Paul Price: What are the Substantive Critiques of Genetic Entropy?

Regardless @PDPrice this all misses point of my original question. Let me try rephrasing. This is a key question for you to answer that can help put to rest a lot of confusion.

  1. We can agree that several scientists, hear and elsewhere, claim to have read Sanford’s work on Genetic Entropy and disagree with it.

  2. Many of them have explained why they disagree with the validity of understanding Genetic Entropy as a challenge for evolution, and why they disagree with key points of Sanford’s reasoning.

  3. Sanford and @PDPrice disagree with these critical scientists.

  4. Without agreeing with these critiques, @PDPrice, can you repeat to us, accurately, these objections and the reasoning behind these objections?

Do you dispute #1, #2, or #3? I don’t think you do. So can you answer #4? That was my question. Can you answer that question? If you can, please do.

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Agreed.

Yes.

Yes.

I’ve seen a few different kinds of arguments in response.

  1. Some try to argue that as more deleterious mutations happen, this opens up the way for more beneficial back-mutations to come in and compensate for them, and at some point an equilibrium is supposed to be reached. This misunderstands the way mutations work at a very fundamental level, as well as greatly misrepresenting the likelihood of back mutations.

  2. Some try to suggest that mutations are only harmful if they affect the coding region, which in humans is a smaller proportion of the genome. This denies most of the recent breakthroughs in genetic science, as we have begun to learn more and more about the functionality of the genome. The assumption of “junk dna” was a great embarrassment, and was entirely philosophical from the start. The problem is, as Dan Graur has noted, “If ENCODE is right, evolution is wrong.” Therefore, those who understand this are holding on to their junk dna with white fingernails.

  1. Some acknowledge most of what Sanford says, but then try to retreat into the unknown areas we cannot directly test, while ignoring the implications of what we can test. They suggest that a large fraction of effectively neutral mutations may be beneficial. This was Dr. Schaffner’s tact. He has suggested that all the many and clear acknowledgements in the literature that ‘most mutations are deleterious’ actually only refer to larger-sized mutations, while telling us nothing at all about the small ones. This response I think fails to do justice to the literature itself, which goes much further than this in what it states. It requires us to come to a conclusion that runs contrary to everything we can actually test about mutations. This also ignores the general principle that “it’s easier to break a machine than to improve it”, which means this is highly unlikely to be correct.
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This is great @PDPrice. Thanks for answering. This gives a good bases for a substantive exchange.

First question is to others. @Joe_Felsenstein and @glipsnort, does this accurately describe any of your objections?

@PDPrice, I note that this is not comprehensive. What other objections and reasoning do you know of?

We don’t need to worry about adjudicating if they are correct critiques or not yet. I just want to lay them out on the table, and clarify if we even understand what the objections are at this time. Adjudicating the objections is a separate activity.

That being said, you did put rebuttals to each point. Do you know why we reject those rebuttals?

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You tacitly assume that all objections must come from population genetics. Is that a valid assumption?

@PDPrice’s #2 at least is a serious distortion of the arguments of others. Once again he confuses protein-coding DNA with functional DNA and non-coding DNA with presumed junk. Once again he misunderstands what ENCODE shows and ignores all the arguments in favor of extensive junk DNA in most eukaryote genomes. So on #2, he gets a definite failure to understand the critics.

And let me repeat that the most telling and clear objections do not come from population genetics.

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Can you cite even one example of someone arguing that? I think you’ll struggle, given that we’ve known about functional non-coding elements for decades prior to Sanford’s book.

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@PDPrice, in addition to the problems with the way you articulated the three objections you mentioned (which I’ll not worry about here), you missed perhaps the most important: Dr. Sanford’s model requires mutation accumulation without purifying selection , and also, ultimately, a decline in reproductive output due to that accumulation . This is simply contradiction; if the mutations in question result in a decline in relative reproductive success, then they are necessarily subject to purifying selection.

I’ve heard and read the retort that the entire population is affected, so absolute reproductive ability declines, but relative output does not, so there can be no purifying selection.

For this to be the case, there would have to be no differences in reproductive output across members of the entire population in question, despite each individual experiencing a unique set of mutations. Which, of course, is not a serious proposition. This means that selection can preserve the “least bad” genotypes, if you will. Not pristine, not non-mutated, not optimal, but least bad.

That’s the objection I would like to see seriously considered and addressed.

(Repeating this comment from the parent thread. Mods, please let me know if that’s not okay. Thank you.)

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I’m interested to see if PDPrice will respond to the most substantive critique of Genetic Entropy: that GE is based on the demonstrably false premise all life on Earth came into existence only 6000 years ago.

I’m not holding my breath.

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I don’t think this is true. Can you produce quotes that demonstrate that it’s conclusions were logically derived from the premise of a young earth?

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Sanford is well known to be a YEC. Even his book GE offers the declining ages of the Biblical patriarchs as part of his “scientific” evidence.

I’ll accept a correction from PDPrice if he assures me GE is not based on the YEC paradigm, but something tells me I won’t get it. :slightly_smiling_face:

I don’t think that is reasonable. He uses the patriarch ages as a possible place of corresponding evidence, but his logical starting point is not those ages, or YEC.

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I forgot to mention Kimura’s own attempt to solve the problem he raised. He suggested that there really is a decline in fitness over time as a result of effectively neutral mutations, but that this decline is offset by occasional mega-beneficial mutations. This was effectively responded to in Dr Sanford’s book. Kimura never offered any evidence for this offset, and on a theoretical level it makes no sense. You can’t make up for the fact that you’re garbling all the information in the genome by simply having occasional mutations that are reproductively beneficial. This type of response ultimately boils down to an oversimplification of genetics to an imaginary ‘substance-like’ metric of “fitness”, when in reality it’s about the integrity and quality of the information in the genome.

Let’s ask PDPrice who claims to have read extensively on GE.

PDPrice, under the GE hypothesis what is the maximum age for all life to have come into existence? If GE is making all genomes constantly degrade to extinction please extrapolate backwards and tell us when GE says all genomes were in their original “perfect” state.

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Curiously, you’ve omitted the point I made despite @glipsnort reminding you of it today, which is that Sanford, Carter, and you can’t even present the evidence accurately.

In the published paper:

In Fig. 2, H1N1 sequence differences are falsely described as “Relative mutation count.” That’s just wrong. The discontinuities are from rearrangements of segments, which are not mutations and which they even describe in the paper! That’s a staggering bit of incompetence, Paul.

Then in the creation.com articles, the same false Y-axis label is used. The Y-axis of the graph actually represents sequence differences, most of which come from reassortment. Calling them all mutations is grossly false and incredibly misleading.

If Sanford and Carter are incapable of distinguishing between segmental reassortment and mutations and misrepresenting the evidence itself, why should anyone (say, an actual virologist) who is capable of distinguishing between them take them seriously?

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You’re getting into an allegation about Carter and Sanford’s basic methodology for their paper, and I’m not qualified to comment on that. There is nothing preventing you from asking them about this yourself. Please do so. Nobody in the peer-review committee clearly felt that what you are saying is the case, nor has anybody in the citing literature since this was published said anything to this effect.

Why in the world was my post on Sanford’s age of the Earth hidden? It is directly relevant to the fact Sanford’s GE hypothesis is based on Sanford’s YEC beliefs.

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I agree. How do we get comment on that?

This is a huge admission on your part, since GE is all about population genetics.

PDPrice I’d really appreciate an answer to this to clear up any confusion.

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