Cornell Geneticist: Deteriorating Genomes Disprove Evolution (Continued)

[Dave Hawkins]

This thread is a continuation of the previous one found here ... Sanford/Crow Discussion

I repeat the chapter titles of Dr. Sanford's book here ...

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).

Dr. Sanford infers that ...

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.

We had a lively discussion of the Crow (1997) paper listed above. Apparently it was little too lively. I will do my part to keep this continued discussion just that ... a discussion. Not a pie throwing match. Now we continue with another paper that Sanford discusses ...

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

Author: Kondrashov A.S.
Source: Journal of Theoretical Biology, Volume 175, Number 4, 1995 , pp. 583-594(12)
Publisher: Academic Press

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.

I do have the paper now and I have studied it quite thoroughly.

Kondrashov begins with a little history of the study of Very Slightly Deleterious Mutations (VSDMs) and cites the familiar names in population genetics ... Haldane, Kimura, Crow, Ohta and others. He states that the study of VSDMs constitutes one of the pillars of population genetics. Hmmm ... pretty important I guess. He says that contamination by VSDMs has been carefully studied by Ohta (1992), but the study of the fitness of individuals has not attracted much attention, hence his study.

Following are some of the quotes from his paper that I want to discuss ...

WHAT IS SYNERGISTIC EPISTASIS?
He proposes this as a possible solution to his shocking question in his title, but what is it? Answer (sort of) ...

Even under the most efficient truncation selection, which is the extreme case of synergistic epistasis, the load is too high if ... [formula] (p. 586)

Apparently S.E. is a softer form of truncation selection which is artificial and simply kills off all the individuals with a mutation count higher than "X". Does S.E. work in the real world? I don't think anyone knows. Personally, I don't think so and I will cite some papers later of real researchers who have their doubts. Remember also, that this journal that Kondrashov is publishing in is called Journal of Theoretical Biology. Notice that word "theoretical." This is not real world stuff. It's theory. And as far as S.E. is concerned, I suspect it's probably wrong.

Moving on ...

The principle question is whether--as my analysis apparently suggests--contamination by VSDMs implies an excessive load, leading to the stochastic mutation load paradox. (p. 589)

And under "SIMPLIFYING ASSUMPTIONS" he says ...

I have assumed m~n. In fact m>=n. Even if only one suboptimal nucleotide is populationally neutral, while the other two have s>1/4Ne and have to be ignored, m=n if mutation rates are symmetric. Thus eqn (8)underestimates the expected contamination.
...
However, if mutations that increase the number of a state are more frequent than backward mutations, weak selection in a finite population may be
unable to prevent the unlimited increase of the average state number and, thus, the unlimited decline of fitness.
...
It is unclear how natural populations can avoid this [unlimited decline of fitness]. One possibility is that after some deviation from the optimum each next mutation becomes very deleterious (synergistic epistasis see below). Anyway, the assumption that there is an equilibrium contamination can only underestimate the impact of VSDMs.
...
Finally, I have extrapolated the results from an individual site to the whole genome. There is a consensus that this leads to underestimation of the
genome contamination (p. 589)

Then under "IS THE STOCHASTIC LOAD PARADOX REAL?" ...

According to Kimura, (1983:247) VSDMs do not cause any problem because (i) they accumulate very slowly and (ii) their impact can be easily counter-balanced by rare fixations of beneficial alleles. I do not think that this is correct. High contamination by VSDMs is reached after Ne of a lineage remains much smaller than G during ~1/m~10^8 generations. This may be the case in some vertebrates. In addition, if after a drop of Ne the expected equilibrium contamination is, say, 100, VSDMs may become important much sooner, ~10^6 generations after the drop. The total mutation rate in mammals is ~100 events per genome. [probably way low] If 10% of them are VSDMs with the average selection coefficient 10^-6 (implying Ne~10^5), they cause the decline of fitness by ~10^5 per generation (if initially all nucleotides were best). This decline will become important ~10^5 generations after the drop of Ne.

Finally, under "POSSIBLE RESOLUTIONS AND IMPLICATIONS OF THE PARADOX" ...

Because the stochastic mutation load paradox appears real, it requires a resolution. Five options must be mentioned.[Lists options including that the properties of equilibrium may be rare, Ne could be higher than he assumed, nucleotide sites with dangerous values of s may be rare, synergistic epistasis may operate, soft selection]

Notice how many times he says that "this assumption leads to an underestimate of genome contamination." This is a common theme in Sanford's book as he chronicles the investigation of Genome Contamination over the last 50 years from Haldane and Muller in the 1950's to Kimura in the 1960's to the modern investigators. In that time, we have gone from an estimated mutation rate of 0.1 (Muller 1950) to more than 100 (Kondrashov 2002). Sanford says Kondrashov has communicated to him directly that it is probably more like 300.

So what Sanford shows (and I will give more quotes of his) is that the more they investigate this Genome Deterioration thing, the worse the news gets.

OK ... I won't provoke anyone by drawing any sweeping conclusions just yet.

Let's see what you have to say.

[Constant Mews]

Originally Posted by afdave

This thread is a continuation of the previous one found here ... Sanford/Crow Discussion
[snipped irrelevant material]

Dr. Sanford infers that ...

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.

This syllogism is unsound, I'm afraid, and that is the base of the problem.

If (species go extinct) therefore (evolution cannot produce species) does not work. The fact is that we know that speciation takes place; we have current examples of speciation - chilchids, anyone? So any given species undergoing 'genetic meltdown' could speciate before that point. Second, Sanford is merely asserting that selection cannot save the species. We have shown you numerous studies which completely refute that point. Third, if you logic were correct, there would be no species in existence at all right now, flies for example would have committed special seppuku as it were.

We had a lively discussion of the Crow (1997) paper listed above. Apparently it was little too lively. I will do my part to keep this continued discussion just that ... a discussion. Not a pie throwing match. Now we continue with another paper that Sanford discusses ... I do have the paper now and I have studied it quite thoroughly.

The discussion was lively because you ignored all the material presented. Sticking your fingers in your ears and screaming "doesn't exist, doesn't exist" at the top of your lungs is bound to irritate folks after a while.

Kondrashov begins with a little history of the study of Very Slightly Deleterious Mutations (VSDMs) and cites the familiar names in population genetics ... Haldane, Kimura, Crow, Ohta and others. He states that the study of VSDMs constitutes one of the pillars of population genetics. Hmmm ... pretty important I guess. He says that contamination by VSDMs has been carefully studied by Ohta (1992), but the study of the fitness of individuals has not attracted much attention, hence his study.

Following are some of the quotes from his paper that I want to discuss ...

WHAT IS SYNERGISTIC EPISTASIS?
He proposes this as a possible solution to his shocking question in his title, but what is it? Answer (sort of) ... Apparently S.E. is a softer form of truncation selection which is artificial and simply kills off all the individuals with a mutation count higher than "X". Does S.E. work in the real world? I don't think anyone knows. Personally, I don't think so and I will cite some papers later of real researchers who have their doubts. Remember also, that this journal that Kondrashov is publishing in is called Journal of Theoretical Biology. Notice that word "theoretical." This is not real world stuff. It's theory. And as far as S.E. is concerned, I suspect it's probably wrong.

You don't know anything about genetics and epistatis - your opinion is meaningless.

This patterns continues throughout your post. All you have presented is two fallacies:

argument from authority

argument from personal incredulity

Neither of which is in the slightest convincing. In addition, you have completely ignored the various studies cited in the previous post which demonstrate that selection is quite effective in keeping 'bad' mutations under control - especially since the vast majority of mutations and recombinations are neutral.

[chapka]

So the paper in question points out an effect that would destroy any species in a small number of generations if left unchecked.

The authors are aware that, in fact, species do not go extinct due to deleterious mutations after a relatively short number of generations.

So, they propose mechanisms for addressing the paradox.

What's the relevance of this to creationism? If there is no mechanism to correct for this issue, it's not just an issue for evolution; it's an issue for common sense. AFAICT, we know of plenty of rapidly-reproducing species that fit the genome size/population size criteria, and they do not in fact go extinct.

So what's the relevance to creationism? Either there is a corrective force or there isn't. If there is, then there is no conflict for evolutionary theory. If there isn't, then the conflict is still not with evolution; it's with the basic observed facts that not all species are currently dying out in order according to their speed of reproduction, initial population size, and size of genome.

[Jedi Mind Trick]

Is this thread gonna take 20 pages for it to sink in that Sanford's YEC is not based upon science but upon a personal issue that caused him to get hit by the church bus? As such he wrote a book quote mining a real geneticist’s words and he is to be taken seriously? Does this topic deserve another thread?

[Jedi Mind Trick]

Oh I just want to add: taking the OP as fact for argument's sake... Is it intelligent design that created a deteriorating genome?

[Constant Mews]

Originally Posted by Blackwater

Is this thread gonna take 20 pages for it to sink in that Sanford's YEC is not based upon science but upon a personal issue that caused him to get hit by the church bus? As such he wrote a book quote mining a real geneticist’s words and he is to be taken seriously? Does this topic deserve another thread?

No - it will never sink in; yes; and no.

[Constant Mews]

Originally Posted by Blackwater

Oh I just want to add: taking the OP as fact for argument's sake... Is it intelligent design that created a deteriorating genome?

Yes. Per Dave, the Curse of Adam's Sin was the act of God. Therefore God created the deteriorating genome. Perhaps the Rapture occurs at just about genetic meltdown for the human species?

[Coragyps]

THIS THREAD WILL BE WATCHED CLOSELY!

KEEP IT CIVIL OR WE'LL LET THE CANDIRU LOOSE IN THE POOL!

---Coragyps the mod.

[ericmurphy]

Originally Posted by afdave

Dr. Sanford infers that ...

1) that populations will ultimately go extinct due to mutational meltdown and that selection, natural or otherwise, cannot save them

Dave, this is a statement of the obvious with an air of discovery. There is probably not a single species in existence today that is more than 10 million years old. Populations do ultimately go extinct, whether from "mutational meltdown" (whatever that actually means, and neither you nor anyone else has provided a rigorous definition), or from failure to adapt to changing enviromental conditions. This is a prediction of evolutionary theory, and it essentially contradicts special creation.

, and

2) that this shows that the "Primary Axiom" of evolution--Random Mutation + Natural Selection--could never have produced species extant today.

How, Dave? It shows no such thing. That species go extinct does not in any way, shape, or form show that new species cannot arise.

We had a lively discussion of the Crow (1997) paper listed above. Apparently it was little too lively. I will do my part to keep this continued discussion just that ... a discussion. Not a pie throwing match. Now we continue with another paper that Sanford discusses ... I do have the paper now and I have studied it quite thoroughly.

So have you finally, at long last, understood that Crow was talking about mutational build-up due to intereference with selection pressures?

WHAT IS SYNERGISTIC EPISTASIS?
He proposes this as a possible solution to his shocking question in his title, but what is it? Answer (sort of) ... Apparently S.E. is a softer form of truncation selection which is artificial and simply kills off all the individuals with a mutation count higher than "X". Does S.E. work in the real world? I don't think anyone knows. Personally, I don't think so and I will cite some papers later of real researchers who have their doubts. Remember also, that this journal that Kondrashov is publishing in is called Journal of Theoretical Biology. Notice that word "theoretical." This is not real world stuff. It's theory. And as far as S.E. is concerned, I suspect it's probably wrong.

Here's the problem with your argument, Dave. If it were correct, one of two things would have to happen. Either most eukaryotes would have to have already gone extinct, or there would have to be something unique to the human genome that makes it much more prone to mutation than any other organism's genome. Since the first is certainly untrue, and you have no evidence or even conjecture for the second, it appears that your argument is a non-starter.

[VoxRat]

Does S.E. work in the real world? I don't think anyone knows. Personally, I don't think so and I will cite some papers later of real researchers who have their doubts.

Seems pretty reasonable to me. I've been studying science for quite a while.

Why do you not think so? and
what are your credentials, that would cause anyone to give your personal opinion a second thought?