A most promising anti-evolutionist

[DMB]

I have invited him to post here, but I'm not at all sure he will. In this thread (http://www.iidb.org/vbb/showthread.php?s=&postid=1118111#post1118111) Charles Darwin (yes, it is a bit cheeky of him, don't you think?) wrote:
The naturalistic models of how the likes of the DNA code or echolocation evolved amount to this: "well, since evolution is true then these must have evolved somehow, let's speculate about it."

I do agree with you that there is a heap of evidence for macro evolution, there also is for the flat earth theory and geocentrism. You can even predict ecclipses with geocentrism. But I assume you think the evidence for macro evolution is compelling. This is not the case -- each evidence, in fact, can be used to argue *against* evolution.

For example, the fossils often shows new species arising fully formed, as though they were planted there. Then they don't change for eons. Even the sequence of horse-like fossils, that old favorite of museums and textbooks, is now admitted to be a series of different, overlapping in time, species. If the different species evolved from each other, then it must have been rapidly so as not to have left any fossils of the transition. As Niles Eldredge admitted:

"There have been an awful lot of stories, some more imaginative than others, about what the nature of that history [of life] really is. The most famous example, still on exhibit downstairs, is the exhibit on horse evolution prepared perhaps fifty years ago. That has been presented as the literal truth in textbook after textbook. Now I think that that is lamentable, particularly when the people who propose those kinds of stories may themselves be aware of the speculative nature of some of that stuff."

Or as paleontologist Robert Carroll explains, the fossil record "emphasizes how wrong Darwin was in extrapolating the pattern of long-term evolution from that observed within populations and species." So to the rescue comes punctuated equilibrium, which isn't so much a theory as a label. We don't observe gradual evolution and the fossil species are static, so evolution must proceed by fits and starts.

There are, of course, many fossil species with similarities, and these rightfully are evidence for evolution. But the many "explosions" with strange and new species appearing out of nowhere are strong arguments against evolution. We certainly cannot simply conclude that the fossils are strong evidence for evolution. As paleontologist Henry Gee of Nature wrote:

"Many of the assumptions we make about evolution, especially concerning the history of life as understood from the fossil record, are, however, baseless. The reason for this lies in the scale of geological time that scientists deal with, which is so vast that it defies narrative. Fossils, such as the fossils of creatures we hail as our ancestors, constitute primary evidence for the history of life, but each fossil is an infinitesimal dot, lost in a fathomless sea of time, whose relationship with other fossils and organisms living in the present day is obscure. Any story we tell against the compass of geological time which links these fossils in sequences of cause and effect—or ancestry and descent—is, therefore, only ours to make. We invent these stories, after the fact, to justify the history of life according to our own prejudices."

Well, I'm afraid it gets worse from here. I'll spare the details, but the comparative anatomy evidence has all kinds of problems for evolution (calling for all sorts of "convergent" evolution and lateral gene transfer). For instance, we are constantly finding similar designs in otherwise distant species. IOW, the similar designs must have been repeated. Good old echolocation, in fact, probably had to have evolved multiple times if evolution is true. Sometimes these similarities are quite striking.
Some of the habitues from here might care to tackle him there if he doesn't turn up here. BTW he claims to be a physicist.

[Data]

I'll spare the details, but the comparative anatomy evidence has all kinds of problems for evolution (calling for all sorts of "convergent" evolution and lateral gene transfer). For instance, we are constantly finding similar designs in otherwise distant species. IOW, the similar designs must have been repeated. Good old echolocation, in fact, probably had to have evolved multiple times if evolution is true. Sometimes these similarities are quite striking.
He doesn't say why this causes problems for evolution, I can't actually see how it could.

[MrDarwin]

Originally posted by DMB
In this thread (http://www.iidb.org/vbb/showthread.php?s=&postid=1118111#post1118111) Charles Darwin (yes, it is a bit cheeky of him, don't you think?) wrote:


I shall have to give him a stern talking-to!

[charlie d]

Originally posted by MrDarwin
I shall have to give him a stern talking-to!
Indeed! ;)

[Happy Wonderer]

For example, the fossils often shows new species arising fully formed, as though they were planted there. Then they don't change for eons.

Well, I'm afraid it gets worse from here. I'll spare the details, but the comparative anatomy evidence has all kinds of problems for evolution (calling for all sorts of "convergent" evolution and lateral gene transfer).


Any of you at a university should really take the time to sneak a recent copy or two of Nature into both the physics and engineering departments. There have been a couple of discoveries since 1950 that may provide tantalizingly new evidence for evolution...

hw

[DMB]

More from the desk of Charles Darwin:

I would argue from science that naturalistic theories of origins are not good. I'm not saying naturalistic theories are literally impossible; simply that from everything we know about science, it is informing us that naturalistic theories are consistently failing, except in circles where only naturalistic theories are allowed, and therefore there is less critical review (ie, naturalistic theories are viewed critically only to the extent that they are inferior to *other* naturalistic theories).

[wade-w]

I just gave him "official" notification that discussions of evolution are off topic in GRD, and if he wishes to continue to discuss the subject he should post here.

From what he has said in various threads in GRD, he seeems to believe in some variation of ID. And he also claims to have a PhD in physics.

I really hope he shows. Should be intersting to watch.

/me wanders off to get the popcorn ready...

[DMB]

This gem from another thread (http://www.iidb.org/vbb/showthread.php?s=&threadid=59858&perpage=25&pagenumber=2) in GRD (he is explaining the impossibility that bats could have evolved echolocation by Natural Selection):
Anyone familiar with today’s sonar or radar systems knows the immense complexity involved with such systems: the problems of sensing the echo in the presence of the transmitted signal which can be billions of times stronger, of filtering out spurious signals such as echoes of older transmissions, of combining the echo information with knowledge of your own motion, and so forth. Yet the bat’s detection abilities are superior to those of the best electronic sonar equipment. To think that things like this just happen to occur via a series of mutations is not scientific thinking.

[KC]

Originally posted by MrDarwin
I shall have to give him a stern talking-to!

And you can actually say to him, "That's Mr Darwin to you"...:D

KC

[Roland98]

Hmm, how bizarre that he chooses to discuss that in GRD but not over here. I look forward to his first thread in this folder...

[Happy Wonderer]

Yet the bat’s detection abilities are superior to those of the best electronic sonar equipment.


I love statements like this. Say again how much better bats are at detecting enemy submarines in 300 meters of water? Maybe Raytheon is on the wrong track here...

hw

[Nic Tamzek]

I bet you've got Cornelius Hunter right there. It sure sounds like him...keeps repeating the same general assertions over and over, rather than picking a specific case to see if he can develop a better answer than evolutionary theory provides, etc.

His most recent book is hilarious -- wild self-contradictions on every page, practically. Later in the book he lays out his cards and makes it pretty clear that the whole evolution thing is a Christian apologetics thing for him -- he starts quoting prophecy and "desiring to become wise, they became fools" (the rallying cry of those who don't have the evidence on their side everywhere) and the whole bit. He doesn't quite come out and say it but I think he's probably actually a YEC or hardcore special creationist. Which is highly ironic since he criticizes Darwin et al. ad nauseum for arguing against special creation.

Darwin's Proof: The Triumph of Religion Over Science
http://enotalone.com/books/ASIN/1587430568.html

There is also a recent episode where Hunter gave a talk up in the Bay Area (IIRC), and asserted that the similarity of wolk and thylacine skulls was too close to be explained by evolution (this kind of thing is his "evidence" against evolution), and documented this by showing pictures of said skulls.

But, there was a paleontologist in the crowd, who observed that Hunter was just using one picture, of a thylacine skull, which he reversed to represent the "wolf" skull! LOL! In fact the skulls are easily distinguishable by anyone who knows mammal skulls, since the convergences are superficial and numerous hallmarks of placental vs. marsupial skulls remain in each skull.

But, by all means, invite him over here, we haven't had a feisty one in awhile.

[Duvenoy]

Indeed, Charlie D's been invited several times, and even given directions by a mod. I rather doubt he'll show up. Perhaps it's a perfectly reasonable fear of picking up a snake that he knows is going to bite him. Can't blame him for that.

I myself would like to read his response to this:

http://www.ucmp.berkeley.edu/mammal/eutheria/chirofr.html

In fact, the oldest known complete fossil bat, the Eocene-age Icaronycteris shown at right, shows specializations of the auditory region of the skull that suggest that this bat could echolocate.

Might be interesting.

doov

[DMB]

He wasn't quite a drive-by, but he seems to have pretty much disappeared as a result of being asked to post here and in other fora besides GRD.

[Charles Darwin]

Originally posted by Duvenoy
Indeed, Charlie D's been invited several times, and even given directions by a mod. I rather doubt he'll show up. Perhaps it's a perfectly reasonable fear of picking up a snake that he knows is going to bite him. Can't blame him for that.

I myself would like to read his response to this:

http://www.ucmp.berkeley.edu/mammal/eutheria/chirofr.html



Might be interesting.

doov

First, a fellow on another section of this forum (the general religious discussion) had this to say:

"Evolution is fact. We know it happens."

Do you fellows believe this? I have to say that I can't quite imagine how one would think this. Perhaps you could lay out the argument. I'm sure there are many details, but how about the general form of the argument?

Now second, as for doov's point, I'm unclear on why echolocation in an extinct bat makes this capability more likely to be a product of evolution. Can you elaborate?

[Secular Pinoy]

Sure, evolution is both a fact and a theory. The fact of evolution is simply the realization that organisms change over time. In more concrete terms, there is a change in alleles in a population. The theory of evolution seeks to provide a mechanism to explain the fact of evolution. These mechanisms include Natural Selection, Genetic Drift, and Neutral Evolution.

For a very good introduction to this, I suggest you read Evolution as Fact and Theory (http://www.stephenjaygould.org/library/gould_fact-and-theory.html) by SJ Gould.

[Charles Darwin]

Originally posted by Secular Pinoy
Sure, evolution is both a fact and a theory. The fact of evolution is simply the realization that organisms change over time. In more concrete terms, there is a change in alleles in a population. The theory of evolution seeks to provide a mechanism to explain the fact of evolution. These mechanisms include Natural Selection, Genetic Drift, and Neutral Evolution.

For a very good introduction to this, I suggest you read Evolution as Fact and Theory (http://www.stephenjaygould.org/library/gould_fact-and-theory.html) by SJ Gould.

I've read Gould's piece, I guess I missed the part where he showed that evolution is a fact (despite the title). Let's see, as I recall he pointed out that fossils exist; that some species are similar to other species; and the we observe small amounts of evolution. Therefore evolution is a fact? I'm sorry, but with all due respect to the late Professor Gould, even my pet cat can't be persuaded by that.

You, OTOH, seem to be saying something different. You're saying that the fact of evolution is changes in alleles in a population over time. This, of course, is not what Gould was talking about. Were you just making an example, or are you making a different claim than Gould's? If so, then why do you cite Gould?

[Data]

Originally posted by Charles Darwin
We observe small amounts of evolution. Therefore evolution is a fact?
You answered your own question there. :boohoo:

[Wounded King]

The direct observational evidence of evolution, the 'small amounts' of evolution are the changes in allele frequency which secular mentioned.

As a paleontologist rather than a geneticst Gould preffered to discuss the fossil record, but the first tier of evidence he mentions is exactly what Secular described.

[Duvenoy]

Hi Charls! welcome to E/C!

I had another post on bats somewhere, but can't seem to find it. Perhaps, I'll re-do it later.

The point is that the extinct bat was very old -- are you YEC?

Also, not all bats echolocate, and, with one exception, those that do use the larynx to produce the sound. The other, one of the fruit bats, uses tongue clicks.

Further, echolocation ain't all that big of a deal. Many animals have evolved the trait, notably toothed whales, the tenrecs of Madagascar, and some species of shrew. Oddly, bats are the only fliers known to have done so.

Seems to me that if echolocation was bestowed upon these animals by some sort of deity, that deity would have also given it to many other creatures, who could use it to advantage.

On a side note, there are species of moth that take wild, evasive action the instant they hear a bat echolocating. Sound (bad pun! :D )evidence of natural selection, no?

doov

[Duvenoy]

Aha! Found it! I'm re-posting it here mainly for the links, which I think are very good.

Originally posted by DMB
"Charles Darwin" seems to be arguing the irreducible complexity of bats' echo location here (http://www.iidb.org/vbb/showthread.php?s=&threadid=60065).

I was hoping.....

The fact is that not all bats echolocate. The old world fruit bats don't use it. Rather, they have evolved enhanced eyesight. I think there is a single species that echolocates, but it is with tongue-clicking, rather than through the larynx.

Echolocation ain't all that rare. Toothed whales do it, the tenrecs of Madagascar and some species of shrew, non-fliers all, also do it.

One wonders how many times it evolved, in one form or another, over the ages.

Interesting sites:

http://www.tenrec.org/fieldolson.htm

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33452

doov

[Charles Darwin]

Originally posted by Duvenoy
The point is that the extinct bat was very old -- are you YEC?
I don't see how evolution is a fact no matter how much time you have. In other words, I don't think the age of the earth has much of a bearing. My point here is that the fact that a bat, with echolocation, is now extinct doesn't add credence to the theory that the bat (or echolocation) evolved.

Originally posted by Duvenoy
Also, not all bats echolocate, and, with one exception, those that do use the larynx to produce the sound. The other, one of the fruit bats, uses tongue clicks.

Yes, it now looks like echolocation must have evolved several times. Just like so many other designs.

Originally posted by Duvenoy
Further, echolocation ain't all that big of a deal. Many animals have evolved the trait, notably toothed whales, the tenrecs of Madagascar, and some species of shrew. Oddly, bats are the only fliers known to have done so.

Why does the fact that many species make use of echolocation make it no big deal? It sounds like you are presupposing evolution to be true. That is fine if you want to talk to other evolutionists, but it doesn't work if you want to promote evolution.

Originally posted by Duvenoy
Seems to me that if echolocation was bestowed upon these animals by some sort of deity, that deity would have also given it to many other creatures, who could use it to advantage.

I thought you just made the point that echolocation is no big deal because it is bestowed upon many different creatures. Looks like you're having it both ways. Apparently what you are saying is that it occurs sufficiently often for it to be no big deal, and yet not often enough to satisfy your opinion of what a deity would do. So now we're about as scientific as yesterday's astrology column. You're making some sort of vague claim that echolocation is no big deal because it is in multiple species (last time I checked echolocation had the US military's systems beat hands down), and then you're telling us about God.

As far as I can tell both these claims are unsupported. Can you help and explain how you found these things out?

Originally posted by Duvenoy
On a side note, there are species of moth that take wild, evasive action the instant they hear a bat echolocating. Sound (bad pun! :D )evidence of natural selection, no?

Yes, indeed, that is evidence for natural selection. By the way, yesterday's astrology column had it right. More evidence for astrology, no?

Originally posted by Duvenoy
The fact is that not all bats echolocate. The old world fruit bats don't use it. Rather, they have evolved enhanced eyesight. I think there is a single species that echolocates, but it is with tongue-clicking, rather than through the larynx.

Echolocation ain't all that rare. Toothed whales do it, the tenrecs of Madagascar and some species of shrew, non-fliers all, also do it.

One wonders how many times it evolved, in one form or another, over the ages.

doov

Well, I guess evolution must be true! {/sarcasm off}. Thank you for the links.

[Charles Darwin]

Quote from Data: You answered your own question there.

Originally posted by Wounded King
The direct observational evidence of evolution, the 'small amounts' of evolution are the changes in allele frequency which secular mentioned.

As a paleontologist rather than a geneticst Gould preffered to discuss the fossil record, but the first tier of evidence he mentions is exactly what Secular described.

You must be kidding me. Don't tell me I'm going to have to suffer through equivocating on evolution and spend a dozen posts clearing that up? If you think evolution is a fact, then explain why. Gould said it is a fact because there are fossils, similarities, and small levels of evolution. Is that really your reasoning too?

[Wounded King]

Are you saying that we don't observe microevolution? If so there are a couple of hundred pieces of primary literature I can refer you to.

Why not tell us what you understand by evolution and then maybe we can tell you if it is a fact, you obviously don't like the definition Secular Pinoy gave.

Where does the equivocation come in? In trying to dismiss the evidence as only microevolution.

I personally think that evolution is a fact because of the various microevolutionary experiments that have been performed, the radical changes in morphology associated with highly specific mutations seen in developmental biology, the highly conserved nature of developmental programs and developmental signalling pathways, the fossil record, numerous studies on isolated population which have diversified and speciated (such as the cichlid fish in Lake Victoria) and a whole lot of other stuff that doesn't come to mind at the moment.

[Doubting Didymus]

Endogenous retroviral insertions confirming phylogenetic trees constructed on independant data prove that species descend from a common ancestor.

[Doubting Didymus]

On the same note, the phylogenetic trees formed by standard genome comparisons confirm the trees built by morphological comparisons. There's no reason to expect that to happen if species aren't related.

[RRoman]

I always thought that dogs are among the better examples of evolution. But I think Charles Darwin should first tell us what he thinks evolution is.

[Doubting Didymus]

Oh yeah... and the widely accepted endosymbiont theory of chloroplast and mitochondria origin is independant evidence that all multicellular species were unicellular at some point in the past. You probably don't buy the aforementioned endosymbiont theory, but if it's not true, then the similarities between mitochondria and bacteria are slightly mysterious, as is the possession of said organelle of its own genetic material.

[Charles Darwin]

Originally posted by RRoman
I always thought that dogs are among the better examples of evolution. But I think Charles Darwin should first tell us what he thinks evolution is.

The theory that the origin of the species can be explained as the result of natural forces and laws at work.

[Charles Darwin]

Originally posted by Doubting Didymus
On the same note, the phylogenetic trees formed by standard genome comparisons confirm the trees built by morphological comparisons. There's no reason to expect that to happen if species aren't related.

I need a bit of help on this one. Why "no reason"? And what do you mean by related? For instance, why does a relationship prove evolution to be a fact?

[The Lone Ranger]

Originally posted by Duvenoy:

Further, echolocation ain't all that big of a deal. Many animals have evolved the trait, notably toothed whales, the tenrecs of Madagascar, and some species of shrew. Oddly, bats are the only fliers known to have done so.

Actually, some birds are known to echolocate -- notably, cave-nesting swiftlets (http://www.pnas.org/cgi/content/abstract/93/14/7091) and oilbirds. Their echolocation abilities aren't nearly as impressive as are those of bats, however.

Cheers,

Michael

[Charles Darwin]

Originally posted by Wounded King
Are you saying that we don't observe microevolution? If so there are a couple of hundred pieces of primary literature I can refer you to.

Why not tell us what you understand by evolution and then maybe we can tell you if it is a fact, you obviously don't like the definition Secular Pinoy gave.

Where does the equivocation come in? In trying to dismiss the evidence as only microevolution.

I personally think that evolution is a fact because of the various microevolutionary experiments that have been performed, the radical changes in morphology associated with highly specific mutations seen in developmental biology, the highly conserved nature of developmental programs and developmental signalling pathways, the fossil record, numerous studies on isolated population which have diversified and speciated (such as the cichlid fish in Lake Victoria) and a whole lot of other stuff that doesn't come to mind at the moment.

No, I don't doubt that instances of microevolution are observed. Nor do I doubt that instances of macroevolution are observed.

The equivocation comes in when you say the evolution is a fact because instances of microevolution are observed. Some moths changed color, therefore it is a fact that fish evolved into giraffes.

Regarding your ideas of why evolution is a fact, I assume that you mean 'public' fact, not 'private' fact. That is, you intend that this fact is objective, for all to see, not your own private inspiration. If I'm on track here, then I utterly fail to track your logic. How did evolution create the adaptation machine that produces microevolution that you now claim as evidence for your theory? And the same for the developmental programs?

I hope you understand my questions are rhetorical. I have no doubt you can provide speculations on these questions. My point is that the evidence you are citing that evolution is a fact does not support evolution in the way you seem to think it does.

On to the fossil record. How does that help to combine with the other evidences to arrive at telling us evolution is a fact? You mean that species appear out of nowhere? Emm, no, that's probably not what you're referring to. You mean that species don't change once they appear? Emm, no, can't be that. You mean that there are similar species in the fossil record? OK, where does that get you?

Do you see my point? To prove evolution to be a (public) fact, we need more than a jumble of evidences which can be interpreted in various ways (including contra evolution).

Even granting you favorable interpretations of these evidences, why do they prove evolution to be a fact?

[The Lone Ranger]

Originally posted by Charles Darwin
No, I don't doubt that instances of microevolution are observed. Nor do I doubt that instances of macroevolution are observed.

The equivocation comes in when you say the evolution is a fact because instances of microevolution are observed. Some moths changed color, therefore it is a fact that fish evolved into giraffes.

<snip>

Even granting you favorable interpretations of these evidences, why do they prove evolution to be a fact?

Whoa, hang on there a moment.

Evolution is changes in populations of organisms over time, specifically, genetic changes. Period. End of statement.

It is an observed fact that populations of organisms change over time, as you note. Therefore, it is a fact that evolution occurs.

When you're talking about the evolution of giraffes from fish (via quite a few intermediaries), you're talking about common descent. Theories of evolution explain this.

This is why we distinguish between the fact that evolution occurs and evolutionary theory which seeks to explain such things as the apparent fact that all organisms share common ancestry.

Cheers,

Michael

[Doubting Didymus]

Originally posted by Charles Darwin
I need a bit of help on this one. Why "no reason"? And what do you mean by related? For instance, why does a relationship prove evolution to be a fact?

When a biologist attempts to construct a phylogenetic tree, they are basically drawing a diagram of how species are related. By 'relationship' here, we aren't talking about the vague colloquial sense (early 1900s church music is 'related' to jazz of the same period, by bent of sharing characteristics). We mean related in the specific sense of family relationships. I am related to my sister, and to my cousin, by blood.

So when a biologist builds a tree of species relationships based on something (morphology, DNA, etc), it's not just an effort in saying "these species look the most alike" but a hypothesis about the lineage relationships. If the tree places humans and chimps on more recently diverging lines than cats, its making a hypothesis about when the ancestors of these species diverged.

Now, if that hypothesis is false, and humans and chimps don't share an ancestor, and neither of us shares an ancestor with cats, then we don't expect the tree we drew based on morphology to agree with our genomes. Our nucleotide sequences shouldn't build a tree that agrees with the hypothesis that certain species are more or less related (again, related in the sense of lineage). It could be anything, building a wildly different tree.

Now, a common objection to this is that there might indeed be a good reason to expect an animals genes to agree with the tree, even if they were never related. Perhaps, goes the argument, animals that just happen to be similar because of the taste of the creator would naturally share more genes with species they look more like, and less than those that don't. The genes would agree with the morphology tree, just because they are more similar in shape to that species. If two cakes taste alike they should have similar recipes, and as the cake becomes less like the first, the recipe should slowly change accordingly. That doesn't mean that all caes are descended from the first cake.

Unfortunately, that argument doesn't hold water for a number of reasons. First, we could test areas of the genome that aren't used: genes that don't make anything, and see if the tree is still produced the same way. It does.

Second, we should then be able to take two species that have similar morphology and expect there to be a consistantly higher genetic similarity. We should expect dolphins to have swimming-thing-with-fins-that-eats-fish genomes that are more similar to sharks than to walking-around-a-field-chewing-grass genomes like elephants. But they don't. We should expect the flying suirrel to be more genetically like an australian flying marsupial possum than to, say, a dog. They don't.

Thus, being able to build the same phylogenetic tree over and over, no matter what method we use, is strong evidence that the hypotheses that the tree generates (i.e. that species are related by lineage) are correct.

[Charles Darwin]

Originally posted by Doubting Didymus
Endogenous retroviral insertions confirming phylogenetic trees constructed on independant data prove that species descend from a common ancestor.

So does the failure of endogenous retrovial insertions to confirm pre established trees disprove evolution? If so, then you should drop evolution as they are all over the map. For instance, there is the HERV that shows up in gorillas and chimps but not humans. In general:

"As has been the case with numerous nuclear DNA markers, there was no consensus among the HERV trees for the relationship among humans, chimpanzees, and gorillas (30). The remaining trees displayed interesting deviations from the predicted separation of the 5' and 3' LTR sequences." PNAS, 96:10254, 1999.

If the failure of endogenous retrovial insertions to confirm pre established trees does not disprove evolution, then how does it tell us that evolution is a fact?

[Duvenoy]

Originally posted by The Lone Ranger
Actually, some birds are known to echolocate -- notably, cave-nesting swiftlets (http://www.pnas.org/cgi/content/abstract/93/14/7091) and oilbirds. Their echolocation abilities aren't nearly as impressive as are those of bats, however.

Cheers,

Michael

Thanks Ranger. Now that you've said it, I get a little nudge in the back of my mind that I read it somewhere. I should'a looked.

Echolocation is no more big a deal than the ever-growing incisors of rodents or the lure possesed by angler fish. It is just another trait that some organisms evolved to give a slight survival advantage.

Here’s another link, on fossils (not bats), one might find interesting:

http://www.gcssepm.org/special/cuffey_05.htm

doov

[Doubting Didymus]

Here is the full text of the article referenced by Charles:

Constructing primate phylogenies from ancient retrovirus sequences (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=17875)

Note that the overwhelming finding of the study found that ERVs support the long standing phylogenetic tree of the old world primates.

An example of findings from this article that support the standard phylogenetic tree:

Three of the loci, HERV-KC4, HERV-KHML6.17, and RTVL-Ia, were detectable in the genomes of OWMs and hominoids, but not New World monkeys, and therefore integrated into the germ line of a common ancestor of the Old World lineages. HERV-K18, RTVL-Ha, and RTVL-Hb were found exclusively in humans, gorillas, chimpanzees, and bonobos, and thus are consistent with a gorilla/chimpanzee/human clade. None of the loci was detected in New World monkeys.

Also note the following paragraph from the papers conclusion:

The study reported here is, to our knowledge, the first to take advantage of special properties of retroelements to provide insight into evolutionary mechanisms. The HERVs analyzed above include six unlinked loci, representing five unrelated HERV sequence families. Except where noted, these sequences gave trees that were consistent with the well established phylogeny of the old world primates, including OWMs, apes, and humans.

The exceptions noted by my emphasis above are, of course, discussed in the article. Evolution does not predict that something so mutable and error-prone as the genome should perfectly preserve every retrovirus it ever includes. we should expect there to be explainations when data is imperfect, which this article devotes some time to doing. I do not believe that a fair reading of this article can lead one to the conclusion that ERVs have "failed" to confirm pre established trees. They overwhelmingly do, and the few exeptions are not mysterious.

[God Fearing Atheist]

Originally posted by Charles Darwin
So does the failure of endogenous retrovial insertions to confirm pre established trees disprove evolution? If so, then you should drop evolution as they are all over the map. For instance, there is the HERV that shows up in gorillas and chimps but not humans. In general:

"As has been the case with numerous nuclear DNA markers, there was no consensus among the HERV trees for the relationship among humans, chimpanzees, and gorillas (30). The remaining trees displayed interesting deviations from the predicted separation of the 5' and 3' LTR sequences." PNAS, 96:10254, 1999.

If the failure of endogenous retrovial insertions to confirm pre established trees does not disprove evolution, then how does it tell us that evolution is a fact?

For everyones sake, lets try quoting the whole passage:

For each HERV locus, the amplified LTRs from each species were directly sequenced, and the aligned sequences were used to generate phylogenetic trees (Fig. 2). The 5' and 3' LTRs of HERV-KHML6.17 fell into two distinct clusters, in accord with prediction (Fig. 2A). Moreover, both LTR cluster topologies are consistent with established versions of primate species phylogeny (26-29). As has been the case with numerous nuclear DNA markers, there was no consensus among the HERV trees for the relationship among humans, chimpanzees, and gorillas (30). The remaining trees displayed interesting deviations from the predicted separation of the 5' and 3' LTR sequences.

Does that make more sense now?

Let's also note Johnson & Coffin's conclusion:

The study reported here is, to our knowledge, the first to take advantage of special properties of retroelements to provide insight into evolutionary mechanisms. The HERVs analyzed above include six unlinked loci, representing five unrelated HERV sequence families. Except where noted, these sequences gave trees that were consistent with the well established phylogeny of the old world primates, including OWMs, apes, and humans

The full text is available here (http://www.pnas.org/cgi/content/full/96/18/10254#FN151).

-GFA

[Doubting Didymus]

http://www.cnnsi.com/events/1996/olympics/daily/aug5/images/marathon01.jpg

Beat you by one minute, GFA.

[God Fearing Atheist]

dag-nabbit DD!

;)

-GFA

[Charles Darwin]

Originally posted by The Lone Ranger
Whoa, hang on there a moment.

Evolution is changes in populations of organisms over time, specifically, genetic changes. Period. End of statement.

It is an observed fact that populations of organisms change over time, as you note. Therefore, it is a fact that evolution occurs.

When you're talking about the evolution of giraffes from fish (via quite a few intermediaries), you're talking about common descent. Theories of evolution explain this.

This is why we distinguish between the fact that evolution occurs and evolutionary theory which seeks to explain such things as the apparent fact that all organisms share common ancestry.

Cheers,

Michael

This is the kind of equivocation I'm talking about. Evolutionists such as Gould are not merely talking about the observed, small-scale, genetic changes in populations when they argue evolution is a fact. Otherwise, they wouldn't need to write at length about it.

[Duvenoy]

Just remembered another echolocater, of sorts; the electric eel (these are not really eels, but one of the South American knifefishs)

The young 'eel' soon becomes blind from electricity-induced cataracs. To navigate and find food, it puts forth a series of electrical discharges that tell it the shape of it's location. It is highly accurate.

I recall reading that the torpedo rays do the same, but it was a popular piece and suspect.

doov

[The Lone Ranger]

Originally posted by Charles Darwin
This is the kind of equivocation I'm talking about. Evolutionists such as Gould are not merely talking about the observed, small-scale, genetic changes in populations when they argue evolution is a fact. Otherwise, they wouldn't need to write at length about it.

Where, exactly, is the "equivocation"?

There is no doubt whatsoever that evolution occurs, so it's utterly proper to say, "Evolution occurs; that's a fact."

As for saying something along the lines of "all living organisms are the results of billions of years of evolution, and are related by common descent", that is a "fact" in the sense that it has long-ago been established beyond any reasonable doubt. It's not improper to call this a "fact" because if it's not true, our perception of the world around us is so mistaken that we obviously can't rely upon evidence at all, and we therefore can't say that anything is true. As Gould points out in the article referenced above: "In science, 'fact' can only mean 'confirmed to such a degree that it would be perverse to withhold provisional assent.' I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms."

He goes on to point out that "Evolutionists have been clear about this distinction between fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred."

I've yet to read any introductory-level science textbook which doesn't emphasize that all scientific knowledge is provisional, and subject to revision in the light of new data. Nonetheless, we can confidently state that there are established facts -- things that are "confirmed to such a degree that it would be perverse to withhold provisional assent." That all extant organisms are related by common descent is just such a fact.

This fact has been confirmed over and over again, by everything from comparative anatomy to molecular biology, any one of which could have disproved it. If there are data which disprove this "fact," no one has presented them yet.

There comes a time when the evidence in favor of a particular conclusion can become so overwhelming that to deny the factuality of the conclusion is to deny reason. Here, we have just such a case.

Cheers,

Michael

[Charles Darwin]

Originally posted by Doubting Didymus
The exceptions noted by my emphasis above are, of course, discussed in the article. Evolution does not predict that something so mutable and error-prone as the genome should perfectly preserve every retrovirus it ever includes. we should expect there to be explainations when data is imperfect, which this article devotes some time to doing. I do not believe that a fair reading of this article can lead one to the conclusion that ERVs have "failed" to confirm pre established trees. They overwhelmingly do, and the few exeptions are not mysterious.

Failure is a strong word. You're the one claiming that the ERVs help make evolution a *fact*. Sure, there is a lot of consistencies, there are also important differences, such as the ERV in the gorilla and chimp but not the human.

[God Fearing Atheist]

Originally posted by Charles Darwin
This is the kind of equivocation I'm talking about. Evolutionists such as Gould are not merely talking about the observed, small-scale, genetic changes in populations when they argue evolution is a fact. Otherwise, they wouldn't need to write at length about it.

Its not equivocation Charles. The thing is, the "change in allele frequency in a population over time" and "decent with modification" definitions are functionally equivalent.

-GFA

[Charles Darwin]

Originally posted by The Lone Ranger
Where, exactly, is the "equivocation"?

There is no doubt whatsoever that evolution occurs, so it's utterly proper to say, "Evolution occurs; that's a fact."

As for saying something along the lines of "all living organisms are the results of billions of years of evolution, and are related by common descent", that is a "fact" in the sense that it has long-ago been established beyond any reasonable doubt. It's not improper to call this a "fact" because if it's not true, our perception of the world around us is so mistaken that we obviously can't rely upon evidence at all, and we therefore can't say that anything is true. As Gould points out in the article referenced above: "In science, 'fact' can only mean 'confirmed to such a degree that it would be perverse to withhold provisional assent.' I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms."

He goes on to point out that "Evolutionists have been clear about this distinction between fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred."

I've yet to read any introductory-level science textbook which doesn't emphasize that all scientific knowledge is provisional, and subject to revision in the light of new data. Nonetheless, we can confidently state that there are established facts -- things that are "confirmed to such a degree that it would be perverse to withhold provisional assent." That all extant organisms are related by common descent is just such a fact.

This fact has been confirmed over and over again, by everything from comparative anatomy to molecular biology, any one of which could have disproved it. If there are data which disprove this "fact," no one has presented them yet.

There comes a time when the evidence in favor of a particular conclusion can become so overwhelming that to deny the factuality of the conclusion is to deny reason. Here, we have just such a case.

Cheers,

Michael

OK, very good. I agree with your definition of what a "scientific fact" is (ie, evidence is overwhelming; if we're wrong about it, then we're wrong about a whole lot of things). I'll use the term "scientific fact" rather than "fact." So now, you write:

"As for saying something along the lines of "all living organisms are the results of billions of years of evolution, and are related by common descent", that is a "fact" in the sense that it has long-ago been established beyond any reasonable doubt. "

and

"This fact has been confirmed over and over again, by everything from comparative anatomy to molecular biology, any one of which could have disproved it. If there are data which disprove this "fact," no one has presented them yet. "

Now Gould utterly fails to make the sort of proof you are talking about. So my question is, why do you think that evolution is a scientific fact? You mentioned comparative anatomy and molecular biology. Can you go down a level deeper and explain why those areas confirm that evolution is a scientific fact?

[The Lone Ranger]

Originally posted by Charles Darwin


Now Gould utterly fails to make the sort of proof you are talking about. So my question is, why do you think that evolution is a scientific fact? You mentioned comparative anatomy and molecular biology. Can you go down a level deeper and explain why those areas confirm that evolution is a scientific fact?

Here's (http://www.talkorigins.org/faqs/comdesc/) a good introduction.

Cheers,

Michael

[Doubting Didymus]

Originally posted by Charles Darwin
Failure is a strong word. You're the one claiming that the ERVs help make evolution a *fact*. Sure, there is a lot of consistencies, there are also important differences, such as the ERV in the gorilla and chimp but not the human.

Didn't you read the results section? If you're talking about the one that this report itself found, then the anomaly was explained within the report.

[Doctor X]

I argued against evolution, but the staphylococcus disagreed with me. . . .

This is all an elaborate complaint that because we do not know "everything"--trace the entire development of species--evolution remains a theory as tenuous as the flat earth.

--J.D.

[Wounded King]

Dear Charles,

You ask
How did evolution create the adaptation machine that produces microevolution that you now claim as evidence for your theory? And the same for the developmental programs?
Do you really expect me to give you a course in evolutionary-developmental biology right here and now? Its a big topic! There is plenty of research into the conservation of developmental programs, wjy not take a look at the primary literature or read a textbook like Gilbert or Wolpert. In fact you can access the text of Gilbert free online at pubmed so you don't even have to go to the library.

As to the 'machinery' for adaptation, its inherent in any population of imperfect replicators, and since it forms the basis of evolution evolution did not 'create' it.

[Oolon Colluphid]

Oh deary dear... Arguing with a creationist with the temerity to call himself Charles Darwin makes my old Darwin’s Terrier moniker rather embarrassing... or perhaps, rather apposite. Watch your ankles, Charles.

Now then...
Can you go down a level deeper and explain why those areas confirm that evolution is a scientific fact?
Start by thoroughly reading the link Michael (TLR) gave you above.

It’s really quite simple, old chap. We have dozens of separate lines of evidence from a range of fields. Not one of them disagrees with evolution, which they could have if evolution were wrong; instead, they all confirm it. We have biogeography, genetics, anatomy and physiology, for instance, plus those annoying fossils. Where would you like to start?

Okay, I’ll get specific. If evolution -- descent with modification -- is not a fact, perhaps you could explain these two pictures:

http://www.talkorigins.org/faqs/comdesc/images/hominids2.jpg

Would you mind telling us please which are the ape fossils, and which are human, and why?

Then there’s this:

http://www.gate.net/~rwms/hum_ape_chrom_2.gif

See www.gate.net/~rwms/EvoEvidence.html for an explanation.

Care to explain why there are telomeres in the middle of our chromosome 2?

These are two, entirely unrelated fields, both saying the same thing: humans and apes share a common ancestor.

These are just two examples, readily to hand. But all of biology and palaeontology is like this, stuffed with observations that only make sense if evolution is correct. I chose humans because, when the chase is cut to, whatever else creationists can be forced to accept, it is human evolution that they cannot countenance.

Ah, to hell with it, I’ll jump the gun anyway, since bats have been mentioned...

The designer was clever enough to make echolocation. Okay... but maybe, Charles, you could explain why this same creator gave bats a respiratory / lung ventilation system that is ten times less efficient than that of birds?

What is it about the lifestyles of bats that meant their designer was right to give them a breathing system so inefficient, compared to one he used elsewhere in other flying creatures?

And why did He use the avian through-flow system in kiwis, and the mammalian tidal system in cheetahs (sprinters), wolves (long-distance runners) and the pinnacle of His purpose, us humans?

TTFN, Oolon

[Jack the Bodiless]

First, a fellow on another section of this forum (the general religious discussion) had this to say:

"Evolution is fact. We know it happens."
That was me.

Others have already dealt with this, but:

We know for a fact that the process of evolution occurrs. This is NOT a controversial statement: even YEC's accept it (even if they insist on calling it "microevolution").

You were attempting to place the "God hypothesis" on the same level as the "evolution hypothesis". But we KNOW that evolution is an actual process, happening right now in the real world. And, even though we cannot be certain that evolution alone is the full and complete explanation for our own descent from primitive organisms, we know of no reason why this should NOT be the case.

...Whereas I am not aware of ANY actual, successful, scientifically-verified examples of intelligences willing Universes into being, or even very small objects into being. There is no known process that the supporter of the God hypothesis can point to and say "look, there, THAT's what I'm suggesting as the process which led to the emergence of humanity".

[Oolon Colluphid]

Originally posted by Charles Darwin
I don't see how evolution is a fact no matter how much time you have. In other words, I don't think the age of the earth has much of a bearing.
So the time needed doesn’t bother you. And even the thickest creationist doesn’t contest ‘microevolution’ -- that is, descent with modification, but only a little of it. Fine.

In which case, perhaps Charles Darwin -- who ought to know, I guess -- could tell us what exactly a ‘kind’ is? Is it roughly a species, a genus, a family, an order... what? IOW, what’s to stop cumulative microevolution making something considerably different? We really need to know, if we’re to tell whether ‘kinds’ are genuinely immutable.

Now take a good hard look at these two pics.

http://www.ucmp.berkeley.edu/mammal/eutheria/battwo.gif

http://www.bio.psu.edu/faculty/strauss/anatomy/misc/skeleton2.jpg

On what grounds could descent with modification not have produced these two organisms from a common ancestor?

TTFN, Oolon

[lpetrich]

"Charles Darwin" has maintained that the following are unevolvable:

* Echolocation

* Altruism (behavior that benefits another rather than oneself)

He points to examples of fancy echolocation, and he seems to think that they had emerged in one big jump. Yet such fancy echolocation does not require one big jump to come into existence; a simpler echolocation system can still be functional, even if its performance is less.

He ought to consider human-technology echolocation: radar and sonar. Present-day radar and sonar systems were not developed instantaneously in one big jump, but over the last century.

There is a close parallel with discussions of the evolution of eyes.

Turning to his second problem, there are two favorite solutions:

* Reciprocal altruism (I'll scratch your back, and you'll scratch mine)

That happens in social animals; some even take care to detect cheaters. Vampire bats will share meals with other bats which have not been able to eat -- but only if those others had helped them out in this fashion in the past.

* Kin selection (they share many of one's genes; part of oneself continues to live in them)

There are numerous examples of that, starting with the cells of a multicellular organism. All but a few will die with the organism, and many of them die before that:

The outermost layer of human skin is dead cells, produced by the multiplication of cells just below. There are several other kinds of sacrificial cells in our bodies, including digestive-system-surface cells and various blood cells.

Tree trunks have only a thin "live" layer, the cambium. Cells on the cambium's inside die and become wood; cells on the cambium's outside die and become bark.

Many trees drop their leaves before wintertime or a dry season. Such "deciduous trees" produce leaves that last only a growing season, and die at the end of it.

Development often involves cells dying at strategic places, such as cells between the digits (fingers, toes).

Going back to the organism level, parental care and provisioning is an obvious form of kin selection; it sometimes takes extremes like plants dying as they go to seed or a female octopus starving to death as she protects her eggs.

Kin selection may be involved in sociality, since social groups are often somewhat inbred. This goes to extremes in "eusocial" insects, where a few reproducers produce the rest of the group's members -- members who does not reproduce. Such worker insects are like the non-germ cells in a body; they assist the reproduction of close relatives.

So "Charles Darwin" ought to study some evolutionary biology some time -- he will be amazed at how far it has gone.

[Roland98]

Originally posted by Charles Darwin
Failure is a strong word. You're the one claiming that the ERVs help make evolution a *fact*. Sure, there is a lot of consistencies, there are also important differences, such as the ERV in the gorilla and chimp but not the human.

Do you understand why the retroviral insertions are such convincing evidence in support of evolution? The insertions are in the same position on the same chromosome in two different species (say, chimps and humans). In some cases, these insertion elements are in the same position in more distant common ancestors as well, but are missing in relatives further down the evolutionary line (say in this case, crocodiles). The most parsimonious reason for there identical position is that they were inheirited from a common ancestor; in the example I outlined, it would have integrated into an ancestor prior to the time the chimp/human lineages diverged, but after those lineages shared a common ancestor with crocodiles. Pretty straightforward stuff, and very unlikely to happen by chance. However, the lack of a viral insertion is not evidence against evolution; and I presume you read the explanations the authors provided?

[Wounded King]

Whats up Roland? No balm in Gilead?

[Roland98]

Originally posted by Wounded King
Whats up Roland? No balm in Gilead?

heh heh...kept hitting quote instead of edit...sorry, it's a Monday. :banghead: Mods, please feel free to delete extraneous posts to keep the thread on track, and my apologies.

[RBH]

I suggest that Charles Darwin's definition of "evolution" needs to be addressed. It's very peculiar:Originally posted by Charles DarwinOriginally posted by RRoman
I always thought that dogs are among the better examples of evolution. But I think Charles Darwin should first tell us what he thinks evolution is.The theory that the origin of the species can be explained as the result of natural forces and laws at work.No mention of allele frequency changes, natural selection, population variability and its generators; just "natural forces and laws." That definition is of "science," not "evolution." Substitute any phenomenon for "the origin of the species" in that sentence and it reads just the same. In other words, Charles Darwin equates "evolution" and naturalism, methodological or (this is my bet) philosophical, with no other distinguishing content. Any naturalistic theory of the origin of species is "evolution" to Charles.

RBH

[Jack the Bodiless]

I've used echolocation myself: I've dropped a stone down a well, and I've even made a clicking sound to get a "feel" for the size of a dark cave. The results weren't particulary precise, but it wasn't exactly difficult to do either.

But maybe I'm just a transitional form between the two species depicted above by Oolon.

[HRG]

Originally posted by Charles Darwin
Failure is a strong word. You're the one claiming that the ERVs help make evolution a *fact*. Sure, there is a lot of consistencies, there are also important differences, such as the ERV in the gorilla and chimp but not the human.

Which (if true) simply means that the gorilla-chimp split occurred after the human-(chimp+gorilla) split.

I wonder why this is apparently so difficult to understand.

Regards,
HRG.

[pangloss]

Originally posted by lpetrich
"Charles Darwin" has maintained that the following are unevolvable:

* Echolocation



I have wondered why creationists find echolocation such a mystery.


I can echolocate. YOU can echolocate. We do it all the time. Blind people have it down to an art, and with training, they can learn to tell the texture of objects by their sound-reflection.

Certainly, bats and such are a level above that, but it seems clear that the basic wiring for the ability is in all mammals, certainly, maybe even most vertebrates.

[Doubting Didymus]

Originally posted by HRG
Which (if true) simply means that the gorilla-chimp split occurred after the human-(chimp+gorilla) split.

It might indicate that independantly, but it contradicts all the other phylogenetic tree evidence that places the chimp-human split after the gorilla-(human, chimp) split, including the evidence of all the other retroviruses. It's an anomaly, and needs an explanation, which is supplied in the paper. There are a number of possibilities. The first one that comes to my mind is a deletion in the chimp line, but I'm confident that the papers authors thought of that.

[Urvogel Reverie]

Charles Darwin writes:

"For example, the fossils often shows new species arising fully formed, as though they were planted there. Then they don't change for eons. Even the sequence of horse-like fossils, that old favorite of museums and textbooks, is now admitted to be a series of different, overlapping in time, species. If the different species evolved from each other, then it must have been rapidly so as not to have left any fossils of the transition. As Niles Eldredge admitted:

"There have been an awful lot of stories, some more imaginative than others, about what the nature of that history [of life] really is. The most famous example, still on exhibit downstairs, is the exhibit on horse evolution prepared perhaps fifty years ago. That has been presented as the literal truth in textbook after textbook. Now I think that that is lamentable, particularly when the people who propose those kinds of stories may themselves be aware of the speculative nature of some of that stuff."

Or as paleontologist Robert Carroll explains, the fossil record "emphasizes how wrong Darwin was in extrapolating the pattern of long-term evolution from that observed within populations and species." So to the rescue comes punctuated equilibrium, which isn't so much a theory as a label. We don't observe gradual evolution and the fossil species are static, so evolution must proceed by fits and starts.

There are, of course, many fossil species with similarities, and these rightfully are evidence for evolution. But the many "explosions" with strange and new species appearing out of nowhere are strong arguments against evolution. We certainly cannot simply conclude that the fossils are strong evidence for evolution."



To claim that the fossil record is a disproof of evolutionary biology is indicative of either a severe misunderstanding of the paleontological data, or, a disingenuous argument. Either way, the assertion is equally fallacious. Combined with genetics and other molecular biology, paleontology is among the most significant of data substantiating common descent. Indeed, the matter of whether or not evolutionary biology's central premise is valid has been solved since 1861, with the discovery of Archaeopteryx lithographica, which by no means our only anatomical intermediate (indeed a conservative list for Archosauromorpha alone, excluding Avialae would include dozens), remains the most emblematic.

The very fact that there are taxa whose anatomy approaches conditions intermediate between other taxa defies creationist logic, which must by necessity advance morphological stasis over time so as to preclude a speciation event. Evolution predicts these fossils, and we find them. Creationism predicts that no such fossils should exist, and yet we have them in abundance. The parsimonious, indeed rational conclusion, is all too obvious.

As for punctuated equilibrium, it has been consistently misrepresented by creationists, thanks in no small part to the specious manner in which S. J. Gould presented it--as a revolutionary panacea to previous problems in deciphering the rate and process of evolution. However, punctuated equilibrium is simply a period of rapid evolution, following a period of fairly gradual morphological variation. It is explained within the framework of more gradual evolution, and evolutionary biology continues to have no need to devise grandiose schemes and their concomitant rubbish about "species selection" to explain that which is already well modeled. It is for this reason that punctuated equilibrium has rarely been taken to the extremes that Gould, Stanley, and Eldgredge took it. Your claim that the fossil record was the impetus for the formulation of this theory is correct, but also misleading because it is the fossil record itself which demonstrates that paleontology is not so supportive of punctuated equilibrium. In your quotation of Carroll (1988) you conveniently forget to mention that fact that he reviews the extensive morphological studies of various Cenozoic mammal fauna undertaken by Hurzeler (1962), Maglio (1973), Gingerich (1982, 1983), Chaline & Laurin (1986), Fahlbusch (1983), Harris & White (1979), MacFadden (1985), and Krishtalka & Stucky (1985) in which progressive morphological variation over time is observed in multiple eutherian lineages, and you utterly ignore Carroll's conclusions that attention to anatomical detail and not taxonomic convention demonstrate that the fossil basis for punctuated equilibrium is in fact very illusory.

Urvogel Reverie
Archaeopteryx lithographica

[lpetrich]

"Charles Darwin" seems to be proposing that an enormous number of species had been specially created over geological time.

But looking at such well-preserved examples as fossil equines, one wonders why each new allegedly-created species closely resembles existing species. Is this all some massive coincidence? Or does it suggest that the process that creates new species is not really very "creative"?

Even the fossil record of human ancestors has that quality; there's a nice picture showing a series of skulls from chimp to various fossils to human -- and showing remarkable continuity.

[Urvogel Reverie]

Originally posted by lpetrich
"Charles Darwin" seems to be proposing that an enormous number of species had been specially created over geological time.

But looking at such well-preserved examples as fossil equines, one wonders why each new allegedly-created species closely resembles existing species. Is this all some massive coincidence? Or does it suggest that the process that creates new species is not really very "creative"?

Even the fossil record of human ancestors has that quality; there's a nice picture showing a series of skulls from chimp to various fossils to human -- and showing remarkable continuity.


Indeed this sort of gradual and more or less continuous morphological variation over time is a hallmark of most lineages, although it is nowhere as well demonstrated as some exemplar Cenozoic eutherian series, which I already listed some examples of. In addition, my beloved Archosauromorpha display a similar pattern in multiple lineages, including to large degree, the Crurotarsi.

Urvogel Reverie

[Charles Darwin]

Originally posted by The Lone Ranger
Here's (http://www.talkorigins.org/faqs/comdesc/) a good introduction.

Cheers,

Michael

The site is entitled "29+ Evidences for Macroevolution" but I came away thinking it is a real misnomer. Though it proposes to be an objective approach to the subject, it is actually a clever attempt to hoodwink those less knowledgable readers. It starts out by stating that "scientific theories are validated by empirical testing against physical observations." This affirming-the-consequent sleight of hand sets up the reader, as the page goes on to site all kinds of dubious "validations." I could give you 29+ validations for the flat-earth model, that doesn't mean it is true.

There is, in fact, no explanation for how life and her species are supposed to have evolved. To head off that minor little problem, the page explains to the reader that "in evolutionary theory it is taken as axiomatic that an original self-replicating life form existed in the distant past, regardless of its origin." How convenient. Now all those thorny complexity problems can be swept under the rug as being outside of scope; but who are we fooling? And of course there still is no explanation for how something like our friend echolocation is supposed to have evolved; or did the first bacteria echolocate too?

The Introduction then ends up with this patronizing (mis) quote:

"Finally, there is this possibility: after I tell you something, you just can't believe it. You can't accept it. You don't like it. A little screen comes down and you don't listen anymore. I'm going to describe to you how Nature is - and if you don't like it, that's going to get in the way of your understanding it." –Feynman

Well if evolution is a fact, then skeptics like me must just be nuts right? Place your opponents in the "irrational" category and everything will be alright. Why is it that evolutionists cannot seem to recognize that their theory is, in fact, not a scientific fact?

I didn't read through the entire site, but went to the first "validation" that caught my eye. It was Section 2.2, Atavisms. It states:

"Probably the most well known case of atavism is found in the whales. According to the standard phylogenetic tree, whales are known to be the descendants of terrestrial mammals that had hindlimbs. Thus, we expect the possibility that rare mutant whales might occasionally develop atavistic hindlimbs."

Aside from the fact that nothing is "known" from phylogenetic trees, the idea that hindlimbs are a prediction of evolution is a joke. You don't really believe that evolution would be rejected if such mutants were never discovered do you? What if tails were never discovered in humans? This has got to be one of the most absurd claims I've ever heard. Of course, the text falls back on the standard cretionist punching bag opponent as if to present a serious rebuttal.

[Charles Darwin]

Originally posted by Doubting Didymus
When a biologist attempts to construct a phylogenetic tree, they are basically drawing a diagram of how species are related. By 'relationship' here, we aren't talking about the vague colloquial sense (early 1900s church music is 'related' to jazz of the same period, by bent of sharing characteristics). We mean related in the specific sense of family relationships. I am related to my sister, and to my cousin, by blood.

So when a biologist builds a tree of species relationships based on something (morphology, DNA, etc), it's not just an effort in saying "these species look the most alike" but a hypothesis about the lineage relationships. If the tree places humans and chimps on more recently diverging lines than cats, its making a hypothesis about when the ancestors of these species diverged.

OK ...

Originally posted by Doubting Didymus
Now, if that hypothesis is false, and humans and chimps don't share an ancestor, and neither of us shares an ancestor with cats, then we don't expect the tree we drew based on morphology to agree with our genomes. Our nucleotide sequences shouldn't build a tree that agrees with the hypothesis that certain species are more or less related (again, related in the sense of lineage). It could be anything, building a wildly different tree.

How do you know it could be anything, such as a wildly different tree?

Originally posted by Doubting Didymus
Now, a common objection to this is that there might indeed be a good reason to expect an animals genes to agree with the tree, even if they were never related. Perhaps, goes the argument, animals that just happen to be similar because of the taste of the creator would naturally share more genes with species they look more like, and less than those that don't. The genes would agree with the morphology tree, just because they are more similar in shape to that species. If two cakes taste alike they should have similar recipes, and as the cake becomes less like the first, the recipe should slowly change accordingly. That doesn't mean that all caes are descended from the first cake.

Unfortunately, that argument doesn't hold water for a number of reasons. First, we could test areas of the genome that aren't used: genes that don't make anything, and see if the tree is still produced the same way. It does.

How do you know that an area isn't used?

Originally posted by Doubting Didymus
Second, we should then be able to take two species that have similar morphology and expect there to be a consistantly higher genetic similarity. We should expect dolphins to have swimming-thing-with-fins-that-eats-fish genomes that are more similar to sharks than to walking-around-a-field-chewing-grass genomes like elephants. But they don't. We should expect the flying suirrel to be more genetically like an australian flying marsupial possum than to, say, a dog. They don't.

Thus, being able to build the same phylogenetic tree over and over, no matter what method we use, is strong evidence that the hypotheses that the tree generates (i.e. that species are related by lineage) are correct.

But (i) dolphins and sharks; and (ii) marsupial and placental flying squirrels have some dramatic differences too. Furthermore, we really do not understand how the phenotype arises from the genotype. Finally, you seem to be conveniently ignoring the many phylogenetic mismatches. If you believe that phylogentic congruence proves evolution, then what about the mismatches?

[Charles Darwin]

Originally posted by Duvenoy
Echolocation is no more big a deal than the ever-growing incisors of rodents or the lure possesed by angler fish. It is just another trait that some organisms evolved to give a slight survival advantage. --doov

Well, if that is the way you think, then there is not much I can say. If echolocation means nothing more to you than teeth then I'm not surprised you think evolution is a fact.

[Valentine Pontifex]

Originally posted by Charles Darwin

The Introduction then ends up with this patronizing (mis) quote:

"Finally, there is this possibility: after I tell you something, you just can't believe it. You can't accept it. You don't like it. A little screen comes down and you don't listen anymore. I'm going to describe to you how Nature is - and if you don't like it, that's going to get in the way of your understanding it." –Feynman


Just how is this a misquote?

[Charles Darwin]

Originally posted by Charles Darwin
Failure is a strong word. You're the one claiming that the ERVs help make evolution a *fact*. Sure, there is a lot of consistencies, there are also important differences, such as the ERV in the gorilla and chimp but not the human.

Originally posted by Doubting Didymus
Didn't you read the results section? If you're talking about the one that this report itself found, then the anomaly was explained within the report.

Oh I have no doubt that there are explanations. I'm not sure that that paper offers an explanation, but no matter, I certainly have read explanations for the [gorilla + chimp but not human] ERV elsewhere; the hand-waving was ferocious. Proving once again that if you allow for any explanation, then any explanation will do.

[Charles Darwin]

Originally posted by Charles Darwin

The Introduction then ends up with this patronizing (mis) quote:

"Finally, there is this possibility: after I tell you something, you just can't believe it. You can't accept it. You don't like it. A little screen comes down and you don't listen anymore. I'm going to describe to you how Nature is - and if you don't like it, that's going to get in the way of your understanding it." –Feynman

Originally posted by Valentine Pontifex
Just how is this a misquote?

Feynman was alluding to far more profound and bizarre theories in the world of QM.

[Charles Darwin]

Originally posted by God Fearing Atheist
Its not equivocation Charles. The thing is, the "change in allele frequency in a population over time" and "decent with modification" definitions are functionally equivalent.

-GFA

Ahh, but who are we fooling? Allele frequencies change all the time. So what? You're not creating anything new. But bird's beak changes shape and size over a few years, and then goes back to the way it was when the environment changes back. Same bird. But since allele frequencies do change, therefore the giraffe came from the fish?

[Charles Darwin]

Originally posted by Doctor X
This is all an elaborate complaint that because we do not know "everything"--trace the entire development of species--evolution remains a theory as tenuous as the flat earth.

--J.D.

So you must like astrology too. Sure we don't know all the details, but so what?

[Charles Darwin]

CD wrote: How did evolution create the adaptation machine that produces microevolution that you now claim as evidence for your theory? And the same for the developmental programs?

Originally posted by Wounded King
Dear Charles,

You ask

Do you really expect me to give you a course in evolutionary-developmental biology right here and now? Its a big topic! There is plenty of research into the conservation of developmental programs, wjy not take a look at the primary literature or read a textbook like Gilbert or Wolpert. In fact you can access the text of Gilbert free online at pubmed so you don't even have to go to the library.

As to the 'machinery' for adaptation, its inherent in any population of imperfect replicators, and since it forms the basis of evolution evolution did not 'create' it.

No I don't expect a crash course. However, I also did not expect you to say that the elaborate adaptation machine is merely present in the initial conditions and therefore not a problem. Now who are we fooling?

[Charles Darwin]

Originally posted by Doubting Didymus
Oh yeah... and the widely accepted endosymbiont theory of chloroplast and mitochondria origin is independant evidence that all multicellular species were unicellular at some point in the past. You probably don't buy the aforementioned endosymbiont theory, but if it's not true, then the similarities between mitochondria and bacteria are slightly mysterious, as is the possession of said organelle of its own genetic material.

You mean the story that a big cell ate up a little cell and forever after the little one was there, working away to produce all those ATPs via that convenient electron transport chain that just happened to be there, with its series of re-dox steps that just happened to be there, and the ATPase which just happened to be there? Well, you're right, I don't buy it. Aside from all this complexity, there is thorny little problem of organelles common to prokaryotes and eukaryotes. Doesn't quite fit the theory of endosymbiosis.

Oh, also, why is the possession of genetic material mysterious for an organelle?

[Charles Darwin]

Originally posted by Oolon Colluphid
Start by thoroughly reading the link Michael (TLR) gave you above.

It hardly seemed worthwhile. Did I accidentally stumble on the worst of it?

Originally posted by Oolon Colluphid
It’s really quite simple, old chap. We have dozens of separate lines of evidence from a range of fields.

Oh really ...

Originally posted by Oolon Colluphid
Not one of them disagrees with evolution

I see, no problems huh? Echolocation and all that has all been explained then? Well evolution must be true.

Originally posted by Oolon Colluphid
Okay, I’ll get specific. If evolution -- descent with modification -- is not a fact, perhaps you could explain these two pictures:

http://www.talkorigins.org/faqs/comdesc/images/hominids2.jpg

Would you mind telling us please which are the ape fossils, and which are human, and why?

I'm afraid I can't ; shucks, evolution must be true huh? Oh, by the way, one little question: why does that make evolution a scientific fact?

Originally posted by Oolon Colluphid
Then there’s this:

http://www.gate.net/~rwms/hum_ape_chrom_2.gif

See www.gate.net/~rwms/EvoEvidence.html for an explanation.

Care to explain why there are telomeres in the middle of our chromosome 2?

These are two, entirely unrelated fields, both saying the same thing: humans and apes share a common ancestor.

I hate to have to be the one to tell you this, but there's a whole bunch we don't know about micro biology. So, no, I'm afraid I can't explain the presence of the telomeres in the middle of chromosome 2 in humans and apes.

Now, getting back to the question at hand, let's see ... How did evolution create all that? You think evolution created these chromosomes, even though you don't know how it could have done said task. Nor do you have the slightest idea of what function said design might serve.

Originally posted by Oolon Colluphid
I chose humans because, when the chase is cut to, whatever else creationists can be forced to accept, it is human evolution that they cannot countenance.

If all else fails, bring on the creationists.

Originally posted by Oolon Colluphid
Ah, to hell with it, I’ll jump the gun anyway, since bats have been mentioned...

The designer was clever enough to make echolocation. Okay... but maybe, Charles, you could explain why this same creator gave bats a respiratory / lung ventilation system that is ten times less efficient than that of birds?

What is it about the lifestyles of bats that meant their designer was right to give them a breathing system so inefficient, compared to one he used elsewhere in other flying creatures?

And why did He use the avian through-flow system in kiwis, and the mammalian tidal system in cheetahs (sprinters), wolves (long-distance runners) and the pinnacle of His purpose, us humans?
TTFN, Oolon

Good questions. I see that we are not talking about a "scientific" fact anymore, or a "scientific" theory. I respect your religious sentiments. I can see that for you, evolution must be a fact.

[Charles Darwin]

Originally posted by Jack the Bodiless
But we KNOW that evolution is an actual process, happening right now in the real world. And, even though we cannot be certain that evolution alone is the full and complete explanation for our own descent from primitive organisms, we know of no reason why this should NOT be the case.

So much for science pursuing likely theories. With evolution, science becomes the pursuit of that which has not (or cannot) be proven wrong. No matter that evolution has no explanation for how life arose or how things like echolocation arose. It may not be likely, but it must be a fact.

[Charles Darwin]

Originally posted by Oolon Colluphid
So the time needed doesn’t bother you. And even the thickest creationist doesn’t contest ‘microevolution’ -- that is, descent with modification, but only a little of it. Fine.

In which case, perhaps Charles Darwin -- who ought to know, I guess -- could tell us what exactly a ‘kind’ is? Is it roughly a species, a genus, a family, an order... what?

I don't know. Do you need all the details to accept an idea? If yes, then how is it that you accept evolution?

Originally posted by Oolon Colluphid
IOW, what’s to stop cumulative microevolution making something considerably different? We really need to know, if we’re to tell whether ‘kinds’ are genuinely immutable.

Nothing, in principle. Perhaps by some magical process species transform themselves into other species. Now why does this make evolution a fact?

Originally posted by Oolon Colluphid
Now take a good hard look at these two pics.

http://www.ucmp.berkeley.edu/mammal/eutheria/battwo.gif

http://www.bio.psu.edu/faculty/strauss/anatomy/misc/skeleton2.jpg

On what grounds could descent with modification not have produced these two organisms from a common ancestor?

TTFN, Oolon

Far be it for me to falsify evolution. But on what grounds to these make evolution compelling?

[Urvogel Reverie]

Originally posted by Charles Darwin
OK ...


But (i) dolphins and sharks; and (ii) marsupial and placental flying squirrels have some dramatic differences too. Furthermore, we really do not understand how the phenotype arises from the genotype. Finally, you seem to be conveniently ignoring the many phylogenetic mismatches. If you believe that phylogentic congruence proves evolution, then what about the mismatches?


This post smacks of significant misunderstandings in the modern methodology for phylogenetic reconstruction, in addition to aspects thereof including outgroup analysis and parsimony analysis. In addition, your claim that we are utterly in the dark as to how the genotype and phenotype interact, and in turn how normalizing selection interacts with the genotype are misleading, as we have learned a great deal about both of these subjects, as any review of, for instance, Maynard-Smith, Dawkins, or Mayr, would illustrate.

Urvogel Reverie

[Charles Darwin]

Originally posted by lpetrich
"Charles Darwin" has maintained that the following are unevolvable:

* Echolocation

* Altruism (behavior that benefits another rather than oneself)

He points to examples of fancy echolocation, and he seems to think that they had emerged in one big jump. Yet such fancy echolocation does not require one big jump to come into existence; a simpler echolocation system can still be functional, even if its performance is less.

He ought to consider human-technology echolocation: radar and sonar. Present-day radar and sonar systems were not developed instantaneously in one big jump, but over the last century.

There is a close parallel with discussions of the evolution of eyes.


I don't say one big jump, nor do I say it cannot have evolved. I say it isn't likely. Also, the analogy with human technology suffers from the fact that human designers were involved.

Originally posted by lpetrich
Turning to his second problem, there are two favorite solutions:

* Reciprocal altruism (I'll scratch your back, and you'll scratch mine)

That happens in social animals; some even take care to detect cheaters. Vampire bats will share meals with other bats which have not been able to eat -- but only if those others had helped them out in this fashion in the past.

Do you know how big the design space is which evolution had to randomly search through and hit upon, and test, this design? How many years were available, and what mutational rates would be required? I don't think we have a good handle on this, so this is really just speculation.

[Urvogel Reverie]

Originally posted by Charles Darwin
Ahh, but who are we fooling? Allele frequencies change all the time. So what? You're not creating anything new. But bird's beak changes shape and size over a few years, and then goes back to the way it was when the environment changes back. Same bird. But since allele frequencies do change, therefore the giraffe came from the fish?


Specious rot. Shift in allele frequency is at the very heart of allopatric speciation in that it precludes the mixture of populations and the maintenance of genotypic homogeneity. It is not possible to construe the variation in the frequency of alleles within populations both isolated and otherwise, as anything but the most compelling of data to substantiate evolutionary biology. It furthermore accounts for the dynamism which was implicit in the Darwinian treatment of organic evolution and yet unquantified due to the lack of genetic understanding comparative to ours, in 1859--after all, it was not even until 1900 that Mendel's work on heredity was rediscovered, and it would be another half century before the composition of the gene would be discovered. Genetics, synthesized with the traditional Darwinian mechanisms, has rather than refuting evolutionary biology, as anti-evolutionists long predicted, overwhelmingly corroborated it.

As a side note, as not a single work of evolutionary biology labels giraffes or any other eutherians as the phyletic progenitors of even a paraphyletic hodgepodge such as "fish", your claim to the contrary is quite simply assinine.


Urvogel Reverie

[Urvogel Reverie]

CD:

I hate to have to be the one to tell you this, but there's a whole bunch we don't know about micro biology. So, no, I'm afraid I can't explain the presence of the telomeres in the middle of chromosome 2 in humans and apes.



And you completely avoid the issue that the fusion of chromosomal elements plesiomorphic in chimps, in humans (constituting an autapomorphy of genus Homo), is compelling evidence for evolutionary biology, not the least of the reasons being that by anti-evolutionary standards, no such fusion should be present. Your response to this particular claim was nothing less than categoric dismissal without examination of the data presented. I believe if you modify it slightly, one could have a Gish Gallop.

Urvogel Reverie

[Charles Darwin]

Originally posted by Roland98
Do you understand why the retroviral insertions are such convincing evidence in support of evolution? The insertions are in the same position on the same chromosome in two different species (say, chimps and humans). In some cases, these insertion elements are in the same position in more distant common ancestors as well, but are missing in relatives further down the evolutionary line (say in this case, crocodiles). The most parsimonious reason for there identical position is that they were inheirited from a common ancestor; in the example I outlined, it would have integrated into an ancestor prior to the time the chimp/human lineages diverged, but after those lineages shared a common ancestor with crocodiles. Pretty straightforward stuff, and very unlikely to happen by chance. However, the lack of a viral insertion is not evidence against evolution; and I presume you read the explanations the authors provided?

Yes, I do understand the retroviral insertion argument. They are supposed to be irreversible markers; which is why, for example, the [Ape + chimp but not human] ERV is interesting since at the homologous human site the DNA sequence clearly shows a clean pre insertion site. I also understand know that ERVs can have site selectivity. And I also understand that, if evolution is true, there must have been a sort of "punctuated equilibrium" in the HERV world; and that HERVs must have played a role in evolution since they, in fact, have a regulatory function.

One can always contrive some sort of explanation if one is willing to invoke enough contingencies, special events, what-if's, and so forth. And so therefore, you may argue this is not evidence against evolution. But the price you pay is your theory becomes less compelling because it is so moldable. And your position that it is a fact is likewise weakened (as if it ever had any strength to it).

[Charles Darwin]

Originally posted by Urvogel Reverie
And you completely avoid the issue that the fusion of chromosomal elements plesiomorphic in chimps, in humans (constituting an autapomorphy of genus Homo), is compelling evidence for evolutionary biology, not the least of the reasons being that by anti-evolutionary standards, no such fusion should be present. Your response to this particular claim was nothing less than categoric dismissal without examination of the data presented. I believe if you modify it slightly, one could have a Gish Gallop.

Urvogel Reverie

Sorry, you have to read down to the bottom of the post. I was typing fast, and meant for that response to go along with my other responses for the remainder of the post, because he was bringing up similar types of claims.

I was not at all disimissing the claim, but merely pointing out the nature of the claim. I fully agreed with him that evolution becomes a fact (for him).

[lpetrich]

Charles Darwin:
(29 evidences for macroevolution, talkorigins.org)
... There is, in fact, no explanation for how life and her species are supposed to have evolved.

What did you expect? These are evidence of a fairly continuous chains of species that have a branching-tree topology.

CD, are you challenging that? And if you think that some alternative is closer to the truth, then what is it?

Do you accept this topology of equine relationships (http://www.talkorigins.org/faqs/horses/horse_evol.html), or do you believe it was something else?

And if you do, do you believe that it represents ancestor-descendant chains or something like

55 myr: *POOF!* Hyracotherium was created
50 myr: *POOF!* Orohippus was created
40 myr: *POOF!* Mesohippus was created
35 myr: *POOF!* Miohippus was created
17 myr: *POOF!* Merychippus was created
12 myr: *POOF!* Dinohippus was created
4 myr: *POOF!* Equus was created
2 myr: *POOF!* Various present-day equine species created

And in human ancestry:

5 myr: *POOF!* Ardipithecus ramidus was created
4 myr: *POOF!* Australopithecus afarensis was created
3 myr: *POOF!* Australopithecus africanus was created
2.7 myr: *POOF!* Paranthropus aethiopicus was created
2.3 myr: *POOF!* Paranthropus boisei was created
2 myr: *POOF!* Paranthropus robustus was created
2.5 myr: *POOF!* Homo habilis was created
2 myr: *POOF!* Homo erectus was created
0.7 myr: *POOF!* Homo heidelbergensis was created
0.3 myr: *POOF!* Homo neanderthalensis was created
0.1 myr: *POOF!* Homo sapiens was created

With each species having a suspicious resemblance to existing species.

And of course there still is no explanation for how something like our friend echolocation is supposed to have evolved; or did the first bacteria echolocate too?

Echolocation is much simpler to develop than CD seems to think -- why does he seem to think that only a full-scale, very-fancy echolocation system could ever be useful?

All you have to do to start echolocating is making sounds and listening for echoes. It's that simple.

[Charles Darwin]

Originally posted by Urvogel Reverie
Specious rot. Shift in allele frequency is at the very heart of allopatric speciation in that it precludes the mixture of populations and the maintenance of genotypic homogeneity. It is not possible to construe the variation in the frequency of alleles within populations both isolated and otherwise, as anything but the most compelling of data to substantiate evolutionary biology.

That's an interesting claim. How could it be that :

"It is not possible to construe the variation in the frequency of alleles within populations both isolated and otherwise, as anything but the most compelling of data to substantiate evolutionary biology."

Starting with the 2nd half of the claim, you are saying that these data are "most compelling." That's awfully strong language for something that, in fact, creates no new sequences. Obviously evolution requires massive genetic changes, and this gives us none. Hmmm.

Then, on to the 1st half of the claim, you seem to think "it is not possible to construe" the data "as anything but" supporting evolution. This is, of course, not a scientific statement. In science we propose theories rather than make metaphysical proclamations. We say, "If P, then Q", not "If and only if P, then Q". The former describes the expected outcome of a theory. The latter is a universal truth claim about Q. But then again, who said this was science.

Originally posted by Urvogel Reverie
As a side note, as not a single work of evolutionary biology labels giraffes or any other eutherians as the phyletic progenitors of even a paraphyletic hodgepodge such as "fish", your claim to the contrary is quite simply assinine.

Urvogel Reverie

Then why is the recurrent laryngeal nerve evidence for evolution?

[Charles Darwin]

Originally posted by lpetrich
Charles Darwin:
(29 evidences for macroevolution, talkorigins.org)
... There is, in fact, no explanation for how life and her species are supposed to have evolved.

What did you expect? These are evidence of a fairly continuous chains of species that have a branching-tree topology.

CD, are you challenging that? And if you think that some alternative is closer to the truth, then what is it?

Do you accept this topology of equine relationships (http://www.talkorigins.org/faqs/horses/horse_evol.html), or do you believe it was something else?

I really don't know, but I do know that the mythical horse sequence convinced many a lay person for the better part of a century before it was finally admitted to be, well, ... mythical. What we have is a bunch of different species which, if evolution is true, must have punctuated into each other. I also know that evolution, beyond handwaving, doesn't explain how any of those species got there in the first place anyway. Why is it you think this makes evolution a scientific fact?



Originally posted by lpetrich
And if you do, do you believe that it represents ancestor-descendant chains or something like

55 myr: *POOF!* Hyracotherium was created
50 myr: *POOF!* Orohippus was created
40 myr: *POOF!* Mesohippus was created
35 myr: *POOF!* Miohippus was created
17 myr: *POOF!* Merychippus was created
12 myr: *POOF!* Dinohippus was created
4 myr: *POOF!* Equus was created
2 myr: *POOF!* Various present-day equine species created

And in human ancestry:

5 myr: *POOF!* Ardipithecus ramidus was created
4 myr: *POOF!* Australopithecus afarensis was created
3 myr: *POOF!* Australopithecus africanus was created
2.7 myr: *POOF!* Paranthropus aethiopicus was created
2.3 myr: *POOF!* Paranthropus boisei was created
2 myr: *POOF!* Paranthropus robustus was created
2.5 myr: *POOF!* Homo habilis was created
2 myr: *POOF!* Homo erectus was created
0.7 myr: *POOF!* Homo heidelbergensis was created
0.3 myr: *POOF!* Homo neanderthalensis was created
0.1 myr: *POOF!* Homo sapiens was created

With each species having a suspicious resemblance to existing species.

I see. You and the other folks -- I see a pattern. Of course we cannot believe they were created, so ..., evolution must be true. We were talking about a scientific fact, but this is a switch. What you are really saying is this is a metaphysical fact. Given your metaphysical position, evolution is a fact. Ok, I'll buy that.

Originally posted by lpetrich
And of course there still is no explanation for how something like our friend echolocation is supposed to have evolved; or did the first bacteria echolocate too?

Echolocation is much simpler to develop than CD seems to think -- why does he seem to think that only a full-scale, very-fancy echolocation system could ever be useful?

All you have to do to start echolocating is making sounds and listening for echoes. It's that simple.

Sorry, it is a little more complicated than that.

[Charles Darwin]

Originally posted by Urvogel Reverie
Charles Darwin writes:

"For example, the fossils often shows new species arising fully formed, as though they were planted there. Then they don't change for eons. Even the sequence of horse-like fossils, that old favorite of museums and textbooks, is now admitted to be a series of different, overlapping in time, species. If the different species evolved from each other, then it must have been rapidly so as not to have left any fossils of the transition. As Niles Eldredge admitted:

"There have been an awful lot of stories, some more imaginative than others, about what the nature of that history [of life] really is. The most famous example, still on exhibit downstairs, is the exhibit on horse evolution prepared perhaps fifty years ago. That has been presented as the literal truth in textbook after textbook. Now I think that that is lamentable, particularly when the people who propose those kinds of stories may themselves be aware of the speculative nature of some of that stuff."

Or as paleontologist Robert Carroll explains, the fossil record "emphasizes how wrong Darwin was in extrapolating the pattern of long-term evolution from that observed within populations and species." So to the rescue comes punctuated equilibrium, which isn't so much a theory as a label. We don't observe gradual evolution and the fossil species are static, so evolution must proceed by fits and starts.

There are, of course, many fossil species with similarities, and these rightfully are evidence for evolution. But the many "explosions" with strange and new species appearing out of nowhere are strong arguments against evolution. We certainly cannot simply conclude that the fossils are strong evidence for evolution."

-------------------

To claim that the fossil record is a disproof of evolutionary biology is indicative of either a severe misunderstanding of the paleontological data, or, a disingenuous argument. Either way, the assertion is equally fallacious.

Urvogel Reverie
Archaeopteryx lithographica

But since I did not, in fact, say that, your point is irrelevant.

[Charles Darwin]

Originally posted by Urvogel Reverie
In addition, your claim that we are utterly in the dark as to how the genotype and phenotype interact,

Urvogel Reverie

But, in fact, I did not say that.

[Doctor X]

One can always contrive some sort of explanation if one is willing to invoke enough contingencies, special events, what-if's, and so forth. And so therefore, you may argue this is not evidence against evolution. But the price you pay is your theory becomes less compelling because it is so moldable. And your position that it is a fact is likewise weakened (as if it ever had any strength to it).

Look OUT! TAKE COVER!!!

http://shanek.ispofusa.net/images/iron-e.gif

--J.D.

[lpetrich]

Charles Darwin:
(on falsehood of evolution implying discrepant family trees...)
How do you know it could be anything, such as a wildly different tree?

What alternative do you think is plausible? Special creation of species with the appearance of evolution?

(unused areas of the genome...)
How do you know that an area isn't used?

Experience with molecular-level genetics: the more functionally-constrained something is, the more the sequences look alike between species. So some rapidly-evolving area implies low constraint.

But (i) dolphins and sharks; and (ii) marsupial and placental flying squirrels have some dramatic differences too.

So what? That's how one can recognize convergent evolution.

Furthermore, we really do not understand how the phenotype arises from the genotype.

Which is just plain wrong. We know how proteins are made from genes, and we are accumulating clues as to how other features are made.

Finally, you seem to be conveniently ignoring the many phylogenetic mismatches.

Like what?

If you believe that phylogentic congruence proves evolution, then what about the mismatches?

Whatever you have in mind. Please explain in more detail.

[The Lone Ranger]

Originally posted by Charles Darwin:

The site is entitled "29+ Evidences for Macroevolution" but I came away thinking it is a real misnomer. Though it proposes to be an objective approach to the subject, it is actually a clever attempt to hoodwink those less knowledgable readers. It starts out by stating that "scientific theories are validated by empirical testing against physical observations." This affirming-the-consequent sleight of hand sets up the reader, as the page goes on to site all kinds of dubious "validations." I could give you 29+ validations for the flat-earth model, that doesn't mean it is true.
How, exactly, is this a “clever attempt to hoodwink those less knowledgable [sic] readers”? And where is the sleight of hand? One tests the validity of scientific hypotheses and theories by testing to see whether their predictions conform to reality, just as the site states. Do you know of some other way?

Every scientific theory makes predictions which can be, in principle, tested. If the theory fails these tests, then it must be modified or abandoned. While it’s true that if the predictions are verified, this doesn’t prove the theory to be true, it does give us more confidence in the theory. Evolutionary theory makes quite a number of predictions, and has a spectacularly good track record. So far, no one has found anything which contradicts it.


I could give you 29+ validations for the flat-earth model, that doesn't mean it is true.
Can you? I don’t believe that you can.

Remember, for the flat-earth model to be a legitimate scientific theory, it must be based upon actual evidence, and it must make specific predictions which can be tested and falsified. If the predictions are shown to be false, they are not "validations" of the theory.

I would assume that a “validation” of the “theory” would be that the Earth appears to be flat to an observer. Upon casual observation, this may be so, but it takes only a little work to show that the prediction does not hold up. Anyone who has observed a ship sailing out to sea, for example, can clearly see that the Earth does not appear to be flat when viewed on a sufficiently large scale.

This is why the flat Earth theory is not taken seriously, because any non-trivial predictions it makes are easily falsified. So, please tell us which of the predictions of evolutionary theory have been falsified, and how. I know of no examples, myself.


There is, in fact, no explanation for how life and her species are supposed to have evolved.
You asked for evidence that evolution is sufficiently well-established to be called a “fact.” That is precisely what the site offers. If it’s an explanation of evolutionary theory that you want, that information is readily available. You have only to ask.


To head off that minor little problem, the page explains to the reader that "in evolutionary theory it is taken as axiomatic that an original self-replicating life form existed in the distant past, regardless of its origin." How convenient. Now all those thorny complexity problems can be swept under the rug as being outside of scope; but who are we fooling?
I’m at a loss to understand why so many people have the erroneous impression that evolutionary theory has anything whatsoever to do with the origins of life. Repeat after me: evolutionary theory is about how living things have evolved over time – since the origin(s) of life. Saying that evolutionary theory is incomplete or invalid because it doesn’t explain the origin of life is like saying that chemistry is an invalid field because it doesn’t explain the origins of atoms.


And of course there still is no explanation for how something like our friend echolocation is supposed to have evolved; or did the first bacteria echolocate too?
The point of the site – as per your request – is to provide evidence for the fact of evolution, not to explain every little adaptation. Do you consult the owner’s manual of your automobile for an explanation of how the Bernoulli effect applies to the function of a carburetor? Do you throw the manual down in disgust and conclude that it's worthless because it doesn't provide that explanation?

Besides, as several posters have pointed out, echolocation isn’t difficult. Any animal with ears and the ability to produce sound can echolocate, at least crudely. Why is it so difficult to conceptualize how the process could have been refined by natural selection? Indeed, we have living examples of animals that can echolocate very crudely (humans, for example), to those that can echolocate rather more effectively (oilbirds, for instance), to those that can echolocate quite well (bats and cetaceans).


The Introduction then ends up with this patronizing (mis) quote:
"Finally, there is this possibility: after I tell you something, you just can't believe it. You can't accept it. You don't like it. A little screen comes down and you don't listen anymore. I'm going to describe to you how Nature is - and if you don't like it, that's going to get in the way of your understanding it." –Feynman
Whether it’s a nice thought or not, Feynman has a legitimate point. If you’re determined not to believe a thing, you’re not going to be convinced by evidence, nor are you likely to gain a very thorough understanding of the subject. With respect, you give every indication of being someone who very much wants for evolution not to be true. If this is the case, it’s going to be difficult to convince you of the legitimacy of evolutionary theory on the basis of something as inconsequential as evidence.


Well if evolution is a fact, then skeptics like me must just be nuts right? Place your opponents in the "irrational" category and everything will be alright. Why is it that evolutionists cannot seem to recognize that their theory is, in fact, not a scientific fact?
Well, to put it bluntly, there are many thousands of evolutionary biologists over the world who have studied the matter quite thoroughly. They’re quite convinced that the evidence in favor of evolution is so voluminous – and the evidence against it is conspicuously nonexistent – that they’re quite comfortable calling it an established fact. Oddly, the only ones who deny that evolution is a fact consistently show themselves to be a.) ignorant of the subject, and/or b.) strongly prejudiced against acceptance of evolution for religious/political/whatever reasons.

I note, in passing, that you still seem to be incapable of distinguishing between the fact of evolution (that all organisms show clear and unmistakable evidence of being related through common descent) and the theory of evolution (which explains that fact). Why is that so difficult a concept? If one didn’t know better, one would suspect that you conflate the ideas because you don’t want to understand the differences.

In a later post, you ask:
Do you know how big the design space is which evolution had to randomly search through and hit upon, and test, this design? How many years were available, and what mutational rates would be required? I don't think we have a good handle on this, so this is really just speculation.

If you think that natural selection is a random process, then yours is a very poor understanding of evolutionary theory indeed. By the way, no one is suggesting that evolution produces "ideal" or "perfect" adaptations – indeed, examples of just how inefficient a process it can be abound.


"Probably the most well known case of atavism is found in the whales. According to the standard phylogenetic tree, whales are known to be the descendants of terrestrial mammals that had hindlimbs. Thus, we expect the possibility that rare mutant whales might occasionally develop atavistic hindlimbs."

Aside from the fact that nothing is "known" from phylogenetic trees, the idea that hindlimbs are a prediction of evolution is a joke. You don't really believe that evolution would be rejected if such mutants were never discovered do you? What if tails were never discovered in humans? This has got to be one of the most absurd claims I've ever heard. Of course, the text falls back on the standard cretionist punching bag opponent as if to present a serious rebuttal.
Perhaps you should re-read that paragraph. Certainly, within the context of phylogenetic trees, it is known that whales are descended from terrestrial mammals with hindlimbs. That’s what the trees predict, and that’s precisely what the author is saying – that it’s a known fact that the phylogenetic trees predict this.

So, one way to test the validity of the phylogenetic trees – and of the evolutionary theory that they’re based upon – is to see if the predictions they make hold up in the real world. The trees predict that whales are descended from ancestors with hindlimbs. A corollary of that prediction is that whales should still possess genes for hindlimbs, and therefore we would expect to occasionally find a whale with hindlimbs. This is a straightforward prediction, and not in the least absurd. We can guage the validity of the theory by looking to see if whales are occasionally born with hindlimbs. If we didn’t see the occasional whale born with hindlimbs, this would indeed be evidence that evolutionary theory was in need of revision. Furthermore, if whales were never observed to have atavistic hindlimbs, and a careful analysis of whales’ DNA showed conclusively that they did not have genes that were homologous to those which cause the growth of hindlimbs in terrestrial mammals, that would indeed be a serious blow to evolutionary theory.

That’s the point. The observations could have provided evidence that evolution is not a fact. If so, we’d have no choice but to accept that. They didn’t though; they did just the opposite.

That’s how science is done. We put our hypotheses and theories on the chopping block by testing their claims against reality. If they fail the tests, out they go. So far, evolutionary theory has not failed any of the tests we’ve been able to devise for it.


******


Let’s simplify things a bit.

[list=1]
According to all the available evidence – from geology, astronomy, cosmology, etc. – the Earth is very old, over four billion years old, in fact.
Molecular biology and genetics provide overwhelming evidence that all living organisms are related and share common ancestry.
The fossil record provides unambiguous evidence that organisms have been evolving for quite some time.
Populations of organisms are observed to evolve in the wild.
Studies of natural populations show not only that they evolve, but that they often evolve at rates that are orders of magnitude faster than is necessary to explain the observed rates of change in the fossil record.*
[/list=1]
A question arises. Since all the evidence we have indicates that the Earth is billions of years old, and since molecular and genetic data clearly indicate that all extant organisms are related through common descent, and since field studies consistently show that populations can and do evolve at rates which are more than adequate to explain the rates of change implied by the fossil record, what evidence do you have that evolution is not true and that 99.99% of the world’s biologists, geologists, paleontologists, astronomers, cosmologists, etc. are completely deluded?

* See this (http://www.sciencemag.org/cgi/content/full/275/5308/1934) study, for example.


Perhaps you think that there exists some sort of “genetic” barrier which would somehow prevent one species from evolving into another, I would like to point out that no studies have ever provided evidence that such barriers exist. Consider ring species, for example.

A ring species occurs when a single species becomes distributed in a circular pattern over a large geographical area. Neighboring populations of the species vary slightly and can interbreed, but those populations at the extremes of the distribution – the opposite ends that link to form the circle – are sufficiently different that they do not interbreed and function as separate species. In fact, they would be considered to be separate species except that the intermediates which link them form a continuum. Ring species are a particularly nice example of evolution in action, because we can see all of the intermediates that link two related “species.”

Perhaps the best-known example of a ring species is the salamander Ensatina eschscholtzi. Here's a picture showing the species' distribution and variation.
http://www.pbs.org/wgbh/evolution/library/05/2/images/l_052_05_l.jpg

The subspecies at the endpoints of the ring (Ensatina eschscholtzi eschscholtzi and Ensatina eschscholtzi klauberi) come into contact with each other, and thus close the ring. Yet they're so different in appearance that the would certainly be classified as separate species were it not for the existence of all the intermediates which connect them.

Here's E. e. eschscholtzi:
http://www.santarosa.edu/lifesciences/esch72.jpg

Here's E. e. klauberi:
http://www.amphibian.co.uk/Images/eeklauberi1.gif

In most areas where they co-occur, E. e. eschscholtzi and E. e. klauberi seldom if ever interbreed, as has been confirmed by both behavioral and genetic studies. See this (http://links.jstor.org/sici?sici=0014-3820%28199406%2948%3A3%3C876%3AEAHAOP%3E2.0.CO%3B2-B) article, for example. Indeed, the genetic differences between E. e. eschscholtzi and E. e. klauberi are equal to or greater than (http://links.jstor.org/sici?sici=0014-3820%28198607%2940%3A4%3C702%3AGVIAIA%3E2.0.CO%3B2-L) the genetic differences between different species.

The point is that this looks exactly like an example of speciation in action. It certainly qualifies as very strong evidence of evolution in action. Moreover, it clearly demonstrates that there is no magical genetic barrier which would prevent one species from evolving into another.


***

Let's simplify even more.

You asked for evidence that evolution is a fact. That evidence is readily available. The genetic unity of life, the fact that species can be organized into a nested hierarchy of apparent relatedness, the fact that independent methods produce similar or identical phylogenies, the existence of intermediate forms, the presence of atavistic structures, the presence of vestigial structures, ontological features, biogeography, and so forth -- all of these provide overwhelming evidence that evolution is a fact.

You can, of course, invent all sorts of ad hoc "explanations" for these lines of evidence. Perhaps a Creator -- for some strange reason -- wished to create life in such a way as to make it look like it evolved over time, but that's not a testable or falsifiable hypothesis, and so is of no use.

The overwhelming verdict of the scientific community is that the evidence in favor of evolution is so complete that it's pointless to call it anything other than a fact. Your choices are simple: 1.) accept this and move on, or 2. show us why we're wrong.

Hint: Whining that no one has explained every little detail is not the same thing as providing evidence that the conclusion is false. If you see and videotape Person "A" shooting Person "B", if you see Person "B" bleeding afterward, if you see the surgeons removing the bullet from Person "B"'s body, if you hear Person "A" confess to the crime -- do you claim that it's not a fact that Person "A" shot Person "B" because you don't know where the bullet was manufactured?

Cheers,

Michael

[RufusAtticus]

Originally posted by Charles Darwin
I could give you 29+ validations for the flat-earth model, that doesn't mean it is true.

Okay. I'll bite. Give me 29+ evidences of the flat-earth, complete with references for each one from the primary scientific literature.

There is, in fact, no explanation for how life and her species are supposed to have evolved.

Completely false. Life evolves via mutation, selection, drift, migration, and the mating system.

To head off that minor little problem, the page explains to the reader that "in evolutionary theory it is taken as axiomatic that an original self-replicating life form existed in the distant past, regardless of its origin." How convenient. Now all those thorny complexity problems can be swept under the rug as being outside of scope; but who are we fooling?

They're not trying to fool anyone, just telling it how it is. Evolution does not concern itself with the origin of life. That is because, for evolution to occur, it requires an imperfect replicator. Therefore, anything that leads up to that first imperfect replicator is logically not evolution.

Aside from the fact that nothing is "known" from phylogenetic trees, the idea that hindlimbs are a prediction of evolution is a joke.

Read the section again. Not to use of the term "possibility."

Ahh, but who are we fooling? Allele frequencies change all the time. So what? You're not creating anything new.

It's creating new allele frequencies. Most people realize that when talking about changing allele frequencies 0.0->0.001 is a change in allele frequency. Clearly mutation falls under that description, and clearly new, novel genes are formed all the time.

I hate to have to be the one to tell you this, but there's a whole bunch we don't know about micro biology. So, no, I'm afraid I can't explain the presence of the telomeres in the middle of chromosome 2 in humans and apes.

Anyone with a good high-school biology background should be able to know how it occured. It is hardly a mystery. Teleomeres are found in the middle of human chromosome 2 because it is the result of an ancient fussion between two chromosomes. In the other apes, these chromosomes are still separate.

You think evolution created these chromosomes, even though you don't know how it could have done said task. Nor do you have the slightest idea of what function said design might serve.

CD, perhaps you shouldn't go around telling people what they can or can't do without first testing them on it. Such rhetoric is no different than lying about someone else, which is not a good way to opperate in an intellectual discussion.
Chromosomes are simply a DNA polymere, packaged with proteins. No mystery there.
Chromosomes function to keep the hereditary information togering in a well controled location(s) so that when cell division occurs there is low chance that one of the daughter cells is missing something. Chromosomes are also important in regulating gene expression.

[caravelair]

Originally posted by Charles Darwin
I see. You and the other folks -- I see a pattern. Of course we cannot believe they were created, so ..., evolution must be true. We were talking about a scientific fact, but this is a switch. What you are really saying is this is a metaphysical fact. Given your metaphysical position, evolution is a fact. Ok, I'll buy that.

i believe you have completely avoided the question that was asked by changing the subject entirely. i would like to know your answer to the question, so i'll post it again:

Originally posted by lpetrich
And if you do, do you believe that it represents ancestor-descendant chains or something like

55 myr: *POOF!* Hyracotherium was created
50 myr: *POOF!* Orohippus was created
40 myr: *POOF!* Mesohippus was created
35 myr: *POOF!* Miohippus was created
17 myr: *POOF!* Merychippus was created
12 myr: *POOF!* Dinohippus was created
4 myr: *POOF!* Equus was created
2 myr: *POOF!* Various present-day equine species created

And in human ancestry:

5 myr: *POOF!* Ardipithecus ramidus was created
4 myr: *POOF!* Australopithecus afarensis was created
3 myr: *POOF!* Australopithecus africanus was created
2.7 myr: *POOF!* Paranthropus aethiopicus was created
2.3 myr: *POOF!* Paranthropus boisei was created
2 myr: *POOF!* Paranthropus robustus was created
2.5 myr: *POOF!* Homo habilis was created
2 myr: *POOF!* Homo erectus was created
0.7 myr: *POOF!* Homo heidelbergensis was created
0.3 myr: *POOF!* Homo neanderthalensis was created
0.1 myr: *POOF!* Homo sapiens was created

With each species having a suspicious resemblance to existing species.

so... do you believe that each of theseb species was created, died out, and then replaced with the creation of another very similar species?

[Jet Black]

Originally posted by Charles Darwin
Yes, I do understand the retroviral insertion argument. They are supposed to be irreversible markers; which is why, for example, the [Ape + chimp but not human] ERV is interesting since at the homologous human site the DNA sequence clearly shows a clean pre insertion site. I also understand know that ERVs can have site selectivity. And I also understand that, if evolution is true, there must have been a sort of "punctuated equilibrium" in the HERV world; and that HERVs must have played a role in evolution since they, in fact, have a regulatory function.


the ape and chimp ERV is easily explainable by saying that it was introduced into the ape-chimp line after the human line split off.

what is the regulatory finction of the HERV?

[lpetrich]

Charles Darwin:
(endosymbiosis:)
You mean the story that a big cell ate up a little cell and forever after the little one was there, working away to produce all those ATPs via that convenient electron transport chain that just happened to be there, with its series of re-dox steps that just happened to be there, and the ATPase which just happened to be there? Well, you're right, I don't buy it.

Except that various bacteria also have electron-transport chains and membrane-based ATP synthesis. And it is not difficult to imagine a process of natural selection that results in the selection of an aerobic organic-eating bacterium as the endosymbiont rather than a bacterium with a different metabolism. Imagine a protoeukaryote eating lots of different kinds of bacteria and some of them staying inside, with the most useful of them helping their hosts reproduce more than the others.

Aside from all this complexity, there is thorny little problem of organelles common to prokaryotes and eukaryotes. Doesn't quite fit the theory of endosymbiosis.

So what? Genome-less organelles like ribosomes and flagella are directly produced by their host cells.

Oh, also, why is the possession of genetic material mysterious for an organelle?

What's the point of an organelle having its own genome, especially a very reduced genome? Especially when cells can create several kinds of genome-less organelles from their cytoplasm.

[Just fixing an inadvertant smiley. -GunnerJ]

[lpetrich]

Charles Darwin:
... Perhaps by some magical process species transform themselves into other species. ...

As opposed to some magical process that poofs species into existence?

How new species form is a subject of active research; and so far, there is no need to consider it a magical process.

That's one reason why the genome of the fruit fly Drosophila pseudoobscura is being sequenced (http://www.hgsc.bcm.tmc.edu/projects/drosophila/); it is close to lab fly Drosophila melanogaster, and comparison of the two flies' genomes should help indicate what distinguishes a species from some very similar species. This is also why there are some proposals (http://www.genome.gov/10002154) to sequence two other close species: D. simulans and D. yakuba.

[lpetrich]

Charles Darwin:
(evolution of echolocation...)
I don't say one big jump, nor do I say it cannot have evolved. I say it isn't likely.

But when you mention the details of the fancier forms of echolocation, you seem like you believe in the one-big-jump theory. So what do you think happened?

Also, the analogy with human technology suffers from the fact that human designers were involved.

Except that human designers do not create fully-developed technologies in one swell foop -- and are not capable of doing so. Even the greatest geniuses work in collaboration with others. As a result, development of technology proceeds incrementally, in a fashion that resembles biological evolution.

(Reciprocal altruism...)
Do you know how big the design space is which evolution had to randomly search through and hit upon, and test, this design? How many years were available, and what mutational rates would be required? I don't think we have a good handle on this, so this is really just speculation.

That would require understanding how genes translate into behavior, which has been much more difficult than understanding how genes translate into proteins.

But one can get around that by studying vampire bats' behavioral repertoire to work how blood-sharing could have evolved.

[lpetrich]

Charles Darwin:
(what topology of horse relationships...)
I really don't know, but I do know that the mythical horse sequence convinced many a lay person for the better part of a century before it was finally admitted to be, well, ... mythical.

My guess is that CD's main "knowledge" of horse evolution comes from creationist quote miners. The only thing that's been discredited is a simple straight-line model of horse evolution -- it is a very bushy sort of tree, with only some recent branchings surviving.

What we have is a bunch of different species which, if evolution is true, must have punctuated into each other.

So what? And I take it that you endorse the *POOF!* theory of origins.

I also know that evolution, beyond handwaving, doesn't explain how any of those species got there in the first place anyway. Why is it you think this makes evolution a scientific fact?

What would you consider acceptable evidence, O CD? Going back in time in a time machine and watching all of those ancestral species?

I see. You and the other folks -- I see a pattern. Of course we cannot believe they were created, so ..., evolution must be true. ...

No, you extrapolate.

All you have to do to start echolocating is making sounds and listening for echoes. It's that simple.

Sorry, it is a little more complicated than that.

How is even the simplest form of echolocation more complicated that that?

[Charles Darwin]

Originally posted by lpetrich
Charles Darwin:
(on falsehood of evolution implying discrepant family trees...)
How do you know it could be anything, such as a wildly different tree?

What alternative do you think is plausible? Special creation of species with the appearance of evolution?

(unused areas of the genome...)
How do you know that an area isn't used?

Experience with molecular-level genetics: the more functionally-constrained something is, the more the sequences look alike between species. So some rapidly-evolving area implies low constraint.

But (i) dolphins and sharks; and (ii) marsupial and placental flying squirrels have some dramatic differences too.

So what? That's how one can recognize convergent evolution.

Furthermore, we really do not understand how the phenotype arises from the genotype.

Which is just plain wrong. We know how proteins are made from genes, and we are accumulating clues as to how other features are made.

Finally, you seem to be conveniently ignoring the many phylogenetic mismatches.

Like what?

If you believe that phylogentic congruence proves evolution, then what about the mismatches?

Whatever you have in mind. Please explain in more detail.


When you say life looks like it evolved you're begging the question. That is the question at hand. I would argue that life, the most complex thing known, does not look like it evolved; not by a long shot.

You also beg the question when you say that rapidly evolving areas have no function (ie, low constraint). You cannot claim unused segments as evidence for evolution, and then support your claim by saying you know they are unused because they are rapidly evolving. You are presupposing evolution in order to present evidence for evolution.

And no, I'm not just "plain wrong" that we still lack many details of how the phenotype is created from the genotype. Knowing how protein synthesis works is only one step in the process.

Regarding phylogenetic mismatches, I'm amazed that I'm even being asked for examples. Look in any research journal or review article dealing with phylogeny. Examples are abundant.

[GunnerJ]

Originally posted by Jack the Bodiless
I've used echolocation myself: I've dropped a stone down a well, and I've even made a clicking sound to get a "feel" for the size of a dark cave. The results weren't particulary precise, but it wasn't exactly difficult to do either.

But maybe I'm just a transitional form between the two species depicted above by Oolon.

[off topic, way old] From your name, I'd have guessed you were a transitional form between homo sapiens sapiens and homo sapiens psionicus. But what would that make Diamond Mask? [/OT,WO]

[GunnerJ]

When you say life looks like it evolved you're begging the question. That is the question at hand. I would argue that life, the most complex thing known, does not look like it evolved; not by a long shot.

Out of curiousity, what do you think life "looks like," in relation to it not "look[ing] like" evolution?

[Urvogel Reverie]

Originally posted by Charles Darwin
That's an interesting claim. How could it be that :

"It is not possible to construe the variation in the frequency of alleles within populations both isolated and otherwise, as anything but the most compelling of data to substantiate evolutionary biology."

Starting with the 2nd half of the claim, you are saying that these data are "most compelling." That's awfully strong language for something that, in fact, creates no new sequences. Obviously evolution requires massive genetic changes, and this gives us none. Hmmm.

Then, on to the 1st half of the claim, you seem to think "it is not possible to construe" the data "as anything but" supporting evolution. This is, of course, not a scientific statement. In science we propose theories rather than make metaphysical proclamations. We say, "If P, then Q", not "If and only if P, then Q". The former describes the expected outcome of a theory. The latter is a universal truth claim about Q. But then again, who said this was science.



Then why is the recurrent laryngeal nerve evidence for evolution?


Creates no new sequences? Are you seriously proposing that meiotic recombination fails to yield variety in the genotype? If in fact this is your claim, references for such a bold assertion are requisite, and if it is not your claim, elaboration of a statement no doubt deliberately nebulous, is in order.

Your summation of basic logic is nice and well, however, as my statements about genetics and evolution are meant in the context that whereas evolutionary biology predicted what has now been confirmed by genetics, it is nothing less than special pleading to say that on the contrary the genetics do not substantiate evolution. Hence, "it is not possible to construe the data as anything but" support for evolutionary biology, and still be true to empirical reality.

Lastly, a recurrent laryngeal nerve is apomorphy which, to my knowledge, has not precluded conventional systematic analysis and identified fish as the phyletic progenitor of eutherians. Your implicit and outright assertions to the contrary demand substantiation.

Urvogel Reverie

[Urvogel Reverie]

Originally posted by Charles Darwin
But since I did not, in fact, say that, your point is irrelevant.

It is implicit in your post, and it is in fact a standard viewpoint of creationists as a whole. Your entire farcical post about how punctuated equilibrium is akin to a ideological conspiracy to mask the defficiencies of the fossil record for evolutionary biology, is built upon (among others) the argument that paleontology fails to vindicate evolution.

Urvogel Reverie

[Urvogel Reverie]

Originally posted by Charles Darwin
But, in fact, I did not say that.


Your post on the matter of chromosome 2 in hominids implied just such a statement. If you do not wish people to misinterpret what you have posted, perhaps you ought to abandon attempts to couch your views in such obfuscation that you can readily change your posts to accomodate whatever particular argument you happen to be making at any one time.

Urvogel Reverie

[Urvogel Reverie]

Originally posted by Charles Darwin


Regarding phylogenetic mismatches, I'm amazed that I'm even being asked for examples. Look in any research journal or review article dealing with phylogeny. Examples are abundant.


And once more you reveal a poor understanding of the methodology of phylogenetic reconstruction, and no doubt, the principals of cladistics as a whole which are so often employed by modern systematists in this endeavor. Of course, it is possible that I am wrong, and thus elaboration of this idea of yours that phylogenetic mapping is a problem, would be in order.

Urvogel Reverie

[lpetrich]

Charles Darwin:
When you say life looks like it evolved you're begging the question. That is the question at hand.

How is it that living things fit into a family-tree-like hierarchy so well?

Is it some obscure whim? Or is it something else? Like descent with modification?

I would argue that life, the most complex thing known, does not look like it evolved; not by a long shot.

Maybe not to you, O CD. But given the success of biological evolution so far, I do think that living things look like the result of evolultion.

You also beg the question when you say that rapidly evolving areas have no function (ie, low constraint). ...

One can test that hypothesis by comparing amounts of constraint to known functionality. And the more critical parts of proteins are indeed found to evolve more slowly.

And no, I'm not just "plain wrong" that we still lack many details of how the phenotype is created from the genotype. Knowing how protein synthesis works is only one step in the process.

However, it's an important step, and you had claimed earlier that we are almost completely ignorant of how the phenotype comes from the genotype.

Regarding phylogenetic mismatches, I'm amazed that I'm even being asked for examples. Look in any research journal or review article dealing with phylogeny. Examples are abundant.

I still don't know what you are talking about. Please give us some examples -- and serious ones.

[Doubting Didymus]

Originally posted by Charles Darwin
How do you know it could be anything, such as a wildly different tree?

What do you think the separate creation hypothesis predicts the tree to look like?

How do you know that an area isn't used?

When an area produces no polypeptide, or a polypeptide is degraded before being put to use, or a finished polypeptide results that does not have a function. You think when geneticists say 'this stretch of nucleotide sequence has no function' they're just making shit up?

But (i) dolphins and sharks; and (ii) marsupial and placental flying squirrels have some dramatic differences too. Furthermore, we really do not understand how the phenotype arises from the genotype. Finally, you seem to be conveniently ignoring the many phylogenetic mismatches. If you believe that phylogentic congruence proves evolution, then what about the mismatches?

Yes, dolphins are different from sharks. However, dolphins have very nearly got the exact genes of a placental mammal. Why should this be? Evolution explains it nicely: dolphins have mammilian genes because they are descended from mammals. How do you explain this with a separate creation model of biodiversity?

Regarding phylogenetic mismatches: they are few and far between. They get a lot of airtime in phylogenetic publications because they are rare, unexpected, and worthy of receiving an explaination. It's not like these things are impossible under the evolutionary framework, just that it should be unlikely. For example, further study of the problem may reveal answers: segments of chromosome can shift and change on rare occasions, it may be that the genetic segment will be found somewhere else, surrounded by the correct fragments that would have been its neighbors. If something is present in two species, but not in a third which is hypothesised to be between them on a tree, there may have been a simple deletion. An extreme example: evolution predicts that humans should have the same number of chromosomes as chimps. They dont. Has evolutionary theory failed? We look at our chromosomes, and find that one of them has frigging telomeres in the center. What seemed a discrepancy vanishes under scrutiny. So, to sum up: where a discrepancy exists, evidence will be found in most cases that explains it.

[GunnerJ]

But... dolphins and sharks... have some dramatic differences too.

However, a dolphin is morphologically more similar to a shark than to an elephant, at least in terms of swimming ability. So if the "Creator" is "re-using" code for similar functional morphologies, why is a dolphin's DNA closer to an elepahnt's than a shark's?


DD seyz: Endogenous retroviral insertions confirming phylogenetic trees constructed on independant data prove that species descend from a common ancestor.

CD replies:

So does the failure of endogenous retrovial insertions to confirm pre established trees disprove evolution?


No. This does not follow from what DD said at all.

Why? Because there are lots of reasons why, for example, an "HERV... shows up in gorillas and chimps but not humans." They have been listed. Thus, it's plausible that an HERV would not conform to the phylogenic tree for reasons other than the falsehood of evolution.

However, outside of evolution (by this we mean the fact of evolution, i.e., common descent) being accurate, there is no reason for HERVs to confirm the phylogenetic trees.*

If you can't tell the difference between this and mere hand-waving and ad-hoc rationalization, then, well, there isn't much I can do to help you.

*Unless, of course, the "Creator" just liked putting the same viral DNA fragments into the genome of independant creations just for the hell of it.

[Charles Darwin]

Originally posted by The Lone Ranger
How, exactly, is this a “clever attempt to hoodwink those less knowledgable [sic] readers”? ...
Cheers,

Michael


How do you dress up an idea that makes no sense, get it accepted as science, and even as a scientific fact? Well it isn't easy. You'll have to stretch the truth in several different ways. First, and most obviously, you have to direct attention away from the fact that your idea is nothing more than handwaving, and doesn't actually explain how life and her intricacies were supposed to have arisen.

One tests the validity of scientific hypotheses and theories by testing to see whether their predictions conform to reality, just as the site states. Do you know of some other way?

It is not a matter of knowing another way, it is a matter of understanding science. One doesn't get carried away with an absurd notion, claiming it is a fact, because it can be used to model some observables. No one believes the earth is flat, though I can give you 29+ validations for that model.

Can you? I don’t believe that you can. Remember, for the flat-earth model to be a legitimate scientific theory, it must be based upon actual evidence, and it must make specific predictions which can be tested and falsified. If the predictions are shown to be false, they are not "validations" of the theory.

The flat-earth theory is probably one of the most successful false models in the history of science. Physicists and engineers use it literally everyday. It has produced an untold number of incredibly accurate predictions and is indispensable in such areas as machine design, projectile motion, construction, architecture, structural engineering, etc., etc.

But since contrived predictions are all you've got, you're going to have to stick with them, and make falsification your king:

If the theory fails these tests, then it must be modified or abandoned.

This, of course, is not at all true. Falsification can be sustained in one of a number of ways short of abandonment or modification. Likewise, you'll have to elevate verification beyond its limit, for remember, you goal is to establish your idea as a scientific fact:

While it’s true that if the predictions are verified, this doesn’t prove the theory to be true, it does give us more confidence in the theory.

Again, without serious qualification, this is not true. False models make plenty of correct predictions. And because your idea is so absurd, you're going to have to stretch things to come up with your supposed "predictions:"

So, one way to test the validity of the phylogenetic trees – and of the evolutionary theory that they’re based upon – is to see if the predictions they make hold up in the real world. The trees predict that whales are descended from ancestors with hindlimbs. A corollary of that prediction is that whales should still possess genes for hindlimbs, and therefore we would expect to occasionally find a whale with hindlimbs. This is a straightforward prediction.

No, in fact, this is not a corollary. Let's read on:

if whales were never observed to have atavistic hindlimbs, and a careful analysis of whales’ DNA showed conclusively that they did not have genes that were homologous to those which cause the growth of hindlimbs in terrestrial mammals, that would indeed be a serious blow to evolutionary theory.

A "serious blow"? Come now, do you really believe this would falsify evolution? Try hard, can you not think up just one explanation for such a finding? Gee, could those genes have been lost in the evolutionary process. After all, remember, it took millions of years.

If we didn’t see the occasional whale born with hindlimbs, this would indeed be evidence that evolutionary theory was in need of revision.

Ah yes, a little revision:

"Researchers at Cambridge University have now discovered that genes are not only altered in the evolutionary process, but that they can be lost altogether. 'We are now gaining a much deeper insight into how evolution really works," said Charles Darwin, great-great-great-great Grandson of the inventor of evolution."

That’s the point. The observations could have provided evidence that evolution is not a fact. If so, we’d have no choice but to accept that. They didn’t though; they did just the opposite. That’s how science is done. We put our hypotheses and theories on the chopping block by testing their claims against reality. If they fail the tests, out they go. So far, evolutionary theory has not failed any of the tests we’ve been able to devise for it.

I'm sorry, but you're confusing mythology for science, but what's new?

Next, you'll have to narrow the scope of your theory. Defending the absurd is hard enough as it is, let's not make it any harder:

I’m at a loss to understand why so many people have the erroneous impression that evolutionary theory has anything whatsoever to do with the origins of life. Repeat after me: evolutionary theory is about how living things have evolved over time – since the origin(s) of life. Saying that evolutionary theory is incomplete or invalid because it doesn’t explain the origin of life is like saying that chemistry is an invalid field because it doesn’t explain the origins of atoms.

The bit about chemistry is a nice touch. Equate the origin of life with matter itself. Who in their right mind expects science to get metaphysical, after all? Meanwhile, evolutionists are busy writing books, conducting conferences, publishing journals, writing research proposals, and so forth, all dedicated to the origin of life problem. They even claim the problem is all but solved. It is not a question of if, but how, they assure us, though they've precious little to show us in the way of actual results. Oh, but I forgot, this is not actually part of evolution.

Not only have we narrowed scope, but we've got a wonderful trash bin to stash all those nasty complexity problems. The DNA code, protein synthesis, the Krebs cycle? No problem, they're not part of evolution.

Now what about all those nasty macro problems. How do we explain the gzillion optimizations and adaptations nature reveals to us? Well, this is really no problem at all. The strategy is two-fold. First, downplay the design. It isn't really all that complex after all. A few mutations here, a few selections there, and who knows what might pop out:

Besides, as several posters have pointed out, echolocation isn’t difficult. Any animal with ears and the ability to produce sound can echolocate, at least crudely. Why is it so difficult to conceptualize how the process could have been refined by natural selection? Indeed, we have living examples of animals that can echolocate very crudely (humans, for example), to those that can echolocate rather more effectively (oilbirds, for instance), to those that can echolocate quite well (bats and cetaceans).

Ignorance is bliss. This is the "just add water" version of biology, and you'll need to stick to it. Second, don't forget to chastise the creationist (always call them creationists by the way) for demanding all the details. Explain that this is the way real scientists do things:

The point of the site – as per your request – is to provide evidence for the fact of evolution, not to explain every little adaptation. Do you consult the owner’s manual of your automobile for an explanation of how the Bernoulli effect applies to the function of a carburetor? Do you throw the manual down in disgust and conclude that it's worthless because it doesn't provide that explanation?

Always differentiate between the "fact" of evolution, which we all know, and the "theory" of evolution, that is, the details, which shouldn't concern us too much. The owner's manual analogy is brilliant. Evolution is like the owner's manual, and the details of evolution are like the details of how the car works. The owner's manual isn't worthless just because it doesn't tell all. And likewise, evolution isn't worthless. This subtle shifting of the claim from "evolution is a fact" to "evolution isn't worthless" works wonders in reducing your evidential burden too.

Next, never forget that offense is the best defense. You're trying to defend the absurd, and it will help to shift the focus onto the skeptic:

If you’re determined not to believe a thing, you’re not going to be convinced by evidence, nor are you likely to gain a very thorough understanding of the subject. With respect, you give every indication of being someone who very much wants for evolution not to be true. If this is the case, it’s going to be difficult to convince you of the legitimacy of evolutionary theory on the basis of something as inconsequential as evidence.

Yes, there must be something wrong with the skeptic to be ignoring all this obvious evidence. Religious motivations no doubt. The next fallacy you'll need to use at some point is the argument from authority:

Well, to put it bluntly, there are many thousands of evolutionary biologists over the world who have studied the matter quite thoroughly. They’re quite convinced that the evidence in favor of evolution is so voluminous – and the evidence against it is conspicuously nonexistent – that they’re quite comfortable calling it an established fact. Oddly, the only ones who deny that evolution is a fact consistently show themselves to be a.) ignorant of the subject, and/or b.) strongly prejudiced against acceptance of evolution for religious/political/whatever reasons.

Notice too how the ad hominem can be inserted just about anywhere. Tell them that they must be ignorant or prejudiced. Now if this battery of fallacies still haven't shut'em up, and they are still raising those thorny complexity problems, you'll need to fall back on the fact vs. theory distinction. Just remember this: every scientific problem they raise falls into the "theory" box, and every supportive argument we can raise falls into the "fact" box:

I note, in passing, that you still seem to be incapable of distinguishing between the fact of evolution (that all organisms show clear and unmistakable evidence of being related through common descent) and the theory of evolution (which explains that fact). Why is that so difficult a concept? If one didn’t know better, one would suspect that you conflate the ideas because you don’t want to understand the differences.

Again, toss those ad hominems in there wherever you can. The key is to enforce the idea that the problems and unknowns with evolution are trivial, and that therefore questioning evolution is no different than doubting the obvious:

Whining that no one has explained every little detail is not the same thing as providing evidence that the conclusion is false. If you see and videotape Person "A" shooting Person "B", if you see Person "B" bleeding afterward, if you see the surgeons removing the bullet from Person "B"'s body, if you hear Person "A" confess to the crime -- do you claim that it's not a fact that Person "A" shot Person "B" because you don't know where the bullet was manufactured?

Next, be on the watch for any criticisms of natural selection. The rules of the game are that the mutations are random, but the selection is not. Whenever they use the word random, tell'em they don't understand the theory to begin with:

If you think that natural selection is a random process, then yours is a very poor understanding of evolutionary theory indeed.

Another trick that comes in handy is to shift the burden of proof. True, science is all about theories that are supposed to be backed up by evidence; and we are the ones making the claim that evolution is a fact. But it never hurts to put'em on their heels by asking them to falsify our theory (don't tell'em that avoiding falsification means very little):

Perhaps you think that there exists some sort of “genetic” barrier which would somehow prevent one species from evolving into another, I would like to point out that no studies have ever provided evidence that such barriers exist.

So now you've got'em where they have to show a genetic barrier, excellent. No matter that they never claimed any such barrier, or that our theory requires enormous amounts of change compared to our puny examples of speciation.

Now at some point you may feel the need to overstate the evidence. Go ahead, have no trepidation, for it will either silence them, or if it doesn't you can fall back any number of explanations:

Molecular biology and genetics provide overwhelming evidence that all living organisms are related and share common ancestry.

The fossil record provides unambiguous evidence that organisms have been evolving for quite some time.

Obviously these are not scientific statements, but if they complain, just shift the burden of proof again:

what evidence do you have that evolution is not true and that 99.99% of the world’s biologists, geologists, paleontologists, astronomers, cosmologists, etc. are completely deluded?

See how easy it is? I'm beginning to believe it myself.

[Muad'Dib]

Hi Charles Darwin,

Could you give an example of something you consider to be a scientific fact, and the ground on which you base that assessment?

Thanks,
Muad'Dib

[Charles Darwin]

Originally posted by RufusAtticus
Completely false. Life evolves via mutation, selection, drift, migration, and the mating system.


I said that there is, in fact, no explanation for how life and her species are supposed to have evolved, and you responded that this is "Completely false. Life evolves via mutation, selection, drift, migration, and the mating system." Very good, and astrology works by the stars right? C'mon, is it not clear that I'm talking about scientific explanations. You know, that actually explain *how* it is supposed to happen. You don't have any details, why not just admit it? This is not trivial. I'm not asking for where the bullet was manufactured in a murder case. I'm asking for the very basics which "mutation, selection, drift, migration, and the mating system" do not come even close to explaining. How did echolocation arise (and no, telling me it is simple is not sufficient). This is an example of a fundamental problem with evolution which you'all cannot just explain away as a minor detail.

I wrote that "You think evolution created these chromosomes, even though you don't know how it could have done said task. Nor do you have the slightest idea of what function said design might serve." And you responded:

CD, perhaps you shouldn't go around telling people what they can or can't do without first testing them on it. Such rhetoric is no different than lying about someone else, which is not a good way to opperate in an intellectual discussion.
1. Chromosomes are simply a DNA polymere, packaged with proteins. No mystery there.
2. Chromosomes function to keep the hereditary information togering in a well controled location(s) so that when cell division occurs there is low chance that one of the daughter cells is missing something. Chromosomes are also important in regulating gene expression.

You missed my point. I was talking about the subject at hand (ie, the presence of the telomeres in the middle of the chromosome) not chromosomes themselves.

[Charles Darwin]

Originally posted by Charles Darwin
I see. You and the other folks -- I see a pattern. Of course we cannot believe they were created, so ..., evolution must be true. We were talking about a scientific fact, but this is a switch. What you are really saying is this is a metaphysical fact. Given your metaphysical position, evolution is a fact. Ok, I'll buy that.

Originally posted by caravelair
i believe you have completely avoided the question that was asked by changing the subject entirely. i would like to know your answer to the question, so i'll post it again:


so... do you believe that each of theseb species was created, died out, and then replaced with the creation of another very similar species?

I'd be delighted to join in on a religious discussion, including personal beliefs, but my personal religous beliefs have precisely zero influence on whether evolution is a scientific fact or not.

Regarding the question of horse evolution, I did not dodge the question but said I don't know how they got there (maybe that was in another post).

[Charles Darwin]

Originally posted by Spike Spiegel
the ape and chimp ERV is easily explainable by saying that it was introduced into the ape-chimp line after the human line split off.

However, for a range of reasons, evolutionists already believe that the ape split off first; then later came the human-chimp split.

[Charles Darwin]

Originally posted by lpetrich

Charles Darwin quote on endosymbiosis: You mean the story that a big cell ate up a little cell and forever after the little one was there, working away to produce all those ATPs via that convenient electron transport chain that just happened to be there, with its series of re-dox steps that just happened to be there, and the ATPase which just happened to be there? Well, you're right, I don't buy it.

Except that various bacteria also have electron-transport chains and membrane-based ATP synthesis. And it is not difficult to imagine a process of natural selection that results in the selection of an aerobic organic-eating bacterium as the endosymbiont rather than a bacterium with a different metabolism. Imagine a protoeukaryote eating lots of different kinds of bacteria and some of them staying inside, with the most useful of them helping their hosts reproduce more than the others.

I'm not doubting that we can contrive explanations, where we are free to imagine.



Charles Darwin quote: Aside from all this complexity, there is thorny little problem of organelles common to prokaryotes and eukaryotes. Doesn't quite fit the theory of endosymbiosis.

So what? Genome-less organelles like ribosomes and flagella are directly produced by their host cells.

I was referring to membrane-bound organelles, independent of the plasma membrane, such as things like acidocalcisomes which are found in both some prokaryotes and eukaryotes.

[Charles Darwin]

Originally posted by lpetrich
Charles Darwin:
(evolution of echolocation...)
I don't say one big jump, nor do I say it cannot have evolved. I say it isn't likely.

But when you mention the details of the fancier forms of echolocation, you seem like you believe in the one-big-jump theory. So what do you think happened?

I really don't know, but again, my personal opinion on the matter has precisely zero influence on whether evolution is a scientific fact or not.

[Charles Darwin]

Originally posted by lpetrich
What we have is a bunch of different species which, if evolution is true, must have punctuated into each other.

So what? And I take it that you endorse the *POOF!* theory of origins.

Yes, I got the point. No need to keep repeating. Evolution is a fact for you.


Originally posted by lpetrich
I see. You and the other folks -- I see a pattern. Of course we cannot believe they were created, so ..., evolution must be true. ...

No, you extrapolate.

I don't follow. How am I extrapolating?

[Charles Darwin]

Originally posted by GunnerJ
Out of curiousity, what do you think life "looks like," in relation to it not "look[ing] like" evolution?

Pretty complicated.

[GunnerJ]

Originally posted by Charles Darwin
Pretty complicated.

This pithy non-answer speaks for itself.

[The Lone Ranger]

Originally posted by Charles Darwin:
How do you dress up an idea that makes no sense, get it accepted as science, and even as a scientific fact? Well it isn't easy. You'll have to stretch the truth in several different ways. First, and most obviously, you have to direct attention away from the fact that your idea is nothing more than handwaving, and doesn't actually explain how life and her intricacies were supposed to have arisen.

First of all, for the umpteenth time, evolutionary theory doesn’t attempt to explain the origin(s) of life. As far as evolutionary biology is concerned, life may be the result of purple goblins from the 12th dimension. What matters is what has happened since the origin(s) of life.

To claim that evolution is a flawed theory because it cannot explain the origin(s) of life is no more logical than would be the claim that quantum mechanics is a flawed theory because it doesn’t explain why some genes are dominant and others are recessive.

Of course, how life arose is relevant to evolutionary biology, since life must first exist in order for it to evolve. Knowing more about how life may have arisen would also be quite useful to biologists, since it could very likely give us clues as to the chemical idiosyncracies displayed by living organisms. [Why do all living organisms use the same 20 amino acids, for example? Are these the “best” combination of amino acids for building proteins, or is it just chance that these were the ones that the first living organisms used?] So, the origin(s) of life is certainly of interest, but it nonetheless lies outside the scope of evolutionary theory.

You seem to want very much for evolutionary theory to be something that it is not, and never was.

Evolutionary biologists consider it a fact – that is, established beyond any reasonable doubt – that all extant organisms are related through common descent. I’m curious as to how this idea could be said to make no sense.


Here’s an overview of evolutionary theory. Please tell us where it breaks down.

[LIST=1]
All populations of organisms have the potential for very high growth rates. If one does the math, it’s easy to show that even very slowly-reproducing animals like elephants produce enough offspring that the planet would be literally covered with elephants in just a few hundred years if all elephants that are born survived and produced young of their own.

Resources (food, nesting sites, etc.) are necessarily limited in supply. Since the Earth is not infinite in size, this is an uncontroversial statement.

Conclusion: Since populations can potentially grow so fast, and since resources are limited in supply, more individuals are born than the available resources can possibly support. Thus, there will inevitably be competition for resources. (Competition does not necessarily mean fighting, by the way.) [If you think this conclusion is false, please explain.]

There is a great deal of variation among individuals within a population.

Variation is largely heritable. That is, individuals tend to resemble their parents, grandparents, and so forth more than they resemble random members of the population.

Survival and reproduction of individuals often depends upon the heritable traits they possess.

Conclusion: Since there is competition for resources, those individuals who happen to possess heritable traits which make them well-suited to their environment are more likely to survive and pass those traits on to offspring than are those individuals unlucky enough to be born with traits which make them poorly-suited to their environment. This phenomenon is called natural selection. [If you think this conclusion is false, please explain why.]

Conclusion: Given that those individuals that are well-suited to their environment are more likely to survive and reproduce than are those that are poorly-suited to it, the genetic makeup of populations is expected to change over time, as traits which make their bearers well-suited to the environment become more common and traits which make their bearers less well-suited to the environment become rarer. This process is called evolution. [If you disagree with this conclusion, please explain why.]
[/LIST=1]


No one disputes that natural selection occurs, and that populations evolve as a result. Nor is there any disagreement within the scientific community that the Earth is more than four billion years old. Fossils have been found in rocks that are almost four billion years old.

Given the age of the Earth and the amount of time that living organisms have been around, and given that populations do evolve, it is an inevitable conclusion that we should expect to see quite a lot of evolutionary change over time. Indeed, field studies often document rates of evolution hundreds or even thousands of times greater than are necessary to explain the rates of change implied by the fossil record.

There are three possible reasons why we wouldn’t expect substantial amounts of evolution to have occurred.

[LIST=1]
The Earth isn’t as old as the evidence indicates and/or life hasn’t existed for as long as the evidence indicates. [If you think this is the case, please explain why the geologists, astronomers, and paleontologists are wrong.]

Some sort of mechanism exists which prevents populations from evolving beyond a certain point. Given that genetic variation within a species sometimes equals or exceeds the genetic variation between species, this seems unlikely, to say the least. Geneticists have consistently found that the genetic variation between species (or genera, or families, or even between kingdoms, for that matter) is qualitative, not quantitative. [If you think such mechanisms exist, please explain why the geneticists are wrong. Also, please show us where the mechanism(s) are: do they prevent evolution between species, and how? Do they work at a higher level and prevent evolution between genera? Do they prevent evolution between families? Where are they, and how do they function?]

Populations of organisms evolve at rates that are far slower than studies indicate, and/or mutations (the ultimate source of new alleles) are far rarer than studies indicate. [If this is the case, please explain to us why the thousands of studies in question are wrong.]
[/LIST=1]


No one believes the earth is flat, though I can give you 29+ validations for that model.
So you say. I don’t believe that you can, and I challenge you to do so. Please provide 29 “validations” for the flat-earth model that are drawn from peer-reviewed literature.


The flat-earth theory is probably one of the most successful false models in the history of science. Physicists and engineers use it literally everyday. It has produced an untold number of incredibly accurate predictions and is indispensable in such areas as machine design, projectile motion, construction, architecture, structural engineering, etc., etc.

Indeed? I was taught in my GIS courses that one must take the curvature of the Earth into account if one wants to locate something accurately even on a small-scale map. Indeed, this is one of the biggest problems that mapmakers face: flat maps that cover an area of more than a few square miles inevitably distort features.

Engineers designing long bridges must take the Earth’s curvature into account, because a bridge that’s more than half a mile long or so must be build with the Earth’s curvature in mind. (Granted, it’s not a major concern, since a half-mile long bridge isn’t a rigid structure. If it were, this would be a major concern.) Artillery officers must take into account both the fact that the Earth’s surface isn’t flat and that the Earth rotates when plotting shell trajectories (after all, artillery pieces have been capable of firing shells over the horizon for over a century). Certainly, navigators of ships and aircraft must take into account the Earth’s curvature when plotting courses.

Physicists and engineers most certainly don’t use models which assume the Earth’s surface isn’t curved. Their models (quite correctly) assume that the curvature is small enough that it doesn’t matter if you’re concerned about something as small as a single building, but must be taken into account on larger scales.


You seem to think that evolution is not a falsifiable theory. In fact, it would be quite easy to falsify it. Ridiculously easy, in fact. Here are just a few ways.

As soon as it was discovered in the 1950s that DNA encodes genetic traits, it was predicted by biologists that there would be a correlation between how closely-related organisms appeared to be, and the similarity of their DNA. Specifically, it was predicted that those organisms which comparative anatomy, the fossil record, and comparative behavior suggested were close relatives would share very similar DNA, while organisms which appeared to be very different would have dissimilar DNA. Exactly as predicted, molecular analyses showed beyond any doubt that those organisms which independent lines of evidence suggested were closely-related were closely-related, genetically. Had the DNA turned out otherwise, this would have been a deathblow to evolutionary theory. We would have had to go back to the drawing board.

While we’re on the subject of genetics, if it had turned out that different species share different genetic codes, this would have completely falsified the notion of common descent.

Another very easy way to falsify evolutionary theory would be to find fossils where they couldn’t possibly exist, according to the theory. The existence of fossils of modern mammals in Precambrian sediments, for example, would immediately falsify evolutionary theory. Interestingly, no such “out of place” fossils have ever been found, despite decades of diligent searching.


The scientific community has concluded that the evidence in favor of the fact of evolution is overwhelming. The evidence which leads to that conclusion is publicly-available, and the reasoning has been explained. Your claim is that we’re wrong in our conclusion. The burden of proof, therefore, is on you to show us why we’re wrong.

Good luck.

Michael

[Charles Darwin]

Originally posted by lpetrich
Charles Darwin:You also beg the question when you say that rapidly evolving areas have no function (ie, low constraint). ...

One can test that hypothesis by comparing amounts of constraint to known functionality. And the more critical parts of proteins are indeed found to evolve more slowly.


Again, all you are doing here is parroting the standard evolution line. Segments that share greater similarity are assumed to have evolved more slowly, and are therefore assumed to have more functional constraint. And even if they are found to have greater functional constraint, so what? One does not need evolution to explain such a finding. You are contriving evidence where there is none.

Originally posted by lpetrich
Charles Darwin: Regarding phylogenetic mismatches, I'm amazed that I'm even being asked for examples. Look in any research journal or review article dealing with phylogeny. Examples are abundant.

I still don't know what you are talking about. Please give us some examples -- and serious ones.

Here are some samples.

"Genomes are evolving in a completely nonuniform way" Science 296:1601

"The phylogenetic position of the platyhelminths within the metazoan tree is examined using two independent sets of molecular characters, the evolution of 18S ribosomal RNA sequences and the diversity of the genes belonging to the HOX cluster. Among the various hypotheses that have been considered by zoologists, a position of the platyhelminths within the protostomes, related to the phyla with typical spiral cleavage, appears to be favoured when taking into account all separate lines of evidence. It is in conflict with the traditional hypothesis of an early emergence at the base of the bilaterally symmetrical animals. This relatively late emergence is compatible with the old idea that flatworms are derived from a coelomate ancestor. New evidence from the sequences of Hox genes suggests that the duplicated genes Ultrabithorax/abdominal-A constitute a genetic synapomorphy of the whole protostome clade." C R Acad Sci III., 320:83

"The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. Taxa previously proposed to be sister groups to the arthropods include Annelida, Onychophora, Tardigrada and others, but hypotheses of phylogenetic relationships have been conflicting. For example, onychophorans, like arthropods, moult periodically, have an arthropod arrangement of haemocoel, and have been related to arthropods in morphological and mitochondrial DNA sequence analyses. Like annelids, they possess segmental nephridia and muscles that are a combination of smooth and obliquely striated fibres. Our phylogenetic analysis of 18S ribosomal DNA sequences indicates a close relationship between arthropods, nematodes and all other moulting phyla. The results suggest that ecdysis (moulting) arose once and support the idea of a new clade, Ecdysozoa, containing moulting animals: arthropods, tardigrades, onychophorans, nematodes, nematomorphs, kinorhynchs and priapulids. No support is found for a clade of segmented animals, the Articulata, uniting annelids with arthropods. The hypothesis that nematodes are related to arthropods has important implications for developmental genetic studies using as model systems the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster, which are generally held to be phylogenetically distant from each other." Nature, 387:489

"Sequence data can sometimes mislead or even give an entirely wrong answer." Science, 276:1032

"Animal relationships derived from these new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present. Growing evidence suggests that phylogenies of animal phyla constructed by the analysis of 18S rRNA sequences may not be as accurate as originally thought." Science, 279:505

You also have distant species with similarities and allied species with similarities that derive from different development paths.

[Charles Darwin]

[QUOTE]Originally posted by Doubting Didymus
QUOTE]

What do you think the separate creation hypothesis predicts the tree to look like?

I don't think the separate creation hypothesis supplies sufficient detail to say how the species comparisons would play out.

When an area produces no polypeptide, or a polypeptide is degraded before being put to use, or a finished polypeptide results that does not have a function. You think when geneticists say 'this stretch of nucleotide sequence has no function' they're just making shit up?

Then if evolution is true, why do segments in the human and mouse genome, which evolutionists say are functionless, show near identity?

Yes, dolphins are different from sharks. However, dolphins have very nearly got the exact genes of a placental mammal. Why should this be? Evolution explains it nicely: dolphins have mammilian genes because they are descended from mammals. How do you explain this with a separate creation model of biodiversity?

"Evolution explains it nicely"? You've got to be kidding? Evolution has no idea (beyond hand waving) how all this change and complexity is supposed to have come about. You see some similarities between the dolphin and other mammals, and say evolution explains this nicely?! There's got to be something behind this, for science doesn't work this way.

You ask about a separate creation model. It is an interesting question. I don't have anything to add beyond the obvious, such as dolphins share genetic similarities because they share many traits with those mammals that evolutionists think they are descended from. But what's that got to do with evolution being a scientific fact?

[lpetrich]

Charles Darwin:
(endosymbiosis -- most successful is naturally selected...)
I'm not doubting that we can contrive explanations, where we are free to imagine.

Let's imagine that we could go back about 1.5-2 billion years ago to where some early protist was eating last year's crop of cyanobacterium colony.

The endosymbiosis hypothesis states that one of those protists swallowed, but did not digest, some alpha-proteobacterium. That bacterium multiplied inside, living off of the protist's waste products, like acetic acid. One day, due to some membrane-synthesis defect, the bacterium's outer membranes became a bit leaky, allowing some synthesized ATP to escape and AMP, ADP, and inorganic phosphate to return for assembly. This ATP supplied extra energy, helping its host eat more cyanobacterium and grow more and reproduce more, assisting the reproduction of that bacterium.

And that's what I would expect to see -- that or something similar. As opposed to this:

One day, some protists popped into existence with a big *POOF!*. They looked like some existing protist inhabited by an alpha-proteobacterium, however.

"Charles Darwin", is this what you believe?

I was referring to membrane-bound organelles, independent of the plasma membrane, such as things like acidocalcisomes which are found in both some prokaryotes and eukaryotes.

That ONLY means that some organelles have not originated by endosymbiosis; I've yet to see anyone claim that they have that origin.

[Doubting Didymus]

Originally posted by Charles Darwin
[B]I don't think the separate creation hypothesis supplies sufficient detail to say how the species comparisons would play out.

Which is exactly why my first statement read with the following sentiment: "There is no particular reason for any two phylogenetic tree creation methods to produce the same results, if species were are not in fact related."

Then if evolution is true, why do segments in the human and mouse genome, which evolutionists say are functionless, show near identity?

You do not appear to understand what I am talking about. Humans and mice are closely related. I should expect functionless DNA from those two species to be similar. I should also expect functionless DNA from a species closer to humans than mice to be more similar still to humans. Why shouldn't human and mouse junk DNA be similar?

"Evolution explains it nicely"? You've got to be kidding? Evolution has no idea (beyond hand waving) how all this change and complexity is supposed to have come about. You see some similarities between the dolphin and other mammals, and say evolution explains this nicely?! There's got to be something behind this, for science doesn't work this way.

Now it's my turn to not understand what you are talking about. Lets stay on this one specific topic: If an organisms genome is created without adapting it from ancestral genomes, we should see genome similarity correspond to similarities in environmental needs. It doesn't. Instead, genomes are more similar when organisms share more recent hypothesised ancestors. We should not be able to build ancestor trees if there were no ancestors, but we can. These ancestor trees should not be borne out by the hypothetical history in the fossil record, but they do (e.g. we should not find transitional forms in the right places. I do hope we can finish with this topic before discussing those, however, as I am no paleontologist, and the topic deserves its own thread. Deal?). This is the same for every phylogentic tree, of which there are many. Every time a new tree agrees with an old tree it is a confirmation of the common descent hypothesis. This particular argument has nothing to do with explaining 'how all this change and complexity is supposed to have come about', so your motivation for mentioning that escapes me.

I don't have anything to add beyond the obvious, such as dolphins share genetic similarities because they share many traits with those mammals that evolutionists think they are descended from. But what's that got to do with evolution being a scientific fact?

First, the idea that genomes are more similar because the genes are catering to similar functions does not work, as I mentioned earlier, because we can get the same phylogenetic tree results with genetic segments that do not do anything to the organism. The similarity we see is therefore not linked to functional similarity.

As for what this has to do with 'fact' status: If a theory makes a prediction, and the prediction is correct, then it helps the theories standing. If a theory makes many many many predictions, and they all turn out right without any falsifying evidence showing up, then eventually the theory is considered a fact. So, what I'm doing is showing you some occasions where evidence confirms evolutionary predictions. As I have demonstrated several times now, evolution expects there to be one true phylogenetic tree of life that shows which species diverged at what times in relation to each other. There is no reason to expect any such thing if species are not related. Therefore, every time a phylogenetic tree based on one thing agrees with the phylogenetic trees based on another method, it is a strong confirmation of evolutionary prediction. Phylogenetics is a very precise science with well established guidelines. I don't see how you can call it handwaving.

If you insist, you can still call the theory of common descent just a 'well evidenced theory' and forget about calling it a fact. The distinction there is purely semantic.

Can I help you with anything else?

[lpetrich]

Charles Darwin:
Again, all you are doing here is parroting the standard evolution line. Segments that share greater similarity are assumed to have evolved more slowly, and are therefore assumed to have more functional constraint. ...

Why don't you look at discussions of protein structure and function some time? Real discussions, not creationist literature.

"Genomes are evolving in a completely nonuniform way" Science 296:1601

So freaking what?

And how is that supposed to mean that new species come into existence by poof-poof-poof?

"The phylogenetic position of the platyhelminths within the metazoan tree is examined using two independent sets of molecular characters, the evolution of 18S ribosomal RNA sequences and the diversity of the genes belonging to the HOX cluster. Among the various hypotheses that have been considered by zoologists, a position of the platyhelminths within the protostomes, related to the phyla with typical spiral cleavage, appears to be favoured when taking into account all separate lines of evidence. It is in conflict with the traditional hypothesis of an early emergence at the base of the bilaterally symmetrical animals. This relatively late emergence is compatible with the old idea that flatworms are derived from a coelomate ancestor. New evidence from the sequences of Hox genes suggests that the duplicated genes Ultrabithorax/abdominal-A constitute a genetic synapomorphy of the whole protostome clade." C R Acad Sci III., 320:83

No real difficulty. That's because there has not been much to work from when working out the relationships between the animal phyla. So if you choose some character that's been affected by multiple evolution, you will get false results.

However, molecular characters are more detailed, and the authors of that paper used two different sets of them -- 16S/SSU rRNA sequences and HOX-gene sequences.

Furthermore, some old ideas about animal-kingdom relationships have survived. Bilateria, Protostomia, and Deuterostomia. And a relatively close relationship between mollusks and annelids, previously suggested from their very similar larvae.

"The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. Taxa previously proposed to be sister groups to the arthropods include Annelida, Onychophora, Tardigrada and others, but hypotheses of phylogenetic relationships have been conflicting. For example, onychophorans, like arthropods, moult periodically, have an arthropod arrangement of haemocoel, and have been related to arthropods in morphological and mitochondrial DNA sequence analyses. Like annelids, they possess segmental nephridia and muscles that are a combination of smooth and obliquely striated fibres. Our phylogenetic analysis of 18S ribosomal DNA sequences indicates a close relationship between arthropods, nematodes and all other moulting phyla. The results suggest that ecdysis (moulting) arose once and support the idea of a new clade, Ecdysozoa, containing moulting animals: arthropods, tardigrades, onychophorans, nematodes, nematomorphs, kinorhynchs and priapulids. No support is found for a clade of segmented animals, the Articulata, uniting annelids with arthropods. The hypothesis that nematodes are related to arthropods has important implications for developmental genetic studies using as model systems the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster, which are generally held to be phylogenetically distant from each other." Nature, 387:489

So what? And how is that supposed to imply poof-poof-poof?

"Sequence data can sometimes mislead or even give an entirely wrong answer." Science, 276:1032

However, biologists have learned how to be careful, and to apply various significance tests.

"Animal relationships derived from these new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present. Growing evidence suggests that phylogenies of animal phyla constructed by the analysis of 18S rRNA sequences may not be as accurate as originally thought." Science, 279:505

Again, so what? Is that the end of the world or something like that?

[lpetrich]

Doubting Didymus:
What do you think the separate creation hypothesis predicts the tree to look like?

Charles Darwin:
I don't think the separate creation hypothesis supplies sufficient detail to say how the species comparisons would play out.

Thank you for being so honest about the gross deficiencies of your pet hypothesis.

Then if evolution is true, why do segments in the human and mouse genome, which evolutionists say are functionless, show near identity?

These are noncoding sequences, which can be involved in gene regulation and production of functional bits of RNA, like ribosomal and transfer RNA.

[Urvogel Reverie]

Originally posted by Charles Darwin
Again, all you are doing here is parroting the standard evolution line. Segments that share greater similarity are assumed to have evolved more slowly, and are therefore assumed to have more functional constraint. And even if they are found to have greater functional constraint, so what? One does not need evolution to explain such a finding. You are contriving evidence where there is none.



Here are some samples.

"Genomes are evolving in a completely nonuniform way" Science 296:1601

"The phylogenetic position of the platyhelminths within the metazoan tree is examined using two independent sets of molecular characters, the evolution of 18S ribosomal RNA sequences and the diversity of the genes belonging to the HOX cluster. Among the various hypotheses that have been considered by zoologists, a position of the platyhelminths within the protostomes, related to the phyla with typical spiral cleavage, appears to be favoured when taking into account all separate lines of evidence. It is in conflict with the traditional hypothesis of an early emergence at the base of the bilaterally symmetrical animals. This relatively late emergence is compatible with the old idea that flatworms are derived from a coelomate ancestor. New evidence from the sequences of Hox genes suggests that the duplicated genes Ultrabithorax/abdominal-A constitute a genetic synapomorphy of the whole protostome clade." C R Acad Sci III., 320:83

"The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. Taxa previously proposed to be sister groups to the arthropods include Annelida, Onychophora, Tardigrada and others, but hypotheses of phylogenetic relationships have been conflicting. For example, onychophorans, like arthropods, moult periodically, have an arthropod arrangement of haemocoel, and have been related to arthropods in morphological and mitochondrial DNA sequence analyses. Like annelids, they possess segmental nephridia and muscles that are a combination of smooth and obliquely striated fibres. Our phylogenetic analysis of 18S ribosomal DNA sequences indicates a close relationship between arthropods, nematodes and all other moulting phyla. The results suggest that ecdysis (moulting) arose once and support the idea of a new clade, Ecdysozoa, containing moulting animals: arthropods, tardigrades, onychophorans, nematodes, nematomorphs, kinorhynchs and priapulids. No support is found for a clade of segmented animals, the Articulata, uniting annelids with arthropods. The hypothesis that nematodes are related to arthropods has important implications for developmental genetic studies using as model systems the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster, which are generally held to be phylogenetically distant from each other." Nature, 387:489

"Sequence data can sometimes mislead or even give an entirely wrong answer." Science, 276:1032

"Animal relationships derived from these new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present. Growing evidence suggests that phylogenies of animal phyla constructed by the analysis of 18S rRNA sequences may not be as accurate as originally thought." Science, 279:505

You also have distant species with similarities and allied species with similarities that derive from different development paths.


These quotes are all fascinating, and they all confirm for any skeptic, that you completely misunderstand phylogenetic reconstruction. You have regurgitated excellent examples of the conflict between phenetic, geological, phylogenetic, and other methods of systematics, and the fact that restoring phylogney is in fact not easy. What you have utterly failed to do, is display why this should be a fatal flaw which undermines systematics, or on a greater scale, evolutionary biology as a whole.

Urvogel Reverie

[Jack the Bodiless]

CD:

Why did you claim to be a "physicist" if you reject the entire basis of the scientific method? Will you now retract your claim to be a physicist, or any other sort of scientist?

And why do you accept that evolution is a fact, while repeatedly questioning this? It seems that you just won't let go of your erroneous (creationist) definition of the word "evolution", despite being corrected many times.

Mutations happen, and you accept this.

Natural selection happens, and you accept this.

Changes in the frequency of alleles in a population happen, and you accept this.

Therefore evolution happens, and you accept this.

Why, then, are you questioning the "fact" of evolution, which you accept?

[Ape31]

This has been a most amusing thread and I, like most here it seems, thought CD was a genuine (mustn't say creationist) anti-evolutionist.

However, he has shown a reasonable understanding of most of the arguments and has shown the ability to read and reference primary literature so the only conclusion I can draw is that we are dealing with a most excellent sock-puppet!

I must offer my most sincere congratulations on such a wonderful creation. :notworthy

Or did he evolve perhaps?

r.

[Charles Darwin]

Originally posted by Muad'Dib
Hi Charles Darwin,

Could you give an example of something you consider to be a scientific fact, and the ground on which you base that assessment?

Thanks,
Muad'Dib

I don't think we need to be overly concerned about how to define "scientific fact." I would agree with arguments evolutionists make about how scientific facts are different from empirical facts.

I think you are raising an interesting question, but I don't think it is highly relevant here for the simple reason that evolution isn't anywhere close. Pick you favorite definition of "scientific fact." I'd probably agree with it.

[Charles Darwin]

Originally posted by The Lone Ranger


quote:
--------------------------------------------------------------------------------
Originally posted by Charles Darwin:
How do you dress up an idea that makes no sense, get it accepted as science, and even as a scientific fact? Well it isn't easy. You'll have to stretch the truth in several different ways. First, and most obviously, you have to direct attention away from the fact that your idea is nothing more than handwaving, and doesn't actually explain how life and her intricacies were supposed to have arisen.
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First of all, for the umpteenth time, evolutionary theory doesn’t attempt to explain the origin(s) of life. As far as evolutionary biology is concerned, life may be the result of purple goblins from the 12th dimension. What matters is what has happened since the origin(s) of life.

To claim that evolution is a flawed theory because it cannot explain the origin(s) of life is no more logical than would be the claim that quantum mechanics is a flawed theory because it doesn’t explain why some genes are dominant and others are recessive.

Of course, how life arose is relevant to evolutionary biology, since life must first exist in order for it to evolve. Knowing more about how life may have arisen would also be quite useful to biologists, since it could very likely give us clues as to the chemical idiosyncracies displayed by living organisms. [Why do all living organisms use the same 20 amino acids, for example? Are these the “best” combination of amino acids for building proteins, or is it just chance that these were the ones that the first living organisms used?] So, the origin(s) of life is certainly of interest, but it nonetheless lies outside the scope of evolutionary theory.

You seem to want very much for evolutionary theory to be something that it is not, and never was.

You missed my point a bit. The point is not that evolution is a flawed theory because it cannot explain the origin(s) of life – it is already plenty flawed, thank you. My point is that evolutionists play a sort of bait-and-switch game with the origin of life. It shows up repeatedly in the evolution literature, from textbooks to popular literature. And it is claimed to be a solved problem (though not all the details are known; have we heard that somewhere before?). The Miller-Urey experiment is a favorite example that shows up repeatedly.

But when someone questions evolution, suddenly evolutionists become minimalists. They'll have nothing to do with the origin of life. Now secondly, having sequestered evolution, they now use the origin of life problem as a great safe-zone in which to place as many difficulties as possible. Protein synthesis, or a million other micro wonders, for which there is nothing more than speculation, are now no longer a problem.

Evolutionary biologists consider it a fact – that is, established beyond any reasonable doubt – that all extant organisms are related through common descent. I’m curious as to how this idea could be said to make no sense.

I'm not sure I put it that way. Something that goes against our scientific understanding and is highly unlikely doesn't necessarily "make no sense."

Here’s an overview of evolutionary theory. Please tell us where it breaks down.

…

Conclusion: Given that those individuals that are well-suited to their environment are more likely to survive and reproduce than are those that are poorly-suited to it, the genetic makeup of populations is expected to change over time, as traits which make their bearers well-suited to the environment become more common and traits which make their bearers less well-suited to the environment become rarer. This process is called evolution. [If you disagree with this conclusion, please explain why.]

But evolution is not equivalent to this process. In other words, what you have described is only part, and the non heroic part, of evolution. Coloration changes in moths, or beaks changing shapes in birds are examples of this process you describe. But with evolution, we have to have microbes changing into monkeys. But this is what evolutionists are forced to do. In order to show that their idea is a scientific fact, they must take a minimalist approach where the theory becomes essentially equivalent to evolution on a small scale, which of course, is a scientific fact. Then, when it comes to the part of theory which is not a fact, they run out of gas, as we see below:

No one disputes that natural selection occurs, and that populations evolve as a result. Nor is there any disagreement within the scientific community that the Earth is more than four billion years old. Fossils have been found in rocks that are almost four billion years old.

So?

Given the age of the Earth and the amount of time that living organisms have been around, and given that populations do evolve, it is an inevitable conclusion that we should expect to see quite a lot of evolutionary change over time.

Ah, hah, now we finally get to the meat of the issue. And what is the claim: that the vast oceans of change, creating everything from echolocation to the brain, is simply the "inevitable conclusion." Amazing – I can see that modern science is working wonders for us.

Indeed, field studies often document rates of evolution hundreds or even thousands of times greater than are necessary to explain the rates of change implied by the fossil record.

Ah, those guppies again. Isn't it amazing what we've been able to learn from their growth patterns (of course, they still look a lot like guppies, but that's another matter). They change so fast, surely frogs must have come from fish.

There are three possible reasons why we wouldn’t expect substantial amounts of evolution to have occurred.

Eh, hum; sorry but I think you've missed just a few reasons, say about ten thousand. But let's make it simple and stick with echolocation (sorry folks, it doesn't "just happen").

The scientific community has concluded that the evidence in favor of the fact of evolution is overwhelming. The evidence which leads to that conclusion is publicly-available, and the reasoning has been explained. Your claim is that we’re wrong in our conclusion. The burden of proof, therefore, is on you to show us why we’re wrong.

Right. And since I can't disprove your mythology, it must be a fact.

[Charles Darwin]

Earlier posted by Ipetrich:

Again, so what? Is that the end of the world or something like that?


Originally posted by Urvogel Reverie
These quotes are all fascinating, and they all confirm for any skeptic, that you completely misunderstand phylogenetic reconstruction. You have regurgitated excellent examples of the conflict between phenetic, geological, phylogenetic, and other methods of systematics, and the fact that restoring phylogney is in fact not easy. What you have utterly failed to do, is display why this should be a fatal flaw which undermines systematics, or on a greater scale, evolutionary biology as a whole.

Urvogel Reverie

Why is it that you cannot seem to follow a thread for more than about one post? No, it is not the end of the world; no it does not undermine systematics. What it does do is answer the question raised earlier about why phylogenetic results fail to prove evolution to be a fact. Earlier, phylogenetic results were raised as one of the critical and compelling evidences for evolution, demonstrating it to be a scientific fact. I pointed out that those results are often conflicting. There is not doubt that explanatory mechanisms can always be brought to bear. Things can be explained by this convergence, or that lateral transfer.

People, this is a good example of the bankruptcy of thought. You will be told evolution is a fact, when you critique the reasons and evidence given, you will be chastised for having failed to disprove the theory. Meanwhile, the absurdity continues: the most amazing of devices are to have merely arisen.

[Doubting Didymus]

Phylogenetic mismatches are rare, and thus do not cause problems for evolutionary theory. You do not damage a major field of science with five questionable quotations, which I highly doubt you even understand.

Do you actually have anything at all to add to the E/C debate other than your overblown personal incredulity? Because that is a singularly unimpressive factor.

[Charles Darwin]

Originally posted by Doubting Didymus



--------------------------------------------------------------------------------
Originally posted by Charles Darwin
I don't think the separate creation hypothesis supplies sufficient detail to say how the species comparisons would play out.
--------------------------------------------------------------------------------

Which is exactly why my first statement read with the following sentiment: "There is no particular reason for any two phylogenetic tree creation methods to produce the same results, if species were are not in fact related."

Perhaps I mispoke, or perhaps you read too much into my sentence. Be that as it may, I did not mean to say that nothing can be said of different phylogenetic trees, of the same species set but based on different features, on the theory of separate creation. It certainly makes sense that design features would converge. The spokes, seats, and gearing of bicycles follow correlated trends. Of course, one can find plenty of exceptions, just as one finds with the species.

quote: Originally posted by Charles Darwin
--------------------------------------------------------------------------------
Then if evolution is true, why do segments in the human and mouse genome, which evolutionists say are functionless, show near identity?
--------------------------------------------------------------------------------

You do not appear to understand what I am talking about. Humans and mice are closely related. I should expect functionless DNA from those two species to be similar. I should also expect functionless DNA from a species closer to humans than mice to be more similar still to humans. Why shouldn't human and mouse junk DNA be similar?

No, I think you aren't following here. When I say "near identity" of functionless segments, I mean just that. ["As researchers begin comparing newly sequenced genomes, numerous surprises are emerging, as described at a genome meeting here held from 7 to 11 May. For one, some of that 'useless' noncoding DNA turns out to be highly conserved among humans and mice." Science, 296:1601.]. There is no explanation for it under evolution, aside from the usual contrivances.

quote: Originally posted by Charles Darwin
--------------------------------------------------------------------------------
"Evolution explains it nicely"? You've got to be kidding? Evolution has no idea (beyond hand waving) how all this change and complexity is supposed to have come about. You see some similarities between the dolphin and other mammals, and say evolution explains this nicely?! There's got to be something behind this, for science doesn't work this way.
--------------------------------------------------------------------------------

Now it's my turn to not understand what you are talking about. Lets stay on this one specific topic: If an organisms genome is created without adapting it from ancestral genomes, we should see genome similarity correspond to similarities in environmental needs. It doesn't. Instead, genomes are more similar when organisms share more recent hypothesised ancestors. We should not be able to build ancestor trees if there were no ancestors, but we can. These ancestor trees should not be borne out by the hypothetical history in the fossil record, but they do (e.g. we should not find transitional forms in the right places. I do hope we can finish with this topic before discussing those, however, as I am no paleontologist, and the topic deserves its own thread. Deal?). This is the same for every phylogentic tree, of which there are many. Every time a new tree agrees with an old tree it is a confirmation of the common descent hypothesis. This particular argument has nothing to do with explaining 'how all this change and complexity is supposed to have come about', so your motivation for mentioning that escapes me.

You could build the exact same argument using automobiles (indeed, evolutionists have done it many times). It is true that automobiles demonstrate a sort of evolutionary process, and would form convergent trees, the analogy also reveals that convergent trees do not imply the sort of evolution you are talking about. In fact, there are a great many exceptions, which is a fact for designed things, but you must explain away with your contrivances.

quote: Originally posted by Charles Darwin
--------------------------------------------------------------------------------
I don't have anything to add beyond the obvious, such as dolphins share genetic similarities because they share many traits with those mammals that evolutionists think they are descended from. But what's that got to do with evolution being a scientific fact?
--------------------------------------------------------------------------------

First, the idea that genomes are more similar because the genes are catering to similar functions does not work, as I mentioned earlier, because we can get the same phylogenetic tree results with genetic segments that do not do anything to the organism. The similarity we see is therefore not linked to functional similarity.

And who gets to decide which segments have function and which do not? It seems that everytime evolutionists discover something they claim it has no function. It is therefore strong evidence for evolution. Years later, when the function is found, the clamor isn't so loud.

As for what this has to do with 'fact' status: If a theory makes a prediction, and the prediction is correct, then it helps the theories standing. If a theory makes many many many predictions, and they all turn out right without any falsifying evidence showing up,

No falsifying evidence? We've discovered a realm of undreamt of complexity. We wouldn't have a clue how to put it all together. Yet you believe it came about on its own? And you see no reason to doubt this? And you call it a scientific fact? This is ridiculous.

Phylogenetics is a very precise science with well established guidelines. I don't see how you can call it handwaving.

"Until about 5 years ago, researchers considered the transfer of genetic material from one species to another an oddity. Since then, genome studies have shown that some genes have moved around quite a bit. [Note, no one has shown any such thing; this all hinges on the assumption evolution is true – CD] Even so, microbiologists assumed this would not be true for genes involved in translating DNA to RNA, for example, or sunlight to biomass; they couldn't see how genes of such mixed ancestry could possibly coordinate these complex processes. But that assumption 'doesn't seem to be true,' says W. Ford Doolittle, an evolutionary biologist at Dalhousie University in Halifax, Nova Scotia. The new work 'clearly shows that photosynthesis genes have moved from one organism to another,' adds Carl Bauer, a biochemist at Indiana University, Bloomington." Science, 298:1538.

[Charles Darwin]

Originally posted by Doubting Didymus
Phylogenetic mismatches are rare, and thus do not cause problems for evolutionary theory.

It is not a matter of causing problems for the theory. They are claimed as part of the evidence that makes evolution a fact. They do no such thing, not even close. There are plenty of mismatches, at every level. If you think they are rare then you are misinformed.

Originally posted by Doubting Didymus
You do not damage a major field of science with five questionable quotations, which I highly doubt you even understand.

Anyone who questions evolution must be ignorant.

Originally posted by Doubting Didymus
Do you actually have anything at all to add to the E/C debate other than your overblown personal incredulity? Because that is a singularly unimpressive factor.

Pay no attention to evidential problems, this man has nothing to offer except personal incredulity. Above all, we must not question evolution.

[Doubting Didymus]

Myself: Phylogenetics is a very precise science with well established guidelines. I don't see how you can call it handwaving.

Thee: "Until about 5 years ago, researchers considered the transfer of genetic material from one species to another an oddity. Since then, genome studies have shown that some genes have moved around quite a bit. [Note, no one has shown any such thing; this all hinges on the assumption evolution is true – CD] Even so, microbiologists assumed this would not be true for genes involved in translating DNA to RNA, for example, or sunlight to biomass; they couldn't see how genes of such mixed ancestry could possibly coordinate these complex processes. But that assumption 'doesn't seem to be true,' says W. Ford Doolittle, an evolutionary biologist at Dalhousie University in Halifax, Nova Scotia. The new work 'clearly shows that photosynthesis genes have moved from one organism to another,' adds Carl Bauer, a biochemist at Indiana University, Bloomington." Science, 298:1538."

I may have to take this as evidence that you havent got the foggiest idea what the hell you're talking about. You seem to have no clue about the biology involved here.

Please, dispel this perception for me. Tell me in your own words what the article is talking about. What kind of species does this happen in? What do you suppose is the mechanism of such gene transfers? Importantly, what on earth is the implication of finding genes of mixed ancestry in a species on the accuracy of phylogenetic research? Lastly, regarding your insert into the above quote: (genes have moved around quite a bit. [Note, no one has shown any such thing; this all hinges on the assumption evolution is true – CD]). In your opinion, can genes move between species as described in the above article, or is there no mechanism for such an occurance?

[Doubting Didymus]

Originally posted by Charles Darwin
It is not a matter of causing problems for the theory. They are claimed as part of the evidence that makes evolution a fact. They do no such thing, not even close. There are plenty of mismatches, at every level. If you think they are rare then you are misinformed.

You were asked several times to provide evidence of phylogenetic mismatches. You utterly failed, and instead displayed for us a series of abominable misquotes that are not even talking about the same thing, or anything like it. I say again: mismatches of significance to evolutionary theory are rare. Mismatches happen, and are the subject of many papers, but they are not problems unless there is no explaition for the mismatch. The fact that you insist on childishly dismissing all explainations offered as contrived handwaving does not make the explaination ineffective unless you actually support your case, which of course you cannot do. You are about rhetoric, and you do not care for real debate.

Anyone who questions evolution must be ignorant.

That was not my first assumption. I came to this suspicion (for that is all it is), based on the things you think are problems for phylogenetics. I suspect you searched for words that sounded good for your case, without really grasping the science. I may well be wrong about that! However, you will need to do more than link to irrelevant nature articles to make your case to the contrary.

Pay no attention to evidential problems, this man has nothing to offer except personal incredulity. Above all, we must not question evolution.

Not a bit of it. Please, all onlookers, pay your fullest attention to any evidential problems charles raises. It would do you all good, however, to note that much of it is empty rhetoric, and to ignore that when you find it.

Would you agree that that is a fairer sentiment?

[God Fearing Atheist]

Charles, there are literally *millions* of phylogenic trees we can construct between taxa. Oddly, even in the worst cases, independent methods rarely arrive at more than a couple dozen or so.

To me, this suggests that independent phylogenies are converging to a highly, highly statistically significant degree.

Their use as support for common decent is as strong as ever.

-GFA

[Urvogel Reverie]

Originally posted by Charles Darwin
Earlier posted by Ipetrich:

Again, so what? Is that the end of the world or something like that?




Why is it that you cannot seem to follow a thread for more than about one post? No, it is not the end of the world; no it does not undermine systematics. What it does do is answer the question raised earlier about why phylogenetic results fail to prove evolution to be a fact. Earlier, phylogenetic results were raised as one of the critical and compelling evidences for evolution, demonstrating it to be a scientific fact. I pointed out that those results are often conflicting. There is not doubt that explanatory mechanisms can always be brought to bear. Things can be explained by this convergence, or that lateral transfer.

People, this is a good example of the bankruptcy of thought. You will be told evolution is a fact, when you critique the reasons and evidence given, you will be chastised for having failed to disprove the theory. Meanwhile, the absurdity continues: the most amazing of devices are to have merely arisen.


You have an amazing ability to imply viewpoints and then categorically dismiss them once they prove to be untenable to your current argument. It is an unenviable trait. Were creationism correct the nested hierarchy revealed by cladistic analysis of all taxa, should not be evident, as this very same pattern reveals evolution in action. Your idiotically labelled phylogenetic "mismatches" are the result of numerical statistical analysis using algorithms designed to isolate the most parsimonious cladograms displaying the greatest character-support at each node, they demonstrate that it is often not easy to establish phylogeny, and not any significant complication nor do they constitute a flaw in using phylogenetic analysis as substantiation of evolution. Given that your posts indicate significant misunderstanding of the practice and methods of phylogenetic reconstruction, it is absurd that you should pontificate on the shortcomings of such analysis in upholding evolution.

The further claim that the "most amazing of devices are to have merely arisen" is even more specious, in that if one bothers to look at a phylogenetic map, most particularly a cladogram, you would see that hiearchical distribution of character states is at the very heart of the method: quantifying the polarity and nature of phenotypic variation is what makes cladograms work--ergo they never have and never will be arguments for derived features appearing as if by magic. If one considers that cladograms are merely shorthand for documenting the process of evolution in any given taxonomic category, one could easily see that on the contrary, evolutionary biologists go to pains to document as meticulously as possible, the changes associated with that process. In other words, the cherished creationist strawman of how evolutionists merely assert that things occurred without bothering to elucidate evidence to substantiate their hypotheses, is nothing less than bunk.

Considering the quality of the posts you have advanced, littered as they are with fallacies and distortions, it is nothing less than laughable that you would be accusing anyone or anything, of intellectual bankruptcy.

Urvogel Reverie

[Doubting Didymus]

"mismatches" are the result of numerical statistical analysis using algorithms designed to isolate the most parsimonious cladograms displaying the greatest character-support at each node

Hell-o Urvogel, that's very "good" technical systematics language you have going there (as opposed to 'bad' technical language: that which suggests unfamiliarity with the terminology, or using unneccesary amounts of jargon). You sound like some of my lecturers. Do you work or study in a related field, by any chance?


Edit: I see that you do!

Interests: Reading, hiking, archosaur paleontology, systematics and taxonomy.

Welcome to Infidels.

[Charles Darwin]

Originally posted by God Fearing Atheist
Charles, there are literally *millions* of phylogenic trees we can construct between taxa. Oddly, even in the worst cases, independent methods rarely arrive at more than a couple dozen or so.

To me, this suggests that independent phylogenies are converging to a highly, highly statistically significant degree.

Their use as support for common decent is as strong as ever.

-GFA

I agree with your sentiment, though not with your numbers, but we can let that go. Let us agree that, for some hypothetical data set, you could infer a set of phylogentic trees using clustering methods or by choosing objective criteria. And it would be quite likely you would not obtain a single tree that unambigously fit the data the best, but rather a set of trees. And there might be some significant topological differences between the set of trees judged to fit the data well. Nonetheless, that set of trees would exhibit a high degree of similarity, when compared to the set of all possible trees.

Now, why exactly is this odd? You say this is "to a highly, highly statistically significant degree." Compared to what? [Hint: answer = randomly arranged traits]. So what? [Hint: the test is meaningless].

You have ignored the many mismatches and their attendant explanations, and have found great meaning in the fact that the species exhibit correlated traits. Amazing.

[Charles Darwin]

Originally posted by Urvogel Reverie
You have an amazing ability to imply viewpoints and then categorically dismiss them once they prove to be untenable to your current argument. It is an unenviable trait. Were creationism correct the nested hierarchy revealed by cladistic analysis of all taxa, should not be evident ...

Very interesting. Would you care to explain this secret knowledge that you have. I'd be fascinated to know why a nested hierarchy would not come from creationism. Oh and also, remember not to "imply viewpoints and then categorically dismiss them."

Originally posted by Urvogel Reverie
Your idiotically labelled phylogenetic "mismatches" are the result of numerical statistical analysis using algorithms designed to isolate the most parsimonious cladograms displaying the greatest character-support at each node, they demonstrate that it is often not easy to establish phylogeny, and not any significant complication nor do they constitute a flaw in using phylogenetic analysis as substantiation of evolution. Given that your posts indicate significant misunderstanding of the practice and methods of phylogenetic reconstruction, it is absurd that you should pontificate on the shortcomings of such analysis in upholding evolution.

Urvogel Reverie

Well you're good at berating me. By the way, what is it that I don't understand about the practice and methods of phylogenetic reconstruction? I thought I had a good handle on it. You say that the mismatches are nothing more than:

"numerical statistical analysis using algorithms designed to isolate the most parsimonious cladograms displaying the greatest character-support at each node, they demonstrate that it is often not easy to establish phylogeny."

Yes, of course this is the case. And there are a dozen or so explanatory mechanisms for every case. So why is this such strong evidence for evolution?

Originally posted by Urvogel Reverie
The further claim that the "most amazing of devices are to have merely arisen" is even more specious, in that if one bothers to look at a phylogenetic map, most particularly a cladogram, you would see that hiearchical distribution of character states is at the very heart of the method: quantifying the polarity and nature of phenotypic variation is what makes cladograms work--ergo they never have and never will be arguments for derived features appearing as if by magic. Urvogel Reverie

And of course, I never said they were. Let's not "imply viewpoints" OK?


Originally posted by Urvogel Reverie
If one considers that cladograms are merely shorthand for documenting the process of evolution in any given taxonomic category, one could easily see that on the contrary, evolutionary biologists go to pains to document as meticulously as possible, the changes associated with that process. In other words, the cherished creationist strawman of how evolutionists merely assert that things occurred without bothering to elucidate evidence to substantiate their hypotheses, is nothing less than bunk. Urvogel Reverie

I don't know what you are talking about. Making things up, or referring to those "creationists" is irrelevent.

[Charles Darwin]

Originally posted by Doubting Didymus
You were asked several times to provide evidence of phylogenetic mismatches. You utterly failed, and instead displayed for us a series of abominable misquotes that are not even talking about the same thing, or anything like it.

What is it about this sentence that you don't understand:

"Animal relationships derived from these new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present." Science, 279:505

How did I utterly fail? Please be specific this time.

[Doubting Didymus]

Now, why exactly is this odd? You say this is "to a highly, highly statistically significant degree." Compared to what? [Hint: answer = randomly arranged traits]. So what? [Hint: the test is meaningless].

Actually, the comparison would be to a number of things. For example, a situation where species share genetic similarity because of morphological similarity would predict a certain tree. This is a falsifyable possibility. This is also a falsified possibility. apart from your egregious assertions earlier that all functionless DNA actually does have undiscovered functions, you have not dealt with the problem of independant confirmation from trees built from junk DNA comparison for the 'similar morphology => similar genes' hypothesis.

[Doubting Didymus]

Originally posted by Charles Darwin
What is it about this sentence that you don't understand:

"Animal relationships derived from these new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present." Science, 279:505

How did I utterly fail? Please be specific this time.

First of all, WHAT new molecular data is the article referring to? also, what is the problem with new molecular data updating old morphology - based trees? Did you expect phylogeneticists to have everything perfect first try? Also: WHICH classical morphology trees have been updated by this new molecular data? In what way have they changed? Is this a mismatch or an update?

You see, you can't just grab desperately at every tasty sentence where a scientist has said "we had such-and-such a problem", and claim to have obliterated an entire scientific field. Your quote is a meaningless soundbite, until it is placed in context. It says nothing at all about anything specific. In other words, another utter failure to provide any evidence of problematic mismatches that are evidence against the theory of common descent. You have evidence of a scientist saying "hmm... ahhh" and nothing more.

[Urvogel Reverie]

Originally posted by Charles Darwin
I agree with your sentiment, though not with your numbers, but we can let that go. Let us agree that, for some hypothetical data set, you could infer a set of phylogentic trees using clustering methods or by choosing objective criteria. And it would be quite likely you would not obtain a single tree that unambigously fit the data the best, but rather a set of trees. And there might be some significant topological differences between the set of trees judged to fit the data well. Nonetheless, that set of trees would exhibit a high degree of similarity, when compared to the set of all possible trees.

Now, why exactly is this odd? You say this is "to a highly, highly statistically significant degree." Compared to what? [Hint: answer = randomly arranged traits]. So what? [Hint: the test is meaningless].

You have ignored the many mismatches and their attendant explanations, and have found great meaning in the fact that the species exhibit correlated traits. Amazing.


This torturous parody of cladistic methodology for phylogenetic reconstruction is simply too egregious to let go, and despite the exasperation of having to provide you with a tutorial of how the process actually works, it would seem that at least something along those lines is necessary. You seem to imply that algorithmic analysis of character-sets and the resultant phylogenetic maps are slapped together piecemeal, and thus that parsimonious maps underwritten by multiple characters at each node, are meaningless as their statistical likelihood is being compared to whimsical aggregates of random traits. This is the most idiotic drivel. Cladistic analyses of any taxon start with the elaboration of a character set to be analyzed, and from that point generate bifurcating patterns by which those characters may have appeared, governed by what we know of the process and pattern of evolution. Subsequent maps are thus potentially equally valid, and as they all are formulated from numerical study of a uniform set of characteristics, there is no "fudging" of the data, as it were--i.e., the analysis is not biased so that one set of parsimonious maps emerges which are lent an illusory credibility by inaccurate comparison to other maps. A parsimonious map, underwritten by a preponderance of characters at each node of the cladogram, is statistically likely to be accurate for the entirely different reason that out of alternatives of equal potential, this map is the most substantiated by the data at hand. Your attempt to introduce reasonable doubt into the methods of cladistics to show that phylogenies only appear to corroborate evolution (via an algorithmic sham), is quite simply bunk. One would suggest that you actually read the literature pertinent to the matter of phylogenetic reconstruction, before attempting to refute it.

Urvogel Reverie

[Doubting Didymus]

By the way, I would appreciate it if you could place publication dates on some of your Science journal references. I am getting a vague feeling that some of them might be quite old and outdated.

[Urvogel Reverie]

Originally posted by Charles Darwin
Very interesting. Would you care to explain this secret knowledge that you have. I'd be fascinated to know why a nested hierarchy would not come from creationism. Oh and also, remember not to "imply viewpoints and then categorically dismiss them."



Well you're good at berating me. By the way, what is it that I don't understand about the practice and methods of phylogenetic reconstruction? I thought I had a good handle on it. You say that the mismatches are nothing more than:

"numerical statistical analysis using algorithms designed to isolate the most parsimonious cladograms displaying the greatest character-support at each node, they demonstrate that it is often not easy to establish phylogeny."

Yes, of course this is the case. And there are a dozen or so explanatory mechanisms for every case. So why is this such strong evidence for evolution?



And of course, I never said they were. Let's not "imply viewpoints" OK?




I don't know what you are talking about. Making things up, or referring to those "creationists" is irrelevent.


A nested hierarhcy is diametrically at odds with any anti-evolutionary model for organic diversity yet advanced, in that their one unifying factor, is the assertion that taxonomic units are typological. If one is to deny evolution, it is a concomitant logical necessity that one maintains morphologic stasis over time. After all, there is nothing about phenotypic variation which would preclude a speciation event, at least to our knowledge, and since speciation is not allowable under anti-evolutionary models, that which would cause it, must be defined out of existence or denied outright. Hence the tired impression of Platonic essentialism into taxonomy by all manner of anti-evolutionists. Therefore, when you claim that a nested hiearchy could be evidence for creationism just as well as anything else, it reveals astonishing ignorance of your OWN worldview.

As for the matter of your lack of understanding about phylogenetic reconstruction--your entire series of posts on the matter has smacked of such. You obfuscate either intentionally or because you lack requisite knowledge, the principles and methods of cladistics, most egregiously in your claims about comparative analysis of cladograms which are formulated during numerical statistical analysis of a character set, which I addressed in an earlier post.

You never claimed they were? Did you not specifically say: "Meanwhile, the absurdity continues: the most amazing of devices are to have merely arisen?" If this is not a statement which indicates the opinion that cladograms merely assert changes in a lineage appeared as if by magic, then I have rarely seen one.

Making up the charge that creationists constantly assert that evolutionary biologists merely say that derived characters appeared without providing evidence of quantifying data? Not at all. Surely I cannot know the creationist argument better than a creationist. All one need do is read the work of Gish, Sarfati, Walker, listen to Hovind, Baugh, or any other number of creationist alumni, to find that very strawman repeated ad nauseum.

Urvogel Reverie

[Coragyps]

"Animal relationships derived from these new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present." Science, 279:505
That quote is in the introductory paragraph of a short "where we are today" review. The rest of the article is about what's being done to address the "central challenge."
Register, for free, at www.sciencemag.org , and use their search function to read the whole thing. (volume 279, page 505 is the easiest search, but it is possible to also give full citations for literature one uses in arguments (/one pet peeve)):
"The Coming of Age of Molecular Systematics"
Laura E. Maley and Charles R. Marshall
Science 1998 January 23; 279: 505-506.

[Charles Darwin]

Originally posted by Urvogel Reverie
This torturous parody of cladistic methodology for phylogenetic reconstruction is simply too egregious to let go, and despite the exasperation of having to provide you with a tutorial of how the process actually works, it would seem that at least something along those lines is necessary. You seem to imply that algorithmic analysis of character-sets and the resultant phylogenetic maps are slapped together piecemeal, and thus that parsimonious maps underwritten by multiple characters at each node, are meaningless as their statistical likelihood is being compared to whimsical aggregates of random traits. This is the most idiotic drivel. Cladistic analyses of any taxon start with the elaboration of a character set to be analyzed, and from that point generate bifurcating patterns by which those characters may have appeared, governed by what we know of the process and pattern of evolution. Subsequent maps are thus potentially equally valid, and as they all are formulated from numerical study of a uniform set of characteristics, there is no "fudging" of the data, as it were--i.e., the analysis is not biased so that one set of parsimonious maps emerges which are lent an illusory credibility by inaccurate comparison to other maps. A parsimonious map, underwritten by a preponderance of characters at each node of the cladogram, is statistically likely to be accurate for the entirely different reason that out of alternatives of equal potential, this map is the most substantiated by the data at hand. Your attempt to introduce reasonable doubt into the methods of cladistics to show that phylogenies only appear to corroborate evolution (via an algorithmic sham), is quite simply bunk. One would suggest that you actually read the literature pertinent to the matter of phylogenetic reconstruction, before attempting to refute it.

Urvogel Reverie

I'm sorry that you missed my point again. You seem to be repeatedly inferring that I am trying to cast doubt on the underlying algorithms and methods of phylogenetic analysis.

Once again, I must ask you to actually read my posts if you are going to make a relevant response. I said nothing about fudging the data or algorithmic shams. I very much trust the phylogenetic methods in use.

The point I was making to the gentleman was in reference to his claim that the results are odd and highly statistically significant. No one is doubting that the best-fit tree is indeed the best fit tree, and that the different characters are reasonably consistent. So what? Why is this so odd and what inference is so signficant?

[Doubting Didymus]

Originally posted by Coragyps
That quote is in the introductory paragraph of a short "where we are today" review. The rest of the article is about what's being done to address the "central challenge."
Register, for free, at www.sciencemag.org , and use their search function to read the whole thing. (volume 279, page 505 is the easiest search, but it is possible to also give full citations for literature one uses in arguments (/one pet peeve)):
"The Coming of Age of Molecular Systematics"
Laura E. Maley and Charles R. Marshall
Science 1998 January 23; 279: 505-506.

Ha! the 'new molecular data' referred to here is actually referring to molecular data period. An entirely new data collection method clarifies old mistakes, and this is supposed to prove that it is an unreliable method!

Charles, your quote is referring to the old mophological relationships that were found to be wrong when molecular phylogenetics first arrived on the scene back in the eighties. Some relationships that taxonomists had inferred turned out to be false when the molecular data showed up. That's not a mismatch at all, its just an update in our knowledge base. And before you say it: I am not just defining the mismatch away. If we went into a detailed morphological analysis on the updated trees, we would find that we were in fact wrong the first time based solely on the morphological data, and more close to the correct tree now. If that were not the case, it would indeed be reported as a mismatch (remember I am not denying that they exists, just that they are sufficiently rare and unimpressive in detail that they do not outweight the support that phylogenetics delivers)

So, as I suspected, the quote does not mean what you think it means. This is not a mismatch that contradicts common descent. Please try again.

[Doubting Didymus]

No one is doubting that the best-fit tree is indeed the best fit tree, and that the different characters are reasonably consistent. So what? Why is this so odd and what inference is so signficant?

Common descent predicts that an ancestor tree should exist. Nothing else (at least, nothing you're mentioned) predicts that result. Therefore the robustness of the ancestor tree confirms that there were, in fact, ancestors. Thus validating the theory that ancestral species existed, namely common descent.

If you want to refute this, you must either show that common descent does not in fact predict the tree to exist in the way it does, or that some other explaination exists that fits the data as well or better. That's how theories are normally treated in science, anyway.

[Muad'Dib]

Originally posted by Charles Darwin
I don't think we need to be overly concerned about how to define "scientific fact."

That wasn't what I asked, since you already answered that question on page 2 (http://www.iidb.org/vbb/showthread.php?threadid=60065&perpage=25&postid=1130087) when you said in response to The Lone Ranger:


I agree with your definition of what a "scientific fact" is (ie, evidence is overwhelming; if we're wrong about it, then we're wrong about a whole lot of things). I'll use the term "scientific fact" rather than "fact."


Rather, I want to know at least one specific thing that you accept as being a scientific fact, and why. This entire discussion is pointless if there is no claim in all of science that you consider to be supported enough to warrant calling a "scientific fact".

With a specific example (assuming one exists), we could qualitatively and quantitatively compare the evidence for whatever X you accept as a scientific fact and the evidence for evolution.

[God Fearing Atheist]

Boy, you're really all over the place Charles. First, you cite a couple incongruent phylogenies, apparently as evidence that there is no convergence. Then, in response to my other post, you seemingly agree that 1) there are an enormous number of potential phylogenies, yet despite this 2) even in cases of the most incongruent sort, they match up with statistical significance where its entirely possible for them not to at all. Indeed, an even greater blow to common decent would be a significant mis-match, a mis-match we do not see.

So what exactly is your point, Charles? What has anything you've said done to even *dent* evolution?

-GFA

[Charles Darwin]

Originally posted by Urvogel Reverie
A nested hierarhcy is diametrically at odds with any anti-evolutionary model for organic diversity yet advanced, in that their one unifying factor, is the assertion that taxonomic units are typological. If one is to deny evolution, it is a concomitant logical necessity that one maintains morphologic stasis over time. After all, there is nothing about phenotypic variation which would preclude a speciation event, at least to our knowledge, and since speciation is not allowable under anti-evolutionary models, that which would cause it, must be defined out of existence or denied outright. Hence the tired impression of Platonic essentialism into taxonomy by all manner of anti-evolutionists. Therefore, when you claim that a nested hiearchy could be evidence for creationism just as well as anything else, it reveals astonishing ignorance of your OWN worldview. Urvogel Reverie

Well I do doubt evolution, but I'm not a Platonist. First, however, I didn't say a nested hiearchy could be evidence for creationism (or if I did it was a mis-type); simply that there is no reason to think that designed or created things should not or cannot form a nested hierarchy. But I gather you got that point.

And I would roughly agree with you that "If one is to deny evolution, it is a concomitant logical necessity that one maintains morphologic stasis over time." But I'm afraid you're off base with your claim that "A nested hierarhcy is diametrically at odds with any anti-evolutionary model for organic diversity yet advanced, in that their one unifying factor, is the assertion that taxonomic units are typological." Without arguing over semantics, let's just say that there is nothing intrinsic about creationism that conflicts with a nested hierarchy (such as it is, full of convergence, etc). Again, I think your advice about "implied views" is relevent. Evolutionists are (rightly) concerned about people mis construing their theory. Let's hope they don't commit the same foible when critiqing other theories.

Originally posted by Urvogel Reverie
As for the matter of your lack of understanding about phylogenetic reconstruction--your entire series of posts on the matter has smacked of such. You obfuscate either intentionally or because you lack requisite knowledge, the principles and methods of cladistics, most egregiously in your claims about comparative analysis of cladograms which are formulated during numerical statistical analysis of a character set, which I addressed in an earlier post. Urvogel Reverie

Hmmm, I wonder how I obfuscated principles and methods of cladistics? I'd certainly like to know, for I'm at a loss to know what I'm missing. Is there some new or secret method I'm unaware of?

Originally posted by Urvogel Reverie
You never claimed they were? Did you not specifically say: "Meanwhile, the absurdity continues: the most amazing of devices are to have merely arisen?" If this is not a statement which indicates the opinion that cladograms merely assert changes in a lineage appeared as if by magic, then I have rarely seen one. Urvogel Reverie

I hate to tell you, but not every sentence in this thread pertains to phylogenetic analysis. My statement that "the most amazing of devices are to have merely arisen" was a reference to your belief that life has evolved. It is funny how evolutionists react when presented with a description of their own theory. They, on the one hand will insist that evolution must be an unguided process -- no teleology. But when they hear that "the most amazing of devices are to have merely arisen", then they say this must be wrong. What am I supposed to say? Are you now a Platonist? When your theory is described in bare terms, do you shy away? Did echolocation not "merely arise"? Was there a goal in sight?

Originally posted by Urvogel Reverie
Making up the charge that creationists constantly assert that evolutionary biologists merely say that derived characters appeared without providing evidence of quantifying data? Not at all. Surely I cannot know the creationist argument better than a creationist. All one need do is read the work of Gish, Sarfati, Walker, listen to Hovind, Baugh, or any other number of creationist alumni, to find that very strawman repeated ad nauseum. Urvogel Reverie

Sorry, I'm not familiar with them. I agree, let's avoid bringing strawmen into this.

[Doubting Didymus]

It is funny how evolutionists react when presented with a description of their own theory. They, on the one hand will insist that evolution must be an unguided process -- no teleology. But when they hear that "the most amazing of devices are to have merely arisen", then they say this must be wrong. What am I supposed to say? Are you now a Platonist? When your theory is described in bare terms, do you shy away? Did echolocation not "merely arise"? Was there a goal in sight?

Our objection is the confusion of naturalistic origin with random happenstance. Biodiversity didn't "just happen to arise". There is of course a process behind its origin. Things did not just fall into place, the processes behind their origin fill a rather hefty textbook or two just with a basic overwiew. Thus, it is not accurate to equate the evolutionary explaination of biodiversity as 'just arose'. See?

[Charles Darwin]

Originally posted by God Fearing Atheist
Boy, you're really all over the place Charles. First, you cite a couple incongruent phylogenies, apparently as evidence that there is no convergence. Then, in response to my other post, you seemingly agree that 1) there are an enormous number of potential phylogenies, yet despite this 2) even in cases of the most incongruent sort, they match up with statistical significance where its entirely possible for them not to at all. Indeed, an even greater blow to common decent would be a significant mis-match, a mis-match we do not see.

So what exactly is your point, Charles? What has anything you've said done to even *dent* evolution?

-GFA

All over the place Huh? How do you get that? Where did I say that there is no convergence? I marvel at the interpretations I'm seeing. How in the world did you infer that I was arguing that nature's species lack convergence?

What is *my* point? Sorry, you're the one making the claim, not me. Evolution is supposed to be a scientific fact, and the congruence of phylogenies is supposed to be an important reason for this conclusion. The fact is, there are plenty of mismatches (no, I'm not saying lack of convergence). Can you explain them? Of course, you can. Isn't LGT wonderful. My point is that evolution is not a fact, and that the nested hierarchies and convergence of phylogenies is not even close to being the compelling evidence you'all believe it is.

[Doubting Didymus]

Originally posted by Charles Darwin
Evolution is supposed to be a scientific fact, and the congruence of phylogenies is supposed to be an important reason for this conclusion. The fact is, there are plenty of mismatches (no, I'm not saying lack of convergence). Can you explain them? Of course, you can. Isn't LGT wonderful. My point is that evolution is not a fact, and that the nested hierarchies and convergence of phylogenies is not even close to being the compelling evidence you'all believe it is.

There are pitifully few significant mismatches that contradict evolution. Dismissing all explainations for the very few apparent mismatches you've managed to raise without actually addressing those explainations is very arrogant. It is also a totally inneffectual debating technique. If all you have to offer is a big fat "is not", then we will counter it with an equally schoolyard "is too". You have to support your claims.

[Charles Darwin]

Originally posted by Doubting Didymus
Our objection is the confusion of naturalistic origin with random happenstance. Biodiversity didn't "just happen to arise". There is of course a process behind its origin. Things did not just fall into place, the processes behind their origin fill a rather hefty textbook or two just with a basic overwiew. Thus, it is not accurate to equate the evolutionary explaination of biodiversity as 'just arose'. See?

No, not really. This reminds me of Dawkin's fallacy for complexity. He claimed it really isn't a problem because it comes in small pieces. Sorry, they still have to add up. You can't sugar-coat the fact that, with evolution, we must believe that random biological variation created the cheetah. Natural selection did not create any of that variation. The words "just arose" means "via natural laws". It says nothing about the time period, or the particulars of the process. I'm sorry, but you believe that the cheetah "just arose." That is simply an amazing thing to believe. It is a wonder that anyone would buy that, much less claim it to be a scientific fact.

[Urvogel Reverie]

Originally posted by Charles Darwin
Well I do doubt evolution, but I'm not a Platonist. First, however, I didn't say a nested hiearchy could be evidence for creationism (or if I did it was a mis-type); simply that there is no reason to think that designed or created things should not or cannot form a nested hierarchy. But I gather you got that point.

And I would roughly agree with you that "If one is to deny evolution, it is a concomitant logical necessity that one maintains morphologic stasis over time." But I'm afraid you're off base with your claim that "A nested hierarhcy is diametrically at odds with any anti-evolutionary model for organic diversity yet advanced, in that their one unifying factor, is the assertion that taxonomic units are typological." Without arguing over semantics, let's just say that there is nothing intrinsic about creationism that conflicts with a nested hierarchy (such as it is, full of convergence, etc). Again, I think your advice about "implied views" is relevent. Evolutionists are (rightly) concerned about people mis construing their theory. Let's hope they don't commit the same foible when critiqing other theories.



Hmmm, I wonder how I obfuscated principles and methods of cladistics? I'd certainly like to know, for I'm at a loss to know what I'm missing. Is there some new or secret method I'm unaware of?



I hate to tell you, but not every sentence in this thread pertains to phylogenetic analysis. My statement that "the most amazing of devices are to have merely arisen" was a reference to your belief that life has evolved. It is funny how evolutionists react when presented with a description of their own theory. They, on the one hand will insist that evolution must be an unguided process -- no teleology. But when they hear that "the most amazing of devices are to have merely arisen", then they say this must be wrong. What am I supposed to say? Are you now a Platonist? When your theory is described in bare terms, do you shy away? Did echolocation not "merely arise"? Was there a goal in sight?



Sorry, I'm not familiar with them. I agree, let's avoid bringing strawmen into this.



Your first paragraph is typical creationist special pleading and vacillating when presented with the necessity of typology in taxonomy if one is to deny evolution. Typological taxonomic units are incapable of reflecting nested hierarchy, since they are not transmutable and are fixed in an endless repetition of the parent taxon's fundamental "essence." At best, such taxonomic units can be mapped as parallel over time--equal in rank but not confluent with each other in a bifurcating pattern. The question should moreover be how can typological taxa be mapped in such a way that they reveal a nested hiearchy? How do creationism or other anti-evolutionary models account for this?

How you obfuscated and distored cladistic methodology? Your little tirade about "mismatches" alone shows you hardly understand phylogenetic reconstruction.

I have no qualms with a process of natural selection devoid of teleological restraints, I do take umbrage when it is argued by creationists that the lack of teleology in evolutionary arguments amounts to invoking magical events to produce phenotypic variety. It that was not implicit in your statements, they were framed within a context which would easily lead one to conclude that you were indeed arguing such.

Urvogel Reverie

[Urvogel Reverie]

Originally posted by Charles Darwin
All over the place Huh? How do you get that? Where did I say that there is no convergence? I marvel at the interpretations I'm seeing. How in the world did you infer that I was arguing that nature's species lack convergence?

What is *my* point? Sorry, you're the one making the claim, not me. Evolution is supposed to be a scientific fact, and the congruence of phylogenies is supposed to be an important reason for this conclusion. The fact is, there are plenty of mismatches (no, I'm not saying lack of convergence). Can you explain them? Of course, you can. Isn't LGT wonderful. My point is that evolution is not a fact, and that the nested hierarchies and convergence of phylogenies is not even close to being the compelling evidence you'all believe it is.


And you have already been shown that not only is your drivel about "mismatches" just that, but the standard results of statistical character analysis in that it yields multiple possibly phylogenies, hardly prevents phylogenetic analysis from being advanced as a support for evolutionary biology.

Urvogel Reverie

[Charles Darwin]

Originally posted by Muad'Dib
Rather, I want to know at least one specific thing that you accept as being a scientific fact, and why. This entire discussion is pointless if there is no claim in all of science that you consider to be supported enough to warrant calling a "scientific fact".

With a specific example (assuming one exists), we could qualitatively and quantitatively compare the evidence for whatever X you accept as a scientific fact and the evidence for evolution.

I could give you some examples (e.g., Charles Darwin invented the theory of evolution) or you could give us your favorite. But we're not talking about fine distinctions here. Don't flatter yourself; your theory is nowhere close to be a fact -- of any sort. It is a bizarre phenomenon of some sort that sociologists of the future will be studying in amazement.

[Mullibok]

Originally posted by Charles Darwin
It is a bizarre phenomenon of some sort that sociologists of the future will be studying in amazement.

But then someone will tell them that all of this evidence they've gathered from the past is theory, not fact, and they can't show it ever happened. Stupid sociologists.

[Charles Darwin]

Originally posted by Urvogel Reverie
Your first paragraph is typical creationist special pleading and vacillating when presented with the necessity of typology in taxonomy if one is to deny evolution. Typological taxonomic units are incapable of reflecting nested hierarchy, since they are not transmutable and are fixed in an endless repetition of the parent taxon's fundamental "essence." At best, such taxonomic units can be mapped as parallel over time--equal in rank but not confluent with each other in a bifurcating pattern. The question should moreover be how can typological taxa be mapped in such a way that they reveal a nested hiearchy? How do creationism or other anti-evolutionary models account for this? Urvogel Reverie

OK, I give. Your metaphysics are such that the alternatives are untenable. For you, non evolutionary models necessarily entail typology which cantradicts nested hierarchy. Hence, for you, evolution is a fact, and anyone who denies this must be wrong, by definition.

[God Fearing Atheist]

Charles my friend, never have i seen someone so capable of talking out of both sides of their mouth. Either there is significant convergence, or there is not. So far, you seem to accept both simultaneously.

- A simply exassperated GFA

[Doubting Didymus]

Originally posted by Charles Darwin
No, not really. This reminds me of Dawkin's fallacy for complexity. He claimed it really isn't a problem because it comes in small pieces. Sorry, they still have to add up. You can't sugar-coat the fact that, with evolution, we must believe that random biological variation created the cheetah. Natural selection did not create any of that variation. The words "just arose" means "via natural laws". It says nothing about the time period, or the particulars of the process. I'm sorry, but you believe that the cheetah "just arose." That is simply an amazing thing to believe. It is a wonder that anyone would buy that, much less claim it to be a scientific fact.

You're not making any sense. What on earth is the fallacy of complexity? How is it relating in any way to anything I was saying? I do not believe that the cheetah 'just arose', and I pointed out why in my last post. There are complicated processes involved in the origin of the cheetah that do not equate with happenstance.

I suspect that you are saying random crap just to get a rise out of us. Do you have any constructive purpose for being here, or are you just trolling?

[Doubting Didymus]

Originally posted by Charles Darwin
OK, I give. Your metaphysics are such that the alternatives are untenable. For you, non evolutionary models necessarily entail typology which cantradicts nested hierarchy. Hence, for you, evolution is a fact, and anyone who denies this must be wrong, by definition.

Alright, simple question: Is nested heirarchy, similar to the sort predicted by common descent, also compatible with special creation?

If yes, How?

[Charles Darwin]

Originally posted by Doubting Didymus
Common descent predicts that an ancestor tree should exist. Nothing else (at least, nothing you're mentioned) predicts that result. Therefore the robustness of the ancestor tree confirms that there were, in fact, ancestors. Thus validating the theory that ancestral species existed, namely common descent.

What do you mean "an ancestor tree should exist." In fact, due to the many mismatches, there is no unambiguous tree. So the prediction is false, and evolution is falsified. Ahh, you didn't quite mean that. You meant to within some predefined fit quality. How did you come up with that criterion? Would evolution really be falsified if it fell just short? [hint: answer is not 'yes'].

Also, surely you don't mean that a successful prediction makes a theory a fact? I'm sure you know that successful predictions don't do this. The flat earth model also makes successful predictions. In fact, when it comes to proving or disproving a theory, predictions can only disprove. And evolution predicts that the species are such that they could have "just arisen." Since species clearly are far too complex to have "just arisen," we know evolution is false.

[Mullibok]

Originally posted by Charles Darwin
Since species clearly are far too complex to have "just arisen"...

You can't possibly have tried to justify this claim, can you? Besides just "no way" assertions I mean? You just have no leg to stand on.

[Doubting Didymus]

Originally posted by Charles Darwin
What do you mean "an ancestor tree should exist." In fact, due to the many mismatches, there is no unambiguous tree.

You have failed to provide any significant mismatches. remember?

However, you have said This Interesting Thing:
Also, surely you don't mean that a successful prediction makes a theory a fact? I'm sure you know that successful predictions don't do this. The flat earth model also makes successful predictions. In fact, when it comes to proving or disproving a theory, predictions can only disprove.

You are more or less right on this one. Predictions can only disprove a theory by merit of their being found untrue, and also, you must be aware that no theory is "proven" in science, ever. Because of this, the only criteria for evaluating the accuracy of a theory is how compatible it is with evidence. You seem to be still seeking some sort of knock down factual support that cannot possibly be explained by any other means, no matter how wacky. That not very realistic. Instead, its best to note that the theory of common descent makes many predictions, all of them are supported by the evidence, and additionally, no evidence to the contrary has ever been found in any field of science in the history of time, ever. That might not be enough to convince you that evolution should be accepted, but it should be enough to make you stop and think for a bit.

[Charles Darwin]

Originally posted by Doubting Didymus
Alright, simple question: Is nested heirarchy, similar to the sort predicted by common descent, also compatible with special creation?

If yes, How?

Well, contrary to our Platonist friend, there are no rules that God cannot create species with similarities. In fact, given that species must operate on the same planet, in the same "environment", under the same set of natural laws, etc., it isn't surprising to see similarities. And just as a very different aspects of machine design are correlated (but also sometimes violate those correlations), so too do the species exhibit such correlations. For instance, the wing shape, engine type, and landing gear are all correlated in aircraft. But then you can get a major shift when you bring in skis instead of wheels.

Please be clear, I am not setting forth anything like a scientific model, complete with predictions and so forth. I'm merely answering your question.

[Doubting Didymus]

Oh, and I hope you don't mind if I quote you selectively and out of context in response to this one:

Originally posted by Charles Darwin
Since species clearly are far too complex to have "just arisen," we know evolution is false.

Originally posted by Charles Darwin
This man has nothing to offer except personal incredulity.

[Doubting Didymus]

Originally posted by Charles Darwin
Well, contrary to our Platonist friend, there are no rules that God cannot create species with similarities. In fact, given that species must operate on the same planet, in the same "environment", under the same set of natural laws, etc., it isn't surprising to see similarities. And just as a very different aspects of machine design are correlated (but also sometimes violate those correlations), so too do the species exhibit such correlations. For instance, the wing shape, engine type, and landing gear are all correlated in aircraft. But then you can get a major shift when you bring in skis instead of wheels.

But if species were similar in their genomes because they are similar in their morphological needs, then functionless DNA would produce an unrelated tree. You remember that, don't you? Also, the functional similarity => genetic similarity argument does not explain why endogenous retrovirusal insertions produce yet another compatible tree. Why does that happen?

[Charles Darwin]

quote:
--------------------------------------------------------------------------------
Originally posted by Charles Darwin
Since species clearly are far too complex to have "just arisen"...
--------------------------------------------------------------------------------


Originally posted by Mullibok
You can't possibly have tried to justify this claim, can you? Besides just "no way" assertions I mean? You just have no leg to stand on.

Well I can turn it around though. How's this: You can't possibly justify that the cheetah could have "just arisen" can you (besides just 'I think it could have')?

Do you see the asymmetry? While I certainly cannot disprove evolution, it requires that you believe in something which is simply way outside of science. The idea that the cheetah "just arose" is so unjustified it is amazing we are even having this discussion.

[Muad'Dib]

Originally posted by Charles Darwin
I could give you some examples

Please do, but see below.

(e.g., Charles Darwin invented the theory of evolution)
<snip>


I'm not interested in what other people call scientific facts. I'm asking for a concrete example from you. What is something that you consider sufficiently well-established to call a "scientific fact"?

In your opinion, is there any claim made by any branch of science that deserves to be called a scientific fact?

[Wounded King]

Actually 'Charles Darwin invented the theory of evolution' is not only not a fact but a blatant lie showing absoloutely no knowledge of the development of evolutionary theory.

[Ape31]

Originally posted by Muad'Dib
I'm not interested in what other people call scientific facts. I'm asking for a concrete example from you. What is something that you consider sufficiently well-established to call a "scientific fact"?

What I think he is saying is that he considers the statement "Charles Darwin invented the theory of evolution" to be a scientific fact.

r.

[Ape31]

Originally posted by Doubting Didymus
There are pitifully few significant mismatches that contradict evolution. Dismissing all explainations for the very few apparent mismatches you've managed to raise without actually addressing those explainations is very arrogant. It is also a totally inneffectual debating technique. If all you have to offer is a big fat "is not", then we will counter it with an equally schoolyard "is too". You have to support your claims.

This is an interesting aspect of this discussion. Can I ask about these mismatches - what kind of numbers are we talking about? 10%, 0.1%, 0.001%?

r.

[markfiend]

I think our friend misunderstands the way cladistic trees are made.

If we take an example of some cars which we wish to classify; lets say we have three colours, red, green and blue, three engine sizes, 3 litre, 4 litre. 5 litre, and two seating patterns 2-seater and 4-seater. From these three traits we can classify 18 different "kind" of car: red 3-litre 2-seater, green 5-litre 2-seater, etc. etc.

How do we classify them in a heirarchy though? We could split them into 2-seater and 4-seater, then colour, then engine size or we could give engine size the highest priority, then number of seats, then colour, and so forth. We would be left with a number of possible trees, all of which would be valid to "classify" our cars. This is to be expected of a designed system, where traits can be applied to any or all of the designed machines.

The difference when it comes to biology, though, is that our traits are not distributed across all species like they are with cars. For example, all birds have feathers, so are grouped together at one level of the tree. Also all birds have backbones, so can be grouped with mammals, reptiles, amphibians and fish into "backboned animals" (vertebrates).

The thing is, that there are no non-vertebrates that have feathers, so we know that having a backbone has a higher priority in our classification than having feathers; feathered animals (birds) are a twig on the branch of backboned animals.

When we take a large enough number of traits like this, we can devise a tree where we know that a trait is a "twig-trait" or a "branch-trait".

Now this tree based entirely on morphology (shapes of living things and their structures) was all we had to go on until biochemical investigation of genes and proteins became feasible. The funny thing is, the trees derived from genetic analysis, from protein structures, and from morphology all agree to an astounding degree. (The "mismatches" that CD alleges are when people said, "Hmmm... I'm not sure whether this branch comes out here or there.")

Now the one correct tree is what is predicted from evolutionary theory, where all organisms descend from a single common ancestor. A creationary/ intelligent design theory (as my example of cars) predicts multiple equally valid trees. This is not found, so ID is refuted. QED.

[Oolon Colluphid]

Excellent post Mark!
Originally posted by markfiend

Now the one correct tree is what is predicted from evolutionary theory, where all organisms descend from a single common ancestor. A creationary/ intelligent design theory (as my example of cars) predicts multiple equally valid trees. This is not found, so ID is refuted. QED.
Yep. This is why it is so strange that good features aren’t used in different groups, and that poor features are spread around amongst (presumably, from creationism) different groups, but within the evolutionary groupings.

Thus it’s odd that the creator gave all birds their efficient through-flow lung system, whether it’s a swift, an ostrich, a penguin or a kiwi (separate creations, presumably)... and gave other separate creations the far inferior ‘mammalian’ tidal system: bats, cheetahs, wolves, sloths, humans all have the inferior system. So the designer made the same mistake over and over: using an inferior system to one he knew about, one that would be advantageous to its owners, is poor design. It’s like giving all four-wheeled vehicles, whether tractor or racing car, a low-power two-stroke engine, while giving trains, say, whether intercity expresses, tourist ‘steam’ trains or Hornby 00-gauge toys, a powerful four-stroke.

Similarly, the creator made the same mistake over and over when he put -- separately into separate creations -- backward-wired retinas into hawks and humans, anteaters and antelopes, rabbits, rhinos and raccoons...

He repeated the stupid design of the laryngeal nerve’s routing in whales, giraffes, humans, pigs and porcupines, lemurs, lions and lemmings -- separate creations all, one assumes.

And so on.

It is the distribution of poor designs, as much as the fact that there are poor designs, that shows the designer to be a bumbling fool (or a refuted hypothesis). For he did not merely make mistakes; he made the same ones repeatedly, but only within certain groups! A giant squid cannot get a detached retina... and nor can a Californian octopus.

Cheers, Oolon

[Ape31]

Originally posted by markfiend
Now this tree based entirely on morphology (shapes of living things and their structures) was all we had to go on until biochemical investigation of genes and proteins became feasible. The funny thing is, the trees derived from genetic analysis, from protein structures, and from morphology all agree to an astounding degree. (The "mismatches" that CD alleges are when people said, "Hmmm... I'm not sure whether this branch comes out here or there.")


Thanks Mark - I like the analogy with the cars.

Presumably then the tree produced from genetic analysis is, in general, considered a more accurate representation of the real tree than those produced by other techniques (morphology, protein structures, etc) even given the level of agreement. Correct?

I understand that in the real world we wouldn't expect 100% agreement across these different techniques due to the difficulties in classification but it would be useful to know how much disagreement we are talking about. This anti-evolution argument (that trees produced with different techniques do NOT match) is not one I had seen before reading this thread.

r.

[markfiend]

Originally posted by Ape31
Thanks Mark - I like the analogy with the cars.

Presumably then the tree produced from genetic analysis is, in general, considered a more accurate representation of the real tree than those produced by other techniques (morphology, protein structures, etc) even given the level of agreement. Correct?

Well... kind of, but only if you had the entire genome for every living thing. At the moment, genetic analysis is done with certain portions of the genome (computer time is a limiting factor I believe).

I understand that in the real world we wouldn't expect 100% agreement across these different techniques due to the difficulties in classification but it would be useful to know how much disagreement we are talking about. This anti-evolution argument (that trees produced with different techniques do NOT match) is not one I had seen before reading this thread.

r.

According to 29 evidences for macro-evolution (http://www.talkorigins.org/faqs/comdesc/section1.html#pred3) at talkorigins, this agreement is to the 41st decimal place. To compare, the charge of the electron is only known to the 7th decimal place. So not very much disagreement at all.

*Edit to add -- caveat -- my previous post on this thread is about the limit of my knowledge on this topic, but there are plenty round these parts that know more about it than I.

[DMB]

Charles Darwin:
What do you mean "an ancestor tree should exist." In fact, due to the many mismatches, there is no unambiguous tree. So the prediction is false, and evolution is falsified. Ahh, you didn't quite mean that. You meant to within some predefined fit quality. How did you come up with that criterion? Would evolution really be falsified if it fell just short? [hint: answer is not 'yes'].
I have hesitated to participate in this thread, because I am a layman in biology, but I do think that we have a basic problem here about the understanding of science. And that is odd, because CD claims to be a scientist. So I too would like some elucidation of what he understands as a "scientific fact".

If we look at the fairly short history(approximately 400 years) of modern science, although there have been some totally discredited theories, most progress has been made by building on and refining what has gone before (e.g. Newton's oft-quoted "standing on the shoulders of giants").

In a very few cases, we do seem to have arrived at a finished state, as in the case of Newtonian mechanics as the basis of modern mechanical engineering. Normally, however, the process of adjustment and refinement goes on. Even when a previously unexplored phenomenon such as radioactivity is investigated, it largely adds to scientific knowledge and theory rather than totally superseding it.

It would have been remarkable indeed if Darwin's publication of the Origin of Species had been the final word on evolution. It is true that he spent a long time gathering evidence for it, but the total evidence available at his death was small in comparison with what has subsequently been gathered. And some of that later evidence has refuted some of Darwin's ideas. This is no more surprising than that the periodic table, when first postulated, had gaps and mistakes that have subsequently been adjusted.

There is no particular reason to suppose that biology has nearly run its course in the way that Newtonian mechanics has. So we should expect to see continued minor adjustments to evolutionary theory as new evidence is forthcoming. There is no paradox in asserting that an ancestor tree should exist but that not quite all the details have yet been established beyond doubt. What is so remarkable is that the work of huge numbers of scientific professionals since Darwin have produced evidence, sometimes in fields that did not even exist in Darwin's day, all of which support the fact of evolution.

[Xixax]

I would just like to point out to Charles Darwin that the cheetah just arose from a very similar cheetah-like ancestor. Likewise, that ancestor came from something very similar to itself, and so on and so on until you have something not much like a cheetah at all.

If Charles Darwin saw a cheetah born without spots, would he scream bloody murder and say that science just can't explain anything like that happening? No. Would he invoke a creator and say "SEE? God just made us a new species, a cheetah without spots!" I'd hope not.

If, for some reason that proved spotless cheetah's were more effective in reproducing and eventually that gene spread throughout a small population, one of the spotless cheetah's then gave birth to a litter with shorter tails, would he see any problem? NO.

Now we have a litter of spotless cheetah's with shorter tails... Charles D, do you see where this is going? Multiply the changes and timeframe by nearly unimaginable quantities and you still fail to understand how evolution works?

I feel similarly to Huxley, it's nearly embarrassing not to understand and recognize that evolution happened and is still happening. It's unavoidable.

[Muad'Dib]

Originally posted by Ape31
What I think he is saying is that he considers the statement "Charles Darwin invented the theory of evolution" to be a scientific fact.

r.

Ah, that makes sense. I think I misunderstood his post then. If that is the case, then I should rephrase my question as follows:

Is there any claim about the world or the universe, made by physics, chemistry, biology, geology, paleontology, astronomy, cosmology, or any other branch of science, that Charles Darwin considers well-established enough to call a scientific fact?

If so, what is one example of such a claim?

If not, why are we having this discussion?

(Thanks for clarifying, Ape31.)

[Ape31]

Originally posted by Muad'Dib
Ah, that makes sense. I think I misunderstood his post then. If that is the case, then I should rephrase my question as follows:

Is there any claim about the world or the universe, made by physics, chemistry, biology, geology, paleontology, astronomy, cosmology, or any other branch of science, that Charles Darwin considers well-established enough to call a scientific fact?

If so, what is one example of such a claim?

If not, why are we having this discussion?

(Thanks for clarifying, Ape31.)

Why not just attack the example he gave? I don't consider his example of a scientific fact anywhere near as well supported as evolution.

r.

[Muad'Dib]

Originally posted by Ape31
Why not just attack the example he gave? I don't consider his example of a scientific fact anywhere near as well supported as evolution.

r. I'd rather not, as I explain below, but you're more than welcome to if you want. :)

I've been interpreting "scientific fact" to mean, among other things, "an established result in at least one of the sciences". The statement about the historical Darwin (;)) inventing the theory of evolution is, to my mind, a historical claim rather than a scientific one. I'd rather compare claims made by science to claims made by science.

Besides that, I don't want to get bogged down in the sematics of what is really meant by "invented", "theory", or "evolution" in the context of CD's example. Evolution's claims aren't always completely crystal clear to me, but they are often easier to pin down than statements about the history of science.

[Jack the Bodiless]

CD:

Perhaps we should review where we're at in this discussion:

1. Evolution is a fact (the process of evolution is a process that actually does occur).

2. The fossil record is perfectly compatible with common descent.

3. Genetic analysis gives results that agree very closely agree with the "Tree of Life" constructed from the fossil record. The very rare discrepancies are entirely to be expected, given both the incompleteness of the fossil record and the ongoing gene-mangling effects of mutation.

Given the above, it's very difficult to see what your argument is. You keep using words like "amazing" to describe belief in evolution, but you are unable to explain what is so "amazing" about it. Meanwhile you occasionally make oblique references to something called "creation" and something called "God", without explaining these terms or providing any evidence at all that these have any real-world significance whatsoever.

Are you seriously arguing that it would be less amazing if millions upon millions of creatures just popped into existence in a sequence that mimics common descent, rather than evolving from very similar antecedents?

Are there any other fields of science in which you prefer magic as an explanation, even when a non-magical explanation fits the evidence?

[Darwin's Beagle]

Charles,

I love your moniker by the way. Since you do not appear to believe Charles Darwin’s theory, one must assume that you chose that moniker to honor his character – the way he took up the challenges to his theory, did not misrepresent his adversaries, and responded to each and every one in an honest forthright manner. I can see how you would admire those qualities in others since they seem to be so lacking in yourself.

Originally you asked for the general form of the argument that the Neo-Darwinian Theory of evolution is a fact. You have received many responses, some good and some bad. I admire your egalitarian nature, you have dismissed all of them with the same contempt. So far all the responses have brought up bits and pieces of the argument but ultimately the argument in the factual nature of evolution lies in the OVERWHELMING preponderance of the evidence. No one piece of information is going to be sufficient to convince a person like you. Actually, I doubt that the entire OVERWHELMING preponderance of the evidence will convince a person like you, but it should convince a rational person with doubts.

I cannot present all the evidence for you. Space limitations probably prevent it. Time limitations definitely prevent it. And there is so much evidence to support it, no one could possibly know it all anyway. So, I will settle for an abbreviated version, much of which has already been presented to you, that should be more than enough to convince a rational person.

Let’s begin by defining what is meant by a scientific fact. I know you have graciously conceded the point SAYING that you do not disagree with the standard explanations, but there is no evidence in your ACTIONS that this is true. If a person had reason to question your sincerity, he might think you are showing a certain level of duplicity here.

Science cannot prove anything to a 100% certainty. Everything is tentative and subject to reinterpretation. However, that doesn’t mean that we know NOTHING. Science is in the business of making predictions and it has been the most successful prediction-making endeavor humanity has ever come up with. There are certain things that have been tested well enough to give us a level of confidence that approaches certainty. There are aspects of evolutionary theory that achieve this level.

What are these aspects? The core of modern evolutionary theory has achieved this level of confidence. For me that core can be divided into two major tenets. First, the diversity of life present today is the result of descent with modification. IOW, all organisms are related by common descent. Second, Natural Selection working on variation created by mutation and recombination is an important, though not necessarily exclusive mechanism underlying descent with modification. In this post, I am going to concentrate on the former and leave the second (natural selection) as being intuitively obvious once we have established descent with modification. Even Michael Behe, an Intelligent Design Creationist who believes in descent with modification, should grant that natural selection is an important process although he would take issue with the idea that the variation was created by mutation and recombination. My argument is that there is abundant evidence from unrelated fields that points clearly to descent with modification and that there is no evidence that refutes it. The sum total of evidence makes it such that any person approaching it from an unbiased and rational perspective would agree that there is no reason to doubt it.

First, let’s look at the fossil record. So far the fossil record has been brought up and you have cavalierly dismissed it. Concerning Stephen Jay Gould’s article “Evolution: Fact and Theory” you say:

CD=
++++++++++++++++++++++++++++++++++++++

Let's see, as I recall he pointed out that fossils exist; that some species are similar to other species; and the we observe small amounts of evolution. Therefore evolution is a fact? I'm sorry, but with all due respect to the late Professor Gould, even my pet cat can't be persuaded by that.

++++++++++++++++++++++++++++++++

Erm… Gould did not say that. It is surprising that someone with your command of the literature would misrepresent him that way. Actually Gould says the exact opposite. He says that in the fossil record we observe the BIG amounts of evolution. It is the small amounts of evolution we do not observe. This is his theory of punctuated equilibrium. It has been around in the literature since 1972. To use your phraseology, I’m “amazed” you seem to have not heard about it.

Ah, perhaps you have heard about it after all. You allude to it with the common creationist misrepresentation of:

++++++++++++++++++++++++++++++++++

On to the fossil record. How does that help to combine with the other evidences to arrive at telling us evolution is a fact? You mean that species appear out of nowhere?

+++++++++++++++++++++++++++++++++++++++++++

Hmm, are you referring to the “sudden” appearance in the fossil of new species that punctuated equilibrium purports to explain? Nobody in modern paleontology has ever thought, said, or even implied that these species come from “nowhere”. Why would such a knowledgeable person like you, misrepresent things so badly? How disappointing.

What punctuated equilibrium says is that in the fossil record we see a certain species and fossils of that species can be seen pretty much unchanged over several bedding planes, and then in the space of a single bedding plane it will disappear and be replaced by a similar species or group of species. The new fossil species did not appear from nowhere, it appeared from exactly what it appears (pun intended) to have appeared from -- the previous species. It is just that the morphological change associated with speciation occurred in the space of a single bedding plane.

Ah, but you may well ask do we have any evidence that this is true? Does speciation occur in such a short period of time? Yes, we do. If comes from – Stephen Jay Gould, himself. I am reciting this from memory so I’m afraid I don’t remember the names of the species, but Gould collected shells on a mud-flat. The shells were from two different but highly related species. Also in that mudflat were shells that formed a continuum from the spiky ones to the smooth ones. One had a smooth shell and the other had spikes. IIRC the smooth-shelled species still existed on the mudflat but the spiky one did not. Gould was struck by the observation that the more spiky the shells were, the more eroded they seemed to be. This suggested to him that the spiky ones were older than the smooth ones, but he could not declare that to be the case just on the impression that the spiky shells seemed to be more eroded. Afterwards, new dating techniques became available that were able to date the shells and sure enough the spiky ones were older. The interpretation was that the spiky-shelled species had evolved into the smooth-shelled species and this had taken place over a period that is consistent with a single bedding plane.

Judging from your other arguments you will ask how this proves evolution? The answer is it doesn’t. There are other possible explanations. However, THIS explanation falls naturally from the results. The other possible explanations are purely ad hoc. This is just one piece of the evidence and it provides support that to the idea that punctuated equilibrium does not violate Neo-Darwinian evolution.

Now that we have covered your stated misconceptions concerning the fossil record, let’s take a look at what the REAL fossil record is telling us. What does it show? The first fossils are microfossils found in rocks dated back 3.6 billion years ago. These are bacteria-like organisms, the most simple life known. There is some biochemical evidence for even earlier life. Apatite granules showing an enrichment in C-12 over C-13 over and above that what would be expected if they were produced from abiotic sources were found in rock dated back 3.85 billion years ago. However, this evidence is controversial and while I do not dismiss it completely, I do not put much stock in it either.

There is evidence that beginning about 1.5 billion years ago, oxygen levels caused a big change in the type of microfossils seen. This corresponds temporally with the elimination in rock of banded-iron formations (BIFs) seen in surface rocks of that time. BIF cannot form in an oxidizing atmosphere. Eukaryotic lifeforms have been found in rock dating back 800 million years. These were single-celled protozoan-like creatures. The first evidence of metazoan (multicellular) organisms come from fossilized worm burrows dating back 700 million years. There are also some microfossils of embryonic cell clumps dating back about 600 million years ago.

Then at about 543 million years ago we have the Cambrian explosion, in which a variety of metazoan organisms make their appearance. Creationists make a big deal about this, so I’ll have to spend some time on it for you. Actually, I do not know for sure you are creationist since you have steadfastly not given us much indication of what you DO believe, only what you DON’T believe. You also complain about people making assumptions about your belief, but if you do not tell us, then the fault does not lie with them. It lies with you. Since your rhetoric SOUNDS like that of a creationist, I will assume that is just what you are.

Creationists often use the Cambrian explosion as evidence against evolutionary theory. It is not. It is strong evidence for descent with modification which is one of the core tenets of evolutionary theory. It is during the Cambrian explosion that virtually all phyla emerge. There hasn’t been a new one since (actually, I think the bryozoans arose after the Cambrian but I’ll set that aside for now). Creationists say this pattern is predicted from the theory of Special Creation, while evolutionists say that the Cambrian is a BIG punctuational event. Who is right?

First, something that creationists do not seem to acknowledge is that NONE of the organisms that were spawned during the Cambrian explosion are around today. There has been a significant change in the make-up of the flora and fauna since then. This change in the make-up of the flora and fauna STRONGLY supports descent with modification (more on this in a moment). Second, creationists also do not seem to acknowledge is this “sudden” appearance actually occurred over several million years, so there is plenty of time for a lot of evolution to happen.

The radiation of species like the 800+ Drosophila species in Hawaii and the Darwin finches in the Galapagos suggest that when new niches to exploit and with little competition there is likely to be rapid evolution. The Cambrian explosion had this in spades. Thus, there is good reason to believe that the Cambrian was a punctuational event.

Furthermore, what the fossil record shows since the Cambrian explosion is a continual change up until present day of the make-up in the flora and fauna. The change is such that organisms in adjacent bedding planes are much more similar to each other than they are in distant bedding planes.

To me the only reasonable conclusion from this data is that there has been continual evolution – descent with modification – from then until now.

Creationists claim that the fossil record and the Cambrian explosion fits with predictions from the theory of Special Creation better. How so? To fit the REAL data with Special Creation one would have to postulate a creator that poofs a number of bacteria-like organism into existence, waits around 2 billion years for them and their descendents to put enough oxygen into the air then poof some different bacteria-like organisms into existence, wait another 700 million years poof some simple eukaryotes into existence, wait another 100 million years and poof the first simple multicellular organisms into exxistence. Then after almost 3 billion years have a sudden fit lasting several million years of poofing new multicellular organisms and then periodically after some go extinct poof some other similar ones into existence until the present time. While this is logically possible, it is not reasonable. The ad hoc nature does not stand up to scrutiny.

Of course, Charles you may be able to show me where this is wrong and give a REASONABLE counter explanation for the real evidence. I’ll doubt that you will do that. Instead you will try and bring up instances in which the fossil record is incomplete and say that it is evidence against evolutionary theory. But the OVERALL picture of the fossil record is quite clear. It is the way I presented it. You are trying to make a case against evolutionary theory based on what we DON’T know. Although your STATED acceptance of the definition of scientific fact acknowledges that we do not have to be able to explain everything, your argument boils down to “if you can’t explain everything then you can’t claim it to be a fact”. You are (or at least have been) totally ignoring and refusing to respond to what we DO know. And what we do know leads us to one reasonable conclusion – evolution as defined by descent with modification is a fact.

You were given links to the REAL fossil record of horse evolution and asked how you would explain it. Here is your response:

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I really don't know, but I do know that the mythical horse sequence convinced many a lay person for the better part of a century before it was finally admitted to be, well, ... mythical. What we have is a bunch of different species which, if evolution is true, must have punctuated into each other. I also know that evolution, beyond handwaving, doesn't explain how any of those species got there in the first place anyway. Why is it you think this makes evolution a scientific fact?

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Charles, Charles … don’t you find it a little hard to look at yourself in the mirror when you intentionally distort the facts. There was no mythical horse sequence. There was incomplete data that led to erroneous assumptions as to the true intermediates but so what? I’ll bet there are some wrong intermediates in our ideas right now that will be modified when we find new data. The REAL data has only gotten stronger over the years supporting evolutionary theory. We could have of course found a Cambrian horse fossil. If we would have done that THEN evolutionary theory would be in real trouble. But we haven’t. Every find so far has only added support to evolutionary theory. The fossils fit in the right places. The new fossils we will find in the future will fit in the right places as well.

You were shown a picture of fossil skulls showing a pretty complete line of intermediate forms between early apes and present-day humans. Even you admitted that you could not tell where the cut-off between apes and humans was. Your next sarcastic statement is a bit of a puzzle:

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Oh, by the way, one little question: why does that make evolution a scientific fact?

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One would think that a clever guy like you could see how this fits well with evolutionary theory while any non-evolutionary theory is going to have be an ad hoc explanation. IOW it is a piece of the evidence that makes it unreasonable to not to view descent with modification as a fact.

I will stop here on fossils and go to the next line of evidence that has been discussed so far – molecular biology.

Your responses along these lines have so far been pretty pathetic. The first piece of evidence presented to you was endogenous retroviruses (ERVs). You seem to acknowledge that ERV are consistent with the predictions of relatedness from evolutionary theory. But you find some exceptions that even you admit evolutionary theory can explain and then you dismiss the evidence as worthless. This is like the fossil record scenario. You look at what it is clearly strong evidence in the overall pattern, but because the data isn’t perfect you feel justified in ignoring it all.

The authors of the paper you (mis)quote found STRONG support for the evolutionary relatedness by examining ERVs. They found this support by looking at insertion sites of a variety of organisms and then by phylogenetic analysis found the most parsimonious fit. Your response was that phylogenetic analysis is not reliable, and that you can come up with anything you want.

This shows an appalling lack of knowledge about not only phlogenetic analysis but about science as well. Scientists do not like to use techniques that do not give reliable results. Reliable results are their bread and butter. Phylogenetic is a technique that has been used in thousands of published works. It would be surprising if the technique has not been verified. Guess what! It has. The reference is:

Hillis DM, Bull JJ, White ME, Badgett MR, Molineaux IJ (1992). Experimental phylogenetics: Generation of a known phylogeny. Science 255:589-592.

To briefly summarize, phylogenetic analyses involving many different factors is invariably done by computer program due to the large number of possible trees needed to evaluate. Hillis et al. took a virus (T7 bacteriophage) and subjected it to mutagenic chemicals in 300 successive generations in which the viruses were split into different lineages. This caused mutations to develop, it also produced a known phylogeny. They then looked at restriction sites and subjected the results to phylogenetic analysis. Out of a possible 135,135 different trees, phylogenetic analysis narrowed it down to the single correct tree. Thus, phylogenetic analysis is not so easily dismissed as you seem to think it is.

In a sense every paper published using that technique is a test of the technique. If the technique gives unreliable results, it is likely to return nonsense solutions. But so far the results it gives fit in well with expectations from theory.

Next, you were shown a picture of human chromosome #2 side-by-side with its G-banding matches in the chimp, gorilla, and orangutan. The picture and the fact that the chromosome contains an extra centromere and telomers in the center STRONGLY suggest that human chromosome #2 was produced by a Robertsonian translocation of chromosomes much like that of chimp/gorilla/orangutan chromosomes 12 and 13.

Here is your response to that data:
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I hate to have to be the one to tell you this, but there's a whole bunch we don't know about micro biology. So, no, I'm afraid I can't explain the presence of the telomeres in the middle of chromosome 2 in humans and apes.

Now, getting back to the question at hand, let's see ... How did evolution create all that? You think evolution created these chromosomes, even though you don't know how it could have done said task. Nor do you have the slightest idea of what function said design might serve.

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It is “amazing” that an intelligent and informed person like yourself doesn’t have a clue about micro biology [sic]. Let me help you out some. Microbiology deals primarily with viruses, bacteria, protozoa, and fungi. Humans, chimps, gorillas and orangutans being metazoan eukaryotes do not fall in its realm. What this picture was referring to falls in the field of genetics.

While there is a lot of genetics we still do not know, we do know the function of telomeres. Since DNA replicase enzymes need to attach to the DNA strand they cannot copy the entire chromosome. There is a bit at the ends that they are incapable of copying. If there were no solution to this problem then after a number of replications the chromosomes would shorten to the point of involving genes. Telomeres are stereotypic sequences that can be added onto the end of chromosomes to prevent this shortening.

Humans have 23 pairs of chromosomes. Chimps, gorillas, and orangutans have 24. Each human chromosome has a G-banding analog in the other apes except Chromosome 2. Chromosome 2’s G-banding aligns up with the two leftover chromosomes from the apes, their chromosomes 12 and 13. The G-banding pattern suggest that human chromosome arose from a fusion of chromosomes very similar to ape chromosomes 12 and 13. Such fusion events have been seen in vivo. They are called Robersonian translocations. The fact that human chromosome 2 has an extra centromeric region and telomeres in the center STRONGLY support the idea that such a chromosomal fusion took place. The OBVIOUS interpretation of this is that human chromosome 2 and the chimp/gorilla/orangutan chromosomes 12 and 13 have a common ancestor. If they have a common ancestor so do humans, chimps, gorillas, and orangutans. Any other explanation for the data requires a bunch of hand-waving and ad hoc explanations. While these may be logically possible, they are not reasonable. The only reasonable explanation is the evolutionary one.

That may not help you much with your ignorance of “micro biology”, but it should help you understand the significance of the data with respect to evolution.

Next, I would like to go into other molecular data that has not been presented that independent of each other lend strong support to descent with modification, and taken together lead to the conclusion that it is a fact.

The correlation of sequence homologies between a variety of proteins (cytochrome C, the hemoglobins, etc) with the phylogenetic trees created from the fossil record is outstanding. Furthermore, the more closely the related the organism the more similar are their chromosomal structure, the more similar is their genome, them more similar is even the non-coding part of their genome.

Amongst mammals, only primates and the guinea pig do not make their own vitamin C. The gene for the enzyme that is essential in its biosynthetic pathway has been located and it turns out that chimps, humans and guinea pigs also have this gene but they have a mutation that puts in a premature stop codon so it is not functional. The mere fact that they have this pseudogene is suggestive of evolution. But even more suggestive is that the mutation that inactivates the gene is at the same place in humans and chimps while it is at a different place in guinea pigs. I will make the prediction that as the genomes of other primates are sequenced you will find a mutation similar to the one in humans and chimps and not like that of the guinea pig. Any takers?

Charles, I’m guessing you would again avoid analyzing the data and fall back on what we don’t know. You would complain that we don’t know how any biochemical pathway evolved so therefore since evolutionary theory can’t explain that how can one say that evolution is a fact. Again, this is avoiding the issue. The overwhelming evidence is not in what we don’t know, it is in what we do know. We do know the above, and any explanation other than the evolutionary one is fraught with so many problems as to make them unreasonable. While we do not know how any biochemical pathway DID evolve, there is no shortage of possible pathways they COULD have evolved.

The next line of evidence that has been gone into is evidence from suboptimal design. The idea here is that these types of structures are just what one would expect from design created by an algorithm without foresight but would be difficult to explain if they were designed by something with the intelligence of a human or better.

So far your response to these has been even more pathetic. The first of these structures you deal with is hind-limb atavisms in whales. You take issue with the author’s presentation claiming that atavisms of this type are to be expected in evolutionary theory:

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I didn't read through the entire site, but went to the first "validation" that caught my eye. It was Section 2.2, Atavisms. It states:

"Probably the most well known case of atavism is found in the whales. According to the standard phylogenetic tree, whales are known to be the descendants of terrestrial mammals that had hindlimbs. Thus, we expect the possibility that rare mutant whales might occasionally develop atavistic hindlimbs."

Aside from the fact that nothing is "known" from phylogenetic trees, the idea that hindlimbs are a prediction of evolution is a joke. You don't really believe that evolution would be rejected if such mutants were never discovered do you? What if tails were never discovered in humans? This has got to be one of the most absurd claims I've ever heard.

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“… one of the most absurd claims [you’ve] ever heard”. You have a led a charmed life, more on this later. First I would like to point out you have totally ignored the content. How else do you explain the presence of atavistic hind limbs in whales (and some snakes for that matter) other than by evolutionary theory? You have responded to similar questions by saying that you don’t know. This suggests that you cannot come up with one and thus as far as you know evolutionary theory is the only one capable of explaining this fact. If it is the only one capable of this fact, then why isn’t evolutionary theory a scientific fact in itself? Because there can be something we don’t know? But again even here your objection to evolutionary theory is based on something we don’t know. When there is so much evidence based on what we DO know that points in one way and one way only then that is sufficient to establish it as a scientific fact.

Now, as to your absurdity remark. What was the author REALLY saying? He was saying that it makes sense for whales to have atavisms such as the one mentioned and it does not make sense in any other light. Knowing what we know now about the genome and genetics if there were no atavisms anywhere then it would most certainly be a severe problem for evolutionary theory to explain.

You were next asked to consider why it is that bats, who function more like birds, have a mammalian respiratory system which is 10 times less efficient than that of birds. You again avoided addressing the issue, instead you decided to take it as a metaphysical question. It is a scientific question as well, Charles. Evolutionary theory explains it very well. The fact that bats have hair, give birth to live young and nurse them on milk says they are mammals. The reason they have a mammalian respiratory system is because that is an evolutionary constraint. Remember evolution has no foresight. No other explanation is nearly so parsimonious.

The same reasoning goes for kiwis. They have a much better respiratory system than they need for what they do. The evolutionary explanation is that it is also an evolutionary constraint. Special creation’s apparent explanation is that that is the way God just happened to do it, or there may be reasons for doing it that way that we do not yet understand. NOW you are talking handwaving.

There are MULTITUDE such questions that can be asked? The evolutionary constraint explanation in every case is the most parsimonious. Special creation’s explanation is handwaving. They include things like:

Why do dolphins and whales have lungs instead of gills?
Why do seals have fur and penguins have feathers?
Why do the halteres (vestigial winglike structures that are used as flight stabilizers) of dipteran (2-winged) insects look just like tiny wings and are positioned exactly the same place as the hindwings of other insects? Etc.

There are other structures that make sense only from an evolutionary perspective. They include teeth in embryonic toothless whales, teeth in chickens that have been incubated with embryonic reptilian jaw tissue, the vermiform appendix, human piloerector muscles, human muscles that wiggle the ears, the long roots of our canine teeth, the fused coccyx, the homology in bone structure of the forelimb of a bat (in which the forelimb is used as a wing), a seal (in which the forelimb is used as a flipper), a mole (in which the forelimb is used as a spade), a dog (in which the forelimb is used as a leg) and humans (in which the forelimb is used for grasping). The evolutionary explanation is that these are remnants of the organism’s evolutionary past. Special creation’s explanation is that they are there (or that way) at the whimsy of the creator. More heavy duty hand-waving.

From your previous responses I guess your answer to the above things will be that some of them have definable functions so they cannot be vestigial. I don’t care what you want to call them, they are best (and in some cases, only) explained by as evolutionary remnants, function or not. I also expect you to object on the grounds that it is impossible to know the purpose the creator may have for these things. This is simply a disingenuous cop-out and again unduly requires evolutionary theory to rule out all possible explanations instead of all reasonable explanations before it can be described as a fact.

There are other unrelated areas of biology that also point to descent with modification. Biogeography for instance. Why are Darwin’s finches limited to Galapagos? Why is the bird that is most closely related to them found on the western coast of South America? Why does Hawaii have 800 plus species of Drosophila? Why are there such an abundance of marsupials in Australia and very few elsewhere? Why do the onset of fossil remains of marsupials elsewhere correspond to times when continents were together?

There are organisms that appear to be in the process of speciating as we speak. I’ll bet you cannot tell a Boat-tailed Grackle from a Great-tailed Grackle but an expert birder can and so can the birds themselves. Eastern Meadowlarks and Western Meadowlarks are the same way. There are four species of Empidonax flycatchers that are difficult to tell apart. A little bit further along the speciation trail are birds like Sharp-shinned Hawks and Cooper’s Hawks – very similar but you could tell them apart if they were side-by-side.

Other evidence that speciation is going on right now includes the abilities of certain animals to produce hybrids. A jack-ass and a horse produce a mule. A lion and tiger can be artificially mated to produce a liger. Many warblers naturally hybridize to form different morphs.

I have discussed only a small percentage of the data that STRONGLY supports evolutionary theory. The data that I have discussed comes from paleontology, molecular biology, comparative anatomy, developmental biology, biogeography, and field biology. Each one taken by itself is STRONG support for descent with modification. Considering the various unrelated fields, all with evidence pointing strongly to the same conclusion the result is such that anybody who gives the data a fair look should agree that descent with modification reaches the lofty heights of scientific fact. And, in case you are wondering, I do think that if you disagree you are not being rational, at least as to evolution. And, yes, I do lump those people in with the nutters that believe in flat-earth and astrology and other silly bug-a-boos of nature. No, not everybody who disbelieves in evolutionary theory is a nutter. There are plenty of people who have not yet given the data a fair look. Of course this is in a large extent due to successful creationist efforts to keep the data out of our schools.

Regards,

Darwin’s Beagle

[Urvogel Reverie]

Originally posted by Darwin's Beagle
Charles,


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Let's see, as I recall he pointed out that fossils exist; that some species are similar to other species; and the we observe small amounts of evolution. Therefore evolution is a fact? I'm sorry, but with all due respect to the late Professor Gould, even my pet cat can't be persuaded by that.

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Erm… Gould did not say that. It is surprising that someone with your command of the literature would misrepresent him that way. Actually Gould says the exact opposite. He says that in the fossil record we observe the BIG amounts of evolution. It is the small amounts of evolution we do not observe. This is his theory of punctuated equilibrium. It has been around in the literature since 1972. To use your phraseology, I’m “amazed” you seem to have not heard about it.

Ah, perhaps you have heard about it after all. You allude to it with the common creationist misrepresentation of:

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On to the fossil record. How does that help to combine with the other evidences to arrive at telling us evolution is a fact? You mean that species appear out of nowhere?

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Hmm, are you referring to the “sudden” appearance in the fossil of new species that punctuated equilibrium purports to explain? Nobody in modern paleontology has ever thought, said, or even implied that these species come from “nowhere”. Why would such a knowledgeable person like you, misrepresent things so badly? How disappointing.

What punctuated equilibrium says is that in the fossil record we see a certain species and fossils of that species can be seen pretty much unchanged over several bedding planes, and then in the space of a single bedding plane it will disappear and be replaced by a similar species or group of species. The new fossil species did not appear from nowhere, it appeared from exactly what it appears (pun intended) to have appeared from -- the previous species. It is just that the morphological change associated with speciation occurred in the space of a single bedding plane.

Ah, but you may well ask do we have any evidence that this is true? Does speciation occur in such a short period of time? Yes, we do. If comes from – Stephen Jay Gould, himself. I am reciting this from memory so I’m afraid I don’t remember the names of the species, but Gould collected shells on a mud-flat. The shells were from two different but highly related species. Also in that mudflat were shells that formed a continuum from the spiky ones to the smooth ones. One had a smooth shell and the other had spikes. IIRC the smooth-shelled species still existed on the mudflat but the spiky one did not. Gould was struck by the observation that the more spiky the shells were, the more eroded they seemed to be. This suggested to him that the spiky ones were older than the smooth ones, but he could not declare that to be the case just on the impression that the spiky shells seemed to be more eroded. Afterwards, new dating techniques became available that were able to date the shells and sure enough the spiky ones were older. The interpretation was that the spiky-shelled species had evolved into the smooth-shelled species and this had taken place over a period that is consistent with a single bedding plane.

Judging from your other arguments you will ask how this proves evolution? The answer is it doesn’t. There are other possible explanations. However, THIS explanation falls naturally from the results. The other possible explanations are purely ad hoc. This is just one piece of the evidence and it provides support that to the idea that punctuated equilibrium does not violate Neo-Darwinian evolution.

Now that we have covered your stated misconceptions concerning the fossil record, let’s take a look at what the REAL fossil record is telling us. What does it show? The first fossils are microfossils found in rocks dated back 3.6 billion years ago. These are bacteria-like organisms, the most simple life known. There is some biochemical evidence for even earlier life. Apatite granules showing an enrichment in C-12 over C-13 over and above that what would be expected if they were produced from abiotic sources were found in rock dated back 3.85 billion years ago. However, this evidence is controversial and while I do not dismiss it completely, I do not put much stock in it either.

There is evidence that beginning about 1.5 billion years ago, oxygen levels caused a big change in the type of microfossils seen. This corresponds temporally with the elimination in rock of banded-iron formations (BIFs) seen in surface rocks of that time. BIF cannot form in an oxidizing atmosphere. Eukaryotic lifeforms have been found in rock dating back 800 million years. These were single-celled protozoan-like creatures. The first evidence of metazoan (multicellular) organisms come from fossilized worm burrows dating back 700 million years. There are also some microfossils of embryonic cell clumps dating back about 600 million years ago.

Then at about 543 million years ago we have the Cambrian explosion, in which a variety of metazoan organisms make their appearance. Creationists make a big deal about this, so I’ll have to spend some time on it for you. Actually, I do not know for sure you are creationist since you have steadfastly not given us much indication of what you DO believe, only what you DON’T believe. You also complain about people making assumptions about your belief, but if you do not tell us, then the fault does not lie with them. It lies with you. Since your rhetoric SOUNDS like that of a creationist, I will assume that is just what you are.

Creationists often use the Cambrian explosion as evidence against evolutionary theory. It is not. It is strong evidence for descent with modification which is one of the core tenets of evolutionary theory. It is during the Cambrian explosion that virtually all phyla emerge. There hasn’t been a new one since (actually, I think the bryozoans arose after the Cambrian but I’ll set that aside for now). Creationists say this pattern is predicted from the theory of Special Creation, while evolutionists say that the Cambrian is a BIG punctuational event. Who is right?

First, something that creationists do not seem to acknowledge is that NONE of the organisms that were spawned during the Cambrian explosion are around today. There has been a significant change in the make-up of the flora and fauna since then. This change in the make-up of the flora and fauna STRONGLY supports descent with modification (more on this in a moment). Second, creationists also do not seem to acknowledge is this “sudden” appearance actually occurred over several million years, so there is plenty of time for a lot of evolution to happen.

The radiation of species like the 800+ Drosophila species in Hawaii and the Darwin finches in the Galapagos suggest that when new niches to exploit and with little competition there is likely to be rapid evolution. The Cambrian explosion had this in spades. Thus, there is good reason to believe that the Cambrian was a punctuational event.

Furthermore, what the fossil record shows since the Cambrian explosion is a continual change up until present day of the make-up in the flora and fauna. The change is such that organisms in adjacent bedding planes are much more similar to each other than they are in distant bedding planes.

To me the only reasonable conclusion from this data is that there has been continual evolution – descent with modification – from then until now.

Creationists claim that the fossil record and the Cambrian explosion fits with predictions from the theory of Special Creation better. How so? To fit the REAL data with Special Creation one would have to postulate a creator that poofs a number of bacteria-like organism into existence, waits around 2 billion years for them and their descendents to put enough oxygen into the air then poof some different bacteria-like organisms into existence, wait another 700 million years poof some simple eukaryotes into existence, wait another 100 million years and poof the first simple multicellular organisms into exxistence. Then after almost 3 billion years have a sudden fit lasting several million years of poofing new multicellular organisms and then periodically after some go extinct poof some other similar ones into existence until the present time. While this is logically possible, it is not reasonable. The ad hoc nature does not stand up to scrutiny.



Regards,

Darwin’s Beagle


First and foremost, I must say you put up a rather excellent post, which I must disagree with in only two regards: the extent of punctuated equilibrium, and the Cambrian "explosion."

While one does not question that evolution and moreoever cladogenesis occur at irregular rates, neither being wholly unformitarian and gradual in the rate of change, nor entirely punctuated (indeed I prefer Simpson's terms bradytely, horotely and tachytely), the real question must be, is punctuation in cladogenetic or anagenetic change as marked as Stanley (1975, 1981, 1982), Eldredge (1984, 1985), Gould and Eldredge (1977), Eldredge & Stanley (1984) and Gould (1980, 1982) have asserted? Given that review of the fossil record specifically geared at testing this supposition has failed to reveal a pattern of morphologic stasis over time (Gingerich 1976, 1980, 1982), followed by rapid appearance of taxa, it seems that Gould et al's presentation of punctuated equilibrium as near dogma for the pattern and process of animal evolution is hardly correct (the worst offender has been Bakker, 1986). Indeed, the vast body of work on morphologic variation over time in Cenozoic mammals has consistently failed to corroborate punctuated equilibrium as elucidated by Gould et al (Hurzeler 1962, Chaline & Laurin 1986, Fahlbusch 1983, Harris & White 1979, Rose & Brown 1984, MacFadden 1985, Krishtalka & Stucky 1985 and Carroll 1988). Curiously, this pattern is extended even to teleost fishes from Upper Miocene lacustrine deposits of Nevada, in which gradualistic morphologic variation was observed by Bell, Baumgarten and Olson (1985). Even such exemplar cases as the punctuated pattern by which the Neornithes were derived (as primarily laid out by Feduccia in 1995, 1996, and 1999), have increasingly been called into question.

That matter aside, we can move on to the Cambrian "explosion," which represents in my opinion a great misnomer of paleontology. Granted, it is not my specialty, but the extensive Vendian fauna combined with our knowledge of developmental genetics--and moreover methods for molecular phylogenetic reconstruction, tax the well-worn notion of the Cambrian witnessing a significant punctuational event. The data seem to suggest a more moderate adapative radiation, in which the incipient phenotypic and genotypic characters of today's phyla were elaborated and differentiated.

Look forward to more of your posts,

Urvogel Reverie

[lpetrich]

Charles Darwin on family-tree discrepancies:
"The phylogenetic position of the platyhelminths within the metazoan tree is examined ..." C R Acad Sci III., 320:83

"The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. ..." Nature, 387:489

However, this is an active area of research, as a result of the progress of gene-sequencing technology, and some new results have been emerging. Some old taxonomic ideas, like Protostomia and Deuterostomia, have continued to be supported, but there have been some rather startling new results, like the division of Protostomia into Ecdysozoa (molters) and Lophotrochozoa (those with lophophores [a certain sort of ring of tentacles for feeding] or trochophore larvae). Arthropods belong to Ecdysozoa and annelids to Lophotrochozoa, though they have often been thought to be closely related on account of their segmentation. However, those trochophore larvae are shared by marine annelids and mollusks, both in Lophotrochozoa.

And as to arthropods, one startling new result that has emerged is that Uniramia (insects and myriapods) is not a natural group. Insects are most closely related to the branchiopod crustaceans, a group which includes the well-known brine shrimp Artemia salina. Myriapods (centipedes and millipedes), however, are an early-branching group, comparable to crustaceans and chelicerates (spiders, scorpions, horseshoe crabs, etc.).

[Charles Darwin]

Originally posted by lpetrich
Charles Darwin:
When you say life looks like it evolved you're begging the question. That is the question at hand.

How is it that living things fit into a family-tree-like hierarchy so well?

Is it some obscure whim? Or is it something else? Like descent with modification?

Whim? Created thinks such as automobiles and aircraft, as evolutionists have pointed out, form "family-tree-like" hierarchies, so why must we resort to the improbable notion of the most advanced machines arising on their own, to explain the observed hierarchy in biology?

[Charles Darwin]

Originally posted by Doubting Didymus
Regarding phylogenetic mismatches: they are few and far between. They get a lot of airtime in phylogenetic publications because they are rare, unexpected, and worthy of receiving an explaination. It's not like these things are impossible under the evolutionary framework, just that it should be unlikely. For example, further study of the problem may reveal answers:

Correction: answers and explanations have already been provided. There is no "problem" with these mismatches (and no, they are not "few and far between" -- take a look at just the few references I supplied) from the evolution perspective. Evolution is a fact, and the anomalies and mismatches are the result of one or more of a dozen or so possible explanations evolutionists can draw on. But the ability to explain so much means the data are not compelling evidence for evolution. That has been my point.

[Charles Darwin]

Originally posted by GunnerJ


CD replies:

So does the failure of endogenous retrovial insertions to confirm pre established trees disprove evolution?


No. This does not follow from what DD said at all.

Why? Because there are lots of reasons why, for example, an "HERV... shows up in gorillas and chimps but not humans." They have been listed. Thus, it's plausible that an HERV would not conform to the phylogenic tree for reasons other than the falsehood of evolution.

However, outside of evolution (by this we mean the fact of evolution, i.e., common descent) being accurate, there is no reason for HERVs to confirm the phylogenetic trees.

If you can't tell the difference between this and mere hand-waving and ad-hoc rationalization, then, well, there isn't much I can do to help you. [/QUOTE]

Actually, the only reasons given have been unacceptable from the evolution perspective (eg, the HERV inserted into the ape/chimp line after the human split-off; sorry that won't work). That's not to say that there is no explanatory mechanism. I'm sure they'll come up with something; or maybe they'll just sweep it under the rug.

You say "there is no reason for HERVs to confirm the phylogenetic trees." This is relatively new data, and we still do not understand it all that well. Evolution has an unfortunate history of pronouncing not-well-understood data as undeniable proof, only to later find out that the devil was in the details. Perhaps we should think a bit more carefully about the HERV data.

For if evolution is true, then there must have been a "punctuated equilibrium" type event or events to explain the jump in numbers. And the HERVs must have serendipitously played a role in evolution itself. And there'll have to be plenty of explanations for all the mismatches (see a quote a gave earlier, for example).

Finally, it is a scientific fact that some retro viruses have quite specific insertion site preferences. Is it not possible that HERVs which are found at homologous sites in different species share site preferences?

So why must we say that there is "no reason for HERVs to confirm the phylogenetic trees" aside from common descent? First of all, they don't always confirm those trees, and there are important exceptions; and secondly, there are reasonable alternative explanations which don't require making a mockery of science and natural laws.

[Charles Darwin]

Originally posted by lpetrich
Charles Darwin:
(endosymbiosis -- most successful is naturally selected...)
I'm not doubting that we can contrive explanations, where we are free to imagine.

Let's imagine that we could go back about 1.5-2 billion years ago to where some early protist was eating last year's crop of cyanobacterium colony.

The endosymbiosis hypothesis states that one of those protists swallowed, but did not digest, some alpha-proteobacterium. That bacterium multiplied inside, living off of the protist's waste products, like acetic acid. One day, due to some membrane-synthesis defect, the bacterium's outer membranes became a bit leaky, allowing some synthesized ATP to escape and AMP, ADP, and inorganic phosphate to return for assembly. This ATP supplied extra energy, helping its host eat more cyanobacterium and grow more and reproduce more, assisting the reproduction of that bacterium.

And that's what I would expect to see -- that or something similar. As opposed to this:

One day, some protists popped into existence with a big *POOF!*. They looked like some existing protist inhabited by an alpha-proteobacterium, however.

"Charles Darwin", is this what you believe?

You are coming through loud and clear. Your imaginary passage is painfully unlikely (not impossible though), yet your metaphysics forces you to accept it. This isn't science.


Originally posted by lpetrich

I was referring to membrane-bound organelles, independent of the plasma membrane, such as things like acidocalcisomes which are found in both some prokaryotes and eukaryotes.

That ONLY means that some organelles have not originated by endosymbiosis; I've yet to see anyone claim that they have that origin.

I wouldn't make the conclusion sound so trivial. It provides plenty of fuel to those evolutionists who are skeptical of endosymbiosis. Also, the conserved organelle in both prokaryotes and eukaryotes forces evolutionists line these species up (I do not know what the implications of this are).

[Charles Darwin]

Originally posted by lpetrich
Charles Darwin:
Again, all you are doing here is parroting the standard evolution line. Segments that share greater similarity are assumed to have evolved more slowly, and are therefore assumed to have more functional constraint. ...

Why don't you look at discussions of protein structure and function some time? Real discussions, not creationist literature.

Not sure what you are referring to. I've been quoting from journals (eg, Science). Do you have a problem with Science?

[Charles Darwin]

Originally posted by lpetrich


CD wrote: Then if evolution is true, why do segments in the human and mouse genome, which evolutionists say are functionless, show near identity?

These are noncoding sequences, which can be involved in gene regulation and production of functional bits of RNA, like ribosomal and transfer RNA.

rRNA and tRNA sequences are not "non-coding." In any case, these sequences were not "involved in gene regulation and production of functional bits of RNA, like ribosomal and transfer RNA." That's the point.

[Charles Darwin]

Originally posted by Ape31
This has been a most amusing thread and I, like most here it seems, thought CD was a genuine (mustn't say creationist) anti-evolutionist.

However, he has shown a reasonable understanding of most of the arguments and has shown the ability to read and reference primary literature so the only conclusion I can draw is that we are dealing with a most excellent sock-puppet!

I must offer my most sincere congratulations on such a wonderful creation. :notworthy

Or did he evolve perhaps?

r.

If all else fails, pull out the ad hominums.

[Charles Darwin]

Originally posted by Doubting Didymus
Phylogenetic mismatches are rare, and thus do not cause problems for evolutionary theory. You do not damage a major field of science with five questionable quotations, which I highly doubt you even understand.

Interesting. If the mismatches were not rare then it would be a problem for evolution? Unfortunately, the answer is not yes. Of course I don't know what you intend by the term "rare" but such mismatches are all over the place. One need only look. I was asked for examples, I gave some. There are plenty more.

[Charles Darwin]

quote:
--------------------------------------------------------------------------------
Myself: Phylogenetics is a very precise science with well established guidelines. I don't see how you can call it handwaving.

Thee: "Until about 5 years ago, researchers considered the transfer of genetic material from one species to another an oddity. Since then, genome studies have shown that some genes have moved around quite a bit. [Note, no one has shown any such thing; this all hinges on the assumption evolution is true – CD] Even so, microbiologists assumed this would not be true for genes involved in translating DNA to RNA, for example, or sunlight to biomass; they couldn't see how genes of such mixed ancestry could possibly coordinate these complex processes. But that assumption 'doesn't seem to be true,' says W. Ford Doolittle, an evolutionary biologist at Dalhousie University in Halifax, Nova Scotia. The new work 'clearly shows that photosynthesis genes have moved from one organism to another,' adds Carl Bauer, a biochemist at Indiana University, Bloomington." Science, 298:1538."


Originally posted by Doubting Didymus
I may have to take this as evidence that you havent got the foggiest idea what the hell you're talking about. You seem to have no clue about the biology involved here.

Please, dispel this perception for me. Tell me in your own words what the article is talking about. What kind of species does this happen in? What do you suppose is the mechanism of such gene transfers? Importantly, what on earth is the implication of finding genes of mixed ancestry in a species on the accuracy of phylogenetic research? Lastly, regarding your insert into the above quote: (genes have moved around quite a bit. [Note, no one has shown any such thing; this all hinges on the assumption evolution is true – CD]). In your opinion, can genes move between species as described in the above article, or is there no mechanism for such an occurance?

Sorry, I should have pasted in the abstract. The article is about photosynthetic prokaryotes of which there are 5 major groups. Looking at representative genomes from each group, the researchers were able to identify 188 reasonably-likely orthologs upon which to construct a phylogeny.

What they found was a rather striking lack of consensus. Of the 15 possible unrooted trees, they found good support for practically all of them (or should I say, no good support for any one of them). This remained true even when the data set was narrowed to subsets, such as hypothetical common function.

They also expanded their dataset with additional genome data, including non photosynthetic species. To summarize the results I'll quote the paper:

"These results bolster the idea that the evolution of photosynthetic genes has been disconnected from divergence and speciation in these organisms, confirming the extensive role that horizontal gene flow has played in prokaryote evolution."

and,

"The most unexpected result from this analysis is the distinct lack of unanimous support for a single topology. Plurality support is seen for the three trees (5, 10, and 15) that group together Synechocystis sp., C. aurantiacus, and H. mobilis separate from a distinct R. capsulatus and C. tepidum cluster. The data suggest that even strongly supported phylogenies and highly conserved genes from these organisms often show very different evolutionary histories."

Unexpected? Yes; but a problem for evolution? Of course, not. There is always HGT to call upon. Remember, this is evidence for the fact of evolution.

[Charles Darwin]

Originally posted by Doubting Didymus
You were asked several times to provide evidence of phylogenetic mismatches. You utterly failed, and instead displayed for us a series of abominable misquotes that are not even talking about the same thing, or anything like it. I say again: mismatches of significance to evolutionary theory are rare. Mismatches happen, and are the subject of many papers, but they are not problems unless there is no explaition for the mismatch. The fact that you insist on childishly dismissing all explainations offered as contrived handwaving does not make the explaination ineffective unless you actually support your case, which of course you cannot do. You are about rhetoric, and you do not care for real debate.

Utterly failed? Misquotes? Sorry, it was claimed thta phylogenies make for one of the compelling evidences of why evolution is a fact. I pointed out that there are plenty of mismatches, and was asked for examples. I gave a few. How were they "misquotes?"

You say they are not problems unless there is no explanation. Oh, there are plenty of ways to explain away any given mismatch. Whether a mismatch is not a problem, as you claim, is an interesting question. But it is not relevant to the point. The point is that the "fact" of evolution is supported by evidence which can be ambiguous and there are plenty of explanatory mechanisms. Why should we believe evolution is a fact when the evidence you cite is so flexible?

Originally posted by Doubting Didymus
Not a bit of it. Please, all onlookers, pay your fullest attention to any evidential problems charles raises. It would do you all good, however, to note that much of it is empty rhetoric, and to ignore that when you find it.

Would you agree that that is a fairer sentiment?

Of course.

[Charles Darwin]

quote:
--------------------------------------------------------------------------------
Originally posted by Charles Darwin
What is it about this sentence that you don't understand:

"Animal relationships derived from these new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present." Science, 279:505

How did I utterly fail? Please be specific this time.


Originally posted by Doubting Didymus
First of all, WHAT new molecular data is the article referring to? also, what is the problem with new molecular data updating old morphology - based trees? Did you expect phylogeneticists to have everything perfect first try?

Its not my dog, he didn't bite you, and besides you hit the dog first. You see you can't win for losing.

The evidence shows evolution is a fact, there are no significant mismatches, if you find any there will be explanations, and in any case what do you expect, perfection?

[Charles Darwin]

Originally posted by Doubting Didymus
Ha! the 'new molecular data' referred to here is actually referring to molecular data period. An entirely new data collection method clarifies old mistakes, and this is supposed to prove that it is an unreliable method!

Charles, your quote is referring to the old mophological relationships that were found to be wrong when molecular phylogenetics first arrived on the scene back in the eighties. Some relationships that taxonomists had inferred turned out to be false when the molecular data showed up. That's not a mismatch at all, its just an update in our knowledge base. And before you say it: I am not just defining the mismatch away. If we went into a detailed morphological analysis on the updated trees, we would find that we were in fact wrong the first time based solely on the morphological data, and more close to the correct tree now. If that were not the case, it would indeed be reported as a mismatch (remember I am not denying that they exists, just that they are sufficiently rare and unimpressive in detail that they do not outweight the support that phylogenetics delivers)

So, as I suspected, the quote does not mean what you think it means. This is not a mismatch that contradicts common descent. Please try again.

Oh, can it be? You've outdone yourself! Now the mismatches aren't even real.

It is not my dog, he didn't bite you, and besides you the dog first, and besides besides, there is no dog.

"I am not just defining the mismatch away." That is exactly what you are doing.

[Charles Darwin]

Originally posted by markfiend
I think our friend misunderstands the way cladistic trees are made.

If we take an example of some cars which we wish to classify; lets say we have three colours, red, green and blue, three engine sizes, 3 litre, 4 litre. 5 litre, and two seating patterns 2-seater and 4-seater. From these three traits we can classify 18 different "kind" of car: red 3-litre 2-seater, green 5-litre 2-seater, etc. etc.

How do we classify them in a heirarchy though? We could split them into 2-seater and 4-seater, then colour, then engine size or we could give engine size the highest priority, then number of seats, then colour, and so forth. We would be left with a number of possible trees, all of which would be valid to "classify" our cars. This is to be expected of a designed system, where traits can be applied to any or all of the designed machines.

The difference when it comes to biology, though, is that our traits are not distributed across all species like they are with cars. For example, all birds have feathers, so are grouped together at one level of the tree. Also all birds have backbones, so can be grouped with mammals, reptiles, amphibians and fish into "backboned animals" (vertebrates).

The thing is, that there are no non-vertebrates that have feathers, so we know that having a backbone has a higher priority in our classification than having feathers; feathered animals (birds) are a twig on the branch of backboned animals.

When we take a large enough number of traits like this, we can devise a tree where we know that a trait is a "twig-trait" or a "branch-trait".

Now this tree based entirely on morphology (shapes of living things and their structures) was all we had to go on until biochemical investigation of genes and proteins became feasible. The funny thing is, the trees derived from genetic analysis, from protein structures, and from morphology all agree to an astounding degree. (The "mismatches" that CD alleges are when people said, "Hmmm... I'm not sure whether this branch comes out here or there.")

Now the one correct tree is what is predicted from evolutionary theory, where all organisms descend from a single common ancestor. A creationary/ intelligent design theory (as my example of cars) predicts multiple equally valid trees. This is not found, so ID is refuted. QED.

You are not trying hard enough. There are some cars with a hatchback; others without. Some with a trunk, others without. Then include trucks, earth movers, mopeds, bicycles, airplanes, .... You get the point. I don't want to push the analogy beyond its point of usefullness, but you've erred in the opposite extreme.

[Charles Darwin]

Originally posted by Doubting Didymus
Common descent predicts that an ancestor tree should exist. Nothing else (at least, nothing you're mentioned) predicts that result. Therefore the robustness of the ancestor tree confirms that there were, in fact, ancestors. Thus validating the theory that ancestral species existed, namely common descent.

If you want to refute this, you must either show that common descent does not in fact predict the tree to exist in the way it does, or that some other explaination exists that fits the data as well or better. That's how theories are normally treated in science, anyway.

Even evolutionists use manufactured objects as examples of hierarchies.

[Charles Darwin]

Originally posted by God Fearing Atheist
Charles my friend, never have i seen someone so capable of talking out of both sides of their mouth. Either there is significant convergence, or there is not. So far, you seem to accept both simultaneously.

- A simply exassperated GFA

There is significant convergence, but there are also numerous and important mismatches (not just a few). None of which cannot be explained away by evolutionists. But they assume evolution is a fact and therefore assume that stretching for whichever explanation is always valid. Never is the theory itself questioned. There is no boundary line beyond which evolution is not allowed to go. Those who claim that this validates evolution are forced to trivialize these important mismatches, and are guilty of not actually setting a criterion for what constitutes confirmation and what does not.

[lpetrich]

Originally posted by Charles Darwin
(origin-of-endosymbiosis scenario...)
You are coming through loud and clear. Your imaginary passage is painfully unlikely (not impossible though), yet your metaphysics forces you to accept it. This isn't science.Except that cells living inside of other cells is not as unlikely as CD seems to believe. CD ought to do some studying of "intracellular parasites" some time.

I wouldn't make the conclusion sound so trivial. It provides plenty of fuel to those evolutionists who are skeptical of endosymbiosis. Also, the conserved organelle in both prokaryotes and eukaryotes forces evolutionists line these species up (I do not know what the implications of this are). That's a STUPID argument. CD, do you honestly think that biologists are unable to distinguish between endosymbiotic and non-endosymbiotic organelles?

Endosymbiotic ones can be recognized by their gene content; they have their own genomes, and their genes are most closely related to certain outside organisms. And some non-endosymbiotic organelles may be derived from endosymbiotic ones; some protists have hydrogen-releasing "hydrogenosomes", which are likely genome-less mitochondria.

[lpetrich]

Originally posted by Charles Darwin
rRNA and tRNA sequences are not "non-coding." In any case, these sequences were not "involved in gene regulation and production of functional bits of RNA, like ribosomal and transfer RNA." That's the point. They may be called "non-coding" if one means by that "not translated into a protein".

[lpetrich]

Originally posted by Charles Darwin
Interesting. If the mismatches were not rare then it would be a problem for evolution? Unfortunately, the answer is not yes. Of course I don't know what you intend by the term "rare" but such mismatches are all over the place. One need only look. I was asked for examples, I gave some. There are plenty more. It must be conceded that there are some circumstances that are likely to produce mismatches, like greatly varying rates of evolution and relatively rapid divergence However, there are ways for testing for such circumstances, such a rerunning a tree-finding algorithm with different randomly-chosen taxon-addition orders, and seeing which topologies consistently appear.

So I don't see why these difficulties support a poof-poof-poof theory of origins.

[lpetrich]

(on lateral transfer of photosynthesis genes...)

That is indeed an oddity, but if the genes are transferred in groups, then some of the coordination difficulty disappears.

[God Fearing Atheist]

I just loved the part about provrial integration being "quite specific" Charles. Certainly, there is some degree of *preferential* targeting, according to base sequence, nuclear localization and, in Saccharomyces cerevisiae, domains of silent chromatin (http://www.genesdev.org/cgi/content/full/13/20/2738#B34).

But saying these sorts of things show shared ERVs to be indicative of something other than common decent is a serious misunderstanding. What are the odds, Charles, of the *same* ERV being found at the *same* locus, even if they perfer to insert near some sequences over others? Creationists love probability calculations, so here's a good one.

-GFA

[Happy Wonderer]

Originally posted by Charles Darwin
quote:

"The most unexpected result from this analysis is the distinct lack of unanimous support for a single topology. Plurality support is seen for the three trees (5, 10, and 15) that group together Synechocystis sp., C. aurantiacus, and H. mobilis separate from a distinct R. capsulatus and C. tepidum cluster. The data suggest that even strongly supported phylogenies and highly conserved genes from these organisms often show very different evolutionary histories."

Unexpected? Yes; but a problem for evolution? Of course, not. There is always HGT to call upon. Remember, this is evidence for the fact of evolution.

This is quite amusing, Charles. A few pages ago you were disputing cladistics for horses, and now you are reduced to quibbling about C. aurantiacus? FYI, that is a bacteria! Should we throw out the whole clade for mammals, then?

hw

[Doubting Didymus]

Correction: answers and explanations have already been provided. There is no "problem" with these mismatches (and no, they are not "few and far between" -- take a look at just the few references I supplied) from the evolution perspective. Evolution is a fact, and the anomalies and mismatches are the result of one or more of a dozen or so possible explanations evolutionists can draw on. But the ability to explain so much means the data are not compelling evidence for evolution. That has been my point.

That would only work if the explainations for mismatches were bad explanations, ad hoc confabulations and unfalsifyable speculations.

Horizontal gene transfer, for example, happens. We have seen it happening in a variety of organisms. Among organisms that do this, we'd expect molecular phylogenies to be unreliable. You wish to dismiss this as ad hoc, but in fact anyone can see that it is perfectly reasonable.

Utterly failed? Misquotes? Sorry, it was claimed thta phylogenies make for one of the compelling evidences of why evolution is a fact. I pointed out that there are plenty of mismatches, and was asked for examples. I gave a few. How were they "misquotes?"

Not misquotes, perhaps. How about "malquotes" then? Your quotes are mainly about problems that phylogeneticists have encountered, or about new data updating less reliable data and refining specific parts of the tree. All your quotes are without context, and are generally useless when we are asking for specific instances of problematic mismatches. Later, for example, you are moving on to expand on one of the quotes that seemed to suggest significant mismatches, and we find you're only having a bitch about horizontal gene transfer.

Unexpected? Yes; but a problem for evolution? Of course, not. There is always HGT to call upon. Remember, this is evidence for the fact of evolution.

Very tiresome, charles. We only expect this to happen in species where horizontal gene transfer actually happens. We have seen horizontal gene transfer, in fact, I saw some just last wednesday. I'm not kidding. Our lab was having a look at hybrid backcrossing in australian plants. Given this, why is it such a terrible thing to find evidence of it in phylogenetic trees of organisms that do it? You seem to have some sort of strange objection to explanations of any kind, and completely ignore the question of whether the explanation is good or not. If it's your contention that any particular scientific theory must explain everything it touches without exception and without any hypothesis testing in any case where it doesn't perform as well as it should, you might as well waltz home in victory now shouting "I disproved molecular phylogenetics by pointing to a species it doesn't work on! Also, I'm suing the kitchen knife industry because I can't cut titanium alloy."

Then, confronted with an exposition of one of your other malquotes, you move into that old time empty rhetoric I was talking about earlier. Observe:

Me (paraphrased): "Your quote is not talking about mismatches. It is about more accurate data (molecular analysis) updating less accurate data (morphological comparison). Note that the new data doesn't actually conflict with the old, but closer inspection reveals that morphological comparisons should have yeilded the new tree in the first place"

Rather than actually address the explaination, you descend into this:

Its not my dog, he didn't bite you, and besides you hit the dog first. You see you can't win for losing.

Oh, can it be? You've outdone yourself! Now the mismatches aren't even real.

It is not my dog, he didn't bite you, and besides you the dog first, and besides besides, there is no dog.

"I am not just defining the mismatch away." That is exactly what you are doing.

These are the desperate antics of one who has utterly failed to make any sort of case at all. You might have struck a terrible blow to the theory of evolution, if only this were a strange paralell universe where your opponents are not allowed to explain things. If one ignores your assertions to the effect that explainations prove unreliability, as they very well should, then what emerges is actually a robust piece of evidence for common descent, the objection to which disappear under a moments light scrutiny.

[Charles Darwin]

Originally posted by Doubting Didymus
You're not making any sense. What on earth is the fallacy of complexity? How is it relating in any way to anything I was saying? I do not believe that the cheetah 'just arose', and I pointed out why in my last post. There are complicated processes involved in the origin of the cheetah that do not equate with happenstance.

Not by happenstance? Was it directed? Happenstance, in fact, is precisely how the evolutionary process is supposed to work. Remember, no teleology or final causes. You say the process is complicated. Fine, make it as complicated as you like, there still is to be no external guidance. The cheetah 'just arose'; whether by millions of years, billions of years, whatever, random biological variation struck upon the cheetah. Natural selection could not have caused any of that variation. You must believe that there is a gradual path from the microbe to the cheetah, and random variations found it.

[Charles Darwin]

Originally posted by Doubting Didymus
You seem to be still seeking some sort of knock down factual support that cannot possibly be explained by any other means, no matter how wacky. That not very realistic.

You're the one making the claim that evolution is a fact. I'm just trying to figure out what's behind it.

Originally posted by Doubting Didymus
Instead, its best to note that the theory of common descent makes many predictions, all of them are supported by the evidence, and additionally, no evidence to the contrary has ever been found in any field of science in the history of time, ever.

Wow, I give. I think I'm beginning to understand now. Anyone who believes that "no evidence to the contrary has ever been found in any field of science in the history of time, ever" is certainly entitled to hold the position that evolution is a fact.

[Charles Darwin]

Originally posted by markfiend
Now the one correct tree is what is predicted from evolutionary theory, where all organisms descend from a single common ancestor.

I hadn't heard that. Why then are evolutionists calling for a different kind of evolution (horizontal rather than vertical) in the early days to explain how the 1st 3 branches formed?

[Charles Darwin]

Originally posted by Oolon Colluphid
Excellent post Mark!

Yep. This is why it is so strange that good features aren’t used in different groups, and that poor features are spread around amongst (presumably, from creationism) different groups, but within the evolutionary groupings.

Thus it’s odd that the creator gave all birds their efficient through-flow lung system, whether it’s a swift, an ostrich, a penguin or a kiwi (separate creations, presumably)... and gave other separate creations the far inferior ‘mammalian’ tidal system: bats, cheetahs, wolves, sloths, humans all have the inferior system. So the designer made the same mistake over and over: using an inferior system to one he knew about, one that would be advantageous to its owners, is poor design. It’s like giving all four-wheeled vehicles, whether tractor or racing car, a low-power two-stroke engine, while giving trains, say, whether intercity expresses, tourist ‘steam’ trains or Hornby 00-gauge toys, a powerful four-stroke.

Similarly, the creator made the same mistake over and over when he put -- separately into separate creations -- backward-wired retinas into hawks and humans, anteaters and antelopes, rabbits, rhinos and raccoons...

He repeated the stupid design of the laryngeal nerve’s routing in whales, giraffes, humans, pigs and porcupines, lemurs, lions and lemmings -- separate creations all, one assumes.

And so on.

It is the distribution of poor designs, as much as the fact that there are poor designs, that shows the designer to be a bumbling fool (or a refuted hypothesis). For he did not merely make mistakes; he made the same ones repeatedly, but only within certain groups! A giant squid cannot get a detached retina... and nor can a Californian octopus.

Cheers, Oolon

Yet another religious thinker has joined (and I thought that was for the GRD forum). Like the others you obviously have strong personal religious beliefs, which I cannot argue with. Clearly, evolution is a fact for you. (but not a "scientific" fact).

[Doubting Didymus]

Originally posted by Charles Darwin
I hadn't heard that. Why then are evolutionists calling for a different kind of evolution (horizontal rather than vertical) in the early days to explain how the 1st 3 branches formed?

That's just silly. Strongly suggest that you not make statements about things you are completely ignorant about.

[Doubting Didymus]

Originally posted by Charles Darwin
You're the one making the claim that evolution is a fact. I'm just trying to figure out what's behind it.

Wow, I give. I think I'm beginning to understand now. Anyone who believes that "no evidence to the contrary has ever been found in any field of science in the history of time, ever" is certainly entitled to hold the position that evolution is a fact.

More empty rhetoric. Are you here for a discussion, or a baloon-filling contest?.

[Doubting Didymus]

Originally posted by Charles Darwin
Not by happenstance? Was it directed? Happenstance, in fact, is precisely how the evolutionary process is supposed to work. Remember, no teleology or final causes. You say the process is complicated. Fine, make it as complicated as you like, there still is to be no external guidance. The cheetah 'just arose'; whether by millions of years, billions of years, whatever, random biological variation struck upon the cheetah. Natural selection could not have caused any of that variation. You must believe that there is a gradual path from the microbe to the cheetah, and random variations found it.

Is it then your opinion that medical textbooks on cancer can be accurately summed up by the sentiment "cancer just arises"? Does that adequately illuminate the causes and processes that must be undertood in order to comprehend and battle cancer? Of course not.

And yes, I beleive that there is a gradual path from protozoans to complex metazoans. Thats not relevant to the question of whether evolution can be properly called 'random'.

In your opinion, are all processes not guided by an intelligent mind 'random'? Ocean waves sort pebbles by weight, for example. Is that a random outcome or not? Note that I'm not drawing any comparisons between evolution and something so simple as basic physical processes, but the point remains that natural processes can have nonrandom, predictable outcomes.

[Charles Darwin]

Originally posted by markfiend
According to 29 evidences for macro-evolution (http://www.talkorigins.org/faqs/comdesc/section1.html#pred3) at talkorigins, this agreement is to the 41st decimal place. To compare, the charge of the electron is only known to the 7th decimal place. So not very much disagreement at all.

I guess an argument is OK if it is for evolution, no matter how specious. Here is the claim:

"So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 10^41 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree. In spite of these odds [CD: what odds?], as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies. Speaking quantitatively, independent morphological and molecular measurements such as these have determined the standard phylogenetic tree to better than 41 decimal places. This phenomenal corroboration of universal common descent is referred to as the 'twin nested hierarchy.' "

Apparently the claim is that evolution predicts the molecular and morphological trees to be identical, and they are, in spite of there being 10^41 trees in all. This is seen as some sort of great coincidence which can only be explained by evolution. If this were the case then evolution would be falsified since there are molecular vs morphological mismatches. But since evolution is considered a fact, then this isn't really the case.

Note also the unspoken assumption here that molecular and morphological characters can be unrelated. Truly bizarre; but then again, this is evolution.

[Charles Darwin]

Originally posted by DMB
I have hesitated to participate in this thread, because I am a layman in biology, but I do think that we have a basic problem here about the understanding of science. And that is odd, because CD claims to be a scientist. So I too would like some elucidation of what he understands as a "scientific fact".

If we look at the fairly short history(approximately 400 years) of modern science, although there have been some totally discredited theories, most progress has been made by building on and refining what has gone before (e.g. Newton's oft-quoted "standing on the shoulders of giants").

In a very few cases, we do seem to have arrived at a finished state, as in the case of Newtonian mechanics as the basis of modern mechanical engineering. Normally, however, the process of adjustment and refinement goes on. Even when a previously unexplored phenomenon such as radioactivity is investigated, it largely adds to scientific knowledge and theory rather than totally superseding it.

It would have been remarkable indeed if Darwin's publication of the Origin of Species had been the final word on evolution. It is true that he spent a long time gathering evidence for it, but the total evidence available at his death was small in comparison with what has subsequently been gathered. And some of that later evidence has refuted some of Darwin's ideas. This is no more surprising than that the periodic table, when first postulated, had gaps and mistakes that have subsequently been adjusted.

There is no particular reason to suppose that biology has nearly run its course in the way that Newtonian mechanics has. So we should expect to see continued minor adjustments to evolutionary theory as new evidence is forthcoming. There is no paradox in asserting that an ancestor tree should exist but that not quite all the details have yet been established beyond doubt. What is so remarkable is that the work of huge numbers of scientific professionals since Darwin have produced evidence, sometimes in fields that did not even exist in Darwin's day, all of which support the fact of evolution.

All good points, but on the whole we will disagree because I don't view evolutionary biology as the kind of successful, progressive process, akin to Newtonian physics, as you are describing. Let me put it this way. The problem lies not with a few missing blanks that have yet to be filled in. I'm not quibbling over some fine points.

The whole idea is, frankly, untenable. Now this alone doesn't mean the thing is all wrong. Science is sometimes bizarre. But when one examines the evidence at hand, things don't get any better.

Now I trust you are well aware (unless you've been living in a hole) that the whole topic is laced with deeper concerns. This thread is no less of an example than the history of the movement. The emotional and religious issues are obvious. With some theories of science, one might argue there are subtle religious influences. Not even here; here the religion is quite overt. There's no hiding it. Just read the posts.

[Godot]

Originally posted by Charles Darwin
I guess an argument is OK if it is for evolution, no matter how specious. Here is the claim:

"So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 10^41 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree. In spite of these odds [CD: what odds?], as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies. Speaking quantitatively, independent morphological and molecular measurements such as these have determined the standard phylogenetic tree to better than 41 decimal places. This phenomenal corroboration of universal common descent is referred to as the 'twin nested hierarchy.' "

Apparently the claim is that evolution predicts the molecular and morphological trees to be identical, and they are, in spite of there being 10^41 trees in all. This is seen as some sort of great coincidence which can only be explained by evolution. If this were the case then evolution would be falsified since there are molecular vs morphological mismatches. But since evolution is considered a fact, then this isn't really the case.

Note also the unspoken assumption here that molecular and morphological characters can be unrelated. Truly bizarre; but then again, this is evolution. You've got a bit of a problem here. There are not 10^41 phylogenetic trees, there are 10^41 alternate ways to arrange the the major taxa into a tree. Big difference. There is only one correct tree. Therefore, your odds are 1:10^41.

[Charles Darwin]

Originally posted by Xixax
I would just like to point out to Charles Darwin that the cheetah just arose from a very similar cheetah-like ancestor. Likewise, that ancestor came from something very similar to itself, and so on and so on until you have something not much like a cheetah at all.

If Charles Darwin saw a cheetah born without spots, would he scream bloody murder and say that science just can't explain anything like that happening? No. Would he invoke a creator and say "SEE? God just made us a new species, a cheetah without spots!" I'd hope not.

If, for some reason that proved spotless cheetah's were more effective in reproducing and eventually that gene spread throughout a small population, one of the spotless cheetah's then gave birth to a litter with shorter tails, would he see any problem? NO.

Now we have a litter of spotless cheetah's with shorter tails... Charles D, do you see where this is going? Multiply the changes and timeframe by nearly unimaginable quantities and you still fail to understand how evolution works?

I feel similarly to Huxley, it's nearly embarrassing not to understand and recognize that evolution happened and is still happening. It's unavoidable.

Yes, I see where it is going. What is "unavoidable" to you is in fact a highly speculative notion that between the microbe and cheetah there lie a tremendous number of finely grained intermediates, each one not so different from its neighbors that it cannot be reached via normal biological variation; that normal biological variation is able to explore the space sufficiently quickly and "experiments" run in the wild with sufficient efficacy to move the process along the path in spite of the astronomical design space involved. What is embarrassing is hearing someone unequivocally claim such speculation is "unavoidable."

Meanwhile, let us consider that fact that known cases of minor evolution are brought about by an incredibly complex adaptation machine. Mutations do not occur randomly, either temporally or spatially, and we find what are essentially preprogrammed pathways of change. Hardly the kind of thing evolution describes. Simply put, evolution would have had to create the marvelous mechanisms that make evolution possible.

[Charles Darwin]

Originally posted by Jack the Bodiless
Are you seriously arguing that it would be less amazing if millions upon millions of creatures just popped into existence in a sequence that mimics common descent, rather than evolving from very similar antecedents?

Are there any other fields of science in which you prefer magic as an explanation, even when a non-magical explanation fits the evidence?

Translation: Mechanistic / naturalistic explanations will always be preferred. It is built into the paradigm.

[Doubting Didymus]

Originally posted by Charles Darwin
Meanwhile, let us consider that fact that known cases of minor evolution are brought about by an incredibly complex adaptation machine. Mutations do not occur randomly, either temporally or spatially, and we find what are essentially preprogrammed pathways of change. Hardly the kind of thing evolution describes. Simply put, evolution would have had to create the marvelous mechanisms that make evolution possible.

Sorry, are you now claiming that muations are not random?

[lpetrich]

Originally posted by Charles Darwin
Apparently the claim is that evolution predicts the molecular and morphological trees to be identical, and they are, in spite of there being 10^41 trees in all. This is seen as some sort of great coincidence which can only be explained by evolution. ...I wonder what CD is claiming -- that it is some sort of irrelevant coincidence?

Note also the unspoken assumption here that molecular and morphological characters can be unrelated. Truly bizarre; but then again, this is evolution. CD ought to tell us why he thinks that this hypothesis is unwarranted -- why he thinks that there is some sort of necessary correlation between cytochrome c sequences and macroscopic features.

[Urvogel Reverie]

Originally posted by Doubting Didymus
Sorry, are you now claiming that muations are not random?


Apparently so. It should be most curious to see his explanation for stochastic replication/transcription errors.

Urvogel Reverie

[markfiend]

In response to my post about phylogenies
Originally posted by Charles Darwin
You are not trying hard enough. There are some cars with a hatchback; others without. Some with a trunk, others without. Then include trucks, earth movers, mopeds, bicycles, airplanes, .... You get the point. I don't want to push the analogy beyond its point of usefullness, but you've erred in the opposite extreme.

Yes I get the point. But you do not. The more "traits" you add to the car-pool, the more possible heirarchies can be constructed. The design argument would predict that all these possible heirarchies are equally valid. With living things, there are 10^41 possible heirarchies, but only one that is valid.

[HRG]

Originally posted by Charles Darwin
Translation: Mechanistic / naturalistic explanations will always be preferred. It is built into the paradigm.

This has nothing to do with a "paradigm" (Oh Kuhn, Kuhn, what nonsense is spread in thy name ...). It has everything to do with the simple fact that only naturalistic explanations are objectively testable.

(How would you distinguish between a water-to-wine transformation by Jesus and a grand illusion by Loki ?)

It is highly doubtful whether supernatural explanations are actually explanations. As someone has said, what can in principle explain everything explains nothing.

Regards,
HRG.

[Oolon Colluphid]

Originally posted by Charles Darwin, in response to my post about dsign flaws:
Yet another religious thinker has joined (and I thought that was for the GRD forum).
Ad hominem. Points not addressed.

I fail to see how my post can be construed as religious thinking. In fact, it is quite the reverse. What I am doing is scientific thinking. I am taking the hypothesis -- that there is a designer behind living things’ complexity -- and testing it. “If there is a designer of great intellect and abilities, what should we see in nature. And what should we not see -- what observations might refute it.”

If there were such a designer, then the one thing we would not expect to see is foolish, poor designs.

Yet we do find poor designs in nature. This means that the designer hypothesis -- ie yours -- is refuted.

It does not matter in the slightest whether we have an alternative explanation or not. Therefore, evolution does not come into my argument at all. It is irrelevant to what I’m saying, and hence there is no ‘religious’ thinking involved about it.

This is why I leave open the possibility that there was a designer, but it has to be an incompetant one. Personally, I’m inclined towards this designer -- if there were one -- being a drunkard, able to accomplish impressive feats at times, but having some off days, days where, hung over or still pissed, he cocked up badly (almightily, one might say).

Now, evolution explains these things more parsimoniously, but an incompetent designer is possible. But it’s not usually one that creationists want to countenance.
Like the others you obviously have strong personal religious beliefs,
:mad: Where? What? I demand that you back up that ludicrous assertion or withdraw it, lest I be forced to emphasise my annoyance with terms such as ‘fuckwit’.
which I cannot argue with.
I do not wish to argue religion. I demand that you explain by your hypothesis the numerous poor designs in nature. So, address the frigging point, and leave the ad hominems out of it pal.
Clearly, evolution is a fact for you. (but not a "scientific" fact).
I know of no other sort than the scientific sort. I have evidence to support it. How about you address the evidence?

[monkenstick]

The whole idea is, frankly, untenable. Now this alone doesn't mean the thing is all wrong. Science is sometimes bizarre. But when one examines the evidence at hand, things don't get any better.

coming from the same person who stated

Note also the unspoken assumption here that molecular and morphological characters can be unrelated. Truly bizarre; but then again, this is evolution.

do you wonder why your personal incredulity doesn't hold much weight?

[Charles Darwin]

Originally posted by Darwin's Beagle



First, let’s look at the fossil record. So far the fossil record has been brought up and you have cavalierly dismissed it. Concerning Stephen Jay Gould’s article “Evolution: Fact and Theory” you say:

CD=
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Let's see, as I recall he pointed out that fossils exist; that some species are similar to other species; and the we observe small amounts of evolution. Therefore evolution is a fact? I'm sorry, but with all due respect to the late Professor Gould, even my pet cat can't be persuaded by that.

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Erm… Gould did not say that. It is surprising that someone with your command of the literature would misrepresent him that way. Actually Gould says the exact opposite. He says that in the fossil record we observe the BIG amounts of evolution. It is the small amounts of evolution we do not observe. This is his theory of punctuated equilibrium. It has been around in the literature since 1972. To use your phraseology, I’m “amazed” you seem to have not heard about it.

Well, let's have a look at the relevant passage:

"The third argument is more direct: transitions are often found in the fossil record. Preserved transitions are not common—and should not be, according to our understanding of evolution (see next section) but they are not entirely wanting, as creationists often claim. The lower jaw of reptiles contains several bones, that of mammals only one. The non-mammalian jawbones are reduced, step by step, in mammalian ancestors until they become tiny nubbins located at the back of the jaw. The "hammer" and "anvil" bones of the mammalian ear are descendants of these nubbins. How could such a transition be accomplished? the creationists ask. Surely a bone is either entirely in the jaw or in the ear. Yet paleontologists have discovered two transitional lineages of therapsids (the so-called mammal-like reptiles) with a double jaw joint—one composed of the old quadrate and articular bones (soon to become the hammer and anvil), the other of the squamosal and dentary bones (as in modern mammals). For that matter, what better transitional form could we expect to find than the oldest human, Australopithecus afarensis, with its apelike palate, its human upright stance, and a cranial capacity larger than any ape’s of the same body size but a full 1,000 cubic centimeters below ours? If God made each of the half-dozen human species discovered in ancient rocks, why did he create in an unbroken temporal sequence of progressively more modern features—increasing cranial capacity, reduced face and teeth, larder body size? Did he create to mimic evolution and test our faith thereby?" - - Gould, "Evolution as Fact and Theory"

I meant no misrepresentation. I gave a quick summary of Gould's argument for why evolution is a fact. He gives 3 areas of evidence: the fossils, comparative anatomy, and small amounts of evolution. Granted I did not go into the detail Gould does about transitionals, but I thought it was obvious that I was intending merely to summarize. Contrary to your claim, Gould's argument is not from large changes in the fossil record, it is from the occasional examples of purported smaller changes.

Ah, perhaps you have heard about it after all. You allude to it with the common creationist misrepresentation of:

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On to the fossil record. How does that help to combine with the other evidences to arrive at telling us evolution is a fact? You mean that species appear out of nowhere?

+++++++++++++++++++++++++++++++++++++++++++

Hmm, are you referring to the “sudden” appearance in the fossil of new species that punctuated equilibrium purports to explain? Nobody in modern paleontology has ever thought, said, or even implied that these species come from “nowhere”. Why would such a knowledgeable person like you, misrepresent things so badly? How disappointing.

Again, I'm afraid it is you who are doing the misrepresenting here. I said nothing about paleontologists believing the species come from “nowhere.” It is true that paleontologists sometimes point out several problems that the fossils pose for evolution. But getting to my point above, I was commenting on the data, not on the paleontologists beliefs about the data. So let's cut the hypocritical finger-pointing, OK?

What punctuated equilibrium says is that in the fossil record we see a certain species and fossils of that species can be seen pretty much unchanged over several bedding planes, and then in the space of a single bedding plane it will disappear and be replaced by a similar species or group of species. The new fossil species did not appear from nowhere, it appeared from exactly what it appears (pun intended) to have appeared from -- the previous species. It is just that the morphological change associated with speciation occurred in the space of a single bedding plane.

Well that describes some of the data. Why do you not also mention that there are instances where species do appear without any obvious precursors?

Ah, but you may well ask do we have any evidence that this is true? Does speciation occur in such a short period of time? Yes, we do. If comes from – Stephen Jay Gould, himself. I am reciting this from memory so I’m afraid I don’t remember the names of the species, but Gould collected shells on a mud-flat. The shells were from two different but highly related species. Also in that mudflat were shells that formed a continuum from the spiky ones to the smooth ones. One had a smooth shell and the other had spikes. IIRC the smooth-shelled species still existed on the mudflat but the spiky one did not. Gould was struck by the observation that the more spiky the shells were, the more eroded they seemed to be. This suggested to him that the spiky ones were older than the smooth ones, but he could not declare that to be the case just on the impression that the spiky shells seemed to be more eroded. Afterwards, new dating techniques became available that were able to date the shells and sure enough the spiky ones were older. The interpretation was that the spiky-shelled species had evolved into the smooth-shelled species and this had taken place over a period that is consistent with a single bedding plane.

Judging from your other arguments you will ask how this proves evolution? The answer is it doesn’t. There are other possible explanations. However, THIS explanation falls naturally from the results. The other possible explanations are purely ad hoc. This is just one piece of the evidence and it provides support that to the idea that punctuated equilibrium does not violate Neo-Darwinian evolution.

No surprises here.

Now that we have covered your stated misconceptions concerning the fossil record, let’s take a look at what the REAL fossil record is telling us. What does it show? The first fossils are microfossils found in rocks dated back 3.6 billion years ago. These are bacteria-like organisms, the most simple life known. There is some biochemical evidence for even earlier life. Apatite granules showing an enrichment in C-12 over C-13 over and above that what would be expected if they were produced from abiotic sources were found in rock dated back 3.85 billion years ago. However, this evidence is controversial and while I do not dismiss it completely, I do not put much stock in it either.

There is evidence that beginning about 1.5 billion years ago, oxygen levels caused a big change in the type of microfossils seen. This corresponds temporally with the elimination in rock of banded-iron formations (BIFs) seen in surface rocks of that time. BIF cannot form in an oxidizing atmosphere. Eukaryotic lifeforms have been found in rock dating back 800 million years. These were single-celled protozoan-like creatures. The first evidence of metazoan (multicellular) organisms come from fossilized worm burrows dating back 700 million years. There are also some microfossils of embryonic cell clumps dating back about 600 million years ago.

No surprises here.

Then at about 543 million years ago we have the Cambrian explosion, in which a variety of metazoan organisms make their appearance. Creationists make a big deal about this, so I’ll have to spend some time on it for you. Actually, I do not know for sure you are creationist since you have steadfastly not given us much indication of what you DO believe, only what you DON’T believe. You also complain about people making assumptions about your belief, but if you do not tell us, then the fault does not lie with them. It lies with you. Since your rhetoric SOUNDS like that of a creationist, I will assume that is just what you are.

Creationists often use the Cambrian explosion as evidence against evolutionary theory. It is not. It is strong evidence for descent with modification which is one of the core tenets of evolutionary theory. It is during the Cambrian explosion that virtually all phyla emerge. There hasn’t been a new one since (actually, I think the bryozoans arose after the Cambrian but I’ll set that aside for now). Creationists say this pattern is predicted from the theory of Special Creation, while evolutionists say that the Cambrian is a BIG punctuational event. Who is right?

No surprises here.

First, something that creationists do not seem to acknowledge is that NONE of the organisms that were spawned during the Cambrian explosion are around today. There has been a significant change in the make-up of the flora and fauna since then. This change in the make-up of the flora and fauna STRONGLY supports descent with modification (more on this in a moment).

This, of course, does not "STRONGLY" support descent with modification. But you say more in a moment, so I'll wait till then.

Second, creationists also do not seem to acknowledge is this “sudden” appearance actually occurred over several million years, so there is plenty of time for a lot of evolution to happen.

This doesn't sound right, but I'm not exactly sure what you are intending here. Can you elaborate a little more? What exactly do you mean by a fossil species appearance occurring over several million years?

The radiation of species like the 800+ Drosophila species in Hawaii and the Darwin finches in the Galapagos suggest that when new niches to exploit and with little competition there is likely to be rapid evolution. The Cambrian explosion had this in spades. Thus, there is good reason to believe that the Cambrian was a punctuational event.

No surprises here.

Furthermore, what the fossil record shows since the Cambrian explosion is a continual change up until present day of the make-up in the flora and fauna. The change is such that organisms in adjacent bedding planes are much more similar to each other than they are in distant bedding planes.

Your word "continual" is loaded. Obviously there were many fossil species that showed essentially no change for long periods. I'm sure you don't doubt that, so you don't really mean continual change. Perhaps you mean "continuous," that is, unbroken or unpunctuated. But this too would be wrong, as there are many post Cambrian examples. I used the horse sequence earlier as an example which the PE'ers used to advance their ideas. More on horses later as I see you bring it up below.

To me the only reasonable conclusion from this data is that there has been continual evolution – descent with modification – from then until now.

Wow. I'm about ready to give. Let's read on:

Creationists claim that the fossil record and the Cambrian explosion fits with predictions from the theory of Special Creation better. How so? To fit the REAL data with Special Creation one would have to postulate a creator that poofs a number of bacteria-like organism into existence, waits around 2 billion years for them and their descendents to put enough oxygen into the air then poof some different bacteria-like organisms into existence, wait another 700 million years poof some simple eukaryotes into existence, wait another 100 million years and poof the first simple multicellular organisms into exxistence. Then after almost 3 billion years have a sudden fit lasting several million years of poofing new multicellular organisms and then periodically after some go extinct poof some other similar ones into existence until the present time.

Yeah, that's about it, and since:

it is not reasonable

then evolution must be a fact. Now is a good time to revisit the question of what a "scientific fact" is. Or in this case, what it is not. One thing a scientific fact is not is a fact that entails religious reasoning. Evolution is a fact for you, not a scientific fact. What is ironic is that they always say that it is the anti-evolutionists who are the religious ones.

You have strong religious beliefs. I respect that, and who knows, you may even be right. And your argument here for why evolution is a fact is perfectly valid. It makes perfect sense for you to state that:

change in the make-up of the flora and fauna STRONGLY supports descent with modification

and,

To me the only reasonable conclusion from this data is that there has been continual evolution – descent with modification – from then until now.

No matter that the idea of the incredibly complicated Cambrian species arising on their own (whether quickly or not) goes against what science tells us about the world. The story is a real stretch, but it is all you have.

Of course, Charles you may be able to show me where this is wrong and give a REASONABLE counter explanation for the real evidence.

No, I think your position is perfectly consistent.

You are trying to make a case against evolutionary theory based on what we DON’T know. Although your STATED acceptance of the definition of scientific fact acknowledges that we do not have to be able to explain everything, your argument boils down to “if you can’t explain everything then you can’t claim it to be a fact”.

That is a misrepresentation. I am very much referring to what we do know about the evidence.

You were given links to the REAL fossil record of horse evolution and asked how you would explain it. Here is your response:

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I really don't know, but I do know that the mythical horse sequence convinced many a lay person for the better part of a century before it was finally admitted to be, well, ... mythical. What we have is a bunch of different species which, if evolution is true, must have punctuated into each other. I also know that evolution, beyond handwaving, doesn't explain how any of those species got there in the first place anyway. Why is it you think this makes evolution a scientific fact?

+++++++++++++++++++++++++++++++

Charles, Charles … don’t you find it a little hard to look at yourself in the mirror when you intentionally distort the facts. There was no mythical horse sequence. There was incomplete data that led to erroneous assumptions as to the true intermediates but so what? I’ll bet there are some wrong intermediates in our ideas right now that will be modified when we find new data. The REAL data has only gotten stronger over the years supporting evolutionary theory. We could have of course found a Cambrian horse fossil. If we would have done that THEN evolutionary theory would be in real trouble. But we haven’t. Every find so far has only added support to evolutionary theory. The fossils fit in the right places. The new fossils we will find in the future will fit in the right places as well.

This is the "evolution is true" version of history, or what Gould calls "whiggish" history. There were never any distortions or biases, just plain old good science at work. Here's what Niles Eldredge had to say about it:

There have been an awful lot of stories, some more imaginative than others, about what the nature of that history [of life] really is. The most famous example, still on exhibit downstairs, is the exhibit on horse evolution prepared perhaps fifty years ago. That has been presented as the literal truth in textbook after textbook. Now I think that that is lamentable, particularly when the people who propose those kinds of stories may themselves be aware of the speculative nature of some of that stuff. --Eldredge

You were shown a picture of fossil skulls showing a pretty complete line of intermediate forms between early apes and present-day humans. Even you admitted that you could not tell where the cut-off between apes and humans was. Your next sarcastic statement is a bit of a puzzle:

F++++++++++++++++++++++++++++++++++++

Oh, by the way, one little question: why does that make evolution a scientific fact?

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One would think that a clever guy like you could see how this fits well with evolutionary theory while any non-evolutionary theory is going to have be an ad hoc explanation. IOW it is a piece of the evidence that makes it unreasonable to not to view descent with modification as a fact.

You think my question was sarcastic; I guess you just can't imagine that those data do not unequivocally support evolution, so any questioning of them must be sarcastic. As you say: "it is a piece of the evidence that makes it unreasonable to not to view descent with modification as a fact." But given your religious beliefs it all makes sense.

Your responses along these lines have so far been pretty pathetic. The first piece of evidence presented to you was endogenous retroviruses (ERVs). You seem to acknowledge that ERV are consistent with the predictions of relatedness from evolutionary theory. But you find some exceptions that even you admit evolutionary theory can explain and then you dismiss the evidence as worthless. This is like the fossil record scenario. You look at what it is clearly strong evidence in the overall pattern, but because the data isn’t perfect you feel justified in ignoring it all.

The authors of the paper you (mis)quote found STRONG support for the evolutionary relatedness by examining ERVs. They found this support by looking at insertion sites of a variety of organisms and then by phylogenetic analysis found the most parsimonious fit. Your response was that phylogenetic analysis is not reliable, and that you can come up with anything you want. This shows an appalling lack of knowledge about not only phlogenetic analysis but about science as well.

That is a blatant misreprentation of my points. The Hillis paper is a fine piece of work. How do you explain an HERV which shows up in the chimp and ape but not human? In the human you have a clean pre-insertion site.

Next, you were shown a picture of human chromosome #2 side-by-side with its G-banding matches in the chimp, gorilla, and orangutan. The picture and the fact that the chromosome contains an extra centromere and telomers in the center STRONGLY suggest that human chromosome #2 was produced by a Robertsonian translocation of chromosomes much like that of chimp/gorilla/orangutan chromosomes 12 and 13.

Here is your response to that data:
++++++++++++++++++++++++++++++++++++++++++++++

I hate to have to be the one to tell you this, but there's a whole bunch we don't know about micro biology. So, no, I'm afraid I can't explain the presence of the telomeres in the middle of chromosome 2 in humans and apes.

Now, getting back to the question at hand, let's see ... How did evolution create all that? You think evolution created these chromosomes, even though you don't know how it could have done said task. Nor do you have the slightest idea of what function said design might serve.

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It is “amazing” that an intelligent and informed person like yourself doesn’t have a clue about micro biology [sic]. Let me help you out some. Microbiology deals primarily with viruses, bacteria, protozoa, and fungi. Humans, chimps, gorillas and orangutans being metazoan eukaryotes do not fall in its realm. What this picture was referring to falls in the field of genetics.

While there is a lot of genetics we still do not know, we do know the function of telomeres. Since DNA replicase enzymes need to attach to the DNA strand they cannot copy the entire chromosome. There is a bit at the ends that they are incapable of copying. If there were no solution to this problem then after a number of replications the chromosomes would shorten to the point of involving genes. Telomeres are stereotypic sequences that can be added onto the end of chromosomes to prevent this shortening.

Humans have 23 pairs of chromosomes. Chimps, gorillas, and orangutans have 24. Each human chromosome has a G-banding analog in the other apes except Chromosome 2. Chromosome 2’s G-banding aligns up with the two leftover chromosomes from the apes, their chromosomes 12 and 13. The G-banding pattern suggest that human chromosome arose from a fusion of chromosomes very similar to ape chromosomes 12 and 13. Such fusion events have been seen in vivo. They are called Robersonian translocations. The fact that human chromosome 2 has an extra centromeric region and telomeres in the center STRONGLY support the idea that such a chromosomal fusion took place. The OBVIOUS interpretation of this is that human chromosome 2 and the chimp/gorilla/orangutan chromosomes 12 and 13 have a common ancestor. If they have a common ancestor so do humans, chimps, gorillas, and orangutans. Any other explanation for the data requires a bunch of hand-waving and ad hoc explanations. While these may be logically possible, they are not reasonable. The only reasonable explanation is the evolutionary one.

Hand-waving and ad hoc explanations huh? Fundamentalists believe they are right and everyone else wrong; and not just wrong but irrational. Only evolution provides a reasonable explanation. And hence it is a fact. But of course it was assumed to be a fact before the evidence was even examined. Which explains why evolutionists are unable to conceive of alternate explanations.

Well, chromosomal fusion is a good explanation for human chromosome 2, but chromosomal fusion does not entail evolution. Indeed, if evolution is true we must say that the fusion event occurred after the human-chimp split. So why is evolution "The only reasonable explanation"?

Next, I would like to go into other molecular data that has not been presented that independent of each other lend strong support to descent with modification, and taken together lead to the conclusion that it is a fact.

The correlation of sequence homologies between a variety of proteins (cytochrome C, the hemoglobins, etc) with the phylogenetic trees created from the fossil record is outstanding. Furthermore, the more closely the related the organism the more similar are their chromosomal structure, the more similar is their genome, them more similar is even the non-coding part of their genome.

Wow, what a coincidence. Similar phenotypes have similar genotypes, certainly there is not explanation for that aside from evolution.{\sarcasm off}.

Amongst mammals, only primates and the guinea pig do not make their own vitamin C. The gene for the enzyme that is essential in its biosynthetic pathway has been located and it turns out that chimps, humans and guinea pigs also have this gene but they have a mutation that puts in a premature stop codon so it is not functional. The mere fact that they have this pseudogene is suggestive of evolution. But even more suggestive is that the mutation that inactivates the gene is at the same place in humans and chimps while it is at a different place in guinea pigs. I will make the prediction that as the genomes of other primates are sequenced you will find a mutation similar to the one in humans and chimps and not like that of the guinea pig. Any takers?

Charles, I’m guessing you would again avoid analyzing the data and fall back on what we don’t know. You would complain that we don’t know how any biochemical pathway evolved so therefore since evolutionary theory can’t explain that how can one say that evolution is a fact. Again, this is avoiding the issue. The overwhelming evidence is not in what we don’t know, it is in what we do know. We do know the above, and any explanation other than the evolutionary one is fraught with so many problems as to make them unreasonable. While we do not know how any biochemical pathway DID evolve, there is no shortage of possible pathways they COULD have evolved.

What you don't mention is that when we look at other pseudogenes, say amongst the primates, they do not fit the accepted phylogeny real well. Yes, of course, there are the explanations.

You also fail to mention that the human and chimp GLO pseudogene alignment shares conserved substitution sites. For example,

The chimp to human alignment has these replacements:
38a to g
55c to t
83c to g
130c to t

and the chimp to orangutan (accession # AB025719) alignment has these replacements:

55c to t
75t to c
83c to g
85a to g
95t to c
96g to a
106a to g
131g to a
144c to t

There are 9/164 = .0549 fraction of residues that are replaced in the latter. So with any given replacement in the human alignment, you have a 0.0549 probability of hitting one of the orangutan's sites, or a .945 probability of not hitting it. Assuming random substitutions, the chances the human alignment not sharing any of the orangutan's substitution sites are ~.945^4 = 80% (this is not quite exact, but close enough to make my point). Or another way to put it, the expected number of hits is about 0.0549*4 ~.22 (again, this is not exact).

So in other words, given this number of residues, this number of replacements in the two cases, we don’t expect to see even a single common substitution site. Instead out of a total of 4 possible, we see two and a third that is off by only 1 residue.

People, what is the point here? Is it that evolution is emprically obvious. No, it is that the "other" explanation is "fraught with so many problems" so as to be unreasonable. There are myriad similarities between the chimp and human. Why do evolutionists dwell on the vitamin C pseudogene? Why is this one so important. Does it make evolution obvious? No, it makes creationism impossible in the fundamentalist's eyes. Don't be fooled by the scientific jargon, this is a religious argument. Religious claims are being handed down as though they were scientific facts. Creationism must be false, so evolution is the only one left standing. It is fact, but not a scientific fact. And here we go again:

The next line of evidence that has been gone into is evidence from suboptimal design. The idea here is that these types of structures are just what one would expect from design created by an algorithm without foresight but would be difficult to explain if they were designed by something with the intelligence of a human or better.

Could the whale have just arisen? Hmm, who knows, but we know it could not have been created.

So far your response to these has been even more pathetic. The first of these structures you deal with is hind-limb atavisms in whales. You take issue with the author’s presentation claiming that atavisms of this type are to be expected in evolutionary theory:

+++++++++++++++++++++++++++++++++++++++++++++

I didn't read through the entire site, but went to the first "validation" that caught my eye. It was Section 2.2, Atavisms. It states:

"Probably the most well known case of atavism is found in the whales. According to the standard phylogenetic tree, whales are known to be the descendants of terrestrial mammals that had hindlimbs. Thus, we expect the possibility that rare mutant whales might occasionally develop atavistic hindlimbs."

Aside from the fact that nothing is "known" from phylogenetic trees, the idea that hindlimbs are a prediction of evolution is a joke. You don't really believe that evolution would be rejected if such mutants were never discovered do you? What if tails were never discovered in humans? This has got to be one of the most absurd claims I've ever heard.

++++++++++++++++++++++++++++++++++++++++++++++

“… one of the most absurd claims [you’ve] ever heard”. You have a led a charmed life, more on this later. First I would like to point out you have totally ignored the content. How else do you explain the presence of atavistic hind limbs in whales (and some snakes for that matter) other than by evolutionary theory?

How else? And since evolutionists can envision no other means, evolution must be true.

You have responded to similar questions by saying that you don’t know. This suggests that you cannot come up with one and thus as far as you know evolutionary theory is the only one capable of explaining this fact. If it is the only one capable of this fact, then why isn’t evolutionary theory a scientific fact in itself? Because there can be something we don’t know?

Do you see where evolution has dragged science. Now something becomes a scientific fact because our religion permits no other answer.

Now, as to your absurdity remark. What was the author REALLY saying? He was saying that it makes sense for whales to have atavisms such as the one mentioned and it does not make sense in any other light.

Say it however you like (no other explanation is reasonable, does not make sense in any other light, etc.), your religious pronouncements don't help evolution to become a scientific fact.

Knowing what we know now about the genome and genetics if there were no atavisms anywhere then it would most certainly be a severe problem for evolutionary theory to explain.

Right. AP Wire (May 14, 2009). Researchers at Cambridge University today announced that evolution must be false. Despite overwhelming evidence for evolution, and its being held as a scientific fact for over a century now, evolutionists have failed to locate even a single atavism. "We're sorry to have to jump horses in mid-stream like this," lamented Charles Darwin, great-great-great-great-great grandson of the inventor of evolution, "but above all else we must maintain our scientific integrity. I guess creationism really is true."

If you believe this then I have a bridge to sell you. On the other hand, if you really do believe that lack of atavism would be a severe problem for evolution, then perhaps you'd believe that the finding of a code, yes a code, would be a problem.

AP Wire (May 14, 1959). Researchers at Cambridge University today announced that evolution must be false. Despite overwhelming evidence for evolution, and its being held as a scientific fact for over half a century now, evolutionists have found in recent years a code within our cells. Even single-celled microbes display a mind-boggling level of complexity which Darwin could only dreamt of. "We're sorry to have to jump horses in mid-stream like this," lamented Charles Darwin, great-great-great grandson of the inventor of evolution, "but above all else we must maintain our scientific integrity. I guess creationism really is true."

You were next asked to consider why it is that bats, who function more like birds, have a mammalian respiratory system which is 10 times less efficient than that of birds. You again avoided addressing the issue, instead you decided to take it as a metaphysical question.

Because it is.

It is a scientific question as well, Charles. Evolutionary theory explains it very well. The fact that bats have hair, give birth to live young and nurse them on milk says they are mammals. The reason they have a mammalian respiratory system is because that is an evolutionary constraint. Remember evolution has no foresight. No other explanation is nearly so parsimonious.

Oh, how conventient are those constraints. The bat *must* posess a mammalian respiratory system. One wonders how the bat obtained echolocation with all those constraints. Oh right, natural selection decided to kick into gear. This is not science.

But, on the other hand, let me say that I absolutely, 100%, give. For you evolution is no doubt a fact. I have no argument there. But I'm not real interested in responding to people's religious dictates which is what the remaining few paragraphs of this post are full of. I could go to church and hear something less dogmatic than this post. I'll let the remaining few paragraphs speak for themselves for those who want to go back and read them. The points have already been made over and over.

[Charles Darwin]

Originally posted by Oolon Colluphid
quote:
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Originally posted by Charles Darwin, in response to my post about dsign flaws:
Yet another religious thinker has joined (and I thought that was for the GRD forum).
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Ad hominem. Points not addressed.

I fail to see how my post can be construed as religious thinking. In fact, it is quite the reverse. What I am doing is scientific thinking.

<and later>

quote:
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Originally posted by Charles Darwin: Like the others you obviously have strong personal religious beliefs,
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Where? What? I demand that you back up that ludicrous assertion or withdraw it, lest I be forced to emphasise my annoyance with terms such as ‘fuckwit’.

No religious thinking huh? Just the facts, right? Tell me, what is it about this sentence that you don't understand:

Originally posted by Oolon: Thus it’s odd that the creator gave all birds their efficient through-flow lung system.

That is a religious claim. Understand? When you tell me about your creator, and use this as evidence for evolution, then you are subjecting me to your personal religious mythology. Get it? Your post is full of it.

Originally posted by Oolon:
Thus it’s odd that the creator gave ...

So the designer made the same mistake over and over ...

Similarly, the creator made the same mistake over and over when he put ...

He repeated the stupid design of the ...


So you can drop the bit about science and not wanting to argue religion; that is exactly what you want to argue.

[GunnerJ]

O.C.: Thus it’s odd that the creator gave all birds their efficient through-flow lung system.

That is a religious claim.

No. It's facetiousness. Stop being dense.

[Urvogel Reverie]

Originally posted by Charles Darwin



Hmm, are you referring to the “sudden” appearance in the fossil of new species that punctuated equilibrium purports to explain? Nobody in modern paleontology has ever thought, said, or even implied that these species come from “nowhere”. Why would such a knowledgeable person like you, misrepresent things so badly? How disappointing.

Again, I'm afraid it is you who are doing the misrepresenting here. I said nothing about paleontologists believing the species come from “nowhere.” It is true that paleontologists sometimes point out several problems that the fossils pose for evolution. But getting to my point above, I was commenting on the data, not on the paleontologists beliefs about the data. So let's cut the hypocritical finger-pointing, OK?

What punctuated equilibrium says is that in the fossil record we see a certain species and fossils of that species can be seen pretty much unchanged over several bedding planes, and then in the space of a single bedding plane it will disappear and be replaced by a similar species or group of species. The new fossil species did not appear from nowhere, it appeared from exactly what it appears (pun intended) to have appeared from -- the previous species. It is just that the morphological change associated with speciation occurred in the space of a single bedding plane.

Well that describes some of the data. Why do you not also mention that there are instances where species do appear without any obvious precursors?


This, of course, does not "STRONGLY" support descent with modification. But you say more in a moment, so I'll wait till then.


This doesn't sound right, but I'm not exactly sure what you are intending here. Can you elaborate a little more? What exactly do you mean by a fossil species appearance occurring over several million years?


Your word "continual" is loaded. Obviously there were many fossil species that showed essentially no change for long periods. I'm sure you don't doubt that, so you don't really mean continual change. Perhaps you mean "continuous," that is, unbroken or unpunctuated. But this too would be wrong, as there are many post Cambrian examples. I used the horse sequence earlier as an example which the PE'ers used to advance their ideas. More on horses later as I see you bring it up below.


Creationists claim that the fossil record and the Cambrian explosion fits with predictions from the theory of Special Creation better. How so? To fit the REAL data with Special Creation one would have to postulate a creator that poofs a number of bacteria-like organism into existence, waits around 2 billion years for them and their descendents to put enough oxygen into the air then poof some different bacteria-like organisms into existence, wait another 700 million years poof some simple eukaryotes into existence, wait another 100 million years and poof the first simple multicellular organisms into exxistence. Then after almost 3 billion years have a sudden fit lasting several million years of poofing new multicellular organisms and then periodically after some go extinct poof some other similar ones into existence until the present time.




You have strong religious beliefs. I respect that, and who knows, you may even be right. And your argument here for why evolution is a fact is perfectly valid. It makes perfect sense for you to state that:

No matter that the idea of the incredibly complicated Cambrian species arising on their own (whether quickly or not) goes against what science tells us about the world. The story is a real stretch, but it is all you have.






How many times must the preponderance of evidence which refutes punctuated equilibrium in the sense of Gould, Stanley & Eldredge be repeated? It is entirely apparent from detailed morphological studies of Cenozoic megafauna, that a pattern of gradual morphologic variation over time as opposed to significant stasis in morphology occurred, and research explicity engineered to uphold or discredit Gouldian-level punc. eq. has revealed it to be nothing but a a series of fluctuations in evolutionary rate, which is far better encompassed by G. G. Simpson's terminology outlined in 1966. I refer the reader to my previous posts--most notably CD, who continues to maintain that the fossil record is saltational--which is an artifact of attention to taxonomic convention, and not indicative of the actual anatomical variation in the fossils at hand. This view, when advanced by either evolutionary biologists (like Gould) or creationists, is entirely fallacious, and no longer supported (if indeed it ever was), by the fossil data previously impressed into service in defense of such a drastically punctuated phylogenetic history of life.

And this brings me to the second point, which I have again and again reiterated. In light of our steadily increasing appreciation of metazoan diversity pre-Cambrian, represented by the enigmatic Vendian fauna, combined with our understanding of the role of regulatory genes such as the Hox and Pax groups in driving morphologic variation within a lineage, and leading to the development of novel traits, it has become increasingly untenable to assert that the appearance of the major metazoan phyla was a massive punctuational or saltational event. Rather, it would seem that around 543 mya, a secondary adaptive radiation of Metazoa occurred which led to the derivation of modern phyla from incipient forms, perhaps represented by the Vendian fauna.

Urvogel Reverie

[Happy Wonderer]

Originally posted by Charles Darwin
Translation: Mechanistic / naturalistic explanations will always be preferred. It is built into the paradigm.

Stop the argument for a second, because I have a serious question. What kind of explanation do you think science should come up with? As soon as we hit a hard problem, should we say "looks like God, better not go further!" Is it blasphemy to try to find a naturalistic explanation? Are we allowed to ask "how did God do it?"

What do you think?

hw

[Happy Wonderer]

Originally posted by GunnerJ
No. It's facetiousness. Stop being dense.

Oh no, Gunner I think that you opened my eyes. I don't believe this. Not another

http://www.collectorsconnection.org/imagesb/28a381.jpg

:eek: Nobody is that dense for real. I mean really, I'd like to talk to a real creationist/anti evolutionist. I have honest questions but all we seem to get are people playing a role.

hw

[Charles Darwin]

Originally posted by Happy Wonderer
Stop the argument for a second, because I have a serious question. What kind of explanation do you think science should come up with? As soon as we hit a hard problem, should we say "looks like God, better not go further!" Is it blasphemy to try to find a naturalistic explanation? Are we allowed to ask "how did God do it?"

What do you think?

hw

Good questions. Let me propose a first step: let's be honest. If your reasoning entails metaphysical truth claims, then let's drop the pretense of scientific objectivity and lay our cards on the table. As scientists, we have a certain responsibility. Non scientists are not in a position to understand the nuances and assumptions of what lies beneath what we are claiming. When we convey the message that "evolution is a scientific fact" to the general public, whether we like it or not, we are impacting lives in important ways. Evolution has a great deal of social impact outside of science. Hence, we shoulder a tremendous responsibility; do not take it lightly.

[Charles Darwin]

Originally posted by markfiend
Yes I get the point. But you do not. The more "traits" you add to the car-pool, the more possible heirarchies can be constructed. The design argument would predict that all these possible heirarchies are equally valid. With living things, there are 10^41 possible heirarchies, but only one that is valid.

You are presupposing evolution. With living things, there are 10^41 possible heirarchies, but only one that is valid *IF* evolution is true.

[Charles Darwin]

quote:
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Note also the unspoken assumption here that molecular and morphological characters can be unrelated. Truly bizarre; but then again, this is evolution.
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Originally posted by lpetrich
CD ought to tell us why he thinks that this hypothesis is unwarranted -- why he thinks that there is some sort of necessary correlation between cytochrome c sequences and macroscopic features.

Careful, let's stick to the argument. This is not a hypothesis; it is an assumption. The claim relies on this *assumption*. I am hardly the one with the burden here, as that is quite a heroic assumption. I disagree with the assumption. I don't claim it must be wrong, though I doubt it.

[Charles Darwin]

quote:
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Originally posted by Charles Darwin
Meanwhile, let us consider that fact that known cases of minor evolution are brought about by an incredibly complex adaptation machine. Mutations do not occur randomly, either temporally or spatially, and we find what are essentially preprogrammed pathways of change. Hardly the kind of thing evolution describes. Simply put, evolution would have had to create the marvelous mechanisms that make evolution possible.
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Originally posted by Doubting Didymus
Sorry, are you now claiming that muations are not random?

Actually, I'm not claiming anything. I'm simply giving a brief description of the state of a particular facet of the research on adaptation. Somehow, there appear to be preprogrammed pathways of change.

[Charles Darwin]

Originally posted by lpetrich
Charles Darwin on family-tree discrepancies:
"The phylogenetic position of the platyhelminths within the metazoan tree is examined ..." C R Acad Sci III., 320:83

"The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. ..." Nature, 387:489

However, this is an active area of research, as a result of the progress of gene-sequencing technology, and some new results have been emerging. Some old taxonomic ideas, like Protostomia and Deuterostomia, have continued to be supported, but there have been some rather startling new results, like the division of Protostomia into Ecdysozoa (molters) and Lophotrochozoa (those with lophophores [a certain sort of ring of tentacles for feeding] or trochophore larvae). Arthropods belong to Ecdysozoa and annelids to Lophotrochozoa, though they have often been thought to be closely related on account of their segmentation. However, those trochophore larvae are shared by marine annelids and mollusks, both in Lophotrochozoa.

And as to arthropods, one startling new result that has emerged is that Uniramia (insects and myriapods) is not a natural group. Insects are most closely related to the branchiopod crustaceans, a group which includes the well-known brine shrimp Artemia salina. Myriapods (centipedes and millipedes), however, are an early-branching group, comparable to crustaceans and chelicerates (spiders, scorpions, horseshoe crabs, etc.).

OK, very good.

[Charles Darwin]

quote:
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I wouldn't make the conclusion sound so trivial. It provides plenty of fuel to those evolutionists who are skeptical of endosymbiosis.
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Originally posted by lpetrich
That's a STUPID argument. CD, do you honestly think that biologists are unable to distinguish between endosymbiotic and non-endosymbiotic organelles?

Endosymbiotic ones can be recognized by their gene content; they have their own genomes, and their genes are most closely related to certain outside organisms. And some non-endosymbiotic organelles may be derived from endosymbiotic ones; some protists have hydrogen-releasing "hydrogenosomes", which are likely genome-less mitochondria.

Well I have to agree the whole thing seems pretty stupid to me. I'm just reflecting the thinking of evolutionists who are skeptical of endosymbiosis. You make it sound so non controversial; it is not.

[Charles Darwin]

Originally posted by lpetrich
It must be conceded that there are some circumstances that are likely to produce mismatches, like greatly varying rates of evolution and relatively rapid divergence However, there are ways for testing for such circumstances, such a rerunning a tree-finding algorithm with different randomly-chosen taxon-addition orders, and seeing which topologies consistently appear.

So I don't see why these difficulties support a poof-poof-poof theory of origins.

And of course (for the umteenth time) that is not what I said. The phylogenetic evidence was used as a compelling reason why evolution is a scientific fact; I pointed out there are mismatches; that was denied; I was asked for examples; I supplied them.

[Charles Darwin]

Originally posted by God Fearing Atheist
I just loved the part about provrial integration being "quite specific" Charles. Certainly, there is some degree of *preferential* targeting, according to base sequence, nuclear localization and, in Saccharomyces cerevisiae, domains of silent chromatin (http://www.genesdev.org/cgi/content/full/13/20/2738#B34).

But saying these sorts of things show shared ERVs to be indicative of something other than common decent is a serious misunderstanding. What are the odds, Charles, of the *same* ERV being found at the *same* locus, even if they perfer to insert near some sequences over others? Creationists love probability calculations, so here's a good one.

-GFA

Great question, but first you are twisting what I said. I said "quite specific." I was not referring to mere preferential targeting with a local segment. I was talking about specific areas within specific chromosomes. As for the odds, that would be very interesting to look into. Unfortunately, the results depend heavily on what site specificity and preferential targeting one assumes. Evolutionists, of course, assume none, so the odds are astronomical even for just one homologous HERV.

[Charles Darwin]

People, sorry but I have to quit out. I've tried to respond to all posts, but I know I've left a few dangling. Sorry about that, but I trust I got my main points across.

If anyone wants to make further replies I will read them, but I will not respond (at least for now). Thank you.

[wade-w]

Originally posted by Charles Darwin
People, sorry but I have to quit out. I've tried to respond to all posts, but I know I've left a few dangling. Sorry about that, but I trust I got my main points across.



All I saw was that you dismiss evolution based on personal incredulity. Not much of a point, in my view. And you never did give a satisfactory answer to what you consider an example of a scientific fact. I'm very disappointed.

[Jack the Bodiless]

CD:

And I am disappointed to note that, after TEN PAGES of this thread (and verious comments on earlier threads), you never made any attempt whatsoever to correct your sloppy, unscientific, deliberately obtuse use of language.

From the context, it is quite clear that you have been arguing against common descent, not evolution. You have persisted in doing this, despite MANY attempts to correct you, because your religious beliefs require this.

You have sought to define "evolution" as a religious label, and then to slap this label on any discussion of the evidence for common descent, in an attempt to belittle or dismiss it. You have also deliberately avoided discussion, not just of the alternatives to Darwinian evolution (which would include theistic evolution), but of the alternatives to common descent (none of which are supportable by the evidence).

Evolution is a fact. Common descent is ALSO a fact. Denying the former makes no sense, and you haven't even attempted to discuss it. To address the latter, we should be able to discuss whether or not the evidence supports common descent, without even needing to mention evolution at all.

But you cannot do this. Your fanatical religion of anti-evolutionism prevents you from being objective, or even relevant.

[markfiend]

Originally posted by Charles Darwin
You are presupposing evolution. With living things, there are 10^41 possible heirarchies, but only one that is valid *IF* evolution is true.

Duh. That is the point. If evolution is *not* true, why do the molecular phylogenies agree so well with the morphological ones?

Forget it. I am rapidly coming to the POV of Happy Wonderer.
http://www.collectorsconnection.org/imagesb/28a381.jpg