Classic case of evolution refuted

[essentialsaltes]

The whole purpose of the experiment was to experomantally test causes of molecular adaptation, that one particular pathway was just their first test case. Everyone asserting it is only about ADH pathway is just ignoring the press release, the abstract and their conclusions.

"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."

Yes, we can experimentally test our hypotheses and find that some are right and some are wrong.

You may have heard of a method used in science called the scientific method. This is a bit of it.

 

[essentialsaltes]

in other words random mutation and natural selection failed. There was some other cause.

Wrong! You made me read the paper, and now you get it full force.

"We did not test any of the innumerable other hypotheses that have been or could be proposed concerning fruit fly adaptation to rotting fruit or ADH evolution. For example, evidence suggests that the increased ethanol tolerance of D. melanogaster may have evolved because of substitutions at other loci 34,36 or in regulatory regions 32,33of Adh and it is possible that these changes were positively selected. The single amino acid replacement that occurred along the D. melanogaster lineage could have affected functions other than ethanol catabolism, such as the breakdown of other substrates, and, if it did, these changes may or may not have increased fitness. For these or any other claims of molecular adaptation, further work would be required to formulate specific adaptive hypotheses and test their causal predictions."

 

[sfs]

Their results were unexpected, in other words random mutation and natural selection failed. There was some other cause.

No. That's a complete misreading of the paper. Natural selection for the hypothesized function didn't explain a particular signal for selection around particular mutation. Based on their data, natural selection probably is responsible for the frequency of a different mutation in the same gene, but some other gene must be responsible for the phenotype they were originally interested in. They can't possibly rule out mutation and selection as having been responsible, since they haven't found the genetic basis for the trait.

 

[Vaccine]

Well, no. Their goal is to test particular hypotheses about the phenotypic effect of particular mutations and the hypothesized selection pressure that drove their success. Their goal is not to test whether natural selection is responsible for genetic differences between species or for adaptive evolution.

I noticed you avoided mentioning fitness. If you cherry pick points while ignoring others you're misrepresenting the article. Fitness was being tested:

"Thus, divergence of the ADH protein sequence along the D. melanogasterlineage had no detectable effect on survival in the presence of ethanol."
Nice try, but they were testing natural selection. And found it (suprise!), had no detectable effect!

 

[Squeegee Beckenheim]

They were TESting a classic well known, appealing historical account of molecular adaptation. Their results were unexpected, in other words random mutation and natural selection failed.

That "in other words" is entirely disconnected from the previous sentence. You're right that they tested one particular hypothesis. That their results refuted it does not mean that they refuted natural selection or random mutation any more than my paper refuting that turning off switch #1 turns off the light refutes switch-flipping.

I note you've not answered my request in post #50. Could you do so, please?

 

[Bugeyedcreepy]

I noticed you avoided mentioning fitness. If your cherry pick points while ignoring others you're misrepresenting the article. Fitness was being tested:

"Thus, divergence of the ADH protein sequence along the D. melanogasterlineage had no detectable effect on survival in the presence of ethanol."
Nice try, but they were testing natural selection. And found it (suprise!), had no detectable effect!

Seriously, how do you not get this, unless you're a Poe?

 

[Squeegee Beckenheim]

I noticed you avoided mentioning fitness. If you cherry pick points while ignoring others you're misrepresenting the article. Fitness was being tested:

"Thus, divergence of the ADH protein sequence along the D. melanogasterlineage had no detectable effect on survival in the presence of ethanol."
Nice try, but they were testing natural selection. And found it (suprise!), had no detectable effect!

That that mutation had no detectable effect on the organism's survival means that they weren't testing natural selection. Instead they demonstrated that this particular mutation didn't make the fly subject to natural selection.

 

[sfs]

I noticed you avoided mentioning fitness.

Huh? I talked about selection pressure. Selection pressure means that different phenotypes have different fitnesses.

Nice try, but they were testing natural selection. And found it (suprise!), had no detectable effect!

They were not "testing natural selection". They were testing whether natural selection was responsible for a particular genetic difference between species. Based on their data, it wasn't. That's an important, interesting question. Really, you seem unable to understand the point of this paper.

 

[Loudmouth]

Since nobody seems to understand the article, it's about a testing a cause: variation aka random mutation.

That is flat out false. They didn't set out to test that claim nor would their experimental method be able to test that claim.

In order to test that claim they would need to trace every single mutation in every single fruit fly gene, and then test each one for changes in fitness. That is not what they did. They looked at the top candidate gene for the evolution of alcohol tolerance in D. melanogaster. Turns out that the top candidate for the production of that trait is not the right one.

It is about more than one isolated case of fruit flies too:
"...and caution against accepting intuitively appealing accounts of historical molecular adaptation that are based on correlative evidence."

That is true. It is telling scientists that they should use a bottom up search for candidate genes responsible for the evolution of a trait, instead of a top down search.

How in the world is this a "refutation of evolution"?

In plain english, they're cautioning about the creative force of random mutations.

That's a flat out misrepresentation of the science.

 

[Papias]

If by .....

First and foremost, thanks.

Thanks for answer the question directly, openly, and honestly. That shows more integrity than we sometimes see on the internet. Before responding, I wanted say that, and to follow up by answering your question to me, as I said I would.

what did you think about this part of the peer reviewed article:
" ..and caution against accepting intuitively appealing accounts of historical molecular adaptation that are based on correlative evidence."

I think it shows quite clearly that their hypothesis of the specific evolutionary pathway was shown to be less likely than a different evolutionary pathway. There are many different genes which could mutate in different ways to give the new ability seen in the flies. They tested one possible mutational route, and found that it wasn't that one. This is no surprise, as other tests on other mutational pathways to new abilities have sometimes found them correct, and sometimes pointed to different mutational routes.
By not, I see that many others have tried to explain that as well, including sfs, who is an expert in this area.

If that answer was not clear, let me know and I'll try again. Now, on to your answers.

If by evolution you meant change over time, no. That is observable, testable and repeatable.I had no intention of casing doubt on that.

If by evolution you meant the variations that happen, are selected for, and produce changes, for example the bacteria enzyme for nylon. Again, no. I have no issues with directed evolution.

Cool. Thanks for clarifying those.

If by evolution you mean purely materialistic mechanisms for change, such as random mutations producing all the genetic differences we see, then yes I absolutely meant cast doubt on that narrative .......

But why try to cast doubt on evolution when it does not require "pure materialism"? It's no different from gravitational theory, which describes gravity without invoking a god, or germ theory, which describes disease without invoking a goddess, or even algebra, which describes equations without invoking a demon.

In any of those, you or I can see God behind it all, as described by Jesus in John 5:17 or in Hebrews 1:3. None of them require you to be "purely materialistic". Why do you see evolution differently than gravity, or germ theory, or, say, obstetrics?

...... and cited a peer reviewed source cautioning against that narriative as well.

But as we saw, the peer reviewed source in no way casts any doubt on evolution, and is no more "materialistic" than chemistry.

In Christ -

Papias

 

[Loudmouth]

If by evolution you mean purely materialistic mechanisms for change, such as random mutations producing all the genetic differences we see, then yes I absolutely meant cast doubt on that narrative and cited a peer reviewed source cautioning against that narriative as well.

Nowhere in the paper does it caution against using the idea that random mutations and natural selection are responsible for evolution. What it cautions against is using human intuition to choose which mutations in which genes are responsible for a specific adaptation. That is actually a good rule in all scientific research.

 

[Loudmouth]

I noticed you avoided mentioning fitness. If you cherry pick points while ignoring others you're misrepresenting the article. Fitness was being tested:

"Thus, divergence of the ADH protein sequence along the D. melanogasterlineage had no detectable effect on survival in the presence of ethanol."
Nice try, but they were testing natural selection. And found it (suprise!), had no detectable effect!

You didn't finish your sentence.

"Nice try, but they were testing natural selection. And found it (surprise!), had no detectable effect on specific protein residues in the D. melanogaster ADH gene." [italicized text added by me]

That would be an accurate description of the paper.

 

[KCfromNC]

The purpose for doing the experiment was to test causes of molecular adaptation, not propose alternative explanations.

If the purpose of this paper wasn't to explore non-materialistic mechanisms for evolution, why are you trying to use it to support this idea :

If by evolution you mean purely materialistic mechanisms for change, such as random mutations producing all the genetic differences we see, then yes I absolutely meant cast doubt on that narrative

 

[TagliatelliMonster]

If you're suggesting "We found that the accepted wisdom about the molecular causes of the flies' evolution is simply wrong." is just a minor adjustment, you're wrong. This challenges the accepted wisdom about adaptation, a fundamental principle of Darwin's theory. They plan on testing more cases and I wouldn't count on it getting better.

They are saying that current accepted ideas about the evolutionary history of flies are wrong. They are not saying that evolution theory itself is wrong.

Count on a creationist, to misrepresent such things.

 

[Vaccine]

They are saying that current accepted ideas about the evolutionary history of flies are wrong. They are not saying that evolution theory itself is wrong.

Count on a creationist, to misrepresent such things.

So the story goes, a gene with function a gets duplicated, random mutation provides a new function b, natural selection refines this new function and viola new species.
So they decide to test this and pick a well known case of the fruit fly. They engineer it back 4 million years where it diverged from a common ancestor. To their suprise there is no detectable difference between the ancestral and extant versions of the gene. So natural selection sits on the sidelines while all this evolving is going on. And they say random mutation isn't the cause:
"The signature of adaptive evolution in the ADH coding sequence is not caused by substitutions on the D. melanogaster lineage. "

So without natural selection or random mutations, what caused all that evolution?

 

[Vaccine]

If the purpose of this paper wasn't to explore non-materialistic mechanisms for evolution, why are you trying to use it to support this idea :

Because they found that random mutation and natural selection had nothing to do with the evolution of the fruit fly.

 

[Vaccine]

You didn't finish your sentence.

"Nice try, but they were testing natural selection. And found it (surprise!), had no detectable effect on specific protein residues in the D. melanogaster ADH gene." [italicized text added by me]

That would be an accurate description of the paper.

So the story goes, a gene with function a gets duplicated, random mutation provides a new function b, natural selection refines this new function and viola new species.
So they decide to test this and pick a well known case of the fruit fly. They engineer it back 4 million years where it diverged from a common ancestor. To their suprise there is no detectable difference between the ancestral and extant versions of the gene. So natural selection sits on the sidelines while all this evolving is going on. And they say random mutation isn't the cause:
"The signature of adaptive evolution in the ADH coding sequence is not caused by substitutions on the D. melanogaster lineage. "

So without natural selection or random mutations, what caused all that evolution?

 

[Vaccine]

Huh? I talked about selection pressure. Selection pressure means that different phenotypes have different fitnesses.

They were not "testing natural selection". They were testing whether natural selection was responsible for a particular genetic difference between species. Based on their data, it wasn't. That's an important, interesting question. Really, you seem unable to understand the point of this paper.

The point was they were testing causes of evolution. Very interesting that natural selection and random mutation are not causes in the evolution of D. melanogaster.

 

[sfs]

The point was they were testing causes of evolution.

Once again, no. They were testing a cause of a particular case of evolution. Repeating your incorrect summary of the paper doesn't make it correct.

Very interesting that natural selection and random mutation are not causes in the evolution of D. melanogaster.

It's very interesting that natural selection was not the cause of the evolution of a single mutation in D. melanogaster. Equally interesting is the fact that natural selection is the cause for the evolution of other loci in the same species, and in other species.

 

[sfs]

Because they found that random mutation and natural selection had nothing to do with the evolution of the fruit fly.

No, they didn't. You're now lying about this paper.