You see the switch here? The first claim is “you don’t seem to understand the reasons people dispute Sanford”, but @PDPrice turns it into an authority claim - tell me who disagrees with Sanford, cite a specific instance - as though that’s what matters, and not the merits of Sanford’s idea.
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No. Dr Schaffner made a specific and far-reaching claim that I found dubious: that “informed biologists in general have considered Dr Sanford’s ideas and have rejected them”. I asked for a citation to back up that claim. That’s not any kind of argument from authority. Since you’re chiming in here, I’ll go ahead and point out that experts in population genetics like Dr Schaffner and Dr Felsenstein don’t say anything remotely like what you have been saying here. They are at least honest enough to admit that most mutations are damaging [edit: well, actually glipsnort is talking out of both sides of his mouth on this point], and most mutations are effectively neutral (at the very least, in humans). From the best I can put it together here, Dr Schaffner’s argument boils down to, “I’m ignoring all the evidence we have about the DFE of mutations because we can only directly test for the DFE of larger-sized mutations. I will, in turn, pin all my hopes for evolution on the class of mutations that are too small to directly measure, and ignore all the logic that would lead to the opposite conclusion.” This is naturalism-of-the-gaps, pure and simple.
You responded to this specific claim:
Perhaps you mistakenly quoted the wrong section of his comment?
Ah yes, the very study of which you still have not answered the basic question as to how a virus can succumb to GE to become extinct in a matter of years over the pandemic, while preserving for millennia in animal hosts. This goes to the heart of the argument, and is a fatal flaw.
This study has been extensively discussed on this forum, if anyone is interested, just use the search and enter Sanford or H1N1.
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There is a least one counter example that refutes your assertion (but probability many others exist), ie ATP synthase.
https://www.pnas.org/content/early/2017/04/24/1700801114
Edit : well, as I thought, it happens that ATP synthase is not at all the only example of near perfection in biology. And this fact alone is a significant challenge to evolutionary theory.
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What I would like to see is the evidence that supports what you think these authors are claiming. Where is the evidence for neutral mutations with slight effects being overwhelmingly deleterious?
In addition, what is the accumulated deleterious effect of these effectively neutral mutations, and how does it compare to the fitness effects of just one beneficial mutation? Does the beneficial mutation increase fitness more or less than the accumulated effect of slightly deleterious mutations?
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That’s a chemical reaction, not a genome.
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What of the genetic differences between humans and chimps? Are there no beneficial differences?
In vertebrates alone we have hundreds of millions of years of evolution recorded in both the fossil record and in the genomes of living species. They haven’t gone extinct because of GE in those hundreds of millions of years. This is why informed biologists ignore Sanford’s claims. When the map doesn’t fit the territory the map is wrong, not the territory. Nature has already done the experiment for us, and they disprove Sanford’s claims.
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No, that doesn’t show ATP synthase to be perfectly fit.
That should be easy to test using ancestor reconstruction. If living organisms were perfect in the past, the reconstructed ancestral states should exhibit higher fitness basically across the board. Do you have ANY evidence that this result obtains?
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Oh man. 
What is it you have against Irony-Meters which makes you want to melt every one on the planet?
Dr Schaffner,
Before I respond any further, I’d like to thank you for discussing this with me, a layman far less educated in this field than you are. This is more than most people in your position are willing to do. I am sorry that @Joe_Felsenstein seems to have dropped out of the discussion, because I was looking forward to hearing more of his perspective on this. I would like to know if he agrees with your statements that we can’t draw any conclusions about the DFE of effectively neutral mutations, or with your implication that a sizable fraction of them (as high as 50%? More?) may be beneficial.
This is an interesting claim, but one I find dubious, even if I cannot directly address it myself. For example we do know that the so-called non-coding region does in fact have function, and that we can even get diseases from mutations in this region:
“…we believe that based on the observations presented above, a considerable proportion of patients will likely have disease-causing mutations outside the exome.”
Scacheri & Scacheri, 2016.
Perfectly functional? Are you really sure about that? There is an unfathomably-large amount of information stored somewhere that codes for a human being’s body, which is the most complicated machine known to exist in the universe. Where, exactly, do you propose all that functional information is stored? Do you think it’s in protein-coding regions only? We aren’t merely a sack of proteins. Somewhere there must be information on how to actually assemble and use those proteins once they’re built, wouldn’t you agree? In fact, building the proteins themselves must be a drop in the bucket compared to the information needed to use those proteins to build a human, just as it’s much simpler to make a brick than it is to make a brick mansion.
Not if you consult nearly any source outside the dusty and rarely-read papers in the hardly-known field of population genetics! Most people, including most scientists, who talk about evolution still make much of the idea of natural selection, as if NS is chiefly responsible for the great “apparent design” we see in nature. But you’re telling a very different story. You’re saying that the “apparent” design in nature is really nothing more than extreme luck. What exactly about the words I used was tendentious, and what did I say that was inaccurate?
This isn’t really helpful. I think my assessment was extremely fair. You’re ignoring all the published data about mutations based upon the technicality that we can’t directly measure very small mutations. You’re also attempting to nullify the plain statements from the literature that I’ve shown here, in a way that winds up contradicting the plain meaning of these statements. Over and over they say: “The vast majority of mutations are deleterious.” You say, "They don’t mean that. What they mean to say is, “We have no idea about the vast majority of mutations.” Those are two very contradictory claims. You can’t say what you’re saying and pretend you’re not contradicting the literature when you say it.
Here’s how you can clear this up. Just point me to a peer-reviewed source that includes an overall DFE of mutations which plots both beneficial and deleterious mutations on the same axis in the same chart.
It was unclear to me how your bringing up an old thread on Carter’s and Sanford’s flu study (in which you did not participate yourself) was supposed to add anything here.
What a coincidence. You’re ignoring all the millions of pieces of published data documenting the evolution of life on the planet over the last 3.8 billion years.
Just give us a simple answer: How did complex life manage to make if from the Cambrian 520 million years ago to the present without everything dying from GE?
C’mon PD, you can’t run from the data your whole life.
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Please quote where they have said this.
And you consider this to be a persuasive argument?
And this? How does this contradict the fact that “in ~90% of the human genome the precise sequence doesn’t matter at all.” I must echo the sentiment of the credentialed experts in this discussion. You have no idea what you are talking about.
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At least tell us if the mutation was beneficial or deleterious.
Bumped for PDPrice on the forlorn hope he may actually find the courage to answer questions about his claims
Just because a very small percentage of non-coding regions have function does not mean the bulk of non-coding regions have function.
We could also look at a genome that has lost the vast majority of its non-coding DNA. The bladderwort is a parasitic plant that isn’t that much different from any other plant. However, it’s genome is just 0.082 billion bases. Compare this to other plants, such as the onion with a genome of about 16 billion bases. Nearly the entire bladderwort genome is considered to be functional DNA.
https://www.nature.com/articles/nature12132
Once again, nature has done the experiment for us.
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YOU brought up the flu study. It has been thoroughly debunked in this forum in a number of threads. Why rehash? So Steve’s original point, that you can’t provide evidence in support, and the entire GE argument is pointless, still stands. Your referenced paper is more of a liability to your position.
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Comments like this really detract from credibility.
Exactly how are the bodies of humans more complicated than the bodies of blue whales or redwoods?
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If accurate, this looks like very good evidence that 1) we’re still a very long way from any meaningful understanding of how DNA works and 2) there must be more information stored in life beyond just the genome. Sugars, maybe?
No, it has never been debunked. This is a common fallacy I see on the internet. Just point to where somebody has talked about something, and assume that suffices as proof it’s been debunked. I’ll call it the Discussion Thread Fallacy.
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If you can’t figure out that humans are more complicated than redwoods, I don’t think there’s even enough common ground for discussion. I think it’s comments like these that actually detract from credibility. Come out of fantasy-land.