Cornell Geneticist: Degenerating Genomes Disprove Evolution

[Dave Hawkins]

Dr. J.C. Sanford, a geneticist from Cornell recently renounced his evolutionary views, has become a young-earth creationist, and has written a very revealing book entitled Genetic Entropy and the Mystery of the Genome (2005) which shows from the published papers of leading population geneticists that deleterious mutations are accumulating in populations. He draws two conclusions from this ... 1) that populations will ultimately go extinct due to mutational meltdown and that selection, natural or otherwise, cannot save them, and 2) that this shows that the "Primary Axiom" of evolution--Random Mutation + Natural Selection--could never have produced species extant today. I began discussing this book last year HERE (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=45d6fd90c5e5eca1;act=ST;f=14;t=3131;st=2106) and HERE (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=45d6ff87c69856ee;act=ST;f=14;t=3131;st=2507) and again here at IIDB just recently in THIS THREAD (http://www.iidb.org/vbb/showthread.php?p=4548790#post4548790). The discussion was veering away from the OP so I have moved it here at the suggestion of a veteran user. I began with a quote from Sanford's book by J.F. Crow below. Please read this quote then read the IIDB link above to see the discussion which followed.
It will take me more time to provide Davidson's data for you, but the Crow quote I can provide easily ... This is from the very end of the paper (free acess) ... The Current Human Population

However efficient natural selection was in eliminating harmful mutations in the past, it is no longer so in much of the world. In the wealthy nations, natural selection for differential mortality is greatly reduced. A newborn infant now has a large probability of surviving past the reproducing years. There are fertility differences, to be sure, but they are clearly not distributed in such a way as to eliminate mutations efficiently. Except for pre-natal mortality, natural selection for effective mutation removal has been greatly reduced.

It seems clear that for the past few centuries harmful mutations have been accumulating. Why don't we notice this? If we are like Drosophila, the decrease in viability from mutation accumulation is some 1 or 2% per generation. This is more than compensated for by much more rapid environmental improvements, which are keeping well ahead of any decreased efficiency of selection. How long can we keep this up? Perhaps for a long time, but only if there remains a social order that permits steady environmental improvements. If war or famine force our descendants to return to a stone-age life they will have to contend with all the problems that their stone-age ancestors had plus mutations that have accumulated in the meantime.

We have seen that quasi-truncation selection can efficiently remove harmful mutations, and the average fitness reduction can be made quite small. This, plus environmental improvements, means that average survival and fertility are only slightly impaired by mutation. Yet, those 80 mutations in a fly---and whatever the number is in the human species---must surely have deleterious effects that don't show up in a life table (or as effects on fitness). How many headaches, stomach upsets, depressed periods, and such things that make life less pleasant, but don't reduce viability or fertility, would be eliminated if our mutation rate had been lower? I suspect the number is substantial.

If the human mutation rate were to drop to zero, we would probably not notice it except for the absence of some of the most loathsome dominant diseases. Loss of variability would not be a problem for a very long time. The genetic variance in the population is enough to satisfy the dreams of even the most wild-eyed eugenist. If we could reduce the mutation rate to zero (without important side effects, of course) I would be for it. If some centuries in the future new mutations are needed, we shall certainly know how to produce them.

I do regard mutation accumulation as a problem. It is something like the population bomb, but it has a much longer fuse. We can expect molecular techniques to increase greatly the chance of early detection of mutations with large effects. But there is less reason for optimism about the ability to deal with the much more numerous mutations with very mild effects. But this is a problem with a long time scale; the characteristic time is some 50-100 generations, which cautions us against advocating any precipitate action. We can take time to learn more.

Meanwhile, we have more immediate problems: global warming, loss of habitat, water depletion, food shortages, war, terrorism, and especially increase of the world population. If we don't somehow reduce the global birth rate to a sustainable level commensurate with economic viability, we won't have the luxury of worrying about the mutation problem.
http://www.pnas.org/cgi/content/full/94/16/8380Note that Crow implies that our Stone Age ancestors had LESS of a load of deleterious mutations than we do. Farther back in time = fewer deleterious mutations. This picture of less harmful mutations further back in time correlates well with Biblical inferences.

[show_no_mercy]

From that quote, the author seems to be saying that since humans are no longer susceptible to natural selection that evolution is false?

[ericmurphy]

300 Generations, Dave.

Sanford claims that complex genomes should deteriorate to the point of extinction after 300 generations.

When we look around, do we see that virtually all complex eukaryotes are extinct, Dave? Do we see that there is virtually no life on the planet outside of simple eukaryotes and prokaryotes?

No. We do not.

Therefore, Sanford was wrong.

Therefore, you are wrong.

Really, Dave, how much more is there to say about this topic? It's dead in the water. Are you ever going to deal with this fatal flaw in Sanford's argument? It's not like it's hard to see. 300 generations, for most eukaryotes, is comfortably less than 500 years. Your flood was 4,500 years ago. Are you going to tell me you don't see the problem here?

[Note to newcomers: I've been asking this question of Dave for easily nine months now, here, at at richarddawkins.net, and at antievolution.org. He has never answered it.]

[RBH]

From the quotation:Yet, those 80 mutations in a fly---and whatever the number is in the human species---must surely have deleterious effects that don't show up in a life table (or as effects on fitness). How many headaches, stomach upsets, depressed periods, and such things that make life less pleasant, but don't reduce viability or fertility, would be eliminated if our mutation rate had been lower? I suspect the number is substantial.If they don't show up as "effects on fitness", as claimed in the quotation, then they're evolutionarily irrelevant. If they don't reduce viability or fertility, they're evolutionarily irrelevant. Sanford is a loon or ignorant, i'm not certain which.

RBH

[chrisharrison]

Sanford's book is reviewed here (http://newtonsbinomium.blogspot.com/2006/10/review-of-mystery-of-genome-i.html) and here (http://newtonsbinomium.blogspot.com/2006/10/review-of-mystery-of-genome-ii.html).

[Toto]

Relevant comments from the BCH thread:

Sanford is the author of Genetic Entropy and the Mystery of the Genome.

Sanford's personal history is contained in his wiki entry -

Bio for Sanford (http://en.wikipedia.org/wiki/John_C._Sanford)Formerly an atheist, in the mid-1980s Sanford and his present wife Helen went through a marital crisis, which led him to become a born again Christian and a young earth creationist. More recently, he has written a book entitled Genetic Entropy & the Mystery of the Genome (2005)[3] in which he claims that the genome is deteriorating and therefore could not have evolved. Sanford's claims have received little attention from the scientific community, and have not been published in peer-reviewed scientific journals.

The book is reviewed here (http://blog.abovetopsecret.com/mattison0922/2006/06/book_review_genetic_entropy_an.html) (fairly charitably) and less charitably here (http://scienceblogs.com/evolgen/2006/06/the_creationists_discover_the.php).

Funny, a marital crisis also led Philip Johnson to abandon rationalism and opt for Christianity and young earth creationism.

[chrisharrison]

Oh wow. Googling Sanford reveals (http://www.raelnews.org/news.php?item.181) some interesting things.

Following the publication of his latest book, Genetic Entropy & the Mystery of the Genome, Rael, founder and spiritual leader of the International Raelian Movement has named Dr. John Sanford an Honorary Priest – a guide for humanity – for his brilliant and courageous way to illustrate that the very foundation of evolutionary premise, the "Primary Axiom", is false.

Well whatever.

His Cornell page (http://www.nysaes.cornell.edu/hort/faculty/sanford/) says "I am presently looking at the theoretical limits of mutation/selection", yet none of his publications (http://www.nysaes.cornell.edu/hort/faculty/sanford/sanford_pubs.html) appear to be aimed at finding this limit.

[deadman_932]

300 generations since the flood, Dave.

Rabbits. Guinea Pigs. Hamsters. Rats. Mice. Bats. Gerbils. Why aren't they all extinct, Dave?

Don't pretend you don't understand what I am asking Dave, It's been asked many times already.

If Sanford were right...why aren't all rapidly reproducing mammals extinct?

[RAFH]

300 generations since the flood, Dave.

Rabbits. Guinea Pigs. Hamsters. Rats. Mice. Bats. Gerbils. Why aren't they all extinct, Dave?

Don't pretend you don't understand what I am asking Dave, It's been asked many times already.

If Sanford were right...why aren't all rapidly reproducing mammals extinct?

Rael prays for them?

[ericmurphy]

300 generations since the flood, Dave.

Rabbits. Guinea Pigs. Hamsters. Rats. Mice. Bats. Gerbils. Why aren't they all extinct, Dave?

Don't pretend you don't understand what I am asking Dave, It's been asked many times already.

If Sanford were right...why aren't all rapidly reproducing mammals extinct?

Dave is blown away that we don't agree that Sanford is correct. He seems to think it's self-evident that "deteriorating genomes" lead to extinction in a few hundred generations.

But then when we show him organisms that according to his own preposterous worldview must have existed for 4,500 generations, we hear what?

The sound of crickets chirping.

[Godless Dave]

From that quote, the author seems to be saying that since humans are no longer susceptible to natural selection that evolution is false?

Actually from the quote, the author is not at all saying that evolution is false. Nowhere in those six paragraphs does he say anything of the kind.

What he's saying is that natural selection is no longer weeding as many deleterious traits out of the human population, because of human-invented medicine and technology. He actually contrasts that with fly populations, where deleterious mutations are removed from the gene pool.

Either the OP is leaving out some crucial part of Crow's work, or the OP is misrepresenting what Crow is saying.

[mung bean]

Either the OP is leaving out some crucial part of Crow's work, or the OP is misrepresenting what Crow is saying.BINGO!

[Dean Anderson]

Either the OP is leaving out some crucial part of Crow's work, or the OP is misrepresenting what Crow is saying.

That is what we have been telling him in the previous thread (here that inspired this one).

He does miss out most of Crow's work. The quoted material is selectively quote mined cropped from the concluding part of a lecture given by Crow, not from any of his actual papers. Besides, if you read the rest of Crow's lecture (follow the link at the bottom of the quoted part), it clearly (to everyone except adfave) shows that Crow's actual meaning is the very opposite of the meaning that afdave takes from it.

I have contacted Crow for clarification on his meaning, and comment on afdfave's (and Sanford's) interpretation of it; and I hope to report his response soon.

[Godless Dave]

Even the Crow quote from Sanford's book doesn't say what afdave says it does. If it's a quote mine it's a pretty poor job of quotemining on Sanford's part. He should have stayed in the junk business with his son.

[Amaleq13]

If they don't show up as "effects on fitness", as claimed in the quotation, then they're evolutionarily irrelevant. If they don't reduce viability or fertility, they're evolutionarily irrelevant.

Those are Crow's words, not Sanford's, and he is not arguing that they are evolutionarily relevant. He is suggesting that they might be the sort of things we experience on a day-to-day basis because of the accumulated mutations that have not been selected out.

Sanford is a loon or ignorant, i'm not certain which.

I suspect he is simply convinced that his recent radical change of heart is genuine and proceeds to interpret all available evidence accordingly. Whether that makes him a loon or ignorant is a subjective call. :)

[Dean Anderson]

Funny, a marital crisis also led Philip Johnson to abandon rationalism and opt for Christianity and young earth creationism.

Yeah - if our collective spouses get sick of us spending all our time on IIDB and leave us, we may end up all converting like this and have to shut down E/C completely...

[Calilasseia]

I've posted this in another thread but it's worth repeating here.

It implies that we have a larger load of deleterious mutations. Yes, the load is even larger because of medical technology, but it is larger even without the technology. Why do I say that? Because Crow says that if the medical technology goes away, then our increased load puts us in worse shape.

Oh dear.

Step 1: "It implies that we have a larger load of deleterious mutations."

No problem here.

Step 2: "Yes, the load is even larger because of medical technology"

Which is what Crow is saying. A common sense extrapolation from the available data. Namely, medical technology is allowing more people to live than would have been possible without it. Some of those people who are now allowed to live carry deleterious mutations - including mutations that would have been fatal to them before reproductive age in the absence of that technology.

Step 3: "but it is larger even without the technology."

Wrong. If modern medical science had not come into being, those people now kept alive by modern medicine would have died. Therefore those deleterious genes that they possessed would never have made it into the present.

Step 4: "Why do I say that? Because Crow says that if the medical technology goes away, then our increased load puts us in worse shape"

A valid conclusion to extract from Steps 1 and 2, but in no way connected to Step 3. Step 3 is an arbitrary insertion of your own devising.

[Dave Hawkins]

You're not a geneticist, Amaleq? Shame on you then for daring to question Dave's interpretation of genetic studies.

Oh, just a minute...... Are you a geneticist, Dave? Or an Egyptologist? Or a palaeontologist? Or an historian? Or an archaeologist? Or a specialist in any of the other areas that you post so knowledgably on?

Just what point were you trying to make with this question?
The point is that Dave is so convinced of his position that he thinks that he can easily surpass a lifetime of learning in any field by reading creationist websites for a few hours. As he has claimed on RD.net.I told CK1 that her statement about me is wrong and to please back it up. She offered this ...Ck1: No one is saying that you need a Ph.D. to engage in discussion, but your claim that someone with no knowledge at all in technical subjects can invalidate 150 years of scientific effort is nothing short of delusional.

AFDave: YOU are delusional if you think I claimed this. My claim is 1) that I now know more than you do about biology and genetics as it relates to Origins, (which is why I want to debate you on this) and 2) that no one here really understands the details of dendrochronology, yet they think it validates C14 dating.She thinks that this supports "Dave is so convinced of his position that he thinks that he can easily surpass a lifetime of learning in any field by reading creationist websites for a few hours."

It clearly does not.

I think you failed to read the words "as it relates to Origins". IOW, what I am saying is that I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand. Examples: I have figured out that mutations have never been shown to produce any biological changes which could be construed as "creative." Also, I have observed that massive variability in taxa is possible in just 5000 years--with NO mutations whatsoever (Ayala's statements). I have figured out similar fundamental realities in geology that highly trained geologists have not figured out.

Why have I figured out these basic things that highly trained specialists have missed? Because I'm smarter than them? No. Not at all. It's because my thinking is unencumbered with a pre-commitment to Darwinism and Deep Time.

[ck1]

Dave,
I have only one thing to add to the previous comments. You referenced Crow to support your belief (apparently shared by Sanford) that genomes have been deteriorating since "the Fall of Adam". However, Crow's article does not support your belief at all since Crow is arguing for the accumulation of deleterious mutations in the human genome in modern times as the direct result of environmental improvements - medicine and sanitation. Not something that has been happening as long as there have been humans.

[Flint]

I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand.The beat goes on. Nothing provides insight that the experts are wrong, so well as ignorance saddled with delusion. Dave isn't smarter than the experts, he enjoyes the freedom of mind that knowledge would encumber so severely.

Along these lines, I know a huge amount the experts don't accept, about nearly everything I know nothing about. I figured it all out by myself, without recourse to any time-wasters like, you know, educational materials. All I needed to know was that I was right, that I had all the answers before I started, and that those who do actual research are too highly trained to see Truth.

The problem with doing actual research is, how can you possibly tell if your results are correct, if you don't know the answers before you start? You might even be wrong. Conversely, if you know the answers before you start, you don't need to do any research. And Making Stuff Up will never violate your preferences, take you by surprise, or cast doubt on your convictions.

[VoxRat]

IOW, what I am saying is that I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand. The rest of us think this is just hilarious.

Examples: I have figured out that mutations have never been shown to produce any biological changes which could be construed as "creative." Nylon eating bacteria? I construe that as "creative".

Also, I have observed that massive variability in taxa is possible in just 5000 years--with NO mutations whatsoever (Ayala's statements). Refresh my memory? What does Ayala say is the ultimate source of genetic variation?

I have figured out similar fundamental realities in geology that highly trained geologists have not figured out. Without ever having cracked a geology book. It's amazing, I tell you!

[ck1]

IOW, what I am saying is that I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand. Examples: I have figured out that mutations have never been shown to produce any biological changes which could be construed as "creative." Also, I have observed that massive variability in taxa is possible in just 5000 years--with NO mutations whatsoever (Ayala's statements). I have figured out similar fundamental realities in geology that highly trained geologists have not figured out.

Why have I figured out these basic things that highly trained specialists have missed? Because I'm smarter than them? No. Not at all. It's because my thinking is unencumbered with a pre-commitment to Darwinism and Deep Time.

Dave, If these are examples of what you have "figured out" on your own then you have a long way to go to present any real challenge to professional scientists.

You continue to misinterpret Ayala who clearly identifies mutations as the source of genetic variability.

I am not sure what you mean by "creative" when referring to mutations, but others have given you the example of nylonase genes generated by frameshift mutations in bacteria as an example of new functional genes produced by mutations. (there are other examples) I do not recall that you have responded.

[Oolon Colluphid]

[snipped he-said-she-said guff]
I think you failed to read the words "as it relates to Origins". IOW, what I am saying is that I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand.
Now, this is interesting. Reason being, I've been in this game quite a while now. And whenever someone not trained in a subject (whether they admit it or not) claims something about the subject -- something, that is, that runs strongly counter to the mainstream of the subject -- it has always turned out that this 'someone' has misunderstood it.

It has always been thus. And it's curious because it shows not only the ignorance, but it so often is accompanied by arrogance. An arrogance that says that the experts are wrong. Now, of course the experts could be wrong. They're human, after all. But there's a reason they are experts. Things like having studied the matter a lot, and having a deep understanding of the issues, for instance. That is, the very things the non-experts don't have (by definition).

So what this "I've not studied it but they're wrong" implies is that the experts are fools. Too daft to spot the claimed problems or insights for themselves, despite being best placed out of everybody to do so. That is why such claims are arrogant. The claim may even be right. What are the chances, eh?

"They laughed at Columbus, they laughed at Fulton, they laughed at the Wright Brothers. But they also laughed at Bozo the Clown."
-- Carl Sagan

And here you are with a textbook example: "I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand."

Unless you are suggesting that biologists don't know much about genetics, do you see why I find such a claim... a bit suspect?


Gotta go work for a bit, back with the remainder shortly.

[ck1]

The point is that Dave is so convinced of his position that he thinks that he can easily surpass a lifetime of learning in any field by reading creationist websites for a few hours. As he has claimed on RD.net.

I am curious. Is there anyone besides Dave who thinks this statement is inaccurate or overstated?

[gregor]

I note dave's on the forum now. Please respond to the 300 generations question. Curious (encumbered) minds want to know.

[Dave Hawkins]

Faid ... Now dave, If I wanted to behave like you and engage in an authority clash, I could easily do it. Comparing geneticists of the magnitude of Crow (and Kondrashov, and others) to the "inventor of the gene gun", would not fare that well for your side.My "authority clash" does not pit Sanford against Crow, Kondrashov and others.

If you go back and read me, you will see that my "authority clash" originally pitted Amaleq13 vs. Sanford--a non-geneticist vs. a geneticist, both of them analyzing the work of some admittedly great geneticists ... yes they are much more accomplished than Sanford in the field of population genetics. I did not at any time try to say "Sanford knows more than Crow." I simply pointed out an inference that Sanford has made from Crow's statements, an inference which I believe is justified.

[FatherMithras]

I did not at any time try to say "Sanford knows more than Crow." I simply pointed out an inference that Sanford has made from Crow's statements, an inference which I believe is justified.

Which shows you´re not qualified to make the judgment, since Sanford COMPLETELY IGNORES THE ENTIRE POINT. The deleterious mutations are a DIRECT RESULT of the loss of selection pressure of death for many conditions. Crow nowhere states that apart from this condition, the genome is degenerating. Yet you keep bullshitting and saying he does, with no support.

Also, you have failed to respond to the refutations of your ´´knowledge´´, clearly showing not only do you have no idea what you´re talking about, you´re not willing to admit it.

[ck1]

I simply pointed out an inference that Sanford has made from Crow's statements, an inference which I believe is justified.

Then instead of providing a long excerpt from a Crow article in your OP, you should provide the details of Sanford's arguments (instead of telling us to buy his book.)

[VoxRat]

The point is that Dave is so convinced of his position that he thinks that he can easily surpass a lifetime of learning in any field by reading creationist websites for a few hours. As he has claimed on RD.net.I told CK1 that her statement about me is wrong and to please back it up. She offered this ...Ck1: No one is saying that you need a Ph.D. to engage in discussion, but your claim that someone with no knowledge at all in technical subjects can invalidate 150 years of scientific effort is nothing short of delusional.

[AFDave:] YOU are delusional if you think I claimed this. My claim is 1) that I now know more than you do about biology and genetics as it relates to Origins, (which is why I want to debate you on this) and 2) that no one here really understands the details of dendrochronology, yet they think it validates C14 dating.She thinks that this supports "Dave is so convinced of his position that he thinks that he can easily surpass a lifetime of learning in any field by reading creationist websites for a few hours."

It clearly does not.

I think you failed to read the words "as it relates to Origins". IOW, what I am saying is that I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand. Examples: I have figured out that mutations have never been shown to produce any biological changes which could be construed as "creative." Also, I have observed that massive variability in taxa is possible in just 5000 years--with NO mutations whatsoever (Ayala's statements). I have figured out similar fundamental realities in geology that highly trained geologists have not figured out. ...
This gets back to that whole concept of consilience I've been trying to bring to afdave's attention for months.

See, you don't get to be more knowledgeable than in biology, or genetics, or geology "as it relates to origins" than the people who have spent lifetimes studying and working in those fields. Not by reading your bible, or cribbing from your creationist websites, you don't. It's all of a piece.

[VoxRat]

The opposite of consilience is compartmentalization.

For instance, pretending that "macroevolution" is unrelated to "microevolution"

Pretending that "origins genetics" is separate from "regular genetics"

Pretending that Crow was talking about mutations, separate from selection.

Pretending that the issue of radiocarbon dating is separable from the calibration methods that are used to cross-check it.

Creationists love compartmentalization.

[Jet Black]

Creationists love compartmentalization.

they love both (note the times when they lump evolution in with cosmology). They love whatever it takes to paper over the vacuous nature of their arguments.

[Dave Hawkins]

E-mail I sent to Dr. Crow this morning ...

Hello Dr. Crow ...

I have some questions about your 1997 paper found here ...

http://www.pnas.org/cgi/content/full/94/16/8380

and I wondered if you would be able to answer them for me. As you may know, Cornell geneticist Dr. John Sanford has quoted you in his recent book, Genetic Entropy and the Mystery of the Genome (2005). He quotes several of your statements, including this one ...

"If war or famine force our descendants to return to a stone-age life they will have to contend with all the problems that their stone-age ancestors had plus mutations that have accumulated in the meantime."

then he writes ...

"He [i.e. you, Dr. Crow] goes on to acknowledge that humanity must now be genetically inferior to our stone-age ancestors [referring to the above statement] - an amazing confession about the reality of genomic deterioration." (Sanford, p. 171)

Now my questions are ...

1) Do you really believe that modern humans are genetically inferior to our stone-age ancestors?
2) If so, is this only because of modern medicine which keeps people alive which would otherwise not reproduce as well and/or die before reproducing?
3) Or would we be genetically inferior anyway (w/o modern medicine) because of the 1-2% per generation decrease in viability that you speak about occurring over the last several centuries?

IOW ... is Dr. Sanford misrepresenting your view by saying that you acknowledge that humanity must now be genetically inferior to our stone-age ancestors? Or is his representation a fair one?

Would you allow me to post your response to this e-mail publicly? If not, that's OK. I still would like to get these questions answered for my own benefit.

Thanks,

Dave Hawkins
Amateur Science Enthusiast :-)

[Oolon Colluphid]

[what I am saying is that I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand.] Examples: I have figured out that mutations have never been shown to produce any biological changes which could be construed as "creative."
In which case, I need you to define "biological changes" and "creative". You don't see any; I have a number of examples that I (using fairly commonplace meanings) consider to fit the bill. But there's no point in me digging up the references (nor even alluding to them) if they'll just be dismissed as not what you mean by the terms.

So, what do you mean by "biological changes" and "creative"?
I have figured out similar fundamental realities in geology that highly trained geologists have not figured out.
Hmmm. Arrogant, much? Okay, let's hear them.
Why have I figured out these basic things that highly trained specialists have missed? Because I'm smarter than them? No. Not at all. It's because my thinking is unencumbered with a pre-commitment to Darwinism and Deep Time.
Perhaps you are unaware of this, but the geologists who laid the foundation for 'Deep Time' were similarly unencumbered, at first. See, people used to think the world was 'young'. It was people who thought so that, when they came to study geology, discovered it wasn't.

So the problem is that this is not a new idea, or something that can only be spotted by Shallow Timers. It is the very idea that Shallow Timers gave up in the face of the evidence. Those who did not have "a pre-commitment to Darwinism and Deep Time" were the very people who discovered deep time.

Don't you find that odd?

Is it not possible that you are misunderstanding stuff? Especially given your proud ignorance of the subject?

[ericmurphy]

300 generations, Dave.

Do you honestly think no one has noticed you have completely ignored this question? A question that points up a fatal flaw in Sanford's (and hence your) argument?

Explain to us why there are any fast-reproducing eukaryotes left, Dave. Your "hypothesis" predicts that they all should be extinct. They're not. Why?

To continue to duck this question throws a spotlight on your intellectual dishonesty, Dave. If you'd like to gain any sort of credibility, I suggest you attempt to answer it.

[Vicious Love]

Amateur Science Enthusiast :-)

MY HEAD ASPLODE

[Dave Hawkins]

Eric ... Sanford claims that complex genomes should deteriorate to the point of extinction after 300 generations.Where does he claim this? Please cite him with a reference. Also, it seems that your refutation of this idea stems from your belief that higher organisms (whatever that includes) have been extant for millions of years. But you have presented no credible evidence for this. It seems to be merely your belief. So your conclusion about Sanford's supposed statement (maybe he did say that, I don't know) is based on your beliefs, not on evidence.

RBH ... If they don't show up as "effects on fitness", as claimed in the quotation, then they're evolutionarily irrelevant. If they don't reduce viability or fertility, they're evolutionarily irrelevant. Sanford is a loon or ignorant, i'm not certain which.They don't show up immediately as "effects on fitness" but they do show up. Note that Crow speaks of a 1-2% per generation decrease in viability in humans resulting from mutation accumulation over the last several centuries. Correct me if I am wrong, but modern medicine does NOT apply to the last several centuries ... only to about the last 100 years or so (maybe less).

Oolon Colluphid ... So what this "I've not studied it but they're wrong" implies is that the experts are fools. But I'm not saying "I've not studied it but they're wrong." I'm saying I HAVE studied it. And Sanford has too. And the only thing we are saying that Crow is wrong about is when he proposes that "quasi-truncation selection" can save the human race. We're not impugning his great reputation as a geneticist. We are not saying we are smarter than he is. We are simply submitting that we think he is mistaken in this idea. What's arrogant about that?

[Jet Black]

Note that Crow speaks of a 1-2% per generation decrease in viability in humans resulting from mutation accumulation over the last several centuries.


decrease in viability? you mean the humans with a lower reproduction rate are actually reproducing more, creating a logical contradiction?

[Vicious Love]

Also, it seems that your refutation of this idea stems from your belief that higher organisms (whatever that includes) have been extant for millions of years.

Might I advise that you become an amateur arithmetic enthusiast?

[hecate]

afdave wrote;
But I'm not saying "I've not studied it but they're wrong." I'm saying I HAVE studied it. And Sanford has too. And the only thing we are saying that Crow is wrong about is when he proposes that "quasi-truncation selection" can save the human race. We're not impugning his great reputation as a geneticist. We are not saying we are smarter than he is. We are simply submitting that we think he is mistaken in this idea. What's arrogant about that?

Nothing, but for the fact you have been shown for the xxxxthiest time to be wrong and not acknowledging that.

[Dave Hawkins]

OC ... So, what do you mean by "biological changes" and "creative"?Well first of all, my understanding of "mutation" is that it is a genetic mistake. My understanding of mutations comes from evolutionary scientists, not creationists. Note the 2006 Prentice Hall High School Biology text by Miller/Levine ... Now and then cells make mistakes in copying their own DNA, inserting an incorrect base or even skipping a base as the new strand is put together. These mistakes are called mutations ... (p. 307)Also, Ayala ... Ayala, Francisco J., “The Mechanisms of Evolution,” Scientific American, vol. 239 (September 1978), pp. 56-69.
p. 58
“A mutation can be considered an error in the replication of DNA prior to its translation into protein.”
p. 59
“The forces that give rise to gene mutations operate at random in the sense that genetic mutations occur without reference to their future adaptiveness in the environment.”But in the same article, Ayala asserts (with no support) that ... mutation is the ultimate source of all genetic variation ... (p. 63)So my first question is "How can a mistake be considered to be creative?" Not language conducive to convincing me that it is. Have you ever heard of a mistake being a creative force in any other context? I have not. It seems that this is just an assertion by proponents of evolutionary theory.

Secondly, for further insight into what I mean by "mutations have never been shown to produce any biological changes which could be construed as 'creative' " please read my analysis of Muller/Newman (http://richarddawkins.net/forum/viewtopic.php?p=121210&highlight=newman#121210) ...

Origination of Organismal Form: The Forgotten Cause in Evolutionary Theory
Gerd B. Müller and Stuart A. Newman
http://mitpress.mit.edu/books/chapters/0262134195chap1.pdf

[ericmurphy]

Eric ... Sanford claims that complex genomes should deteriorate to the point of extinction after 300 generations.Where does he claim this? Please cite him with a reference.

You claim this, Dave.

WHAT IS TRUNCATION SELECTION? QUASI? SYNERGISTIC EPISTASIS?
TRUNCATION SELECTION
Crow (1997) has a good explanation of Truncation Selection (which he says is totally unrealistic) here
http://www.pnas.org/cgi/content/full/94/16/8380
Instead he proposes "Quasi" Truncation Selection. Crow's theory has been modeled using computer simulations by both YEC's (ReMine) and non-YECs (Schoen et al, 1998) and the bottom line is that the mutations still accumulate disastrously and the species goes extinct in 300 generations. And this, only if we can actually select effectively. If all the mutations are nearly neutral, then they are unselectable, and Crow's model breaks down completely.

Permalink (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=SP;f=14;t=3131;p=39657)

(my emph.)

And if you no longer claim this, then please provide a figure for how many generations you believe it will take for higher genomes to degenerate to the point of extinction, and evidence that this happens.


Also, it seems that your refutation of this idea stems from your belief that higher organisms (whatever that includes) have been extant for millions of years.
No it does not. You claim that everything alive today is descended from organisms that were alive 4,500 years ago. If 300 generations are enough to drive species to extinction, virtually everything should be extinct by now. They are not. What is your explanation for this failure of a prediction of your "hypothesis."

But you have presented no credible evidence for this. It seems to be merely your belief. So your conclusion about Sanford's supposed statement (maybe he did say that, I don't know) is based on your beliefs, not on evidence.

I don't need to produce evidence for my beliefs, Dave. You're not shifting the burden of proof here. We're talking about your beliefs. Nothing about my question has anything to do with my beliefs. It has to do with your claim, and how it fails to match up to observation. I'm asking you to explain your belief, which is that 300 generations is enough for complex genomes to deteriorate to the point of extinction, or if you don't think 300 generations is enough, than how many would be enough.

[ericmurphy]

Have you ever heard of a mistake being a creative force in any other context? I have not.

All the time, Dave. Do a little research into the vulcanization process. That should get you started.

[Dave Hawkins]

Dean Anderson ... would you please post your e-mail that you sent to Dr. Crow? Thx

[Dave Hawkins]

Eric ... please read carefully and quote me accurately so as not to clutter up the board with corrections. You are mistaken in two ways. First you incorrectly attribute MY statement to Sanford. Then you misunderstand by not reading carefully. That quote of mine was referring to humans, not "higher genomes" generally, and I was discussing a program ReMine has reportedly run, which I now understand is being modeled in a more robust manner by ICR in their GENE Project. Note that Crow gives an even worse prognosis for humans than ReMines program does. He says we've only got 50-100 generations left.

[ck1]

But I'm not saying "I've not studied it but they're wrong." I'm saying I HAVE studied it. And Sanford has too.
You have NOT studied any of this (by any accepted definition of "study"). You have admitted that you never managed to read a book dealing with a scientific subject by a mainstream (non-creationist) scientist. When I suggested that you might find it interesting to attend science programs/lectures for the general public at your local university or natural science museum your response was (I paraphrase here): "Why would I want to do that?"


And the only thing we are saying that Crow is wrong about is when he proposes that "quasi-truncation selection" can save the human race. We're not impugning his great reputation as a geneticist. We are not saying we are smarter than he is. We are simply submitting that we think he is mistaken in this idea. What's arrogant about that?

So you disagree with Crows's science, but use his paper because you can extract a few useful (from your viewpoint) quotemines.

[argystokes]

Oolon,
No doubt you noticed that Dave opted not to provide definitions of "biological changes" and "creative." Since I had the same discussion with him several months ago, I feel obligated to tell you what Dave means before he obfuscates further and wastes more time. A mutation is not considered to be creative by Dave if it results in the modification of a previously existing protein. Only changes which essentially cause a new structure to essentially pop out of nowhere are deemed creative by Dave. Novel function doesn't count, either.

[Porky Pine]

So my first question is "How can a mistake be considered to be creative?" Not language conducive to convincing me that it is. Have you ever heard of a mistake being a creative force in any other context? I have not. It seems that this is just an assertion by proponents of evolutionary theory.

This just boggles the mind. :eek:

Someone earlier mentioned the nylon eating bacteria. Was that not a mistake in the genetic coding and did it not produce something creative?

[ericmurphy]

Eric ... please read carefully and quote me accurately so as not to clutter up the board with corrections. You are mistaken in two ways. First you incorrectly attribute MY statement to Sanford.
Okay, first explain how a direct quote from you can possibly be inaccurate. I copied and pasted your quote, and supplied a link. In what way is my quote inaccurate?

Second, I corrected myself, and imputed the claim to you, not Sanford. Now, do you stand by your claim, or not?

Then you misunderstand by not reading carefully. That quote of mine was referring to humans, not "higher genomes" generally, and I was discussing a program ReMine has reportedly run, which I now understand is being modeled in a more robust manner by ICR in their GENE Project. Note that Crow gives an even worse prognosis for humans than ReMines program does. He says we've only got 50-100 generations left.

So let's pin you down to what you actually believe, Dave. Are you saying that only the human genome is deteriorating? Is there some different number of generations that other eukaryotic genomes take to deteriorate to extinction?

Do you even know what you're saying, Dave?

And if you think only the human genome is "deteriorating," you need to explain how the human genome is in so much worse shape than other eukaryotic genomes, given that the average biblical "kind" has radiated into a thousand species in the past 4,500 years, whereas humans have not radiated into any additional species. Which "fact" implies a higher mutation rate, Dave?

And why can you simply not be made to understand what Crow is really saying, which is bone-simple: modern medicine is allowing deleterious mutations to pile up in the human genome at a higher-than-normal rate, because it is interfering with the operation of natural selection. Why can't you understand this? Could it be because your mind is encumbered with a 3,000-year-old belief system?

[JonF]

Have you ever heard of a mistake being a creative force in any other context? I have not.
All the time, Dave. Do a little research into the vulcanization process. That should get you started.
Saran wrap.

[Vicious Love]

Still nothing? I realize this may seem like advanced stuff, but it really is only an intermediate-level population genetics problem. Most biology Ph.Ds would get it right on the first try. C'mon, give it a shot:

x = 300
y = 1
5,000 > z < 10,000
f = 4,500

(1) xy > z
(2) xy > f

For what values of z does the inequality (1) hold?
For what values of f does the inequality (2) hold?

Edit: Hm. Could've sworn I hit refresh before posting. Right then, what ericmurphy said. Are other species' genomes deteriorating at all? If so, how many generations before guinea pigs conk out? If not, why are other species exempt?

[TomboyMom]

I'm confused about the quote in the OP. The thread is about Sanford, right? But the quote is from Crow? Or Sanford? Who is Crow???

[ericmurphy]

Oolon,
No doubt you noticed that Dave opted not to provide definitions of "biological changes" and "creative." Since I had the same discussion with him several months ago, I feel obligated to tell you what Dave means before he obfuscates further and wastes more time. A mutation is not considered to be creative by Dave if it results in the modification of a previously existing protein. Only changes which essentially cause a new structure to essentially pop out of nowhere are deemed creative by Dave. Novel function doesn't count, either.

If Dave actually could find what he thinks is proof that evolution can create true novelty, he would have disproved evolution, and found proof that there is an intelligent designer. Dave has his argument exactly backwards.

[Faid]

The point is that Dave is so convinced of his position that he thinks that he can easily surpass a lifetime of learning in any field by reading creationist websites for a few hours. As he has claimed on RD.net.

I am curious. Is there anyone besides Dave who thinks this statement is inaccurate or overstated?

How could we, after dave's post? He reaffirms it, as he supposedly tries to dispute it!

IOW, what I am saying is that I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand.


What's more to say? DaveLogic(TM) in all its glory.

[Faid]

Oh and, dave, here's my post from the other thread, in case you missed it:

Hi dave.

So, you say this:



I would consider the statements of another geneticist who contradicts Sanford carefully.


Fine. In that case, why don't you consider the statements of Crow carefully?

Crow states (and you are in no position to deny this, since it's there in the paper you quoted, plain as plain) that in the past, Natural Selection purged deleterious mutations from our genome (by thwarting the survival of those individuals), which does not happen now because of our advances in medical technology. Sanford claims that this is incorrect, and that natural selection cannot possibly remove these acumulating mutations.

This certainly sounds like a contradiction to me, dave.

So, Why don't you consider Crow's contradicting statements carefully, like you said you would? Why do you handwave them away, exactly like Sanford does?

Now dave, If I wanted to behave like you and engage in an authority clash, I could easily do it. Comparing geneticists of the magnitude of Crow (and Kondrashov, and others) to the "inventor of the gene gun", would not fare that well for your side.

But there's no need to. You see, as we have already told you a dozen times, Crow (and Kondrashov, and Kimura, iirc) have produced calculations and models, published in scientific papers, that demonstrate how natural selection can, in fact, work to purge the genome of those mutations and stop them from accumulating.

Now, where is Sanford's scientific response, to back up his assertions? Where does he address these calculations by these scientists, to show exactly why and how they are inaccurate or misleading?

We have asked you this question many months ago, at AtBC, and we are still waiting for a response.

All we have is Sanford's "300 generations till complete deterioration" claim, which is ridiculous by itself (since it's disproved by reality), and an irrelevant reference- the famous Schoen paper, that, as we found out, actually refers to mutation accumulation in seed storage.

But an attempt to directly address and refute the work of those scientists? None that we know of.



As usual, dave, we have the data. As usual, we win.

[ck1]

Well first of all, my understanding of "mutation" is that it is a genetic mistake. So my first question is "How can a mistake be considered to be creative?" Not language conducive to convincing me that it is. Have you ever heard of a mistake being a creative force in any other context? I have not. It seems that this is just an assertion by proponents of evolutionary theory.

Secondly, for further insight into what I mean by "mutations have never been shown to produce any biological changes which could be construed as 'creative' " please read my analysis of Muller/Newman (http://richarddawkins.net/forum/viewtopic.php?p=121210&highlight=newman#121210) ...

Origination of Organismal Form: The Forgotten Cause in Evolutionary Theory
Gerd B. Müller and Stuart A. Newman
http://mitpress.mit.edu/books/chapters/0262134195chap1.pdf

Dave, You seem to be caught up in semantics here : mistake = bad. Please think for a moment about the types of "mistakes" we are referring to here. The most common mutation is a point mutation, a base substitution that can sometimes result in a substitution of a new amino acid. This does not necessarily have deleterious consequences. Examples can be provided.

There are also frameshift mutations, like the nylonase example given to you over and over. This frameshift generates a completely new protein with a previously unneeded function in bacteria that has a clear survival benefit. Why have you not addressed this example.

We have also previously discussed that Muller/Newman paper. Several times. I hope we do not have to go through that again here.

[JLK]

I'm confused about the quote in the OP. ... the quote is from Crow? Or Sanford? Who is Crow???The quote's from James Crow (http://www.genetics.wisc.edu/faculty/profile.php?id=102), professor emeritus at the U of Wisconsin (where Sanford received his degrees in plant breeding and genes), Crow's one of the two or three most famous/greatest, living population geneticists and his textbook and notes are classics of the field.

[Faid]

And dave, since the only part of my post you deemed worthy of your response was the one about the "authority clash"...

I did not at any time try to say "Sanford knows more than Crow." I simply pointed out an inference that Sanford has made from Crow's statements, an inference which I believe is justified.

...Let me get this straight.

You do NOT claim that Sanford knows more than Crow, right?

So, if they take opposite sides on an issue (and they do), Whose opinion would you be more sceptical of?

Just curious. :)

[TomboyMom]

I'm confused about the quote in the OP. ... the quote is from Crow? Or Sanford? Who is Crow???The quote's from James Crow (http://www.genetics.wisc.edu/faculty/profile.php?id=102), professor emeritus at the U of Wisconsin (where Sanford received his degrees in plant breeding and genes), Crow's one of the two or three most famous/greatest, living population geneticists and his textbook and notes are classics of the field.

Thanks. So if the OP wants to discuss Sanford's theories, why does he give us a post from Crow? Why doesn't he give us a quote from Sanford, or that summarizes Sanford, or that states what Sanford's theory is???

[Dave Hawkins]

CK1 ... You have NOT studied any of this (by any accepted definition of "study"). You have admitted that you never managed to read a book dealing with a scientific subject by a mainstream (non-creationist) scientist. When I suggested that you might find it interesting to attend science programs/lectures for the general public at your local university or natural science museum your response was (I paraphrase here): "Why would I want to do that?"Again, you are misrepresenting me. Curious that you are so concerned about me misrepresenting Crow, yet you have misrepresented me twice now at this forum.

I have read several books dealing with a scientific subject by a mainstream (non-creationist) scientists. My latest ones have been a book on Mendel's life and research work, significant portions of Darwin's Origin and Popper's two main works, Libby's Radiocarbon and a later Nobel Symposium on Radiocarbon, and also Miller/Levine's 2006 High School Biology text from Prentice Hall. I have subscriptions to both Nature and Science and I read them regularly. I also read other scientific papers as I have interest. I am currently reading about the ENCODE project in Nature and also Craig Venter's new synthetic biology company in the latest issue of Science. Fascinating stuff. I think ENCODE is going to wind up showing that creationist predictions about "junk DNA" are correct and evolutionist predictions are wrong. I think Venter's work will highlight just how difficult it is to create a functional organism from scratch. This will have major implications on OOL and evolution studies.

What I admitted is that I don't like reading "Darwin Apologetics" books like the ones Prof. Dawkins writes.

I also don't see the point of spending hours at science programs/lectures, when I can get the same information much more quickly online. Also, I can interact with scientists online pretty well. Yes, in person conversation is valuable too, but I don't have the time for much of that now.

[Dave Hawkins]

The quote's from James Crow (http://www.genetics.wisc.edu/faculty/profile.php?id=102), professor emeritus at the U of Wisconsin (where Sanford received his degrees in plant breeding and genes), Crow's one of the two or three most famous/greatest, living population geneticists and his textbook and notes are classics of the field.

Thanks. So if the OP wants to discuss Sanford's theories, why does he give us a post from Crow? Why doesn't he give us a quote from Sanford, or that summarizes Sanford, or that states what Sanford's theory is???I did. Dr. J.C. Sanford, a geneticist from Cornell recently renounced his evolutionary views, has become a young-earth creationist, and has written a very revealing book entitled Genetic Entropy and the Mystery of the Genome (2005) which shows from the published papers of leading population geneticists that deleterious mutations are accumulating in populations. He draws two conclusions from this ... 1) that populations will ultimately go extinct due to mutational meltdown and that selection, natural or otherwise, cannot save them, and 2) that this shows that the "Primary Axiom" of evolution--Random Mutation + Natural Selection--could never have produced species extant today.That's pretty much Sanford's book in a nutshell.

[ck1]

Useful things resulting from "mistakes":


All the time, Dave. Do a little research into the vulcanization process. That should get you started.
Saran wrap.

And teflon

[ck1]

I have read several books dealing with a scientific subject by a mainstream (non-creationist) scientists. My latest ones have been a book on Mendel's life and research work, significant portions of Darwin's Origin and Popper's two main works, Libby's Radiocarbon and a later Nobel Symposium on Radiocarbon, and also Miller/Levine's 2006 High School Biology text from Prentice Hall. I have subscriptions to both Nature and Science and I read them regularly. I also read other scientific papers as I have interest. I am currently reading about the ENCODE project in Nature and also Craig Venter's new synthetic biology company in the latest issue of Science. Fascinating stuff. I think ENCODE is going to wind up showing that creationist predictions about "junk DNA" are correct and evolutionist predictions are wrong. I think Venter's work will highlight just how difficult it is to create a functional organism from scratch. This will have major implications on OOL and evolution studies.

Well, good to hear this. I hope the "portions" of the works you mentioned are not quotemined sections you find at AIG or ICR. (I believe it was me who pointed you to the ENCODE paper - don't forget to look at the free access associated papers from the ENCODE consortium in Genome Research - there are 3 commentaries there written for a more general audience in addition to more detailed scientific reports. And even you would have to admit that the evolutionary foundation for this project is very clear.)

My statement about your refusal to read mainstream science may have been too harsh, but it is still clear that your interpretation and understanding of what you read leaves much to be desired. Isolated papers cannot be read in a vacuum. That ENCODE material is not easy reading, especially for someone who just learned the definition of "allele".

Please point me to creationist predictions about "junk" DNA and explain the theoretical and experimental basis for those predictions.

[ninewands]

Useful things resulting from "mistakes":


Saran wrap.

And teflon
and Gor-Tex, not to mention silicone adhesives, which will stick to damn-near anything, when what the chemists were looking for was silicone lubricants.

[TomboyMom]

Thanks. So if the OP wants to discuss Sanford's theories, why does he give us a post from Crow? Why doesn't he give us a quote from Sanford, or that summarizes Sanford, or that states what Sanford's theory is???I did. Dr. J.C. Sanford, a geneticist from Cornell recently renounced his evolutionary views, has become a young-earth creationist, and has written a very revealing book entitled Genetic Entropy and the Mystery of the Genome (2005) which shows from the published papers of leading population geneticists that deleterious mutations are accumulating in populations. He draws two conclusions from this ... 1) that populations will ultimately go extinct due to mutational meltdown and that selection, natural or otherwise, cannot save them, and 2) that this shows that the "Primary Axiom" of evolution--Random Mutation + Natural Selection--could never have produced species extant today.That's pretty much Sanford's book in a nutshell.

1. That's too much of a nutshell for anyone to respond to intelligently. To evaluate a hypothesis, we need some detail on what it is and why its proponent asserts its validity.

2. Without some direct information from the author, it's impossible to evaluate how accurately you have described his hypothesis.

[VoxRat]

CK1 ... You have NOT studied any of this (by any accepted definition of "study"). You have admitted that you never managed to read a book dealing with a scientific subject by a mainstream (non-creationist) scientist. Again, you are misrepresenting me. Curious that you are so concerned about me misrepresenting Crow, yet you have misrepresented me twice now at this forum.stop with the accusations of "misrepresenting". Ck1 has done nothing of the sort. Look at that quote, above: "You have NOT studied any of this". What is "this"? GENETICS.
I have read several books dealing with a scientific subject by a mainstream (non-creationist) scientists. My latest ones have been a book on Mendel's life and research work, significant portions of Darwin's Origin
...
I am currently reading about the ENCODE project in Nature and also Craig Venter's new synthetic biology company in the latest issue of Science. Fascinating stuff. I think ENCODE is going to wind up showing that creationist predictions about "junk DNA" are correct and evolutionist predictions are wrong. ...
"significant portions" of Darwin? What would that mean? Most of it? Half of it? The parts that AiG likes to quotemine?

Please share with us what you think are creationist predictions about "junk DNA" that have been made, and what you think are evolutionist predictions about it. Creationists have a habit of telling us after discoveries that they "predicted it all along". However, they can't point to anything specific. That's why I'm asking. That's why you'll probably not respond.

[ericmurphy]

CK1 ... You have NOT studied any of this (by any accepted definition of "study"). You have admitted that you never managed to read a book dealing with a scientific subject by a mainstream (non-creationist) scientist. When I suggested that you might find it interesting to attend science programs/lectures for the general public at your local university or natural science museum your response was (I paraphrase here): "Why would I want to do that?"Again, you are misrepresenting me. Curious that you are so concerned about me misrepresenting Crow, yet you have misrepresented me twice now at this forum.

No one's misrepresenting you, Dave. You have been asked, point-blank, if you've ever read anything about evolution by non-creationist writers, and your answer (when you have bothered to answer) has always been "no." You said you'd read a few chapters, and then bailed when it got boring.

I have read several books dealing with a scientific subject by a mainstream (non-creationist) scientists. My latest ones have been a book on Mendel's life and research work, significant portions of Darwin's Origin and Popper's two main works, Libby's Radiocarbon and a later Nobel Symposium on Radiocarbon, and also Miller/Levine's 2006 High School Biology text from Prentice Hall.
This is a new claim, one you've never made previously. Even if it's true (and let's just say I'm skeptical), that would not change the fact that you are on record as having said up to this point that you have not read any books in their entirety on evolution from non-creationist writers. So cut with the "misrepresentation" crap. Karl Popper is a philosopher of science, not a scientist, and certainly not an evolutionary biologist. Reading a high school textbook on biology hardly prepares you for a discussion of evolution, since most high school textbooks barely even address the issue, and certainly not in any depth.

Whether you have or have not read any books on evolution is irrelevant, in any event, because your profound ignorance on the subject speaks for itself.

I have subscriptions to both Nature and Science and I read them regularly. I also read other scientific papers as I have interest. I am currently reading about the ENCODE project in Nature and also Craig Venter's new synthetic biology company in the latest issue of Science. Fascinating stuff. I think ENCODE is going to wind up showing that creationist predictions about "junk DNA" are correct and evolutionist predictions are wrong.
Creationists haven't made any predictions about "junk DNA" that could be confirmed. Saying "all DNA has a function" is not really a prediction, and it certainly doesn't answer any questions about any purported functions.

I think Venter's work will highlight just how difficult it is to create a functional organism from scratch. This will have major implications on OOL and evolution studies.

Um, No. No one disputes that it's difficult to create a functional organism "from scratch." If you think this is news to legitimate scientists, you're wrong.

What I admitted is that I don't like reading "Darwin Apologetics" books like the ones Prof. Dawkins writes.

When asked what books on evolution by non-creationsts you have ever read in their entirety, your answer was "none."

I also don't see the point of spending hours at science programs/lectures, when I can get the same information much more quickly online. Also, I can interact with scientists online pretty well. Yes, in person conversation is valuable too, but I don't have the time for much of that now.

No, you can't, Dave. What you can do is pick up a lot of misinformation to misinterpret very quickly. You have demonstrated conclusively that your method of surfing the web to develop knowledge about complex subjects simply doesn't work. You're exhibit "A" to support the contention that "a little knowledge is a dangerous thing.

[ericmurphy]

And in case you've forgotten, Dave; you owe BWE a respons in your debate on rd.net.

[Amaleq13]

The point is that Dave is so convinced of his position that he thinks that he can easily surpass a lifetime of learning in any field by reading creationist websites for a few hours. As he has claimed on RD.net.

I am curious. Is there anyone besides Dave who thinks this statement is inaccurate or overstated?

I have to admit I don't understand how the phrase "as it relates to Origins" makes the two statements say anything significantly different. They appear to me to be conveying the same concept.

Dave believes he knows more about the subject as it pertains to his beliefs than experts who have spent their professional lives studying it.

I guess he thinks that the italicized portion makes a difference but I don't see how.

[Mike PSS]

I'm not going to wade too deep into this morass, just enough to indicate to others the history behind some of these claims of Dave's.Examples: I have figured out that mutations have never been shown to produce any biological changes which could be construed as "creative."Dave,
Go to Wiki and find "Nylon Eating Bacteria". I think we walked through this whole mutation episode from the referenced papers on Wiki (honestly, I forget if it was you or someone else). The two step protien path that the bugs need to convert nylon to a more basic sugar for digestion I think. This is a creative process, and the referenced papers actually show how each step was attained. The latest experiments actually "create" the nylon eating bug from scratch (i.e. from non-nylon eating bugs to start with). I believe the original bugs were found in the waste pits of the nylon plant itself.
So much we could talk about, so little you would actually believe.
Also, I have observed that massive variability in taxa is possible in just 5000 years--with NO mutations whatsoever (Ayala's statements).
Dave,
Are you ready to take up the discussion with ericmurphy and I about how at least 61 alleles have formed in 250 years (or the entire set of 600+ in 4500 years). That question has been around since your time at AtBC last year. I never said Ayala's statement wasn't true, but only that his statement wasn't applicable to our discussion involving the immediate post-flood population since your didn't have all that "genetic diversity" available to share between populations.

Are you ready to talk this through here on IIDB?
I have figured out similar fundamental realities in geology that highly trained geologists have not figured out.Dave,
Ummmmm.....
Oh hell, this whole line of discussion is off-topic anyway so I'll just end my statement with....
PPpphhphhhhhhhhtttttttt........ :Cheeky:
Why have I figured out these basic things that highly trained specialists have missed? Because I'm smarter than them? No. Not at all. It's because my thinking is unencumbered with a pre-commitment to Darwinism and Deep Time.Dave,
Your thinking is fully encumbered by a commitment to Biblical Innerrency.

So who's "more" correct? R.H.Brown or RATE? Hmmmmmm....????

[VoxRat]

and speaking of misrepresenting people, are you planning to address this (moved from the Pyramid thread)?

In discussing this paper with a microbiology professor from Ohio, he admitted something to the effect of "the human race is probably headed for mutational meltdown." I could provide the link upon request, but it would be some work.When challenged to support this:Last year I discussed these papers with a microbiology professor (I think that's what he was) named Dr. Russell Durbin ("Russell" at AtBC). The context was the same as the present discussion. We were discussing accumulating mutations and he said this ... Sure enough. Just as I retrodicted. You have misrepresented your source. The fact that 99% of species have gone extinct, and the fact that Homo sapiens is likely to join them, says nothing about "mutational meltdown". Species go extinct from all kinds of causes.

[ericmurphy]

Also, I have observed that massive variability in taxa is possible in just 5000 years--with NO mutations whatsoever (Ayala's statements).

You've observed no such thing, Dave. Where do you think the 600+ HLA-B alleles came from, if not from mutations? We have established (and you do not disagree, anymore) that there could have been no more than 10 HLA-B alleles on the ark. Where did the rest of them come from, if not from mutations?

And again: how can the following statements both be true:

4,500 years is plenty of time to get from several thousand "kinds" to several million species; and
4,500,000,000 years isn't nearly enough time to get from several thousand to several million species.


You've never answered this question, Dave, and you never will.

[Amaleq13]

Note that Crow speaks of a 1-2% per generation decrease in viability in humans resulting from mutation accumulation over the last several centuries.

What he actually wrote (emphasis mine):
"If we are like Drosophila, the decrease in viability from mutation accumulation is some 1 or 2% per generation."

"It seems clear that for the past few centuries harmful mutations have been accumulating."

Correct me if I am wrong, but modern medicine does NOT apply to the last several centuries ... only to about the last 100 years or so (maybe less).

First, Crow doesn't restrict the obstruction of natural selection to "modern medicine" but refers to the more broad category of "environmental improvements".

Second, unless one applies a very narrow definition of "modern medicine", it certainly does apply to the last few centuries. There is no question that the current state of medical science has done more than the last few centuries but it is simply incorrect to suggest or assume that the medical advances of the 18th and 19th centuries did nothing.

[ericmurphy]

Here's a question for you, Dave:

Are modern humans more "reproductively fit" than the humans of 200,000 years ago (feel free to pick a more recent number if the 200,000 makes you uncomfortable)?

Now, if you think modern humans are less reproductively fit, then perhaps you'd like to explain the greater likelihood that a human will survive to reproduce now than he or she would have even 2,000 years ago.

And if you agree that humans are more "reproductively fit" now than they were in the distant past, then perhaps you'd like to explain to us why you think ancient humans were "genetically superior" to modern humans, and why that is.

[deadman_932]

Useful things resulting from "mistakes":



And teflon
and Gor-Tex, not to mention silicone adhesives, which will stick to damn-near anything, when what the chemists were looking for was silicone lubricants.

Penicillin.

I'm still curious as to why Dave thinks only humans are affected, and not other mammals, for instance. It looks as though a new "list of unanswered direct questions" is on the horizon.

[ppnl]

Useful things resulting from "mistakes":



And teflon
and Gor-Tex, not to mention silicone adhesives, which will stick to damn-near anything, when what the chemists were looking for was silicone lubricants.

How about the entire field of combinatorial chemistry. But when you make "mistakes" on an industrial scale is it still a mistake?

[FatherMithras]

Dave, you continue to fail to address the significant rebuttals made in this thread, selectively replying only to almost insignificant bits you can generally misrepresent. Please go back and address some of the points, most notably your failure to acknowledge the reason we have more deleterious mutations in the population is because of modern medicine, not a natural thing we see in nature. And don´t forget the nylon eating bacteria. It´s telling.

[Calilasseia]

I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand.

Wow. Hubris on a galactic scale here. But where have we seen this before folks?

As for this:

Hello Dr. Crow ...

I have some questions about your 1997 paper found here ...

http://www.pnas.org/cgi/content/full/94/16/8380

and I wondered if you would be able to answer them for me. As you may know, Cornell geneticist Dr. John Sanford has quoted you in his recent book, Genetic Entropy and the Mystery of the Genome (2005). He quotes several of your statements, including this one ...

"If war or famine force our descendants to return to a stone-age life they will have to contend with all the problems that their stone-age ancestors had plus mutations that have accumulated in the meantime."

then he writes ...

"He [i.e. you, Dr. Crow] goes on to acknowledge that humanity must now be genetically inferior to our stone-age ancestors [referring to the above statement] - an amazing confession about the reality of genomic deterioration." (Sanford, p. 171)

Now my questions are ...

1) Do you really believe that modern humans are genetically inferior to our stone-age ancestors?
2) If so, is this only because of modern medicine which keeps people alive which would otherwise not reproduce as well and/or die before reproducing?
3) Or would we be genetically inferior anyway (w/o modern medicine) because of the 1-2% per generation decrease in viability that you speak about occurring over the last several centuries?

IOW ... is Dr. Sanford misrepresenting your view by saying that you acknowledge that humanity must now be genetically inferior to our stone-age ancestors? Or is his representation a fair one?

Would you allow me to post your response to this e-mail publicly? If not, that's OK. I still would like to get these questions answered for my own benefit.

Thanks,

Dave Hawkins
Amateur Science Enthusiast :-)

Anyone else waiting to discover what explosions will result from this particular ticking time bomb?

I feel sorry for poor Dr Crow. His in-tray must be overflowing with this sort of thing.

[ck1]

Also, I can interact with scientists online pretty well.

If you define "interact" as "two ships passing in the night."

[deadman_932]

Hmm..Dave put his debate post up at RD's and he's essentially accusing dendrologist Ferguson of conspiracy and fraud...because he didn't allow a biochemist creationist to examine the tree ring data directly. Cute.

[Sven]

I think you failed to read the words "as it relates to Origins". IOW, what I am saying is that I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand. Examples: I have figured out that mutations have never been shown to produce any biological changes which could be construed as "creative." Also, I have observed that massive variability in taxa is possible in just 5000 years--with NO mutations whatsoever (Ayala's statements). I have figured out similar fundamental realities in geology that highly trained geologists have not figured out.

Why have I figured out these basic things that highly trained specialists have missed? Because I'm smarter than them? No. Not at all. It's because my thinking is unencumbered with a pre-commitment to Darwinism and Deep Time.
:huh: :eek: :banghead:

It of course does not matter at all to Dave that Evolution replaced Creationism (including a young Earth) despite scientists fervently trying to rescue Creationism because of their religious convictions (just as Dave does today).

[Constant Mews]

Hmm..Dave put his debate post up at RD's and he's essentially accusing dendrologist Ferguson of conspiracy and fraud...because he didn't allow a biochemist creationist to examine the tree ring data directly. Cute.More amusingly, he claims the data questionable because the sample is limited and no one is allowed to examine it.

The only problem, of course, is that Dave's source of this information is thirty-years old. The amount of data available for dendrochronology master-tree sequence establishment has moved in that amount of time.

Dave might consider examining the WSL data and other NOAA Paleoclimatology Tree Ring data located here. (http://www.ncdc.noaa.gov/paleo/treering-wsl.html)

[ck1]

OK Dave,

While we are waiting for a response from Crow, why don't you deal with a question at least 5 people have asked on this thread:

Can you please explain the generation of nylonase in bacteria from your perspective? Why is this not an example of a novel protein created by mutation?

This is the 4th time I have asked about this on this thread.

Thanks.

[Steviepinhead]

All the time, Dave. Do a little research into the vulcanization process. That should get you started.
Saran wrap.
Post-it notes.

[the Radio Star]

Didn't know it was possible for a real geneticist to be a YEC. I'm scared. :worried:

[argystokes]

OK Dave,

While we are waiting for a response from Crow, why don't you deal with a question at least 5 people have asked on this thread:

Can you please explain the generation of nylonase in bacteria from your perspective? Why is this not an example of a novel protein created by mutation?

This is the 4th time I have asked about this on this thread.

Thanks.

Betcha he'll say it's not a new protein because it is only a modification of a previous protein :nostradamus:

[ericmurphy]

Yep: the one thing that would convince Dave evolution can happen--the discovery of an entirely novel structure in biology without antecedent--would be the one thing that would disprove evolution and would essentially force a belief in intelligent design.

[mung bean]

Also, I can interact with scientists online pretty well.

If you define "interact" as "two ships passing in the night."CK, I think it's more like Dave is the "Andrea Doria" and he's interacting with the "Stockholm".

[Worldtraveller]

Ok folks, enough with the personal comments. Let's keep this on the topic of the OP.

Lane, E/C Moderator.

[Steviepinhead]

Hello Dr. Crow ...

I have some questions about your 1997 paper found here ...

http://www.pnas.org/cgi/content/full/94/16/8380

and I wondered if you would be able to answer them for me. As you may know, Cornell geneticist Dr. John Sanford has quoted you in his recent book, Genetic Entropy and the Mystery of the Genome (2005). He quotes several of your statements, including this one ...

"If war or famine force our descendants to return to a stone-age life they will have to contend with all the problems that their stone-age ancestors had plus mutations that have accumulated in the meantime."

then he writes ...

"He [i.e. you, Dr. Crow] goes on to acknowledge that humanity must now be genetically inferior to our stone-age ancestors [referring to the above statement] - an amazing confession about the reality of genomic deterioration." (Sanford, p. 171)

Now my questions are ...

1) Do you really believe that modern humans are genetically inferior to our stone-age ancestors?
2) If so, is this only because of modern medicine which keeps people alive which would otherwise not reproduce as well and/or die before reproducing?
3) Or would we be genetically inferior anyway (w/o modern medicine) because of the 1-2% per generation decrease in viability that you speak about occurring over the last several centuries?

IOW ... is Dr. Sanford misrepresenting your view by saying that you acknowledge that humanity must now be genetically inferior to our stone-age ancestors? Or is his representation a fair one?

Would you allow me to post your response to this e-mail publicly? If not, that's OK. I still would like to get these questions answered for my own benefit.

Thanks,

Dave Hawkins
Amateur Science Enthusiast :-)

Dave, any particular reason you didn't more correctly identify yourself *smile* as an "Anti-Evolutionary Creationist Curmudgeon" or <edited>? Something along those lines? I mean, you wouldn't want to start your relationship with Dr. Crow off with a blatant misrepresentation of your affection for science, would ya?

Any particular reason you didn't link him to any of your oh-so-science-friendly "Flud Hypothesis" threads at dawkins.net or AtBC? You certainly don't seem to be shy about supplying those links to all and sundry in almost any other context...

You couldn't possibly have been concerned about being "mistaken" for, oh, a <possibly over-the-top reference to a fruit dessert deleted>, couldja, davey...?

And giving Dr. Crow "permission" not to respond publicly may have been polite, but you do realize that we're never gonna take your, ahem, word for whatever it is that Dr. Crow should happen to tell you "off-line," don't ya?

Wouldn't the better approach have been to email Dr. Crow, provide him with a link to this thread--that is, y'know, to actually let him know what's going on and what he might be letting himself in for--and invite him to respond right here?

Just politely wondering, dave, as I often do where your antics are concerned.

[mung bean]

O pointy-headed one, fear not for Davey's propensity to misunderstand Crow. I was tempted to email Crow the necessary links but Dean Anderson has already contacted him as noted on the first page of this thread. Should be interesting when we get a response.

Davey boy, why is it that you are the only one here who apparently misconstrues Crow? His point is quite clear to everyone else, even those of us who aren't trained geneticists.

[Gamera]

OC So my first question is "How can a mistake be considered to be creative?" Not language conducive to convincing me that it is. Have you ever heard of a mistake being a creative force in any other context? I have not. It seems that this is just an assertion by proponents of evolutionary theory.

Short Answer: The heterozygous form of sickle-cell anemia produces limited immunity to malaria infection.

Long Answer: there are no "mistakes" in nature, just processes that we give terms to. In this case, a replication variant. From our perspective, we call it a mistake because we tend to try to replicate things accurately. But of course genes aren't "trying" to do anything. They are simply part of a biological process, which sometimes (predictably in fact) involve replication variants. Further, "creative force" is meaningless in this context. Variant genes are beneficial or detrimental not because of the presence of some creative force, but because of the environment. In a malaria infested environment, it pays to have the heterozygous form of sickle cell anemia. In another environment, it doesn't. There is no "creative force" in evolution: just genetic mutations resulting in variant phenotypes that reproduce better or worse depending on the environment they're in. There are no good or bad mutations per se; just mutations that increase or decrease survival, and that (for the most part, short of one so dysfunctional that life processes cease no matter what the context) has to do with environmental factors (hence natural selection)

[deadman_932]

Ha-HA! I'd like to take this opportunity to point out that a moderator has issued a small reminder and neither Occam's nor Louis or myself was involved in the least. :p And I must agree with our noble host --frankly, I was shocked...SHOCKED to see such goings-on. :angel:

Edit: Personally, I blame society and the unsavoury lot they associate with. Please don't judge them too harshly, for they know not what they do.

[Steviepinhead]

Oops!

Just in case dave saw the now-moderated language afore it was deleted, I agree in retrospect that it was inappropriate to the forum and apologize for any offense.

And I have now read a bit more carefully and see that Dr. Crow has indeed also been asked to comment by Dean Anderson. Which probably renders my, er, critique of dave's message even more redundant.

(Not that I necessarily would've minded sharing virtual off-line libations with such as louis, deadman, bwe, and oa during an absence...but in this case the line-crossing was unintentional, or at least unconscious...!)

[Godless Dave]

It clearly does not.

I think you failed to read the words "as it relates to Origins". IOW, what I am saying is that I, not being formally trained in genetics, have figured out some very fundamental realities about genetics that you, a highly trained biologist, do not seem to understand. Examples: I have figured out that mutations have never been shown to produce any biological changes which could be construed as "creative." Also, I have observed that massive variability in taxa is possible in just 5000 years--with NO mutations whatsoever (Ayala's statements). I have figured out similar fundamental realities in geology that highly trained geologists have not figured out.

You've just made ck1's point better than ck1 ever could.

[Godless Dave]

So my first question is "How can a mistake be considered to be creative?" Not language conducive to convincing me that it is. Have you ever heard of a mistake being a creative force in any other context?

Yes, I have. Ever listened to musicians improvise?

[mung bean]

Ha-HA! I'd like to take this opportunity to point out that a moderator has issued a small reminder and neither Occam's nor Louis or myself was involved in the least. :p You will be......

[RAFH]

Also, I can interact with scientists online pretty well.

If you define "interact" as "two ships passing in the night."

In different oceans?

[RAFH]

Yep: the one thing that would convince Dave evolution can happen--the discovery of an entirely novel structure in biology without antecedent--would be the one thing that would disprove evolution and would essentially force a belief in intelligent design.

Not if it were from another planet. But then it probably wouldn't convince anybody about anything with regard to evolution, especially if it blasted them with its dna-disruptor ray.

[ericmurphy]

Yep: the one thing that would convince Dave evolution can happen--the discovery of an entirely novel structure in biology without antecedent--would be the one thing that would disprove evolution and would essentially force a belief in intelligent design.

Not if it were from another planet. But then it probably wouldn't convince anybody about anything with regard to evolution, especially if it blasted them with its dna-disruptor ray.

I was thinking of some novel structure appearing right in the middle of an organism that could already be fit into the phylogenetic tree. You know, like a ceramic-bearing pump in the heart muscle of a teleost fish, or something. That would be hard to explain other than as an "Oopsie! forgot to hide that one little detail" from an intelligent designer who was otherwise pretty damned adept at hiding any signs of its existence.

[TaO!]

I was thinking of some novel structure appearing... ...like a ceramic-bearing pump in the heart muscle of a teleost fish, or something.

Transcription factor point mutation creates additional functional heart chamber. (http://www.sciencedaily.com/releases/2006/09/060930094021.htm)

Not quite a fish, but still.

[ericmurphy]

I was thinking of some novel structure appearing... ...like a ceramic-bearing pump in the heart muscle of a teleost fish, or something.

Transcription factor point mutation creates additional functional heart chamber. (http://www.sciencedaily.com/releases/2006/09/060930094021.htm)

Not quite a fish, but still.

And not quite a ceramic-bearing pump, either.

[mung bean]

Very interesting, though. So, here we have a genetic "mistake" resulting in a fully functional and more advanced, structurally different heart in the space of one generation.
Dave, what say you to this? Would you regard this as "creative"?

[Goathead]

Wow, you guys are great.

Should right for "The Onion" lol.

[Dave Hawkins]

NYLON EATING BACTERIA
It seems clear that plasmids are designed features of bacteria that enable adaptation to new food sources or the degradation of toxins. The details of just how they do this remains to be elucidated. The results so far clearly suggest that these adaptations did not come about by chance mutations, but by some designed mechanism. This mechanism might be analogous to the way that vertebrates rapidly generate novel effective antibodies with hypermutation in B-cell maturation, which does not lend credibility to the grand scheme of neo-Darwinian evolution.11 Further research will, I expect, show that there is a sophisticated, irreducibly complex, molecular system involved in plasmid-based adaptation—the evidence strongly suggests that such a system exists. This system will once again, as the black box becomes illuminated, speak of intelligent creation, not chance. Understanding this adaptation system could well lead to a breakthrough in disease control, because specific inhibitors of the adaptation machinery could protect antibiotics from the development of plasmid-based resistance in the target pathogenic microbes.
http://www.answersingenesis.org/tj/v17/i3/bacteria.asp
ANTIBIOTIC RESISTANT BACTERIAEvolutionists frequently point to the development of antibiotic resistance by bacteria as a demonstration of evolutionary change. However, molecular analysis of the genetic events that lead to antibiotic resistance do not support this common assumption. Many bacteria become resistant by acquiring genes from plasmids or transposons via horizontal gene transfer. Horizontal transfer, though, does not account for the origin of resistance genes, only their spread among bacteria. Mutations, on the other hand, can potentially account for the origin of antibiotic resistance within the bacterial world, but involve mutational processes that are contrary to the predictions of evolution. Instead, such mutations consistently reduce or eliminate the function of transport proteins or porins, protein binding affinities, enzyme activities, the proton motive force, or regulatory control systems. While such mutations can be regarded as “beneficial,” in that they increase the survival rate of bacteria in the presence of the antibiotic, they involve mutational processes that do not provide a genetic mechanism for common “descent with modification.” Also, some “relative fitness” cost is often associated with such mutations, although reversion mutations may eventually recover most, if not all, of this cost for some bacteria. A true biological cost does occur, however, in the loss of pre-existing cellular systems or functions. Such loss of cellular activity cannot legitimately be offered as a genetic means of demonstrating evolution.
http://www.trueorigin.org/bacteria01.aspSee also ... ANOTHER ICON OF EVOLUTION BITES THE DUST – ANTIBIOTIC RESISTANCE - 4/3/07
Molecular Mechanisms of Antibacterial Multidrug Resistance
Cell Magazine 22 March 2007
Michael N. Alekshun and Stuart B. Levy
Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
Center for Adaptation Genetics and Drug Resistance, Department of Molecular Biology & Microbiology and Department of Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
Treatment of infections is compromised worldwide by the emergence of bacteria that are resistant to multiple antibiotics. Although classically attributed to chromosomal mutations, resistance is most commonly associated with extrachromosomal elements acquired from other bacteria in the environment. These include different types of mobile DNA segments, such as plasmids, transposons, and integrons. However, intrinsic mechanisms not commonly specified by mobile elements—such as efflux pumps that expel multiple kinds of antibiotics—are now recognized as major contributors to multidrug resistance in bacteria. Once established, multidrug-resistant organisms persist and spread worldwide, causing clinical failures in the treatment of infections and public health crises.
http://www.uncommondescent.com/science/another-icon-of-evolution-bites-the-dust-antibiotic-resistance/ As for Teflon and Goretex and such, these seem to be examples of something which, while found by chance, required intelligent design to implement as a useful product. These hardly seem like examples of evolution.

If someone really wants to get into this topic thoroughly, I might suggest a separate thread in this forum. My plan is to stick fairly close to Dr. Sanford's book and examine the papers that he quotes.

[Boro Nut]

If war or famine force our descendants to return to a stone-age life they will have to contend with all the problems that their stone-age ancestors had plus mutations that have accumulated in the meantime.Hmmm. Interesting. Seems to be pretty bad news for the creationists cause. No matter which way I read this it certainly seems to take all the gloss off their plans to return to the stone age.

Boro Nut

[Dave Hawkins]

CK1 ... My statement about your refusal to read mainstream science may have been too harsh, but it is still clear that your interpretation and understanding of what you read leaves much to be desired. Isolated papers cannot be read in a vacuum. That ENCODE material is not easy reading, especially for someone who just learned the definition of "allele".

Please point me to creationist predictions about "junk" DNA and explain the theoretical and experimental basis for those predictions.I wouldn't call it "harsh." Just naive. You seem to have this odd idea that creationists don't read science papers. That was true of me a year and a half ago because I was still involved in business. But not now. Here's several more I read just last week: Kitagawa (1993) and Kitagawa (1998) in Radiocarbon and Kitagawa (1998) in Science.

CREATIONISTS HAVE BEEN WRITING ABOUT JUNK DNA FOR A LONG TIME
Wieland, Carl, “Junk moves up in the world”, Creation Ex Nihilo Technical Journal, Volume 8, Issue 2, August 1994, p. 152 (No link available)
http://www.creationontheweb.com/content/view/1789 (Batten 1998)
http://www.creationontheweb.com/content/view/1631 (Walkup 2000)
http://www.creationontheweb.com/content/view/145 (Sarfati 2003)
http://www.creationontheweb.com/content/view/1588/ (Batten 2005)

The basis for these predictions is that the Creator would not create junk. I suppose you have read the latest issues of Science and Nature pertaining to this issue? Pretty interesting stuff.

[VoxRat]

Dave:
Your c&p's completely fail to even touch the issue of the genesis of the nylonase gene.

If your "plan is to stick fairly close to Dr. Sanford's book and examine the papers that he quotes" - and dodge all the relevant questions, what's the point? To convince someone, anyone, that Sanford's book is worth reading, despite all the indications to the contrary?

[Calilasseia]

With respect to the heart modification gene ...

Better still, here is the original paper (http://www.genesdev.org/cgi/reprint/20/19/2634.pdf) (PDF available free online) on the regulatory genes in Ciona intestinalis, the Chordate under investigation, and the means by which altered expression of the Ets1/2 gene results in a two-chambered instead of a one-chambered heart.

This should make interesting bedtime reading!

As an avid aquarist, I'm a sometime fan of tunicates. Unfortunately, several of them - even the tropical coral reef ones - are not the prettiest of animals to put in your reef aquarium alongside your corals, social polyps and Sabellid fanworms. Some tunicates look like recently extruded dog faeces, which explains why only a few tunicate species (i.e., the brightly coloured ones) tend to find their way into marine aquarium dealers.

[VoxRat]

The basis for these predictions is that the Creator would not create junk.Predictions? What predictions???

I looked up your links, and - in addition to seriously misrepresenting the predictions of real scientists - I couldn't find a single creationist prediction.

What did I miss?

[Dave Hawkins]

Note that Crow speaks of a 1-2% per generation decrease in viability in humans resulting from mutation accumulation over the last several centuries.

What he actually wrote (emphasis mine):
"If we are like Drosophila, the decrease in viability from mutation accumulation is some 1 or 2% per generation."

"It seems clear that for the past few centuries harmful mutations have been accumulating."

Correct me if I am wrong, but modern medicine does NOT apply to the last several centuries ... only to about the last 100 years or so (maybe less).

First, Crow doesn't restrict the obstruction of natural selection to "modern medicine" but refers to the more broad category of "environmental improvements".

Second, unless one applies a very narrow definition of "modern medicine", it certainly does apply to the last few centuries. There is no question that the current state of medical science has done more than the last few centuries but it is simply incorrect to suggest or assume that the medical advances of the 18th and 19th centuries did nothing.But from the context, he clearly believes we ARE like Drosophila in this respect, i.e. that human decrease in viability from mutation accumulation is some 1 or 2% per generation. Why else would he ask how long we can keep outpacing this number with environmental improvements? Again, please study Crow's statement carefully ... It seems clear that for the past few centuries harmful mutations have been accumulating. Why don't we notice this? If we are like Drosophila, the decrease in viability from mutation accumulation is some 1 or 2% per generation. This is more than compensated for by much more rapid environmental improvements, which are keeping well ahead of any decreased efficiency of selection. How long can we keep this up? Perhaps for a long time, but only if there remains a social order that permits steady environmental improvements. If war or famine force our descendants to return to a stone-age life they will have to contend with all the problems that their stone-age ancestors had plus mutations that have accumulated in the meantime.
http://www.pnas.org/cgi/content/full/94/16/8380From this it appears that Crow believes ...
1) That harmful mutations have been accumulating for the last several centuries (What's several? 3? 4?)
2) Humans are like Drosophila in that for at least the time period above, we have experienced a decrease in viability from mutation accumulation is some 1 or 2% per generation.
3) Environmental improvements have been more than compensating for this, but he expresses doubt about how long we can keep this up

You all seem to believe that Crow is simply talking about the ability of modern medicine to keep people alive longer, thus causing many harmful mutations to be retained in the population. However, this only applies to the last hundred years (or less). A careful reading of this indicates that Crow is talking about keeping a good social order, i.e. no huge wars or famines. Nothing there about modern medicine.

But if you want to talk about medicine, see the Wiki article on the History of Medicine here ...
http://en.wikipedia.org/wiki/History_of_medicine
This has really only applied in the last hundred years or so, and that primarily in industrialized nations.

So it seems that YOU have misinterpreted Crow ... not me.

Over to you.

*********************************

No, I'm not going to discuss HLA alleles in this thread. This thread is for Sanford's book and the papers he quotes.

[Mike PSS]

NYLON EATING BACTERIA
{snip the vacuous prose of "Dr." Don Batten}http://www.answersingenesis.org/tj/v17/i3/bacteria.asp
ANTIBIOTIC RESISTANT BACTERIASee also ...

Dave,
Here's a VERY short but VERY concise paper about the nylon bug mechanism.
http://aem.asm.org/cgi/reprint/61/5/2020.pdf#search=%22Irfan%20nylon%20Pseudomonas%22

Experimental Proposal: In this study, we investigated the possibility of creating a new metabolic activity that would degrade the Ahx oligomer in a strain that is not inherently capable of such degradation.
...
Some Experimental Results: After the cells accumulated the required genetic alteration to make a cryptic region active, cells grew in the nylon oligomer medium. The high frequency (1023) of the hypergrowing mutants of parental strain PAO1 on medium containing Ahx might be a result of a high mutation rate under the condition of starvation.
...
Experimental Conclusion: In the present study, it was shown that microorganisms can acquire an entirely new ability to metabolize xenobiotic compounds such as a by-product of nylon manufacture through the process of adaptation.

From your quoted AiG paper, Don Batten references this paper and shows the following "technical" rebuttal...
5. The Japanese researchers demonstrated that nylon degrading ability can be obtained de novo in laboratory cultures of Pseudomonas aeruginosa [strain] POA, which initially had no enzymes capable of degrading nylon oligomers.9 This was achieved in a mere nine days! The rapidity of this adaptation suggests a special mechanism for such adaptation, not something as haphazard as random mutations and selection.
So Batten's ONLY objection to this experiment is a hand-waving polemic about the "rapidity" of the experiment.

But it seems Mr. Batten couldn't even read for comprehension because the paper clearly states its procedures in a matter of a couple paragraphs on page 1.

After 9 days of incubation at 30C, hypergrowing colonies were obtained at a frequency of 10^-3.
One of the hypergrowing mutants (PAO5501) was purified... {snip technical purification description}... for 3 days.
The culture broth ... was then transferred to Ald minimal medium ... After observing slight growth ... in the third week, this culture was retransferred to the Ald minimal medium ...
It was only in the third month that the turbidity of the culture broth reached 1 at A600.

By my math, the experimenters took almost four whole months to accomplish this.

Now, how does "Dr." Don Batten respond to this? Not at all of course because Don has moved on to other more prosporous fields of speculation, like designing saddles for triceritops or something.

Bring ANY creationist paper you want Dave. There will always be egregious errors contained.

Why don't you read the VERY short paper and tell me WHY you don't think it represents random mutation.

Back at you Dave.

And here's one for "Dr." Don Batten. :down:

[Dave Hawkins]

Dave:
Your c&p's completely fail to even touch the issue of the genesis of the nylonase gene.You have to actually click the links and read the articles. The first one is the relevant one about nylon-eating bacteria.

[Calilasseia]

Double post.

Oh dear, the familiar Dave aetiology manifests itself again .... blind assertion accompanied by AiG cut and pastes.

As for the so-called "refutation" of the evolution of Nylonase in Japanese Flavobacterium, well I'm afraid some actual accredited scientists beg to differ ...

... Finally, Mr Cerutti is out of date about this new nylon digesting ability allegedly from a frame shift. New evidence shows that the ability was due to plasmids [e.g. K. Kato, et al., ‘A plasmid encoding enzymes for nylon oligomer degradation: Nucleotide sequence analysis of pOAD2’, Microbiology (Reading) 141(10):2585–2590, 1995. In fact, more than one species of bacteria have the ability, residing on plasmids. This suggests that the information probably already existed, and was just passed between different types of bacteria. ...

However, the people from Sandia National Laboratory say this in reply:

Sorry, AiG, but just because something is on a plasmid doesn't mean it's always been there! In fact, the plasmid involved in this case is very well known and characterized. Scientists have studied both the original (pre-mutation) plasmid and the novel (post-mutation) plasmid, in great detail. It turns out that the novel plasmid's mutated DNA for production of nylonase is almost identical to a non-coding repetitive DNA sequence on the original plasmid; the difference is the single nucleotide that triggered the Frame Shift. This mutation did not exist 60 years ago. If this gene was always there, whether in a plasmid or not, we can reasonably wonder why a bacteria would have a gene for hydrolysing an artificial polymer that did not exist until just a few decades ago; and why, in the absence of such a substrate, was the gene not mutated to uselessness over the millenia?

Was the plasmid slipped in from another bacterium? NO!! The plasmid in question, pOAD2, is just one of three plasmids that are harbored by the bacterium under investigation here, Flavobacterium Sp. K172. Here are some citations to back this up:

"Sequence analysis of a cryptic plasmid from Flavobacterium sp. KP1, a psychrophilic bacterium," (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9919674) Makoto Ashiuchi, Mia Md. Zakaria, Yuriko Sakaguchi, Toshiharu Yagi, FEMS (Federation of European Microbiological Societies) Microbiology Letters 170 (1999), 243-249.

"Bacteria of genus Flavobacterium, Gram-negative bacteria, are widely distributed in soil and fresh marine waters. Some of them harbor plasmid(s) involved in metabolism of synthetic organic compounds. Flavobacterium sp. K172 harbors plasmids, pOAD1, pOAD2 and pOAD3; pOAD2 (43.6 kbp) encodes nylon oligomer degradation genes."

"A New Nylon Oligomer Degradation Gene (nylC) on Plasmid pOAD2 from a Flavobacterium sp.," (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1459943) Seiji Negoro, Shinji Kakudo, Itaru Urabe, and Hirosuke Okadam, Journal of Bacteriology, Dec. 1992, p. 7948-7953.

"The EI-encoding gene (F-nylA) and EII-encoding gene (F-nylB) of Flavobacterium sp. K172 are located on plasmid pOAD2 (44 kb), one of the three plasmids harbored in strain K172."

"Birth of a unique enzyme from an alternative reading frame of the pre-existed, internally repetitious coding sequence" (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=345072), Susumu Ohno, Proc. Natl. Acad. Sci. USA, Vol. 81, pp. 2421-2425, April 1984. PDF (http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=345072&action=stream&blobtype=pdf)

MY ADDITION HERE : THAT PDF JUST LINKED ABOVE IS ONE OF THE ORIGINAL PAPERS ON THE SUBJECT ...

"Analysis of the published base sequence residing in the pOAD2 plasmid of Flavobacterium sp. K172 indicated that the 392-amino acid-residue-long bacterial enzyme 6-aminohexanoic acid linear oligomer hydrolase involved in degradation of nylon oligomers is specified by an alternative open reading frame of the preexisted coding sequence that originally specified a 472-residue-long arginine-rich protein."

It's interesting to note that the precise plasmid of Flavobacterium sp. K172, namely pOAD2, was cited by Susumu Ohno fully eleven years before the publication of the "new evidence" that AiG claims "shows that the ability was due to plasmids..."

The Bottom Line: Just because this mutation wasn't confined to a cell's main chromosomes does not mean it didn't happen. (A plasmid is defined as a replicon - a replicating piece of DNA - that is inherited in an extrachromosomal state.) This case still provides an excellent example of a New Protein that evolved without the assistance of an Intelligent Designer.

Full text to be found on this page (http://www.nmsr.org/nylon.htm#update) along with a full explanation of the evolution of nylonase starting here (http://www.nmsr.org/nylon.htm), complete with gene sequences. In particular I direct the interested reader to the following paragraphs on that latter page dealing with the gene sequences, which state:

The image below shows just a part of the 400+-long nucleotide string for the key enzyme (see the Susumu Ohno paper). The original ("old") enzyme's amino acid sequence appears on top, and the frame-shifted ("new") sequence on bottom. The DNA nucleotides appear in the middle for both the old species and the new (one T inserted). Over this small portion of the enzyme, the old DNA coded for the amino acids Arginine, Glutamic Acid, Arginine, Threonine, Phenylalanine, Histidine, Arginine and Proline.

<Image on Page>

But the NEW DNA strand, which includes one extra T nucleotide, is shifted, and the new string of amino acids is completely changed. The addition of the thymine nucleotide produces a new Methionine amino acid, which, like the conductor tapping his baton, indicates the Start of a new Protein. This is followed by other new amino acids because of the frame shift: Asparagine, Alanine, Arginine, Serine, Threonine, Glycine and Glutamine. The new string of amino acids - the new protein - is completely different from the original.

While most frame shifts of such a key enzyme would destroy the enzyme, resulting in immediate death of the organism, this particular protein happened to react with nylon oligomers. And so it was that a drastic mutation suddenly gave an ordinary sugar-eating bacterium the unusual ability to digest nylon, which just happened to be present in abundance in the little waste pond behind a Japanese factory. The Japanese scientists who discovered strange bacterial mats growing in their scum ponds became very interested in this new ability, and finally found it was all due to a single Frame Shift mutation. The new enzyme is not active on common substrates - the bacteria's old "food" - and plenty were checked. Whether or not these bacteria retain enzymes to digest their former food source, the fact is that the former food source became much less important because of the new-found ability to ingest food from a novel source - nylon waste.

The creationist argument that all mutations must destroy information is clearly wrong. In this case, a mutation has clearly produced new information. That is, unless you want to quibble that the detailed three-dimensional structure and composition of a protein that reacts specifically to nylon is not "information."

Creationists usually counter this example by claiming that the bacterium is, after all, "still a bacterium." It didn't mutate into a whale or a dinosaur. But that's changing the subject. The subject of this essay is "Can Mutations Create New Information."

Science and logic both show the answer is a resounding YES.

Now, any more canards to deal with before I continue? Oh, that "antibiotic resistance isn't evolution" canard. I'll leave that for someone else to have fun with. I've done sufficient here I think ... :)

[Jet Black]

I realise there might be history and frustration with peoples' posting styles, but lets keep the personal remarks out of it and focus on the actual arguments as much as we can :) Everybody's doing pretty well so far but I can see a couple of little slips coming in

cheers

Jet Black [EC] Mod

[ck1]

Although you stated you do not wish to discuss these points further, since you posted this information I would like to make a brief reply

NYLON EATING BACTERIA
It seems clear that plasmids are designed features of bacteria that enable adaptation to new food sources or the degradation of toxins. The details of just how they do this remains to be elucidated. The results so far clearly suggest that these adaptations did not come about by chance mutations, but by some designed mechanism... (snip) http://www.answersingenesis.org/tj/v17/i3/bacteria.asp

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=345072

This is probably the key paper on this subject. Ohno's analysis and other studies have identified 3 different genes capable of digesting nylon. The major player is now called nylB and contrary to your claims that no details are known, sequencing indicates that this gene was formed from a deletion of a single base (a T) that generated a start codon and subseqeunt frameshift in a pOAD2 plasmid repetitive element (a key point since such elements are less likely to produce stop codons in alternative reading frames). It is telling that AIG does not even attempt to discuss the molecular biology done on any of the genes involved in this novel phenotype. If there is evidence for a design mechanism involved in this process please produce it - this is clearly an assertion with no supporting data.

ANOTHER ICON OF EVOLUTION BITES THE DUST – ANTIBIOTIC RESISTANCE - 4/3/07
Molecular Mechanisms of Antibacterial Multidrug Resistance
Cell Magazine 22 March 2007
Michael N. Alekshun and Stuart B. Levy.....(snip)

Treatment of infections is compromised worldwide by the emergence of bacteria that are resistant to multiple antibiotics. Although classically attributed to chromosomal mutations, resistance is most commonly associated with extrachromosomal elements acquired from other bacteria in the environment. These include different types of mobile DNA segments, such as plasmids, transposons, and integrons. However, intrinsic mechanisms not commonly specified by mobile elements—such as efflux pumps that expel multiple kinds of antibiotics—are now recognized as major contributors to multidrug resistance in bacteria. Once established, multidrug-resistant organisms persist and spread worldwide, causing clinical failures in the treatment of infections and public health crises.
http://www.uncommondescent.com/science/another-icon-of-evolution-bites-the-dust-antibiotic-resistance/.

You did not read this paper, did you? Otherwise you would not have claimed that antibiotic resistance is unconnected to evolutionary processes. The first half of this paper explains the mutations that produce resistance to various antibiotics. The second part of this paper describes the genetic basis for intrinsic resistance mechanisms like efflux systems (systems that have a normal function in bacteria but that also can protect against specific antibiotics) - the evolution of some of these is also described.

You and AIG seem to have the idea that if a gene is on a plasmid rather than a chromosome it is not subject to mutation and can't evolve. Where did you get this idea?

If someone really wants to get into this topic thoroughly, I might suggest a separate thread in this forum. My plan is to stick fairly close to Dr. Sanford's book and examine the papers that he quotes.

If your aim is to defend Sanford here, why not stop beating around the bush, and provide some specifics on HIS argument, not quotemines from mainstream scientists like Crow.

[Jet Black]

AiG saying "New evidence shows that the ability was due to plasmids" is a complete non-answer. plasmids are just a particular arrangement of DNA.

[Mike PSS]

Dave:
Your c&p's completely fail to even touch the issue of the genesis of the nylonase gene.You have to actually click the links and read the articles. The first one is the relevant one about nylon-eating bacteria.
What's funny about this discussion is that there are two bugs to discuss.
We have previously isolated two microorganisms, Flavobacterium sp. strain KI72 (7) and Pseudomonas sp. strain NK87 (6), that grow with the Ahx cyclic dimer (Acd) as the sole source of carbon and nitrogen.
http://aem.asm.org/cgi/reprint/61/5/2020.pdf#search=%22Irfan%20nylon%20Pseudomonas%22

Now, each bug may mutate differently but the end result is the same; the breakdown of nylon for food.

Go for it Dave, your choice about which bug to pooh-pooh.

Cali started on Flavobacterium and I started on Pseudomonas.

Pick and choose, pick and choose, so much information, so much to lose.

So now, along with the Brown vs. RATE decision you get the Flav vs. Pseudo decision too.

If only I had this many choices in my life. :rolleyes:

[Worldtraveller]

Lemme see if I got this straight.

The OP starts with a paper (which, if I understand, was really a creationist misinterpretation of a real scientific paper?) that claims that due to modern medicine, we are 'degrading' (whatever that means) our genome.

Along with this comes multiple assertions of mutation and natural selection not being 'creative' (again,a completely undefined, scientifically speaking, term). And at least a few references to all genomes that should be degrading for whatever reason (I assume afdave blames it on the fall?).

Then we have a demonstration of 'creative' process through mutation and natural selection with the nylon bug.

Now the nylon bug isn't creative, but the gene was there all along just waiting to be 'turned on' (by a mutation, natch).

So which is it?? Our genomes are degrading, so any abilities (like, for instance, the latent ability to digest nylon, which wasn't around for the last few billion few thousand years) we might have had will be lost, or is it that our genome is so robust because th creator made them to last forever (or at least until rapture) that natural selection acting our 'designed variability' makes it so we will last more than the 300 generations predicted?

Is it just me, or is afdave trying to eat his cake, and have it created too?

Cheers,
Lane

[VoxRat]

Dave:
Your c&p's completely fail to even touch the issue of the genesis of the nylonase gene.You have to actually click the links and read the articles. The first one is the relevant one about nylon-eating bacteria.

So why didn't you c&p the relevant part? Why would I click a link listed after a bunch of irrelevant stuff about antibiotics and plasmids?

I have read their nonsense on the nylonase gene, though, and find it indefensible. Is that why you chose not to excerpt that part?

[Calilasseia]

Lemme see if I got this straight.

The OP starts with a paper (which, if I understand, was really a creationist misinterpretation of a real scientific paper?) that claims that due to modern medicine, we are 'degrading' (whatever that means) our genome.

Along with this comes multiple assertions of mutation and natural selection not being 'creative' (again,a completely undefined, scientifically speaking, term). And at least a few references to all genomes that should be degrading for whatever reason (I assume afdave blames it on the fall?).

Then we have a demonstration of 'creative' process through mutation and natural selection with the nylon bug.

Now the nylon bug isn't creative, but the gene was there all along just waiting to be 'turned on' (by a mutation, natch).

So which is it?? Our genomes are degrading, so any abilities (like, for instance, the latent ability to digest nylon, which wasn't around for the last few billion few thousand years) we might have had will be lost, or is it that our genome is so robust because th creator made them to last forever (or at least until rapture) that natural selection acting our 'designed variability' makes it so we will last more than the 300 generations predicted?

Is it just me, or is afdave trying to eat his cake, and have it created too?

Cheers,
Lane

I think you'll find it's covered adequately above now. Courtesy of those nice people from Sandia National Laboratory. :)

[deadman_932]

Dave, I'm very sure that you don't even grasp the implications of the "citations" you posted.
1. The AIG "article" by "dr." Don Batten says nothing about the origins of the mutations responsible for the enzymatic activity conferred by horizontal transfer of plasmids. There ARE articles on this subject available, though, including:

Negoro, Seiji, Taku Ohki, Naoki Shibata, et. al. (2005) X-ray Crystallographic Analysis of 6-Aminohexanoate-Dimer Hydrolase: Molecular Basis for the Birth of a Nylon-Degrading Enzyme.J. Biol. Chem., Vol. 280, Issue 47, 39644-39652, November 25.

"6-Aminohexanoate-dimer hydrolase (EII), responsible for the degradation of nylon-6 industry by-products, and its analogous enzyme (EII') that has only 0.5% of the specific activity toward the 6-aminohexanoate-linear dimer, are encoded on plasmid pOAD2 of Arthrobacter sp. (formerly Flavobacterium sp.) KI72...we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the -lactamase fold resulted in the evolution of the nylon oligomer hydrolase."

You'll note that the amino acid replacements on the pOAD2 plasmid are a mutation, Dave. If I bothered to do so, I'm sure there's been work on the other plasmids in Pseudomonas NK87.

"Dr." Don Batten's "explanation" was hand-waving claims about the origins of such novelty being analogous to immunological antibody production...which he specified is "hypermutation"-based. Let's look at what Batten claimed: "This mechanism might be analogous to the way that vertebrates rapidly generate novel effective antibodies with hypermutation "

So, Dave, please tell me how this contradicts molecular models for evolution.

2. Look at your OWN post on antibiotic resistance, Dave: Mutations, on the other hand, can potentially account for the origin of antibiotic resistance within the bacterial world, but involve mutational processes that are contrary to the predictions of evolution . Instead, such mutations consistently reduce or eliminate the function of transport proteins or porins, protein binding affinities, enzyme activities, the proton motive force, or regulatory control systems. While such mutations can be regarded as “beneficial,” in that they increase the survival rate of bacteria in the presence of the antibiotic, they involve mutational processes that do not provide a genetic mechanism for common “descent with modification.”

Also, some “relative fitness” cost is often associated with such mutations, although reversion mutations may eventually recover most, if not all, of this cost for some bacteria.

Do you recall me posting examples of antibiotic resistance at AtBC that did NOT result in fitness loss, Dave? Directly in contradiction to the Kevin Anderson article you just reposted. The contradictory data that you said you were not qualified to judge?

I do.

The citation you give acknowledges mutations while simultaneously tossing up red herrings about such mutations not being consistent with current evolutionary thinking, Dave. That's all it does. More importantly when you were shown contradictory data at AtBC,you just ran.

3. Your final citation has me puzzled. Because Dave Scot at Uncommon descent posted this article, it's supposed to be ...what? We already know that mobile elements like plasmids play a part in antibacterial resistance. That's OLD, old news. Efflux pumps that can be turned on inside existing bacteria is not exactly new, either.

WHAT ICON OF EVOLUTION is being OVERTURNED here, Dave? Are you saying no mutations cause such changes in plasmids or bacteria? If you are, you're wrong. I can cite recent papers galore on mutation conferring antibiotic resistance.

Here's one: Kugelberg, E., Lofmark, S., Wretlind, B., Andersson, D. I. (2005). Reduction of the fitness burden of quinolone resistance in Pseudomonas aeruginosa. J Antimicrob Chemother 55: 22-30 Quinolone resistance in the opportunistic pathogen Pseudomonas aeruginosa is commonly caused by mutations that alter the target molecules DNA gyrase/topoisomerase IV, or cause activation of various efflux systems

Notice how it mentions intrinsic efflux systems being activated by ...mutations, Dave. This is not NEW except to idiots like Dave Scot at Uncommon Descent who don't know about keeping up on the subjects or their ass from a hole in the ground and believe me, Dave Scot is plenty stupid.

Don't like those, Dave? How about these?
Cirz, R. T., Romesberg, F. E. (2006). Induction and Inhibition of Ciprofloxacin Resistance-Conferring Mutations in Hypermutator Bacteria. Antimicrob. Agents Chemother. 50: 220-225

Trong, H. N., Prunier, A.-L., Leclercq, R. (2005). Hypermutable and Fluoroquinolone-Resistant Clinical Isolates of Staphylococcus aureus. Antimicrob. Agents Chemother. 49: 2098-2101

Rafii, F., Park, M., Novak, J. S. (2005). Alterations in DNA Gyrase and Topoisomerase IV in Resistant Mutants of Clostridium perfringens Found after In Vitro Treatment with Fluoroquinolones. Antimicrob. Agents Chemother. 49: 488-492

[deadman_932]

Ooops, sorry, Calilasseia, I duplicated this one that you had previously posted. Easily available material that DAVE COULD HAVE FOUND HIMSELF THOUGH IF HE HAD A SHRED OF GENUINE DESIRE TO FIND OUT ABOUT THE TOPICS IN A SCIENTIFIC SENSE AND NOT MERELY DEFEND CREATIONISM. : Negoro, Seiji, Taku Ohki, Naoki Shibata, et. al. (2005) X-ray Crystallographic Analysis of 6-Aminohexanoate-Dimer Hydrolase: Molecular Basis for the Birth of a Nylon-Degrading Enzyme.J. Biol. Chem., Vol. 280, Issue 47, 39644-39652, November 25.

"6-Aminohexanoate-dimer hydrolase (EII), responsible for the degradation of nylon-6 industry by-products, and its analogous enzyme (EII') that has only 0.5% of the specific activity toward the 6-aminohexanoate-linear dimer, are encoded on plasmid pOAD2 of Arthrobacter sp. (formerly Flavobacterium sp.) KI72...we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the -lactamase fold resulted in the evolution of the nylon oligomer hydrolase."

You'll note that the amino acid replacements on the pOAD2 plasmid are a mutation, Dave. If I bothered to do so, I'm sure there's been work on the other plasmids in Pseudomonas NK87.

[FatherMithras]

Af dave, how lame can it possibly get? ´´it managed to do what was predicted, through a mutations... It must have been intelligently mutated!´´ that´s the most bullshit ad hoc I´ve ever heard, and doesn´t address the fact nothing like that was observed. what was observed was a random mutation adding a survival benefit. and stop using non science, dishonest sources. The´re using the same old, discredited ´´Mutations only destroy information´´ crap that geneticists and biologists, and people who can read have been telling them was fake for centuries.

[Calilasseia]

The more references the merrier Deadman. Welcome to the DumbBuster squadron (I'm manning a Lancaster, is that a B-17 you're flying?) :)

[deadman_932]

The basic problems here are clear, Dave. Despite your claims on objectivity, you consistently hold evolutionary biologists to incredibly high standards while simultaneously lowering the bar for creationists.

You are also so unfamiliar with the subjects that you (contrary to your grandiose claims) haven't the slightest idea when you are posting material designed to fleece the creationist sheep.

You consistently use tactics designed to obfuscate, avoid, and divert while engaging in the use of fallacies so dense that it's difficult to penetrate that thicket to show each use. You should be ashamed of such...and avoid it, but instead you do not, and that doesn't say a great deal that is good.

[FatherMithras]

I also wonder, why did Afdave´s e-mail not state what he has stated here? It seemes deliberately obfuscatory. why not mention creationism?

[VoxRat]

afdave discussed Sanford, Crow, etc. here (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=SP;f=14;t=3131;p=37676).

Are you planning to bring up something new now, afdave? Because, if not, why don't people just go to the discussion from last year? Seems like a monumental waste of time, effort, and bandwidth.

[Mike PSS]

Let's see now.
In reference to JUST the nylon bug nonsense that Dave dug up here from "dr." Don Batten.
In a matter of less than an hour....

I have a post with reference and rebuttal,
Cali has a post with reference and rebuttal,
ck1 has a post with reference and rebuttal,
deadman has a post with reference and rebuttal,
Voxrat has a post with rebuttal.

And almost all the references are independent of each other (except deadman's admitted cross-reference to Cali).

Now, in the real world this would be damning evidence that Batten doesn't know what he's talking about. It would also leave the neutral observer with the impression that Batten's scholorship on this issue was anything but robust.

So Dave. Will this whole nylon issue be another cut-and-run or will you dive in and get down to the nitty-gritty details contained in these papers. The evidence in these papers is VERY specific and VERY detailed so a hand-waving rebuttal to the pertinent points isn't going to cut it in this discussion.

I'm always amazed at the quantity of material available on subjects brought up. And for some reason Dave doesn't agree with the findings in most of this material. Strange that.

[Calilasseia]

Double post. (Unless someone else inserts one before I finish typing this as happened last time ... :) )

AiG saying "New evidence shows that the ability was due to plasmids" is a complete non-answer. plasmids are just a particular arrangement of DNA.

Actually, if you take a peek at the material I obtained from Sandia National Laboratory's Dave Thomas, you'll find that AiG didn't even alight upon anything new. The very scientists who discovered the mutation reported it as existing upon plasmid DNA eleven years before AiG woke up to the fact. As stated in the actual original 1984 paper whose PDF can be downloaded via the link I provided above.

Unfortunately, Dave has yet to disentangle himself from his attachment to AiG, even though the same thing happens every time he posts a cut and paste from them - the content is roundly demolished with little effort, and indeed numerous extant demolitions of AiG's nonsense abound on the web, many written by accredited professionals in the relevant fields.

[Oolon Colluphid]

Has anyone mentioned the antifreeze glycoproteins of Antarctic notothenioid fish yet? Derived from a pancreatic trypsinogen gene...? Chen's string of papers from about 1997 onward...?


(I don't know whether to be proud or geekily embarrassed that I rattled that off off the top of my head.)

[Calilasseia]

Has anyone mentioned the antifreeze glycoproteins of Antarctic notothenioid fish yet? Derived from a pancreatic trypsinogen gene...? Chen's string of papers from about 1997 onward...?


(I don't know whether to be proud or geekily embarrassed that I rattled that off off the top of my head.)

Drat! forgot all about that one ... and me an aquarist too ...

* admonishes self *

Let me check if I've downloaded any papers on that subject ...

Found one!

Convergent Evolution Of Antifreeze Glycoproteins In Antarctic Notothenioid Fish And Arctic Cod (http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=20524&blobtype=pdf)

Enjoy!

[Mike PSS]

The more references the merrier Deadman. Welcome to the DumbBuster squadron (I'm manning a Lancaster, is that a B-17 you're flying?) :)
Forget the WWII stuff.

I'm on a B-58 Hustler.
http://www.aviation-history.com/convair/b58.html

That baby had four GE J-79 engines and Mach2 performance. Two of those engines were on the F4 PhantomII.

Screaming Baby!!!

[ericmurphy]

You all seem to believe that Crow is simply talking about the ability of modern medicine to keep people alive longer, thus causing many harmful mutations to be retained in the population. However, this only applies to the last hundred years (or less). A careful reading of this indicates that Crow is talking about keeping a good social order, i.e. no huge wars or famines. Nothing there about modern medicine.

There's more to it than just modern medicine, Dave. Who do you think had a better chance of surviving to reproduce: someone who lived in a hunter-gatherer society who had been blind from birth, or someone who lived in a Medieval agrarian society who had been blind from birth?

No matter how you try to wriggle, Dave, you're not going to get around Crow's central point: human civilization, and especially modern medicine, are interfering with natural selection's ability to remove deleterious mutations from the gene pool. No amount of wriggling is going to get Crow to be saying that ancient humans were genetically superior to modern humans. And you are never, ever going to be able to support the claim that ancient humans were healthier and lived longer than modern humans. The evidence is against you.

But if you want to talk about medicine, see the Wiki article on the History of Medicine here ...
http://en.wikipedia.org/wiki/History_of_medicine
This has really only applied in the last hundred years or so, and that primarily in industrialized nations.

So it seems that YOU have misinterpreted Crow ... not me.

Nope. It's still you, Dave. You're still wrong, as always. Your "Crow" moment, to go along with your "Portuguese moment," your "Churchill moment," your "water sprinkler moment," and all your other moments caused by your inability to admit error.

No, I'm not going to discuss HLA alleles in this thread. This thread is for Sanford's book and the papers he quotes.

Then stop claiming that you don't need mutations to get variability. Don't make stupid claims and then refuse to discuss rebuttals of those claims.

[Dave Hawkins]

AiG saying "New evidence shows that the ability was due to plasmids" is a complete non-answer. plasmids are just a particular arrangement of DNA.Yes, I think they are VERY particular. In fact, the evidence indicates that they were designed. Sure, they undergo mutation just as all other DNA does, but this cannot be construed as 'constructive' or 'creative.'

Note Bergman's article on viruses, plasmids and other replicons and their role with bacteria ... A critical role that viruses play relates to the fact that bacteria contain a constant, stable genetic system (the large replicon), but they function in the world by acquiring and exchanging a diverse set of variable genetic systems (several small replicons, including plasmids, viruses, and so forth). The small replicons are physically separated from the major bacterial DNA, called the genophore. New DNA can be inserted into the genophore; and it usually divides synchronously with it, but some is able to start self-replicating autonomously (Figure 5).

Mathieu and Sonea claim that viruses convert all bacteria into one giant, global ‘superorganism’, and that viruses ‘possess a remarkable mechanism for the creation and exchange of genetic material’.[23] A major class of genes exchanged are antibiotic-resistance genes (see figure 6), along with genes that allow bacteria to degrade toxins (such as polychlorinated biphenyls) or convert mercury to less noxious forms.[24] This ability is significant in the development of resistance to antibiotics produced by other organisms, allowing bacteria to survive and helping to maintain the balance so critical for ecology.

...

The incorporation of plasmids or prophages into the bacterial chromosomes is called transfection. The incorporation of only genes by a virus carrier or free DNA is called transformation. Transfection and transformation are not random, but tightly controlled processes. Specific surface receptors determine which genes or gene packets enter the cell.

...

Plasmids rarely become integrated into a bacterial chromosome, but instead are like ‘book-mobile’ genes, passed around and used where needed, otherwise discarded (Figure 6). Not all viruses serve this function; many may serve some totally unknown function in the natural world. The realisation that some kinds of viruses have a wider role in life led to a revolution in biology. Using the past research as a guide, it is likely that the extant bacteria and viruses whose function we do not understand likewise will be found to have important roles in the natural world.
http://www.trueorigin.org/virus.asp

[Oolon Colluphid]

:Let me check if I've downloaded any papers on that subject ...
I've already got:

Chen et al (1997): 'Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish'. PNAS 1997; 94; 3811-3816.

Chen et al (1997): 'Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod'. PNAS 1997; 94; 3817-3822.

Cheng & Chen (1999): 'Evolution of an antifreeze glycoprotein'. Nature 401 p.443-444.

Cheng et al (2003): 'Functional antifreeze glycoprotein genes in temperate-water New Zealand Notothenioid fish infer an Antarctic evolutionary origin'. Mol. Biol. Evol. 20(11):1897-1908 (Free full text (http://mbe.oxfordjournals.org/cgi/reprint/20/11/1897) pdf)

Cheng et al (2006): 'Nonhepatic origin of Notothenioid antifreeze reveals pancreatic synthesis as common mechanism in polar fish freezing avoidance'. PNAS 2006;103;10491-10496.

... but if you know of some more, add 'em to the pile. And if youv'e not got those, PM me your email addy.


ETA: From the first one above:
ABSTRACT Freezing avoidance conferred by different
types of antifreeze proteins in various polar and subpolar
fishes represents a remarkable example of cold adaptation,
but how these unique proteins arose is unknown. We have
found that the antifreeze glycoproteins (AFGPs) of the predominant
Antarctic fish taxon, the notothenioids, evolved
from a pancreatic trypsinogen. We have determined the likely
evolutionary process by which this occurred through characterization
and analyses of notothenioid AFGP and trypsinogen
genes. The primordial AFGP gene apparently arose
through recruitment of the 5' and 3' ends of an ancestral
trypsinogen gene, which provided the secretory signal and the
3' untranslated region, respectively, plus de novo amplification
of a 9-nt Thr-Ala-Ala coding element from the trypsinogen
progenitor to create a new protein coding region for the
repetitive tripeptide backbone of the antifreeze protein. The
small sequence divergence (4–7%) between notothenioid
AFGP and trypsinogen genes indicates that the transformation
of the proteinase gene into the novel ice-binding protein
gene occurred quite recently, about 5–14 million years ago
(mya), which is highly consistent with the estimated times of
the freezing of the Antarctic Ocean at 10–14 mya, and of the
main phyletic divergence of the AFGP-bearing notothenioid
families at 7–15 mya. The notothenioid trypsinogen to AFGP
conversion is the first clear example of how an old protein gene
spawned a new gene for an entirely new protein with a new
function. It also represents a rare instance in which protein
evolution, organismal adaptation, and environmental conditions
can be linked directly.

[ericmurphy]

And before this point gets lost in all the discussion of bacterial evolution, I want to bring up a question Dave was asked yesterday, but predictably failed to answer:

You originally claimed that the genomes of all complex eukaryotes are degenerating rapidly, leading to extinction in approximately 300 generations. Now you've revised your claim, saying that it is only the human genome that is degenerating rapidly.

This makes little sense, even in terms of your own worldview, since in the time between the "flood" and now, the average complex eukaryotic "kind" has diverged into hundreds if not thousands of species, and yet in the same time humans have not diverged at all. So what is the mechanism, Dave, which prevents humans from radiating into different species, despite a very high mutation rate that will have us extinct in another two thousand years?

[Dave Hawkins]

Thanks to everyone for the wonderful discussion about supposedly 'creative' evolution. It's not convincing to me, but I appreciate your efforts. I find it telling that there are so few examples of supposedly creative evolution offered by evolution advocates, and even the few examples that there are turn out to be equivocal at best upon close inspection.

But the subject of this thread is Sanford and his argument that genomes are deteriorationg.

Does anyone have any rebuttal to my post earlier today found here ... ?
http://www.iidb.org/vbb/showthread.php?p=4565825#post4565825

I apologize if I missed it. There have been so many posts on the 'supposedly creative evolution' issue that I may have missed your rebuttal.

[deadman_932]

In response to Dave posting Kevin Anderson's "paper" at After the Bar Closes, I posted a number of citations reflecting a CURSORY search on my part. Remeber, Kevin Anderson specifically states that antibiotic resistance is INEVITABLY associated with immediate fitness costs.

When Dave was presented with these ciatations, he refused to deal with them, saying he was UNQUALIFIED to do so. Naturally, though, Dave suggested I go "debate" with Kevin Anderson...rather than Dave questioning his OWN source, Kevin Anderson.

P. Sander, B. Springer, T. Prammananan, A. Sturmfels, M. Kappler, M. Pletschette, and E. C. Bottger (2002).Fitness Cost of Chromosomal Drug Resistance-Conferring Mutations. Antimicrob. Agents Chemother. 46: 1204-1211

"We found that the chromosomal drug resistance mutations studied often had only a small fitness cost; compensatory mutations were not involved in low-cost or no-cost resistance mutations. "

A. I. Nilsson, A. Zorzet, A. Kanth, S. Dahlstrom, O. G. Berg, and D. I. Andersson (2006). Reducing the fitness cost of antibiotic resistance by amplification of initiator tRNA genes. (on rifampin resistance)

"Conclusions: The fitness impact imposed on E. coli 345-2 RifC by carriage of antibiotic resistance elements was generally low or non-existent, suggesting that once established, resistance may be difficult to eliminate through reduction in prescribing alone."

N. Luo, S. Pereira, O. Sahin, J. Lin, S. Huang, L. Michel, and Q. Zhang (2005).
PNAS 102: 541-546. Enhanced in vivo fitness of fluoroquinolone-resistant Campylobacter jejuni in the absence of antibiotic selection pressure.

"The prolonged colonization in chickens did not result in loss of the FQ resistance and the resistance-conferring point mutation (C257-> T) in the gyrA gene. Strikingly, when coinoculated into chickens, the FQ-resistant Campylobacter isolates outcompeted the majority of the FQ-susceptible strains"

This last one was particularly telling, given that C. jejuni fitness was actually enhanced by antibacterial resistance without evidence of compensatory mutations.

Final Note: While it is clear that initial fitness may be affected by antibacterial resistance, the reproductive rates of bacteria lead to compensatory mutations taking place relatively rapidly that dissipate the negative fitness effects in many species.

To top that, there are certainly examples cited above that simply run counter to what Kevin Anderson claimed.

[Oolon Colluphid]

Thanks to everyone for the wonderful discussion about supposedly 'creative' evolution. It's not convincing to me, but I appreciate your efforts. I find it telling that there are so few examples of supposedly creative evolution offered by evolution advocates, and even the few examples that there are turn out to be equivocal at best upon close inspection.
Dave, PM me your email address, I'll send you a copy of the Chen paper above, and then you can critique it and explain why it is not convincing. I'll go one better: if you provide a critique, I'll help you knock it into a shape that can be submitted to PNAS or Nature, and we can do so. How's that?

[deadman_932]

Yeah, apparently you can't see the posts on that little nylonase critter, eh, Dave? It's too difficult for you to see? I find it telling that there are so few examples of supposedly creative evolution offered by evolution advocates, and even the few examples that there are turn out to be equivocal at best upon close inspection.


The problem for you is that you have suggested multiple times that there are NO examples of such evolution, Dave. And when you are confronted with detailed data on such, like that APO AI Milano, you ...avoid it and pretend it doesn't exist.

Let me repeat this little adage of logic, Dave : as soon as you find one black goose, it shows the person claiming all geese are white...is wrong.

[ck1]

CREATIONISTS HAVE BEEN WRITING ABOUT JUNK DNA FOR A LONG TIME
Wieland, Carl, “Junk moves up in the world”, Creation Ex Nihilo Technical Journal, Volume 8, Issue 2, August 1994, p. 152 (No link available)
http://www.creationontheweb.com/content/view/1789 (Batten 1998)
http://www.creationontheweb.com/content/view/1631 (Walkup 2000)
http://www.creationontheweb.com/content/view/145 (Sarfati 2003)
http://www.creationontheweb.com/content/view/1588/ (Batten 2005)

The basis for these predictions is that the Creator would not create junk. I suppose you have read the latest issues of Science and Nature pertaining to this issue? Pretty interesting stuff.

Well creationists may have been writing about "junk" DNA since 1994, but that is not nearly as long as mainstream biologists have been actually working on the stuff. As you know Ohno (who also wrote the key paper on nylonase) coined the term in 1972, but his key papers are in book chapters and hard to get. Other investigators working at the same time were also thinking about of all of this repetitive non-coding DNA. For example:

Britten, RJ AND Davidson, EH. 1971. Quart. Rev. Biol. 46:111
"Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty"

From page 120:

At this time the view which seems most consistent with classical views of natural selection is that stochastic events initiate the chains of steps leading to each family of repeated DNA. In other words, repetitive sequence families originate accidentally. We assume that, later on, some or all of their member sequences become useful to the species, and only at this stage does selective pressure become important. There is no evidence to decide between this view and the alternative one that certain classes of function in the cell cause the excessive duplication of certain useful sequences in the germ line DNA.

they go on to speculate that such sequences provide a reservoir for further evolutionary change.

While this paper is highly speculative, I mention it to illustrate the point that as soon as repetitive non-coding DNA was identified, biologists were thinking about its possible function and reasons for its retention. Specific studies focused on noncoding DNA were begun in the 1970s and continue to the present (ENCODE). And none of this relies on a Design hypothesis or a Creator.

And on what basis do you KNOW that your Creator would not create junk? Isn't this the same creator whose creations are mostly (99%) extinct?

[MrDarwin]

I'm mortified to know that this is going on at my alma mater but it's important to note that he is no longer a professor or researcher at Cornell, and this wouldn't be the first time a respected scientist went a bit nutty in retirement. It's just a shame that, like too many other creationists, he's using an affiliation that he earned for something else entirely to lend a credibility to his ideas that they don't deserve.

[ericmurphy]

Thanks to everyone for the wonderful discussion about supposedly 'creative' evolution. It's not convincing to me, but I appreciate your efforts. I find it telling that there are so few examples of supposedly creative evolution offered by evolution advocates, and even the few examples that there are turn out to be equivocal at best upon close inspection.

No one expected in would be convincing to you, Dave. Over the past year, you've shown yourself impervious to logic when it comes to challenges to your world view.

But if you want examples of "supposedly creative evolution," I would point you to anything living today, which is an example of what four billion years of evolution can accomplish. Sure, you think everything alive was designed (well, except for the millions of species which have evolved from biblical "kinds" in the past 5,000 years), but you've never been able to present evidence for this putative design, nor a mechanism by which this "design" could have occurred.

But the subject of this thread is Sanford and his argument that genomes are deteriorationg.

Does anyone have any rebuttal to my post earlier today found here ... ?
http://www.iidb.org/vbb/showthread.php?p=4565825#post4565825

I apologize if I missed it. There have been so many posts on the 'supposedly creative evolution' issue that I may have missed your rebuttal.

How about if you answer my question, which I doubt you missed, since it appears immediately above your post.

[Calilasseia]

Thanks to everyone for the wonderful discussion about supposedly 'creative' evolution. It's not convincing to me

Note the evidence people ...

Numerous scientific papers citing documented instances of novel features arising in organisms, complete in several instances with full analyses of the genomes involved, are not convincing to Dave.

Yet the kind of turgid pseudoscience that appears at AiG and ICR is convincing to him. Despite being roundly refuted time and time again by people with critical faculties intact, including in numerous instances accredited professional scientists with expertise in the relevant fields.

Dave is wedded inseparably to Biblical inerrancy, a view that the Genesis myth is historical fact (including the global flood, despite it being demonstrated on numerous occasions that every creationist global flood scenario in existence violates the laws of physics and yields manifestly absurd conditions for Planet Earth), is additionally wedded inseparably to creationism regardless of the mountain of evidence in favour of the Modern Synthesis of Evolution and the demonstrable incompetence of creationist "scholarship" in this area, and as a corollary of that is wedded to absurd notions about our genomes "disintegrating as a result of The Curse and The Fall".

We are not dealing here with a person who is willing to engage. We are dealing with a person whose purpose is proselytising. Newcomers to this thread should examine the above carefully and deduce that the above provides evidence of this.

[ck1]

Dave, Here is another novel gene that recently evolved in Drosophila. It encodes a protein involved in motility and was formed by duplication of two adjacent genes followed by their fusion and mutation:

http://www.ncbi.nlm.nih.gov/sites/entrez


Genetica. 2003 Jul;118(2-3):233-44.

Origin and evolution of a new gene expressed in the Drosophila sperm axoneme.
Ranz JM, Ponce AR, Hartl DL, Nurminsky D.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 33143, USA.
Sdic is a new gene that evolved recently in the lineage of Drosophila melanogaster. It was formed from a duplication and fusion of the gene AnnX, which encodes annexin X, and Cdic, which encodes the intermediate polypeptide chain of the cytoplasmic dynein. The fusion joins AnnX exon 4 with Cdic intron 3, which brings together three putative promoter elements for testes-specific expression of Sdic: the distal conserved element (DCE) and testes-specific element (TSE) are derived from AnnX, and the proximal conserved element (PCE) from Cdic intron 3. Sdic transcription initiates within the PCE, and translation is initiated within the sequence derived from Cdic intron 3, continuing through a 10 base pair insertion that creates a new splice donor site that enables the new coding sequence derived from intron 3 to be joined with the coding sequence of Cdic exon 4. A novel protein is created lacking 100 residues at the amino end that contain sequence motifs essential for the function of cytoplasmic dynein intermediate chains. Instead, the amino end is a hydrophobic region of 16 residues that resembles the amino end of axonemal dynein intermediate chains from other organisms. The downstream portion of Sdic features large deletions eliminating Cdic exons v2 and v3, as well as multiple frameshift deletions or insertions. The new protein becomes incorporated into the tail of the mature sperm and may function as an axonemal dynein intermediate chain. The new Sdic gene is present in about 10 tandem repeats between the wildtype Cdic and AnnX genes located near the base of the X chromosome. The implications of these findings are discussed relative to the origin of new gene functions and the process of speciation.

[Sven]

Thanks to everyone for the wonderful discussion about supposedly 'creative' evolution. It's not convincing to me, but I appreciate your efforts. I find it telling that there are so few examples of supposedly creative evolution offered by evolution advocates, and even the few examples that there are turn out to be equivocal at best upon close inspection.
That's quite insulting. At least six people devote much work to this, provide loads of references, explain many details - and all they get is "It's not convincing to me, they are equivocal at best."

Dave may be comfortable to deny the evidence in this childish way, but he should realise that he damages his credibility greatly. If he's out to evangelize (for creationism), he has just achieved the opposite.

[Jet Black]

The problem for you is that you have suggested multiple times that there are NO examples of such evolution, Dave. And when you are confronted with detailed data on such, like that APO AI Milano, you ...avoid it and pretend it doesn't exist.


a concerning point for dave should be that we are managing to show that these mutations are occuring in what he thinks is a 4000 year time frame since Noah's flood, and in small and isolated populations (i.e. a town, or a puddle of nylon)

Since the actual time frame is of the order of a million times longer than that, and there are far more and far larger populations that the biased sample chosen, it then shows that there is ample time for significant numbers of mutations to occur.

[Oolon Colluphid]

Say, Dave, I just realised that you may be unfamiliar with these:
“There are no beneficial mutations.”
This is not true, since some changes do confer an advantage in some situations. Rather, we should say, “We have yet to find a mutation that increases genetic information, even in those rare instances where the mutation confers an advantage.” For examples of information loss being advantageous, see Q&A: Mutations

“No new species have been produced.”
This is not true—new species have been observed to form. In fact, rapid speciation is an important part of the creation model. But this speciation is within the “kind,” and involves no new genetic information. See Q&A: Speciation.
From Answers in Genesis's Arguments we think creationists should NOT use (http://www.answersingenesis.org/home/area/faq/dont_use.asp), specifically under the heading of 'Which arguments should definitely not be used?'

So this leaves me wondering. You have a problem with antibacterial resistance; and you deny any "creative" mutations. But here's these guys telling us that there are beneficial mutations and that even speciation is no problem.

Seems your beef is with those AiG slackers more than us even.

[Jet Black]

Thanks to everyone for the wonderful discussion about supposedly 'creative' evolution. It's not convincing to me, but I appreciate your efforts. I find it telling that there are so few examples of supposedly creative evolution offered by evolution advocates, and even the few examples that there are turn out to be equivocal at best upon close inspection.
That's quite insulting. At least six people devote much work to this, provide loads of references, explain many details - and all they get is "It's not convincing to me, they are equivocal at best."

Dave may be comfortable to deny the evidence in this childish way, but he should realise that he damages his credibility greatly. If he's out to evangelize (for creationism), he has just achieved the opposite.

fortunately the lurkers can see that all the creationists can offer is handwaving and links to AiG, which are immediately refuted. afdave is doing us a service by letting us show these people the vacuous nature of the creationist arguments.

[Jet Black]

Seems your beef is with those AiG slackers more than us even.

aah but those god-hating heathens at AiG aren't taking the bible literally enough! Let one beneficial mutation, or a speciation event slip in, and the entire Bible is instantly false.

[Sven]

A recent article, both relevant to the "junk DNA" argument and to "mutations being creative":

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (http://www.nature.com/search/executeSearch?sp-q=monodelphis&sp-c=10&sp-x-9=cat&sp-s=date&submit=go&sp-a=sp1001702d&sp-sfvl-field=subject%7Cujournal&sp-sfvl-field=subject%7Cujournal&sp-x-1=ujournal)

The abstract:
We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

[deadman_932]

On your digression on mobile elements above, Dave: I am stating quite clearly that you don't know what you are talking about. Try asking yourself where plasmids come from, how they themselves can change, and how they wind up in other organisms.

How you can say this is not part of modern evolutionary theory is beyond me, given that huge books like Berg and Howe's "Mobile DNA" ...collections of work done in previous decades...were being published in the 1980's.

The essence of Darwinian evolution is heritable change (variation), reproduction, selection in a dynamic environment.

"Change" can be accomplished in many ways, AS YOU HAVE BEEN TOLD MANY TIMES. It's not JUST about mutation, it's about plasmids, polyploidy, robertsonian fusion, virus acquisition, symbiosis and much more. All of that is part of modern evolutionary theory.

Quit trying to define it according to your limited and flawed knowledge of the subject ...particularly since you have admitted you don't read books on the subjects that are not by creationists, and especially since you have shown no evidence that you actually read the Nature and Science journals that you claim to subscribe to.

[Oolon Colluphid]

Awww, he's gone offline, and without PMing me his email. He can't be all that keen on seeing the Chen antifreeze protein paper. :huh:

[ericmurphy]

—nor did he answer my question about why only the human genome is deteriorating, apparently unique among complex eukaryotes. This is a question from yesterday, based on his changing a position he's taken for more than six months.

[VoxRat]

afdave discussed Sanford, Crow, etc. here (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=SP;f=14;t=3131;p=37676).

Are you planning to bring up something new now, afdave? Because, if not, why don't people just go to the discussion from last year? Seems like a monumental waste of time, effort, and bandwidth.Seriously, Dave.

I would really like you to answer this question.

So far it appears to be "deja vu all over again".

Are you planning on introducing anything new? Anything that wasn't thoroughly aired here (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=SP;f=14;t=3131;p=37676). ?

[VoxRat]

In fact, the evidence indicates that they [plasmids] were designed. '

Yet another baseless assertion.

Since you think everything in life was "designed", isn't it kind of vacuous to say "the evidence indicates that" plasmids were designed, without even suggesting what that evidence is? What evidence? Is there something particular about plasmid DNA for which there's evidence that's more compelling than - or even different from - the "evidence" that any other DNA was "designed"?

[deadman_932]

From Answers in Genesis's Arguments we think creationists should NOT use, specifically under the heading of 'Which arguments should definitely not be used?'

That's part of Dave's M.O., unfortunately...he equivocates constantly between definitions, he says things directly contrary to his own previous claims, he puts himself in the middle of creationist claims like the RATE group and R.H. Brown and finds himself unable to make a decision on which "authority" to follow because he can't think logically about the subjects himself, since he rejects any refutations of biblically literalism a priori AND he has no meaningful knowledge of his own to follow.

His unsupported repeating of Batten claiming "the evidence indicates that they [plasmids] were designed" is a case in point, particularly when NO such "designed, irreducibly complex" cases have EVER been shown. Yet he'll reject available, dissectable, repeatable, testable data in favor of that level of crap-artistry.

[ericmurphy]

Dave: "The evidence indicates that [utterly preposterous belief, e.g., the universe is a few thousand years old, the world drowned in a mile of water within historical times, T. rex was a vegetarian, Portuguese = Spanish + French + some Madeira wine] is true."

Everyone else: "Oh, really? And what is this "evidence" you speak of?"

Dave: [cue sound of footsteps rapidly receding into distance]

[deadman_932]

Eric: that question of why ONLY the human genome is deteriorating is something that needs to be hammered into dave's skull a lot more. he's trapped , there. Sanford will be removed from his arsenal based on that alone.

I thought about tossing an e-mail to Crow saying who Dave is and his agenda, but I rejected that considering Dave's propensity for conspiracy theories. He'd just claim Crow was part of the cabal against him when he gets an answer he doesn't like.

edit: Hell, he'll still most likely do that anyway, eventually.

[Dave Hawkins]

Oolon ... yes, I am very much aware of those arguments that should not be used. Careful readers will note that I do not use them. I fully acknowledge that speciation occurs ... in fact, it is required in the Creationist/Diluvialist model to account for the number of species extant today. Also, I don't say that mutations can never be beneficial. Of course they can be sometimes in very limited contexts. I will PM you my e-mail for the article you mention.

[ericmurphy]

And yet again Dave fails to answer my question: why is it that only the human genome is degenerating?

And yet, some other mechanism is preventing humans from speciating, while all the other complex eukaryotes have speciated like there was no tomorrow, all in the space of 5,000 years.

[Dave Hawkins]

Again ... does anyone have any convincing rebuttal to this post given earlier this morning?
http://www.iidb.org/vbb/showthread.php?p=4565825#post4565825

You know ... regarding the Crow paper? The subject of this thread?

[Dave Hawkins]

It is only the human genome that we are discussing. I suspect that we would find the same deterioration if we studied other genomes, but I have no comment on them now. As it happens, there is one mentioned right there in the Crow paper ... Drosophila.

[ericmurphy]

Again ... does anyone have any convincing rebuttal to this post given earlier this morning?
http://www.iidb.org/vbb/showthread.php?p=4565825#post4565825

You know ... regarding the Crow paper? The subject of this thread?

Yes. I posted it this morning. But first, answer my question from yesterday:

And yet again Dave fails to answer my question: why is it that only the human genome is degenerating?

And yet, some other mechanism is preventing humans from speciating, while all the other complex eukaryotes have speciated like there was no tomorrow, all in the space of 5,000 years.

[VoxRat]

By the way, Dave.

From your discussion of Sanford at AtBC (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?):Dr. John Sanford has been a Cornell University professor for more than 25 years in the area of plant breeding and plant genetics. He has published over 70 scientific publications, and was granted over 25 patents. His most significant scientific contributions involved three inventions -- the biolistic ("gene gun") process, pathogen-derived resistance, and genetic immunization. Most of the transgenic crops grown in the world today were genetically engineered using the gene gun technology developed by John and his collaborators. John also started two successfull businesses deriving from his research -- Biolistics, Inc. and Sanford Scientific, Inc.Now, since you didn't attribute that to anyone else, I guess we should assume that you wrote it. Though it does look to me suspiciously like a C&P.

Anyway, you might want to check your sources, because - while I believe he was responsible for the "biolistic process" - pathogen-derived resistance and genetic immunization are definitely not his inventions.

[ericmurphy]

Again ... does anyone have any convincing rebuttal to this post given earlier this morning?
http://www.iidb.org/vbb/showthread.php?p=4565825#post4565825

You know ... regarding the Crow paper? The subject of this thread?

Yes. I posted it this morning. Perhaps you didn't read it, since you claim not to read my posts? Here it is again:

You all seem to believe that Crow is simply talking about the ability of modern medicine to keep people alive longer, thus causing many harmful mutations to be retained in the population. However, this only applies to the last hundred years (or less). A careful reading of this indicates that Crow is talking about keeping a good social order, i.e. no huge wars or famines. Nothing there about modern medicine.

There's more to it than just modern medicine, Dave. Who do you think had a better chance of surviving to reproduce: someone who lived in a hunter-gatherer society who had been blind from birth, or someone who lived in a Medieval agrarian society who had been blind from birth?

No matter how you try to wriggle, Dave, you're not going to get around Crow's central point: human civilization, and especially modern medicine, are interfering with natural selection's ability to remove deleterious mutations from the gene pool. No amount of wriggling is going to get Crow to be saying that ancient humans were genetically superior to modern humans. And you are never, ever going to be able to support the claim that ancient humans were healthier and lived longer than modern humans. The evidence is against you.



Nope. It's still you, Dave. You're still wrong, as always. Your "Crow" moment, to go along with your "Portuguese moment," your "Churchill moment," your "water sprinkler moment," and all your other moments caused by your inability to admit error.

No, I'm not going to discuss HLA alleles in this thread. This thread is for Sanford's book and the papers he quotes.

Then stop claiming that you don't need mutations to get variability. Don't make stupid claims and then refuse to discuss rebuttals of those claims.

And once again: WHY IS IT THAT ONLY THE HUMAN GENOME IS DEGENERATING? WHY ARE OTHER COMPLEX EUKARYOTIC GENOMES ALSO NOT DEGENERATING?

[deadman_932]

I fully acknowledge that speciation occurs ... in fact, it is required in the Creationist/Diluvialist model to account for the number of species extant today. Yes, that would be "Dave's hyper-speciation model" where evolution takes off like a rocket due to "front-loaded" (pre-installed, "created") hyper-variable heterozygosity.

This had Dave claiming that there were a whole BUNCH of alleles per loci. LOTS AND LOTS -- screw TWO, hell, he wanted MORE and MORE!!!...thereby revealing the abysmal level of Dave's "knowledge"

[deadman_932]

Say, Dave...about Sanford's claims...how is it that only the human genome is deteriorating, in your view? Can you clarify that?

[VoxRat]

Again ... does anyone have any convincing rebuttal to this post given earlier this morning?
http://www.iidb.org/vbb/showthread.p...25#post4565825

You know ... regarding the Crow paper? The subject of this thread?Yeah, I've seen several.

Oh, you mean convincing to you?

It is only the human genome that we are discussing. I suspect that we would find the same deterioration if we studied other genomes, but I have no comment on them now. As it happens, there is one mentioned right there in the Crow paper ... Drosophila.You mean Drosophila bred in laboratory conditions, where - once again - all selective pressure has been removed? Or Drosophila in the wild? Kind of important distinction, in light of the discussion about the effects of modern civilization on selective pressures on humans, wouldn't you say?

[ericmurphy]

It is only the human genome that we are discussing. I suspect that we would find the same deterioration if we studied other genomes, but I have no comment on them now. As it happens, there is one mentioned right there in the Crow paper ... Drosophila.

You can't just discuss the human genome, when if other genomes were also degenerating, everything would be extinct!

You can't just limit the discussion to what you want to talk about, when there are huge problems with your positions based on other data.

If the Drosophila genome is also degenerating, then why are there any Drosophila left, Dave? Do you know how long 300 generations of Drosophila takes?

You're not ducking this question, Dave. And you're certainly not having it both ways. Either humans and all other complex eukaryotes are suffering from runaway genetic deterioration, or only humans are, or nothing is. You're not going to be allowed to simultaneously hold two mutually-contradictory positions, as you did with Brown and RATE.

Now explain yourself. If you think it's only the human genome that's deteriorating, than you need to explain why that is. If you think it's all complex eukaryotes, then you need to explain why there are any left.

Pick your poison, Dave. But you will pick one, or everyone will know you're a fraud. Oh, wait...

[VoxRat]

You know ... regarding the Crow paper? The subject of this thread?The title of the thread, "Cornell Geneticist: Degenerating Genomes Disprove Evolution" led me to conclude we were talking about Sanford.

Silly me.

[ericmurphy]

One other thing, Dave: it's not a Crow "paper" that Sanford (the supposed subject of this thread, about which I'm pretty sure we haven't even seen a quote from) is discussing. It's the transcript of a speech Crow gave. Big difference.

[deadman_932]

On a side note: I wonder if Dave knows that his beloved Wikipedia also notes mobile elements like plasmids are part of variation.

But on the more important subject of Dave's claims about Sanford...which IS the title of this thread...why is it that there are any fast-reproducing species alive, Dave...and why are you NOW claiming that only humans are affected by genomic meltdown?

Please clarify this, or does politeness also not matter? I know you're a busy, busy, man, but don't you think you should address the subjects derived from the topic of this thread?

[ericmurphy]

On a side note: I wonder if Dave knows that his beloved Wikipedia also notes mobile elements like plasmids are part of variation.

But on the more important subject of Dave's claims about Sanford...which IS the title of this thread...why is it that there are any fast-reproducing species alive, Dave...and why are you NOW claiming that only humans are affected by genomic meltdown?

Please clarify this, or does politeness also not matter? I know you're a busy, busy, man, but don't you think you should address the subjects derived from the topic of this thread?

Dave's caught in a contradiction now, and he's going to try the same thing he's trying with BWE in his dendrochronology debate. He's going to try to limit discussion to just the human genome, so he doesn't have to deal with the problem of claiming that either just the human genome is deteriorating (must be something awfully defective about the flower of God's creativity), or that all genomes are deteriorating (in which case it should be pretty lonely out there with all the rapidly reproducing—which, to a first approximation, is all—eukaryotes already extinct).

I'm waiting for Dave to say, "but you guys already claim that 99% of everything that's ever lived is extinct!" Which is true, but we're talking about 99% of everything that's ever lived in the past four billion years, not everything that's ever lived in the past four millennia. Why are there bunnies, Dave? Or pigeons? Or cats? Or dogs? Or wheat, or corn, or bamboo? We should be down to redwoods, elephants, etc. But strangely, we're not.

[ck1]

But from the context, he clearly believes we ARE like Drosophila in this respect, i.e. that human decrease in viability from mutation accumulation is some 1 or 2% per generation. Why else would he ask how long we can keep outpacing this number with environmental improvements? Again, please study Crow's statement carefully
Sorry to beat a dead horse here, but you continue to misunderstand this paper. Crow's argument considers measured mutation rates and the number of generations a mutation persists and ultimately argues that the accumulation of mutations is balanced by quasi-truncation selection. He says:

I conclude that for flies, and very likely for human populations in the past, mildly harmful mutations were balanced by quasi-truncation selection.

The 1-2% mutation accumulation is what he estimates happens IN THE ABSENCE OF SELECTION. And in the absence of selection due to environmental improvements (he does not specifically mention modern medicine), he argues humans are currently accumulating mutations and this is a bad thing.

[Dave Hawkins]

But from the context, he clearly believes we ARE like Drosophila in this respect, i.e. that human decrease in viability from mutation accumulation is some 1 or 2% per generation. Why else would he ask how long we can keep outpacing this number with environmental improvements? Again, please study Crow's statement carefully
Sorry to beat a dead horse here, but you continue to misunderstand this paper. Crow's argument considers measured mutation rates and the number of generations a mutation persists and ultimately argues that the accumulation of mutations is balanced by quasi-truncation selection. He says:

I conclude that for flies, and very likely for human populations in the past, mildly harmful mutations were balanced by quasi-truncation selection.The 1-2% mutation accumulation is what he estimates happens IN THE ABSENCE OF SELECTION. And in the absence of selection due to environmental improvements (he does not specifically mention modern medicine), he argues humans are currently accumulating mutations and this is a bad thing.He concludes this, but he does not demonstrate this. It is speculation born from his preconceptions of the 'fact' of evolution. I.e. he is firmly convinced that H. sapiens has roamed the planet for 200,000 years and we should have died b/c of mutation accumulation, yet "Here we are!" So, given his pre-commitment, he HAS to propose some explanation of how we could have possibly survived this long.

[Dave Hawkins]

DR. A.S. KONDRASHOV--ANOTHER PROMINENT GENETICIST--ASKS A REALLY TELLING QUESTION

This is probably a good time to introduce another paper quoted by Sanford which echoes the same themes voiced by Crow.

"Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?"

Kondrashov A.S., Journal of Theoretical Biology, Volume 175, Number 4, 1995 , pp. 583-594(12)

Abstract:

It is well known that when s, the selection coefficient against a deleterious mutation, is below ~ 1/4 N e , where N e is the effective population size, the expected frequency of this mutation is ~ 0.5, if forward and backward mutation rates are similar. Thus, if the genome size, G, in nucleotides substantially exceeds the N e of the whole species, there is a dangerous range of selection coefficients, 1/ G < s < 1/4 N e . Mutations with s within this range are neutral enough to accumulate almost freely, but are still deleterious enough to make an impact at the level of the whole genome. In many vertebrates N e ~ 10 , while G ~ 10 , so that the dangerous range includes more than four orders of magnitude. If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10 , an average individual carries ~ 100 lethal equivalents. Some data suggest that a substantial fraction of nucleotides typical to a species may, indeed, be suboptimal. When selection acts on different mutations independently, this implies to high a mutation load. This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations. Several possible resolutions are considered, including soft selection and synergistic epistasis among very slightly deleterious mutations.
http://www.ingentaconnect.com/content/ap/jt/1995/00000175/00000004/art00167Sanford comments ... If Dr. Kondrashov woUld just believe his own data, he would conclude that the Primary Axiom [RM+NS] is wrong, and that genomes must degenerate. Instead, he eventually appeals to "synergistic epistasis" to wave away the problems which he has so brilliantly characterized. (Sanford, p. 168)

[VoxRat]

Again, Kondrashov... all this was discussed at AtBC. Do you have anything new, Dave? Because, as you'll recall, no one found your Sanford very persuasive last time 'round.

[ericmurphy]

Still no answer, Dave. Either you think that the human genome is uniquely fragile, in which case you need an explanation for that surprising "fact," or you think that all eukaryotes are suffering from the same genetic fragility, in which case you need to explain why there are any organisms left with a generation time of less than 15 years (which would be most of them).

You're not going to dodge this question, Dave. Eventually, the few people who have not already asked you this question are also going to start asking this question.

[VoxRat]

Dave? Drosophila? Wild or laboratory? You do see why I ask, don't you?

[Sven]

The 1-2% mutation accumulation is what he estimates happens IN THE ABSENCE OF SELECTION. And in the absence of selection due to environmental improvements (he does not specifically mention modern medicine), he argues humans are currently accumulating mutations and this is a bad thing.He concludes this, but he does not demonstrate this.
Let's accept this for the sake of argument (it's wrong, but let's not beat this dead horse any longer).
Dave, do you realize that you've just admitted that you have been wrong the entire time you'Ve argued about Crow? You just said that Crow concludes the opposite of what you used to claim he said!

It is speculation born from his preconceptions of the 'fact' of evolution. I.e. he is firmly convinced that H. sapiens has roamed the planet for 200,000 years and we should have died b/c of mutation accumulation, yet "Here we are!" So, given his pre-commitment, he HAS to propose some explanation of how we could have possibly survived this long.
:rolling:
Dave, what exacltly about selection weeding out bad things is hard to understand? Why exactly is this explanation not perfectly valid and sound?

Maybe it's because of your precommitment that humans have only been here for 6000 years? :wave:

[deadman_932]

If Sanford's interpretation of Kondrashev is correct, Dave....why are there so many fast-breeding species left alive?

Why do you NOW say that ONLY man is subject to the kind of deleterious mutation accumulation you feel is so relevant....

and why can't you answer direct questions on the subject of the thread, Dave...like Sanford's claims?

To the moderators: I am strongly suggesting that Dave is merely preaching here. He is certainly not discussing the subject of the thread when politely questioned.

[ericmurphy]

Sorry to beat a dead horse here, but you continue to misunderstand this paper. Crow's argument considers measured mutation rates and the number of generations a mutation persists and ultimately argues that the accumulation of mutations is balanced by quasi-truncation selection. He says:

The 1-2% mutation accumulation is what he estimates happens IN THE ABSENCE OF SELECTION. And in the absence of selection due to environmental improvements (he does not specifically mention modern medicine), he argues humans are currently accumulating mutations and this is a bad thing.He concludes this, but he does not demonstrate this. It is speculation born from his preconceptions of the 'fact' of evolution. I.e. he is firmly convinced that H. sapiens has roamed the planet for 200,000 years and we should have died b/c of mutation accumulation, yet "Here we are!" So, given his pre-commitment, he HAS to propose some explanation of how we could have possibly survived this long.

Dave, what factors were interfering with natural selection in humans 200,000 years ago? Was there any sort of civilization, or advanced medical care? How about 50,000 years ago? None then, either, was there? How about 10,000 years ago? Just barely a civilization, and nothing in the way of medical care. How about 5,000 years ago? More civilization, but still not much medical care.

How about 2,000 years ago, Dave? Not much medical care then, either, right? What about 1,000 years ago? Did anyone even know that germs existed? Maybe 200 years ago? Things were looking a little better? In terms of medical care? Can we agree that the benefits of civilization and what medical care there was might have had some effect on the efficacy of natural selection?

Regardless of whether you believe evolution happens, or whether natural selection even exists, you have to agree, do you not, that Crow doesn't have anything to explain here, does he? If evolution does happen, if mutations happen (you don't deny that mutations happen, do you, Dave?) and if natural selection exists, then what is left for Crow to explain?

You're acting like Crow is not seeing the implications of his own findings. That's far from the case. All Crow is saying is that the blessings of civilization, including medical care, have interefered with the workings of natural selection. Even if you don't think natural selection exists, you simply cannot maintain that Crow has not provided an explanation for how mutations have been removed from the human genome until very recently. It's the same explanation it always is: natural selection.

And you still haven't answered my question, which I've now asked at least half a dozen times:

Do you think only the human genome is deteriorating? If so, why only the human genome? Do you think all complex eukaryotic genomes are deteriorating? If so, then why are there any complex eukaryotes left?

[Mike PSS]

Again, Kondrashov... all this was discussed at AtBC. Do you have anything new, Dave? Because, as you'll recall, no one found your Sanford very persuasive last time 'round.
Voxrat,
Was this in the UCGH1 or UCGH2 or one of the other snot-fests?

Your link in a prior message just went to the AtBC front page. Not too helpful.

[ck1]

He concludes this, but he does not demonstrate this. It is speculation born from his preconceptions of the 'fact' of evolution. I.e. he is firmly convinced that H. sapiens has roamed the planet for 200,000 years and we should have died b/c of mutation accumulation, yet "Here we are!" So, given his pre-commitment, he HAS to propose some explanation of how we could have possibly survived this long.
So now you are insisting that Crow's conclusions are wrong! One minute you base your arguments on his paper and the next you claim his conclusions are base-less speculations. Make up your mind!.:rolleyes:

[ericmurphy]

So now you are insisting that Crow's conclusions are wrong! One minute you base your arguments on his paper and the next you claim his conclusions are base-less speculations. Make up your mind!.:rolleyes:

Dave believes that all complex eukaryotic genomes are deteriorating rapidly, and he believes that only the human genome is deteriorating rapidly. Do you see a problem here? Dave doesn't.

[Mike PSS]

Dave,
Don't you think the whole timeline of what Crow is talking about kind of matches with the population growth figures from the past?

Like this....
http://www.globalchange.umich.edu/globalchange2/current/lectures/human_pop/worldpop.jpg

It reads to me that Crow is discussing the mutation effect of the human population at the point where this population curve takes an upward bend. There are a lot of reasons this curved upward and medicine is a big, but not sole, reason.

Now,
I'm not even going to start discussing the timeline at the bottom except to state that your graph would start with 8 people 4700 years ago. I'll let you and BWE discuss the formulaes needed to get to the pyramid builders from that point.

[Dave Hawkins]

He concludes this, but he does not demonstrate this. It is speculation born from his preconceptions of the 'fact' of evolution. I.e. he is firmly convinced that H. sapiens has roamed the planet for 200,000 years and we should have died b/c of mutation accumulation, yet "Here we are!" So, given his pre-commitment, he HAS to propose some explanation of how we could have possibly survived this long.
So now you are insisting that Crow's conclusions are wrong! One minute you base your arguments on his paper and the next you claim his conclusions are base-less speculations. Make up your mind!.:rolleyes:I believe that Crow is correct in his observations. It is in his conclusions from those observations--i.e. his suggestion that QTS can solve it--that I believe he is wrong.

[ericmurphy]

So now you are insisting that Crow's conclusions are wrong! One minute you base your arguments on his paper and the next you claim his conclusions are base-less speculations. Make up your mind!.:rolleyes:I believe that Crow is correct in his observations. It is in his conclusions from those observations--i.e. his suggestion that QTS can solve it--that I believe he is wrong.

But Dave, we've already shown you a million times what is going on here! There is nothing to solve!

The problem Crow is discussing is that environmental factors like living in a civilization and having access to medical care is interfering with the ability of natural selection to remove deleterious mutations from the gene pool.

There is nothing that needs solving.

And stop ignoring my question: why is the human genome uniquely fragile in the entire biological world? Why is it that only the human genome is deteriorating? Or, if you don't believe that's the case, then why are there any rapdidly reproducing eukaryotes left?.

Message to mods: Dave is simply disregarding serious, fatal problems with his argument. This needs to be addressed.

[Gamera]

Oolon ... yes, I am very much aware of those arguments that should not be used. Careful readers will note that I do not use them. I fully acknowledge that speciation occurs ... in fact, it is required in the Creationist/Diluvialist model to account for the number of species extant today. Also, I don't say that mutations can never be beneficial. Of course they can be sometimes in very limited contexts. I will PM you my e-mail for the article you mention.

Sounds like you have conceded that the theory of evolution is valid and you're just quarreling about dating. Taking what you concede here, and place it in the context of 3.5 billion years of organic life, and you got evolution.

[ericmurphy]

He concludes this, but he does not demonstrate this. It is speculation born from his preconceptions of the 'fact' of evolution. I.e. he is firmly convinced that H. sapiens has roamed the planet for 200,000 years and we should have died b/c of mutation accumulation, yet "Here we are!" So, given his pre-commitment, he HAS to propose some explanation of how we could have possibly survived this long.

One more thing. Crow does not "conclude" that since humans have been around for 200,000 years "we should have died b/c of mutation accumulation." You conclude that, Dave, not Crow. Crow doesn't need to "propose some explanation of how we could have possibly survived this long." That "explanation" already exists. What needs to be "explained" is why mutations are currently accumulating so quickly. The explanation for that is simple and obvious, and the only reason you can't grasp it is because you do not wish to grasp it.

[Sven]

Hey, I see that Dave is busy answering many people, but AFAIK, he has not answered one of the posts I directed to him in at least two different threads.
Am I invisible? :wave: Hey, guys, can you see (read) me?

[VoxRat]

Voxrat,
Was this in the UCGH1 or UCGH2 or one of the other snot-fests?

Your link in a prior message just went to the AtBC front page. Not too helpful.Sorry about that. I must have clicked the wrong button.

Yes, it was the UCGH2 around beginning of November.
http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=SP;f=14;t=3131;p=37676

[VoxRat]

Hey, I see that Dave is busy answering many people, but AFAIK, he has not answered one of the posts I directed to him in at least two different threads.
Am I invisible? :wave: Hey, guys, can you see (read) me?Heh!

Join the club!

You'll notice Dave studiously avoiding all my input as well.

[ericmurphy]

Hey, I see that Dave is busy answering many people, but AFAIK, he has not answered one of the posts I directed to him in at least two different threads.
Am I invisible? :wave: Hey, guys, can you see (read) me?

I've been asking him the same question about why the human genome is so fragile since he changed his mind and decided that it was only the human genome, and not all eukaryotic genome, that was crap. Now all he'll say is that he doesn't want to talk about other genomes. In other words, he's explicitly refusing to answer the question.

Which won't keep me from continuing to ask it, believe me.

[Constant Mews]

So now you are insisting that Crow's conclusions are wrong! One minute you base your arguments on his paper and the next you claim his conclusions are base-less speculations. Make up your mind!.:rolleyes:

Dave believes that all complex eukaryotic genomes are deteriorating rapidly, and he believes that only the human genome is deteriorating rapidly. Do you see a problem here? Dave doesn't.It's worse than that: Crow makes reference to Drosophila which are decaying by that 1-2%. Given that there have been considerably more than 300 fly generations since the 'flood', flies must be extinct except, of course, in the lab where we keep a few to study.

How about that, Dave? Notice any flies around recently down there in Missouri? According to you, they don't exist.

Eric, the principle reason that Dave is suddenly ignoring posts - more so than usual, at any rate - is that he suddenly realized that he was, in fact, wrong. We are now reaching the 'stubbornly refusing to admit error' stage.

[Coragyps]

Folks - if you want moderator attention, please use the exclamation point button in the lower left corner of the post you wish to draw attention to. The thread itself is not the place for this.

[Amaleq13]

From this it appears that Crow believes ...
1) That harmful mutations have been accumulating for the last several centuries (What's several? 3? 4?)...

Why do you keep avoiding the word Crow actually uses (ie few)? I don't know how many centuries Crow had in mind but 3 or 4 seems like a reasonable guess.

...2) Humans are like Drosophila in that for at least the time period above, we have experienced a decrease in viability from mutation accumulation is some 1 or 2% per generation....

Why do you think Crow used the word "IF" to qualify his statement?

What I am objecting to is your turning an "if" statement into an assertion.

Just use the actual words Crow wrote, Dave, and you will be much better off.

You all seem to believe that Crow is simply talking about the ability of modern medicine to keep people alive longer, thus causing many harmful mutations to be retained in the population. However, this only applies to the last hundred years (or less). A careful reading of this indicates that Crow is talking about keeping a good social order, i.e. no huge wars or famines.

I just pointed this out to you after you referred only to "modern medicine" as a factor. :rolleyes:

Correct me if I am wrong, but modern medicine does NOT apply to the last several centuries ... only to about the last 100 years or so (maybe less).

First, Crow doesn't restrict the obstruction of natural selection to "modern medicine" but refers to the more broad category of "environmental improvements".

Nothing there about modern medicine.

You don't think Crow would include modern medicine as one of the "environmental improvements" that impeded natural selection? :eek:

But if you want to talk about medicine, see the Wiki article on the History of Medicine here ...

Yes and everything from the section titled "European Renaissance and Enlightenment medicine" until the end is part of the "environmental improvements" to which Crow is referring. I think you will find that it actually goes well beyond the "few" centuries Crow suggests.

So it seems that YOU have misinterpreted Crow ... not me.

You turned an "if" into an assertion, "few" into "several", and failed to comprehend that the Wiki article you referenced actually goes beyond Crow in suggesting when medical advances started making a difference.

It would seem that, contrary to your assertion, all you've managed to do is provide additional evidence that you don't understand Crow as well as evidence that you are also capable of misreading a Wikipedia article.

[Steviepinhead]

Dave, you are--apparently--determined to dance around the question.

You claim that, over the last five thousand years or so, all the kinds, taxa, whatever--exactly at what taxonomic level these were, how we would rigorously define them, why most of them show no evidence of recent genetic bottlenecks, etc., are all questions you have failed to address--have madly speciated to produce the thousands of land-dwelling metazoan species that we currently see all around us.

This claim necessarily requires a huge mutation rate.

You claim that few if any mutations can create new information or confer any but the "narrowest" of benefits.

You claim, along with Sanford, and in contradiction to Crow, that accumulation of harmful, non-creative, non-information generating, non-benefit conferring at such a rate will inevitably lead to extinction at the rate of 1-2% per year or 300 hundred generations.

You claim this explicitly at least for Drosophila, based on your and Sanford's mis-reading of Crow, and for humans (likewise). You necessarily claim it for all other metazoan species which have recently and furiously radiated from their kinds.

Yet, as eric and others have repeatedly pointed out to you, if you continue to hold to all these claims, and their inevitable logical corollaries, then you need to explain why--except as to a very few long-generation species--none of these metazoan species have accumulated such a load of non-beneficial mutations so as to go extinct.

Being's how almost all these critters--with the few exceptions noted above--have gone through many more than 300 generations in the past 5,000 years.

You haven't come forward with any such explanation. Or for any mechanism which would explain why Drosophila and Homo are accumulating the degenerative mutational load, but no other species are: what safeguards all the other species? Why does God just have it in for humans and fruit flies? Why have all the other ill-defined taxa/kinds speciated madly, but the "human" kind has not? Particularly given the high degree of degenerative mutation you are claiming for humanity? Why, for that matter, are there only four non-human great apes, compared with all the members of the mustelid, canid, or felid "kinds"?

Because you are determinedly refusing to engage questions of this kind, which necessarily arise based upon the claims you are making, we are now in a position to reliably presume that you simply have no adequate responses to these questions.

Which, in turn, allows us to authoritatively reject your claims as incorrect.

Where exactly in your chain of reasoning you have gone wrong is left as an exercise for the reader.

[Calilasseia]

You turned an "if" into an assertion, "few" into "several", and failed to comprehend that the Wiki article you referenced actually goes beyond Crow in suggesting when medical advances started making a difference.

It would seem that, contrary to your assertion, all you've managed to do is provide additional evidence that you don't understand Crow as well as evidence that you are also capable of misreading a Wikipedia article.

I have to tell you that this is actually an improvement upon past performance with respect to egregious quantifier abuse in discourse upon his part. Previously, he's been known to extrapolate from "observation X applies to a small section of the genome" (Professor Roy Britten's Indels paper from 2002) to "observation X applies to the whole genome" courtesy of a quote mine. I can reproduce the requisite material on demand if you wish.

His habit of deciding that he knows better what scientists mean by their words than the scientists themselves has been in other places, quite frankly, a serious irritant. Britten isn't the first instance - when I introduced him to the work of Professor Sir Cyril Clarke, who was a member of the same entomology society as me prior to his death, Dave claimed to know better what Prof. Clarke was saying that Prof. Clarke himself did, until I pulled up the Wellcome Seminar on Prof. Clarke's work which included seminar dissertations delivered by extant members of Prof. Clarke's team.

[Worldtraveller]

It's already been mentioned once. Keep your posts directed at the posts and material and not the poster. Behavior at other boards is irrelevant here, as is discussion of who may or may not have been banned, suspended, or otherwise disciplined at other boards.

Further discussion of afdave, and not afdave's posts here will be moved and could result in this thread being locked.

Lane, E/C Moderator

[VoxRat]

I give up.

I'll check back tomorrow to see if any of my questions is at least acknowledged:

"significant portions" of Darwin? What would that mean? Most of it? Half of it? The parts that AiG likes to quotemine?

Please share with us what you think are creationist predictions about "junk DNA" that have been made, and what you think are evolutionist predictions about it. Creationists have a habit of telling us after discoveries that they "predicted it all along". However, they can't point to anything specific. That's why I'm asking. That's why you'll probably not respond.and speaking of misrepresenting people, are you planning to address this...
Sure enough. Just as I retrodicted. You have misrepresented your source. The fact that 99% of species have gone extinct, and the fact that Homo sapiens is likely to join them, says nothing about "mutational meltdown". Species go extinct from all kinds of causes.
The basis for these predictions is that the Creator would not create junk.Predictions? What predictions???

I looked up your links, and - in addition to seriously misrepresenting the predictions of real scientists - I couldn't find a single creationist prediction.

What did I miss?You have to actually click the links and read the articles. The first one is the relevant one about nylon-eating bacteria.

So why didn't you c&p the relevant part? Why would I click a link listed after a bunch of irrelevant stuff about antibiotics and plasmids?

I have read their nonsense on the nylonase gene, though, and find it indefensible. Is that why you chose not to excerpt that part?
afdave discussed Sanford, Crow, etc. here (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=SP;f=14;t=3131;p=37676).

Are you planning to bring up something new now, afdave? Because, if not, why don't people just go to the discussion from last year? Seems like a monumental waste of time, effort, and bandwidth.Seriously, Dave.

I would really like you to answer this question.

So far it appears to be "deja vu all over again".

Are you planning on introducing anything new? Anything that wasn't thoroughly aired here (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=SP;f=14;t=3131;p=37676). ? In fact, the evidence indicates that they [plasmids] were designed. '

Yet another baseless assertion.

Since you think everything in life was "designed", isn't it kind of vacuous to say "the evidence indicates that" plasmids were designed, without even suggesting what that evidence is? What evidence? Is there something particular about plasmid DNA for which there's evidence that's more compelling than - or even different from - the "evidence" that any other DNA was "designed"?By the way, Dave.

From your discussion of Sanford at AtBC (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?):Dr. John Sanford has been a Cornell University professor for more than 25 years in the area of plant breeding and plant genetics. He has published over 70 scientific publications, and was granted over 25 patents. His most significant scientific contributions involved three inventions -- the biolistic ("gene gun") process, pathogen-derived resistance, and genetic immunization. Most of the transgenic crops grown in the world today were genetically engineered using the gene gun technology developed by John and his collaborators. John also started two successfull businesses deriving from his research -- Biolistics, Inc. and Sanford Scientific, Inc.Now, since you didn't attribute that to anyone else, I guess we should assume that you wrote it. Though it does look to me suspiciously like a C&P.

Anyway, you might want to check your sources, because - while I believe he was responsible for the "biolistic process" - pathogen-derived resistance and genetic immunization are definitely not his inventions.It is only the human genome that we are discussing. I suspect that we would find the same deterioration if we studied other genomes, but I have no comment on them now. As it happens, there is one mentioned right there in the Crow paper ... Drosophila.You mean Drosophila bred in laboratory conditions, where - once again - all selective pressure has been removed? Or Drosophila in the wild? Kind of important distinction, in light of the discussion about the effects of modern civilization on selective pressures on humans, wouldn't you say?Again, Kondrashov... all this was discussed at AtBC. Do you have anything new, Dave? Because, as you'll recall, no one found your Sanford very persuasive last time 'round.
Dave? Drosophila? Wild or laboratory? You do see why I ask, don't you?

[Calilasseia]

Meanwhile ...

Which of these two options do you subscribe to Dave?

[1] The human genome (and possibly the Drosophila genome as well) is sufficiently fragile that it will disintegrate and result in our extinction in 300 generations, but no other eukaryote genome is affected;

[2] All eukaryote genomes are sufficiently fragile to result in extinction within 300 generations.

Either way, you have some explaining to do. And we've been waiting for some time now. Pick one OR the other, but do NOT try to switch between them for the sake of convenience as the moment dictates.

[Rhaedas]

It reads to me that Crow is discussing the mutation effect of the human population at the point where this population curve takes an upward bend. There are a lot of reasons this curved upward and medicine is a big, but not sole, reason.

Might we also see a similar trend in domesticated species as well, given they would be artificially protected from natural selection by man? The first obvious example would be dogs, compared to wild canines.

Ironically, introducing this seems off topic even though it is related to the OP's cited paper. :Cheeky:

[ck1]

Meanwhile ...

Which of these two options do you subscribe to Dave?

[1] The human genome (and possibly the Drosophila genome as well) is sufficiently fragile that it will disintegrate and result in our extinction in 300 generations, but no other eukaryote genome is affected;

[2] All eukaryote genomes are sufficiently fragile to result in extinction within 300 generations.

Either way, you have some explaining to do. And we've been waiting for some time now. Pick one OR the other, but do NOT try to switch between them for the sake of convenience as the moment dictates.

what about

[3] All eukaryotic genomes are headed for extinction, but the rate of "genomic decay" varies for each species and may be controlled by factors such as number of genes, amount of noncoding DNA, selection pressure...

Also, why is 300 the magic number? I missed that explanation.

[ck1]

Dave,

Since this thread is about Sanford's book, why not present a succinct outline or summary of the main points of Sanford's thesis instead of listing the mainstream papers he cites. This would be particularly helpful for this discussion since this book is not widely available.

Also, I just noticed this from a few pages ago:


Note Bergman's article on viruses, plasmids and other replicons and their role with bacteria ... ...(big snip)
http://www.trueorigin.org/virus.asp

I have not finished reading this article about viruses in Trueorigin. So far, it reads like the author spent a day or so reading random things about viruses just before he wrote the article. Imagine my surprise to see he claims to teach college level microbiology!

[RBH]

Izzat Jerry Bergman? Community college (http://www.northweststate.edu/). Long-time old-style creationist.

RBH

[ericmurphy]

Dave,

Since this thread is about Sanford's book, why not present a succinct outline or summary of the main points of Sanford's thesis instead of listing the mainstream papers he cites. This would be particularly helpful for this discussion since this book is not widely available.

As far as I can tell, Dave has merely paraphrased Sanford to say that, since Crow has demonstrated that the human genome is falling apart at the seams and no mechanism can stop it, humans can't be more than a few thousand years old as a species.

Anything you'd care to add to my summary, Dave?

[Mike PSS]

Might we also see a similar trend in domesticated species as well, given they would be artificially protected from natural selection by man? The first obvious example would be dogs, compared to wild canines.

Ironically, introducing this seems off topic even though it is related to the OP's cited paper. :Cheeky:
Not OT at all.

Dave and others have narrowed a part of this discussion to the effect of medicine alone on the limiting of selection to the human genome.

The other factors for humans like cities, agriculture, stability, etc. would contribute in some quantity to this selection avoidance too.

A counter point would be that agriculture, although providing a benefit to the species, would only change the equilibrium population that's sustainable to a new level and wouldn't infer any advantage/disadvantage to the genome overall. There is a case either way since some genetic mutations that are exhibited in an agrarian society would no longer be selected because of societal support of these "mutants" compared to a hunter gatherer society (more comparable to other animal organizations).

The domesticated animals are a very good point. Human selection is imposed to overcome natural selection through breeding.

[FatherMithras]

afdave, you still have noy used a reliable source, or shown any evidence of ´´design´´ as far as evolution is concerned. The nylon eating bacteria acquired a novel trait through a specific mutation. The AIG nonsense (and remember, they aren´t relevant scientists, so they´re arguments don´t even matter) of it beig ´´so fast and weird!´it had to be designed is a farce. Who says mutations can´t be selected for at that rate? Nothing contradicts the evidence, and nothing indicates design.


Why do you only use non scientific sources? Why does no one who knows science agree with you Dave? Are you so smart that you´re smarter, and better able to understand genetics than people who´ve worked their whole lives? Why are you, AIG, or Trueorigins, none of whom have even a hint of credibility, more reliable than these people? If you want to respond in PM, fine. But your continuous dodging is getting old. Please just answer the question. it isn´t difficult, even among all these replies, to answer this one thing many of us have asked.

Why do you not use valid sources? You´re like someone quoting Chinese history on the Great Leap forward, or L Ron Hubbard on mental health.

[Faid]

Sorry to beat a dead horse here, but you continue to misunderstand this paper. Crow's argument considers measured mutation rates and the number of generations a mutation persists and ultimately argues that the accumulation of mutations is balanced by quasi-truncation selection. He says:

The 1-2% mutation accumulation is what he estimates happens IN THE ABSENCE OF SELECTION. And in the absence of selection due to environmental improvements (he does not specifically mention modern medicine), he argues humans are currently accumulating mutations and this is a bad thing.He concludes this, but he does not demonstrate this. It is speculation born from his preconceptions of the 'fact' of evolution. I.e. he is firmly convinced that H. sapiens has roamed the planet for 200,000 years and we should have died b/c of mutation accumulation, yet "Here we are!" So, given his pre-commitment, he HAS to propose some explanation of how we could have possibly survived this long.

Here we go again.

Dave,

What you just wrote is a gross inaccuracy. And you are fully aware of it, and have been for months now.

It was pointed out to you here. (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=SP;f=14;t=3131;p=41925)

You were pointed to the fact that Crow, Kondrashov and Kimura do, in fact, "demonstrate" their claims, and provide models and calculations which show how they can work:

http://www.pnas.org/cgi/reprint/76/1/396

http://www.genetics.org/cgi/reprint/120/3/853.pdf

While it is Sanford who, apparently, simply asserts his claims, with no support.

You gave no meaningful response to this, dave. None whatsoever, as everyone can see- except that you would "get Sanford to explain it" to us. Which remains an unfulfilled promise until now.

Can you please explain then why, after many months and in a different forum, you simply reassert that Crow et al "do not demonstrate" their claims, in spite of being thoroughly refuted back then, and left unable to support this claim?

I await your answer with great interest.

[JLK]

Yes, Faid has summed up the key point Dave has an issue with in the OP.
That's what Dave wants to discuss apparently, rather than all this stuff about new functions etc.
Crow's suggestion that QTS (quasi-truncation selection) can solve it--that I believe he is wrong.Ok. As Faid said, you have to point out what is wrong with Crow's paper on truncation selection (http://www.pnas.org/cgi/reprint/76/1/396.pdf).
Then explain why truncation selection has been applied to analyze human genetic disease (http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16175512).
Truncation selection is mostly about rejecting the ridiculous simplistic idea that deleterious mutations' effects are simply multiplicative in decreasing reproductive success. Although bacteria and viri have found ways to overcome truncation via epistasis, a higher organism with multiple deleterious mutations is likely less fit than the multiple of the fitness coef of those with the single deleterious mutations.
But the subject of this thread is Sanford and his argument that genomes are deteriorating.We're on page 9 and, besides Crow's human oriented paper in your OP, you still have not told us what papers about non-human organisms Sanford claims show "genome deterioration".

[Godless Dave]

Sorry to beat a dead horse here, but you continue to misunderstand this paper. Crow's argument considers measured mutation rates and the number of generations a mutation persists and ultimately argues that the accumulation of mutations is balanced by quasi-truncation selection. He says:

The 1-2% mutation accumulation is what he estimates happens IN THE ABSENCE OF SELECTION. And in the absence of selection due to environmental improvements (he does not specifically mention modern medicine), he argues humans are currently accumulating mutations and this is a bad thing.He concludes this, but he does not demonstrate this. It is speculation born from his preconceptions of the 'fact' of evolution. I.e. he is firmly convinced that H. sapiens has roamed the planet for 200,000 years and we should have died b/c of mutation accumulation, yet "Here we are!"

No, that's not what he says at all. Where do you think he says that?

[Calilasseia]

So when are those outstanding questions going to be answered I wonder?

Plus, I wonder when Dave will actually present a detailed presentation of Sanford's arguments, preferably backed up with the man's own words quoted liberally and with full surrounding context?

And no, "why don't you go buy his book" doesn't qualify as an answer.

YOU are the one who claims to possess this knowledge Dave, demonstrate to us that you have this knowledge. If you don't possess this knowledge, admit it.

[Godless Dave]

Might we also see a similar trend in domesticated species as well, given they would be artificially protected from natural selection by man? The first obvious example would be dogs, compared to wild canines.

I know domestic cattle cannot survive in the wild, as have great difficulty giving birth without human assistance.

[deadman_932]

I know domestic cattle cannot survive in the wild, as have great difficulty giving birth without human assistance. No offense, GD, but I seem to recall there were feral cattle running around the U.S. for ..well, centuries. Texas Longhorn and Florida "Cracker" cattle, for example, featured in histories/tales of the areas and descended from Spanish cattle. I was born in New Mexico, so I have no idea whether other breeds can go feral, but I'm pretty sure about those. Apparently ( I just did a quick search) there's a bunch of 'em in Oz, too: http://www.abc.net.au/news/australia/wa/kimberley/200610/s1760484.htm
I dunno about the dairy cattle you probably have up there, though, either...I'm sure there's a continuum at play here. A smart German shepherd or..well, a dingo..should be able to handle itself in the wild for a lot longer than a freaky teacup poodle, I'm sure.

[Godless Dave]

I was referring to dairy cattle, but I may be mistaken altogether.

However, I'm not aware of Texas Longhorns ever being feral. They were herded over the open range, but they weren't just left unattended. Maybe you're thinking of wild horses? They are descendents of domestic horses that live wild.

[Dean Anderson]

I now have a response from Professor Crow (and permission to reprint it here), clarifying what his lecture was about.

Here is my email to him and his response (I have included the full text of each, so no accusations of quote-mining or taking-out-of-context can be made):

Professor Crow,

My name is Dean Anderson, and I am one of the Administrators of the Internet Infidels Discussion Board (www.iidb.org), a web forum which aims to provide scholarly debate on Evolution/Creation issues (amongst other things).

Recently, we have had a Young Earth Creationist register with us, and he is citing some of your work – specifically your November 14th 1996 lecture to the National Academy of Sciences entitled “The high spontaneous mutation rate: Is it a Health Risk” (an online copy of which is at http://www.pnas.org/cgi/content/full/94/16/8380).

More specifically, he is citing this lecture in support of Young Earth Creationism – and says (although without a direct quote) that the article is also cited as evidence supporting Creationism by Dr John C. Sanford (Bio here: http://en.wikipedia.org/wiki/John_C._Sanford) in his book “Genetic Entropy & the Mystery of the Genome”.

His claim (and, I think, Sanford’s claim – although I have not been able to get a quote from Sanford confirming this) is not just that your lecture can be used to support Creationism, but that it is actively making Creationist claims. He interprets your conclusion as follows:

1) Harmful mutations have been accumulating over the past few centuries.

2) Therefore our ancestors of a few hundred to a few thousand years ago had fewer harmful mutations that we do.

3) Therefore our ancestors of a few hundred to a few thousand years ago would have been stronger, fitter and more fertile than we are.

4) Therefore our species cannot be more than a few thousand years old, because if we were then the number of harmful mutations would have already reached a critical point and we would be extinct.

5) This decrease in genetic quality also supports the Biblical account in Genesis, because:

a) The further back we go, the fewer mutations we have and the closer to the genetically “perfect” Adam we get.

b) The better genes and better health of our ancestors supports incredibly the long ages for people listed in Genesis, since people could have lived to 900+ years old.

c) The better genes and greater fertility of our ancestors allow for the rapid post-Flood repopulation of the world within a few hundred years.

Needless to say, the vast majority of users of our forum disagree, and take the very opposite meaning from your lecture – that our ancestors were less healthy than us, and more prone early deaths as natural selection weeded out the same harmful mutations that we can carry with little (short term) problem due to advances in medicine.

I would be very grateful if you could provide me some kind of comment on this Creationist interpretation, and give me permission to post your comment on Internet Infidels as a response to those Creationists who are (in our opinion) badly misrepresenting your views.

Kindest Regards,

Dean AndersonDear Dean Anderson,

Here are my point-by-point comments on the comments of the Young Earth Creationist,

1) Harmful mutations occur every generation, but are eliminated by natural selection. Although most mutations are harmful, some are favorable and these are retained and increased by natural selection. This has been going on for billions of years.

2) I suggested in the article that in recent years, as a result of environmental improvement, the effect of natural selection was diminished, If this is correct, there are probably more harmful mutations in the population than there were a thousand or so years ago. The reason we don't notice this is because we have greatly improved living conditions so that mutations that would have been harmful at an earlier time are much less so now.

3) If my conjecture is correct, our ancestors of a few hundred to a few thousand years ago would have had more mutations than we do. This does not mean that they were stronger, fitter, or more fertile. They lived in a time of great environmental stress and would have been less strong, less fit, and less fertile than we are, thanks to the fact that our life is a lot easier than that of our ancestors..

4) My comments had to do with only the recent past (a few thousand years). In the long run, harmful mutations are eliminated by natural selection. Both mutations and natural selection have been going on since life began, billions of years ago.

5) My work (and my conjecture) offer no support for the Genesis account.
They are entirely consistent wit the neo-Darwinian theory.

I hope this is useful. I would welome your comments.

Sincerely, James F. Crow

[deadman_932]

Ah, thank you, Dean. One more sharp pair of scissors removed from the hands of our young running creationist.

G.D. I'll give it a search, but I think we're kind of misunderstanding each other...what I meant was Longhorns come from Spanish cattle that went feral and were truly feral for a long time, like the Spanish horses. Finding cattle bones in a dig is a pain, they throw everyone off and look a lot like Bison. Hah, I'm just happy about that little e-mail Dean got.

Yo, AFDave? Do ya like apples?

G.D.: Yeah, it looks like they were feral...However, the cattle did not descend directly from Spanish stock. Rather, the first cattle to be imported by the early Spanish explorers were from the Canary Islands. These cattle, in turn, were imported from Portugal, and the closest relatives of Texas Longhorns among existing European breeds are Portuguese cattle breeds (such as the Alentejana and Mertolenga). These early imports of Iberian cattle from the Canary Islands soon became feral in northern Mexico (which included lands that became the Republic of Texas in 1836, and part of the United States in 1845). http://home.austin.rr.com/doublehelix/FAQ.html
There's a bunch on 'em here: http://home.austin.rr.com/doublehelix/longhornlinks.html and the best history I see is this one:
http://home.austin.rr.com/doublehelix/History.html
That's way more info on Longhorns than I imagined.

[mung bean]

Well this doesn't look good for Davey, although I expect he will simply claim that Crow is wrong except when he agrees with Dave.Dear Dean Anderson,

Here are my point-by-point comments on the comments of the Young Earth Creationist,

1) Harmful mutations occur every generation, but are eliminated by natural selection. Although most mutations are harmful, some are favorable and these are retained and increased by natural selection. This has been going on for billions of years.

2) I suggested in the article that in recent years, as a result of environmental improvement, the effect of natural selection was diminished, If this is correct, there are probably more harmful mutations in the population than there were a thousand or so years ago. The reason we don't notice this is because we have greatly improved living conditions so that mutations that would have been harmful at an earlier time are much less so now.

3) If my conjecture is correct, our ancestors of a few hundred to a few thousand years ago would have had more mutations than we do. <snip>I'm curious about this last sentence before the snip, however. It appears to have a typo in it. My understanding was that our ancestors would not have had more mutations, just that the ones they did have would have affected them more severely. Can someone clear this bit up for me? Is it a typo or not?

[deadman_932]

our ancestors of a few hundred to a few thousand years ago would have had more mutations than we do. This does not mean that they were stronger, fitter, or more fertile. They lived in a time of great environmental stress and would have been less strong, less fit, and less fertile than we are, thanks to the fact that our life is a lot easier than that of our ancestors..
I worked in paleoanth for a long time, then archaeology, Dave...and the one thing that I can say for just about every early agricultural group...like those of 4,000 BCE in the middle east..is that they lived shorter lives, had more disease and infant mortality was enormous. This is why Rohl mentioned lots of dead egyptian young, Dave.

We find the same decline in lifespan and increase in infant mortality across the world as agriculturalism comes into focus, dave...neolithic hunter-gatherers lived much healthier lives, hitting pretty advanced ages in comparison.

This is one reason why I opted for prehistoric archaeology --as soon as people move from hunter-gatherer bands and start engaging in horticulturalism and then agriculture, you can see what living sedentary lives in cramped little boxes in large groups does. Disease and nutrition problems due to narrower ranges of foodstuffs...go look at some teeth from the Natufian early agriculturalists, or the Amerind Moundbuilders, or the early chinese , or the africans collecting and then farming barley and sorghum.

Thier teeth become stubs because you have to grind grain. Imagine eating sand/grit/detritus from grinding on stones, or even grinding in wood that contains silicates....imagine that in your food every day all your life ---and guess what kills people who have no dentists, dave?

Additionally, their water sources can become depleted...forests get ravaged to collect firewood...trash piles up, domesticated animals become reservoirs of disease, etc.

Archaeology teaches people a few things, Dave.
One is "don't shit in your own nest" because that's what brought down a lot of groups.
Another thing you learn is people tend NOT to change until disaster strikes. You might want to keep that in mind as you face reality.

Of course, I had already given you this little talk when I described LONG AGO ..WHY written languages don't come into play up until recently --when large-scale chiefdoms and states begin to appear. The reasons for increasing social complexity, sedentism and domestication vary due to geographical and environmental differences , but when people begin using storage, sedentary habitation sites, hierarchical social systems with increased specialization, etc...WRITING becomes necessary in many instances to keep track of goods and trade -- in a word, economics. Religion/ideology can also play a part as they codify former oral traditions, then mystify it ...make it "sacred" so it can control entire populations where priests and kings work together and ...stratification happens. Look at the early writing centers. Notice how they coincide with agriculturalism/city-states across the world? I TOLD you about all this, describing how circumscription works, both geographical and social...but you don't LISTEN to or READ anything that doesn't fit in your narrow little fantasy world.

Take a few damn university courses, Dave...read a book other than "The L'il Thumper Baptist Guide to History"
LEARN something and quit depending on others to constantly teach you while you sit on your ass and pretend at knowledge.

[Godless Dave]

G.D. I'll give it a search, but I think we're kind of misunderstanding each other...what I meant was Longhorns come from Spanish cattle that went feral and were truly feral for a long time, like the Spanish horses. Finding cattle bones in a dig is a pain, they throw everyone off and look a lot like Bison. Hah, I'm just happy about that little e-mail Dean got.

...

G.D.: Yeah, it looks like they were feral...However, the cattle did not descend directly from Spanish stock. Rather, the first cattle to be imported by the early Spanish explorers were from the Canary Islands. These cattle, in turn, were imported from Portugal, and the closest relatives of Texas Longhorns among existing European breeds are Portuguese cattle breeds (such as the Alentejana and Mertolenga). These early imports of Iberian cattle from the Canary Islands soon became feral in northern Mexico (which included lands that became the Republic of Texas in 1836, and part of the United States in 1845). http://home.austin.rr.com/doublehelix/FAQ.html
There's a bunch on 'em here: http://home.austin.rr.com/doublehelix/longhornlinks.html and the best history I see is this one:
http://home.austin.rr.com/doublehelix/History.html
That's way more info on Longhorns than I imagined.

OK, thanks, I didn't know that. I stand corrected.

[deadman_932]

Mung: yeah, the context shows it as a typo. He had "increased" on the mind when he should have written "fewer"

Being subject to more stringent selection pressures, they had fewer mutations than we have...they'd die where --- with our modern tech and science -- we live and accumulate more.

Crow's paper in question states it quite clearly:
However efficient natural selection was in eliminating harmful mutations in the past, it is no longer so in much of the world. In the wealthy nations, natural selection for differential mortality is greatly reduced. A newborn infant now has a large probability of surviving past the reproducing years. There are fertility differences, to be sure, but they are clearly not distributed in such a way as to eliminate mutations efficiently. ....James F. Crow (1997) : The high spontaneous mutation rate: Is it a health risk? Proc. Natl. Acad. Sci. USA Vol. 94, pp. 8380-8386, August. http://www.pnas.org/cgi/content/full/94/16/8380

Bah, I reverse things like that a lot, which is why you'll see so many "edits" in my posts

[Jet Black]

... I TOLD you about all this, describing how circumscription works, both geographical and social...but you don't LISTEN to or READ anything that doesn't fit in your narrow little fantasy world.......

but we're reading it, and it's pretty interesting stuff :) remember dave isn't the only person reading your posts although they are directed at him, so explaining it again won't be wasted :)

[mung bean]

Mung: yeah, the context shows it as a typo. He had "increased" on the mind when he should have written "fewer"

Being subject to more stringent selection pressures, they had fewer mutations than we have...they'd die where --- with our modern tech and science -- we live and accumulate more.
Yep, clear enough. Beats me why Dave refuses to see it when everyone else can. I thought I'd better bring up the typo mainly because I know Dave will pick on any discrepancy he spots, although he may well have missed this one since it doesn't help his case.
Interesting about the change from hunter/gatherer to agrarian society. I'd read something similiar before (Jared Diamond, maybe). From memory he said that not only was tooth wear and the resulting bacterial infection a problem for health but also the more restricted diet, resulting in malnutrition.
Of course disease also spreads more rapidly in crowded conditions as you mentioned.

[Dean Anderson]

Mung: yeah, the context shows it as a typo. He had "increased" on the mind when he should have written "fewer"

I've asked Professor Crow to confirm whether this is a typo or not, so that there can be no ambiguity or quote-mining of his text.

[VoxRat]

Well, here it is "tomorrow"

I checked back. And sure enough, afdave has still not addressed any of my outstanding questions.

I think I've seen this movie several times already.

[Oolon Colluphid]

To be fair, he has PMedme his email, and I've forwarded some of the Notothenioid papers. So I guess he's busy writing his critique for me to forward to Henry Gee...

[mung bean]

To be fair, he has PMedme his email, and I've forwarded some of the Notothenioid papers. So I guess he's busy writing his critique for me to forward to Henry Gee...Yowza. Critique will state teh antifreeze fishies are an example of microevolution within a kind. God gave em oodles of genetic richness coz he knew the Antarctic would be bloody cold one day.

[Dave Hawkins]

Dr. Crow wrote ... Dear Dean Anderson,

Here are my point-by-point comments on the comments of the Young Earth Creationist,

1) Harmful mutations occur every generation, but are eliminated by natural selection. Although most mutations are harmful, some are favorable and these are retained and increased by natural selection. This has been going on for billions of years.

2) I suggested in the article that in recent years, as a result of environmental improvement, the effect of natural selection was diminished, If this is correct, there are probably more harmful mutations in the population than there were a thousand or so years ago. The reason we don't notice this is because we have greatly improved living conditions so that mutations that would have been harmful at an earlier time are much less so now.

3) If my conjecture is correct, our ancestors of a few hundred to a few thousand years ago would have had more mutations than we do. This does not mean that they were stronger, fitter, or more fertile. They lived in a time of great environmental stress and would have been less strong, less fit, and less fertile than we are, thanks to the fact that our life is a lot easier than that of our ancestors..

4) My comments had to do with only the recent past (a few thousand years). In the long run, harmful mutations are eliminated by natural selection. Both mutations and natural selection have been going on since life began, billions of years ago.

5) My work (and my conjecture) offer no support for the Genesis account.
They are entirely consistent wit the neo-Darwinian theory.

I hope this is useful. I would welome your comments.

Sincerely, James F. CrowI got a reply similar to this, but he forgot to give me permission to post it. From his e-mail to me and also his paper it seems clear that the typo identified was truly a typo. We'll see if he confirms this.

Some analysis of his reply to Dean ... 1) Harmful mutations occur every generation, but are eliminated by natural selection. Although most mutations are harmful, some are favorable and these are retained and increased by natural selection. This has been going on for billions of years.This is a mixture of fact and Evolutionary doctrine, typical of mainstream scientists today. It is a fact that harmful mutations occur. It is a fact that SOME of them are eliminated by NS. It is a fact that most are harmful and that some are favorable. But the ratio of favorable to harmful are more like a teaspoonful of water compared to a lake. There are only a tiny handful of favorable ones, and these are equivocal at best. I have personally investigated several of them and they turn out to be favorable only in a very limited context. For example, the A-I Milano mutation (discussed at AtBC beginning Oct 20) is favorable because of a loss of specificity. No one knows what would happen if it were homozygous. This is a little like a man who lives in Antartica saying, "My car heater switch is broken--it's stuck on HIGH and HOT. Gee, isn't that lucky? A mistake that is beneficial to me!" Well, sure it's beneficial in that narrow, limited context, but it would not be if introduced in a wider context and it can in no way be thought of as 'creative.' It's a mistake. It's broken. So yes, a very few are favorable in these limited contexts, but the problem for evolutionists is that so many of these favorable mutations would have to line up just right and not be eliminated so they could ultimately form new genes, new proteins, new cell types, new organs and new body plans, etc. And the problem is huge because at every step, they need to confer an advantage or they may be eliminated before they reach the next "island of functionality."
3) If my conjecture is correct, our ancestors of a few hundred to a few thousand years ago would have had more mutations than we do. This does not mean that they were stronger, fitter, or more fertile. They lived in a time of great environmental stress and would have been less strong, less fit, and less fertile than we are, thanks to the fact that our life is a lot easier than that of our ancestors..Deadman says that he meant to say "would have had fewer mutations than we do." I agree and this would be consistent with his paper and consistent with Sanford's interpretation of what he said. Where it gets confusing for an evolutionist is where he says on one hand, that our ancestors had fewer mutations than we do, yet on the other hand, he inserts his opinion that they would have been less strong, less fit, and less fertile. How can this be? How can an organism with fewer mutations--mistakes according to Miller/Levine and Ayala--be less strong, less fit and less fertile? This is backwards. Why is a leading population geneticist saying something totally contradictory to known facts? The only reason I can think of is that he has subscribed to Evolutionary Doctrine which says that "mutations are the ultimate source of genetic variation." (Ergo, they are 'good' in the long run) This doctrine is misleading because, while it is true that mutations provide variation, it is almost always the "something is broken" kind of variation and usually does improve fitness in the wild. I gave this analogy a while back ...

"Man, I bought this beautiful new Ford Mustang back in 1967. It was red and it had an 8-track and chrome wheels and leather seats. Boy was it sharp. That was 40 years ago and you should see it now. It's got tears in the leather seats and the pretty foam shows through, the headliner has fallen down and I can see the bare metal roof, the front windshield has this beautiful spider web crack pattern on it, and the paint is no longer just a boring red ... it's got several earth tone and rust colored shades now. The left blinker has a new function--it stays on all the time instead of blinking ... isn't that cool? And my seat slides forward when I brake and slides backward when I hit the gas ... all by itself!! Man this is a cool car!" http://richarddawkins.net/forum/viewtopic.php?t=15972&start=266
4) My comments had to do with only the recent past (a few thousand years). In the long run, harmful mutations are eliminated by natural selection. Both mutations and natural selection have been going on since life began, billions of years ago.Conjecture again that sufficient harmful mutations are eliminated by NS to keep the species from mutational meltdown. And of course, conjecture that life began billions of years ago.

*******************************************

So again, while I agree that Dr. Crow has not become a creationist, and I agree that his comments were not intended to support Dr. Sanford's conclusions, they in fact DO support his conclusions.

[VoxRat]

Well, I have to admit that last time we went through this, we just had a half dozen people explaining the clear meaning of Crow's words to Dave. We didn't have Crow explaining the clear meaning of Crow's words to Dave. Perhaps we will now learn that Crow is wrong about what he meant.

[Dean Anderson]

Mung: yeah, the context shows it as a typo. He had "increased" on the mind when he should have written "fewer"

I've asked Professor Crow to confirm whether this is a typo or not, so that there can be no ambiguity or quote-mining of his text.

And he has confirmed that it is a simple typo, and that he meant "fewer".

[Dave Hawkins]

I don't think anyone has addressed Kondrashov's Question (http://www.iidb.org/vbb/showthread.php?p=4566297#post4566297) yet. The title of his paper ... "Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?" ... is quite an eye-catcher, wouldn't you say? Notice that Kondrashov says "This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations", which is why I keep saying that I'm not interested in talking about beneficial mutations on this thread. They are irrelevant according to Kondrashov, at least for the purpose of keeping our species alive. And my question is, "If VSDMs are contaminating the genome so much that beneficial mutations and environmental fluctuations cannot reverse their effect, then how in the world could mutations have EVER created our species? Or ANY species?"

My answer: they cannot. Only a Super Intelligence from somewhere could have created life.

[mung bean]

I don't think anyone has addressed Kondrashov's Question (http://www.iidb.org/vbb/showthread.php?p=4566297#post4566297) yet. The title of his paper ... "Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?" ... is quite an eye-catcher, wouldn't you say?Sure. It's eye catching. So what?
Notice that Kondrashov says "This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations", which is why I keep saying that I'm not interested in talking about beneficial mutations on this thread.Really. So what you're saying is that you refuse to discuss two of the main parts of evolutionary theory, namely beneficial mutations and environmental change. Well, aint that just dandy?

They are irrelevant according to Kondrashov, at least for the purpose of keeping our species alive.They are not irrelevant according to the vast majority of biologists.

And my question is, "If VSDMs are contaminating the genome so much that beneficial mutations and environmental fluctuations cannot reverse their effect, then how in the world could mutations have EVER created our species? Or ANY species?"If? Isn't that a rather big if?

Edit: Oi Dave, if you're so keen on Kondrashov's opinions why do you insist on discounting his solutions to the questions he raises?

[ck1]

I don't think anyone has addressed Kondrashov's Question (http://www.iidb.org/vbb/showthread.php?p=4566297#post4566297) yet. The title of his paper ... "Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?" ... is quite an eye-catcher, wouldn't you say? Notice that Kondrashov says "This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations",

Dave, How much of this paper did you actually read? The quote you give is in the abstract.

[shirley knott]

Leave it to anit-factDave to abandon one expert in favor of another as soon as his distortions of the first's points are exposed. Could it be we've seen this before? perhaps even repeatedly?
It makes one wonder if anti-factDave even *has* an argument, as opposed to mere opposition?
Hardly a way to make anyone take any of the points he raised seriously, now isn't it?

hugs,
Shirley Knott

[ck1]

Dave said:
For example, the A-I Milano mutation (discussed at AtBC beginning Oct 20) is favorable because of a loss of specificity. No one knows what would happen if it were homozygous.

I don't know whether homozygous individuals have been identified in human populations, but the mutation has been introduced into mice. The transgenic mice with two alleles are fine and I believe the mutation's effects are dose dependent - two are better than one.

http://atvb.ahajournals.org/cgi/content/full/19/5/1257

[Dave Hawkins]

CK1 wanted to know the chapter titles of Sanford's book ... OK ... here they are.

Sanford, J.C., Genetic Entropy and the Mystery of the Genome (2005)

Chapter 1: The Genome is the book of life. Where did it come from?
Newsflash - The genome is an instruction manual
Chapter 2: Are mutations good?
Newsflash - Mutations consistently destroy information
Chapter 3: How much mutation is too much?
Newsflash - Human mutation rates are much too high
Chapter 4: All powerful Selection to the rescue?
Newsflash - Selection capabilities are very limited
Chapter 5: Can Genomic problems be solved?
Newsflash - Selection cannot rescue the genome.
Chapter 6: A closer look at noise.
Newsflash - The problems are not really so bad --they're much worse!
Chapter 7: Crow to the rescue?
Newsflash - Crow solution [QTS] fails reality test
Chapter 8: Man to the rescue?
Newsflash - Eugenics, cloning cannot stop genomic degeneration.
Chapter 9: Can natural selection create?
Newsflash - Mutation/selection cannot realistically create a single gene.
Chapter 10: Is the downward curve real?
Newsflash - All evidence points to human genetic degeneration.
Personal Postlude: What hope?
Newsflash - There is a hope.

And of course, that hope is that the same Creator who created life has promised a new life for those who choose to accept it. Sanford concludes, "I humbly put before you this alternative paradigm for your consideration - Jesus is our one true hope."

In his Appendix, Sanford lists the primary papers which support his thesis, beginning with Haldane (1957) then Kimura (1968), Muller (1950 & 1964), Neel (1986), Kondrashov (1995 & 2002), Nachman/Crowell (2000), Walker/Keightley (1999), Crow (1997), Lynch et. al. (1995), Higgins/Lynch (2001), Hoyle (1999), and Howell (1996).

NOTE: Dr. Sanford limits his scope to the human genome but I see no reason why we should expect other genomes to be deteriorating also. I think there are far fewer studies to confirm this. I think most of the studies of this nature are on humans.

[Worldtraveller]

afdave, shirley knott (love the name, BTW!) makes a good point. If you want to talk about Kondrashov's paper, you should start a new thread.

This thread was started as a discussion of Crow's paper, and Sanford's apparent misinterpretation of it (now that misinterpretation has been confirmed by Crow). If you want to concede the argument and move on, that's fine. But if you want to chagne the subject because it's been shown that you are wrong, we will go ahead and lock this thread and you can start a new one on Kondrashov.

There are, in case you haven't noticed, at least a dozen or so outstanding questions still pending for you regarding your (mis)interpretation of Crow's paper.

Lane, E/C Moderator.

[mung bean]

Dave, I've just done a bit of scanning and according to VoxRat Kondrashov's paper was dealt with way back at AtBC. Now, surely you wouldn't simply be resurrecting an argument that had already been dealt with and claiming nobody had responded to it, would you?
Anyone got a link for AtBC so we can check on this?

[ck1]

So again, while I agree that Dr. Crow has not become a creationist, and I agree that his comments were not intended to support Dr. Sanford's conclusions, they in fact DO support his conclusions.

Dave, This is truly bizarre. The only way that Crow's statements "support" Sanford is if you completely discount what he says.

[Dave Hawkins]

I don't think anyone has addressed Kondrashov's Question (http://www.iidb.org/vbb/showthread.php?p=4566297#post4566297) yet. The title of his paper ... "Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?" ... is quite an eye-catcher, wouldn't you say? Notice that Kondrashov says "This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations",

Dave, How much of this paper did you actually read? The quote you give is in the abstract.I didn't claim to read the whole paper. The title and abstract is telling enough. But I could obtain it if you think it's necessary.

MB ... I have no problem discussing beneficial mutations in general as a proposed mechanism to prevent mutational meltdown ... what I don't want to get into on this thread is dissecting individual examples of beneficial mutations and arguing over whether they represent an increase in information or not, and whether they are capable of creating new genes, new cell types, new organs, new body plans, etc. This seems like a separate discussion to me.

[Steve_F]

Here's an interesting paper which demonstrates that genome decay can be reversed:

Estes, M. and Lynch, M. (2003) Rapid fitness recovery in mutationally degraded lines of Caenorhabditis elegans. Evolution, 57, 1022-1030.

Deleterious mutation accumulation has been implicated in many biological phenomena and as a potentially significant threat to human health and the persistence of small populations. The vast majority of mutations with effects on fitness are known to be deleterious in a given environment, and their accumulation results in mean population fitness decline. However, whether populations are capable of recovering from negative effects of prolonged genetic bottlenecks via beneficial or compensatory mutation accumulation has not previously been tested. To address this question, long-term mutation-accumulation lines of the nematode Caenorhabditis elegans, previously propagated as single individuals each generation, were maintained in large population sizes under competitive conditions. Fitness assays of these lines and comparison to parallel mutation-accumulation lines and the ancestral control show that, while the process of fitness restoration was incomplete for some lines, full recovery of mean fitness was achieved in fewer than 80 generations. Several lines of evidence indicate that this fitness restoration was at least partially driven by compensatory mutation accumulation rather than a result of a generic form of laboratory adaptation. This surprising result has broad implications for the influence of the mutational process on many issues in evolutionary and conservation biology.

[Steve_F]

NOTE: Dr. Sanford limits his scope to the human genome but I see no reason why we should expect other genomes to be deteriorating also. I think there are far fewer studies to confirm this. I think most of the studies of this nature are on humans.

As far as I am aware, genomic decay isn't limited to human population's, there are examples in other species. The accumulation of deleterious mutations, leading to extinction is called Muller's Ratchet and is a commonly recognised phemomena. There are various solutions to this. For example:

Khakhlova, O. and Bock, R. (2006) Elimination of deleterious mutations in plastid genomes by gene conversion. Plant Journal, 46, 85-94.

Asexual reproduction is believed to be detrimental, mainly because of the accumulation of deleterious mutations over time, a hypothesis known as Muller's ratchet. In seed plants, most asexually reproducing genetic systems are polyploid, with apomictic species (plants forming seeds without fertilization) as well as plastids and mitochondria providing prominent examples. Whether or not polyploidy helps asexual genetic systems to escape Muller's ratchet is unknown. Gene conversion, particularly when slightly biased, represents a potential mechanism that could allow asexual genetic systems to reduce their mutation load in a genome copy number-dependent manner. However, direct experimental evidence for the operation of gene conversion between genome molecules to correct mutations is largely lacking. Here we describe an experimental system based on transgenic tobacco chloroplasts that allows us to analyze gene conversion events in higher plant plastid genomes. We provide evidence for gene conversion acting as a highly efficient mechanism by which the polyploid plastid genetic system can correct deleterious mutations and make one good genome out of two bad ones. Our finding that gene conversion can be biased may provide a molecular link between asexual reproduction, high genome copy numbers and low mutation rates.

[mung bean]

Dave, How much of this paper did you actually read? The quote you give is in the abstract.I didn't claim to read the whole paper. The title and abstract is telling enough. But I could obtain it if you think it's necessary.

MB ... I have no problem discussing beneficial mutations in general as a proposed mechanism to prevent mutational meltdown ... what I don't want to get into on this thread is dissecting individual examples of beneficial mutations and arguing over whether they represent an increase in information or not, and whether they are capable of creating new genes, new cell types, new organs, new body plans, etc. This seems like a separate discussion to me.
Dave, reading the title and abstract is not enough to fully comprehend Kondrashov's position. If it was he wouldn't have bothered to write the rest of the bloody paper. You may have noticed that in the abstract he suggests solutions to the problems he raises. These will be explained in the paper, obviously.

Re mutations, natural selection is what prevents "mutational meltdown".

[Dave Hawkins]

Dave, I've just done a bit of scanning and according to VoxRat Kondrashov's paper was dealt with way back at AtBC. Now, surely you wouldn't simply be resurrecting an argument that had already been dealt with and claiming nobody had responded to it, would you?
Anyone got a link for AtBC so we can check on this?I don't remember anyone "dealing with" it. Here's the beginning of the Sanford discussion at AtBC.
BEGINNING OF SANFORD DISCUSSION: GENOMES ARE DETERIORATING, RM+NS IS WRONG (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=45d6ff87c69856ee;act=ST;f=14;t=3131;st=2507)

I remember statements like this from Jeannot ... jeannot
Posts: 629
Joined: Jan. 2006
(Permalink) Posted: Nov. 21 2006,12:51
...
Mutation rates and sexual reproduction are/were their fields of research. (Well, Kondrashov is interested in theoretical evolutionnary biology in general.)

The most famous paper produced by Kondrashov (it was in Nature) is a landmark in evolutionary biology. It explains the existence of sexual reproduction as a mean to purge deleterious mutations. It relies on high mutation rates. Muller had a similar hypothesis (Muller's ratchet) but it involve longer timescales.

Now, it seems quite normal that these scientists want to prove their point by measuring high mutations rate. Does it prove they are creationists? Only a clown like yourself would think so.Which of course, doesn't even address the issue. It creates a strawman ... that I am somehow trying to say that these guys are now creationists ... which is ludicrous. I never suggested this.

[Steve_F]

It's also worth pointing out that Sanford might be a little premature in writing his book, since we haven't got a full handle on the degree to which genomes decay. For example:

We need more precise estimates of the basic parameters in mtDNA, including the mutation rate in the coding region, the extent of mutation rate heterogeneity, potential low levels of recombination and the distribution of deleterious mutational effects. These may allow more detailed predictions of the molecular signatures (Charlesworth & Charlesworth, 2000) of decaying populations and may elucidate the solutions to the genomic decay paradox in human mtDNA, if combined with models that include more details like rate heterogeneity, different mutational effects (Butcher, 1995), rare recombination (McVean & Charlesworth, 2000) and spatial structure (Higgins & Lynch, 2001). It will be thrilling to see which of the various potential solutions actually solves the genomic decay paradox in mtDNA.

From the following paper:

Loewe, L. (2006) Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA. Genetical Research, 87, 85-94.

Does Sanford mention that we (including him) don't fully have a handle on this situation yet or does he gloss over this kind of complexity?

[mung bean]

Thanks. I'll read up on that link.
Btw Dave, did you notice that a mod has threatened to lock your thread due to your reluctance to answer outstanding questions here? These guys take their discussion board seriously. You are expected to actually discuss things.

[Steve_F]

Which of course, doesn't even address the issue. It creates a strawman ... that I am somehow trying to say that these guys are now creationists ... which is ludicrous. I never suggested this.

It does address the issue since it mentions some of the solutions that are being proposed. There is a vast amount of literature in this area.

[ck1]

(snip chapter headings)...
Sanford concludes, "I humbly put before you this alternative paradigm for your consideration - Jesus is our one true hope."

(snip ref list)

NOTE: Dr. Sanford limits his scope to the human genome but I see no reason why we should expect other genomes to be deteriorating also. I think there are far fewer studies to confirm this. I think most of the studies of this nature are on humans.

Well that is certainly an interesting set of chapter headings. But, for some reason, not an incentive to rush out and buy this book.

Dave, how can you tout this as a serious science book when it ends with that Jesus statement?

Certainly humans are the major focus in genetics/genomics, but much of what we know about eukaryotic genetics was developed in studies on flies and mice (as you can tell from the papers you cite - Crow and Muller).