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Refutation of a “Classic Case of Molecular Adaptation”


As new techniques arise in sequence analysis, as well as in genetic engineering, new frontiers open up to test the direction and power of natural selection. A new such experiment has been performed by a team including Joe Thornton.

Here’s the opening sentences from the paper:

We generated a large alignment of ADH sequences, determined the best-fit evolutionary model, inferred the maximum likelihood phylogeny and calculated the posterior probability distribution of amino acid states at key ancestral nodes. We synthesized coding
sequences for the maximum a posteriori sequence of AncMS, which was inferred with high confidence and only one ambiguously reconstructed amino acid (Fig. 1b, Supplementary Fig. 1), and for an alternative version of AncMS (Alt-AncMS), which contained the other plausible state at the ambiguous site and was identical to D.simulans ADH. We also characterized the inferred ancestral D.melanogaster ADH, the amino acid sequence of which is identical to that of the ‘slow’ allele present in extant populations, which is known to be older than other ADH variants.”

At Phys.Org, here’s what the PR has to say:

Thornton and Siddiq reasoned that by combining ancestral gene reconstruction with techniques for engineering transgenic animals, they could study how genetic changes that occurred in the deep past affected whole organisms-their development, physiology, and even their fitness.

“This strategy of engineering ‘ancestralized animals’ could be applied to many evolutionary questions,” Thornton said. “For the first test case, we chose a classic example of adaptation-how fruit flies evolved the ability to survive the high alcohol concentrations found in rotting fruit. We found that the accepted wisdom about the molecular causes of the flies’ evolution is simply wrong.

Did I hear that correctly? The “accepted wisdom about the molecular causes of the fly’s evolution is SIMPLY WRONG?

Yes, that’s right. Because later on in the PR we read:

Siddiq and Thornton realized that this hypothesis could be tested directly using the new technologies. Siddiq first inferred the sequences of ancient Adh genes from just before and just after D. melanogaster evolved its ethanol tolerance, some two to four million years ago. He synthesized these genes biochemically, expressed them, and used biochemical methods to measure their ability to break down alcohol in a test tube. The results were surprising: the genetic changes that occurred during the evolution of D. melanogaster had no detectable effect on the protein’s function.

What’s that you say? No detectable effect?

One supposes that the gene selected is one, among very many, that can be best ‘reverse-engineered’ to give a facsimile of the ‘ancient’ form. Yet, when tested in vivo, there is no difference found between the supposed ‘slow’ ancestral gene, and the ‘fast’ extant form. This is not how neo-Darwinism is supposed to work. Something is seriously wrong, no?

It might be that the techniques employed to identify the ‘ancestral’ form are bad. Maybe that’s it, and it alone. But, OTOH, maybe something is seriously wrong with current neo-Darwinian theory.

From the very end of the “Discussion” section:

Some notions concerning adaptation will
therefore remain difficult to study rigorously. Nevertheless, because
of technical and conceptual advances, it should now be possible to
experimentally assess the causal predictions of many previously
untested or weakly tested hypotheses of historical molecular adaptation,
allowing them to be corroborated or, like the classic hypothesis
of ADH divergence in D.melanogaster, decisively refuted

One wonders what’s really left of Darwinism. Between Behe’s Edge of Evolution, Shapiro’s “Natural Genetic Engineering,” the whole field of epigenetics, the disappearing of “Junk-DNA”, and now the disappearance of a ‘fitness’ change in a “classic case” of molecular adaptation, can anyone seriously believe that Darwinism has much to say about how life evolves?

This is the Phys.Org Press Release.

It would seem that no one is more "surprised" these days than Darwin-directed scientists doing experiments. It's one surprise after another. It reminds one of Inspector Clouseau. PaV
Dr JDD @13 & PaV @14, If that's what they would expect, then why do they write 'unexpectedly' and 'surprisingly' so many times in their papers these days? :) Dionisio
PaV, Sometimes I'm on 'auto-pilot' too. :) In any case, the paper you referenced in your OP is very interesting. Dionisio
Dionisio: I needed to fix the link in any event; so, no problem. But, yes, it's the same link. I should have looked closer at the link address, but was on 'auto-pilot' at the time. PaV
Dr JDD: LOL. You're right, of course. PaV
PaV @9: And they will say that this is exactly what we would expect from evolution. Dr JDD
PaV @11: Thank you for the information. BTW, this is a funny example that illustrates my poor communication skill (assuming I have any): Note that the links at the end of the comments posted @10 (mine) & @11 (yours) match. :) Here's the direct link to the PDF document: http://www.nature.com/articles/s41559-016-0025.pdf Again, thank you for referencing this interesting paper in your OP. BTW, did you have adjust the implicit link "paper" in your OP? Now it works for me. Dionisio
Dionisio: Here's the link to the Nature paper. You'll have to download the paper as a pdf yourself: http://www.nature.com/articles/s41559-016-0025 PaV
PaV: Thank you for referencing this interesting paper. BTW, this link doesn't seem to work for me:
Here’s the opening sentences from the paper: https://uncommondesc.wpengine.com/Users/Pasquale/Downloads/Experimental%20Test%20and%20Refutation%20of%20a%20Classic%20Case%20of%20Molecular%20Adaptation%20in%20Drosophila%20melanogaster--Siddiq-Thornton%202017%20Nature.pdf
I get this error message:
Error 404: page not found The page you are looking for is not here
This link
At Phys.Org, here’s what the PR has to say: https://phys.org/news/2017-01-scientists-animals-ancient-genes-evolution.html
points to this link: http://www.nature.com/articles/s41559-016-0025 Dionisio
Dr JDD: They will also tell us that they knew this all along. PaV
PaV: ERVs, SINEs, LINEs, repetitive sequences - they will all be found to have significant function. Of course it will he argued that the function has been adapted by evolution but it was originally junk. How great though art oh evolution! Another just so load of pseudoscience. Dr JDD
Dr JDD: And just think of what fun it will be when the ENCODE experimentalists find greater evidence of function for virtually all of the genome. Now that will be fun, too, since it will be a blow to neutral drift. PaV
PaV: it's very easy to make untestable statements. Evolutionists do it all the time. Why does a giraffe have a long neck? It adapted to reach food. Not testable. Fantasy, pseudoscience. The genetic arguments have sounded more convincing to those who do not think about it. In fact they are circular. Why has this enzyme changed sequence and conserved? It is important in the evolution of the organism. Thus demonstrating the power of RM+NS in evolution. Yet that is non-sciebce and self-referential circular arguments used all the time. Now we can finally test some of these things. It's game over. Load up your bucket with a heavy helping of popcorn my friend. The next few years are going to be entertaining! Dr JDD
gpuccio: Yes, that quote from the abstract is devastating, isn't it? PaV
Dr JDD: Thanks for your comment. Yes, I see it exactly as you do: both about the experimental prowess biology now has, and as to the entrenched dilettantes. As Dr. Cornelius Hunter often writes, "Religion drives science, and it matters." It is incredible how limited Darwinian evolution is proving to be. Even here at UD, years ago, when I expressed doubts about the basic adaptational power of RM+NS, I was severely criticized by some; yet, I'm being proven right. Time will tell. You can run; but, you can't hide. PaV
Wow! This is big news. Truth Will Set You Free
The significance of these results should not be underestimated. Finally discovered techniques like CRISPR are allowing us to answer questions previously unanswerable which led to sloppy science where one could simply make up a just so story and they could remain unchallenged. Slowly but surely the foundation is slipping away. The religious fanatics will never give up though. They have too much to lose. Dr JDD
PaV: Very interesting! If the (few) neodarwinian hypotheses about specific cases of molecular evolution can be really tested by new methodologies, that would really be something. I believe we have no doubts about the results... :) This is from the abstract, and I really like it:
Our experiments strongly refute the predictions of the adaptive ADH hypothesis and caution against accepting intuitively appealing accounts of historical molecular adaptation that are based on correlative evidence. The experimental strategy we employed can be used to decisively test other adaptive hypotheses and the claims they entail about past biological causality.

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