Classic case of evolution refuted

[essentialsaltes]

it's about a testing a cause: variation aka random mutation.

No, it seems to be about testing one particular proposed molecular pathway. And finding it wanting.

 

[Vaccine]

No it's not. It was testing one particular hypothesis about the cause of one particular adaptation in one particular species of fruit fly. It demonstrates that the hypothesis was false, and the authors caution against utilising the correlative methods which led to the hypothesis, as well as saying that the methodology they used can be used to test other hypotheses.

And you don't have to keep referring back to the article - I posted the paper itself upthread. You'd do better to read that, not least because it's interesting.

It wasn't just about one particular case of adaptation in a fruit fly. They had a much broader goal in mind, see the part in bold:
"But hypotheses about adaptive divergence between species or at higher taxonomic levels are explicitly historical, so testing them requires the effect of genetic changes that occurred on phenotype and fitness in specific evolutionary lineages from the distant past to be measured. Here we address this challenge."

No they're not. In plain English they're cautioning creating hypotheses based on nothing more that correlative data. There is no reference to "random mutations", and I'm not even sure what you think you mean by the phrase "creative force", but it is neither a scientific term nor one that the authors use or allude to.

What do you think they meant by "forged by chance"?

 

[Squeegee Beckenheim]

I thought it interesting they experimentally tested a cause of evolution.

They didn't. They tested the hypothesis that one specific protein caused one specific adaptation in one specific species of fruit fly.

I thought people could understand the difference between refuting a mechanism (variation) for macroevolution and refuting a theory in general.

They didn't refute any mechanism of evolution, and certainly not variation. They refuted one specific hypothesis that one specific protein caused one specific adaptation in one specific species of fruit fly.

I thought wrong, people here think you are either a cheerleader for Darwin or some really weird YEC.

I think you're grossly misrepresenting what the article says.

Considering you accused me of blasphemy for doubting Darwinism, 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."

They're cautioning against creating hypotheses based on nothing more than correlative data.

 

[Squeegee Beckenheim]

It wasn't just about one particular case of adaptation in a fruit fly.
They had a much broader goal in mind, see the part in bold:
"But hypotheses about adaptive divergence between species or at higher taxonomic levels are explicitly historical, so testing them requires the effect of genetic changes that occurred on phenotype and fitness in specific evolutionary lineages from the distant past to be measured. Here we address this challenge."

The specific experiment detailed in the paper tests one specific hypothesis about one specific adaptation in one specific species of fruit fly. The methodology used can be used going forwards to test other hypotheses about other animals.

What do you think they meant by "forged by chance"?

I can only assume you're talking about this quote, taken from the paper:

But sequence signatures of selection can be forged by chance or demographic processes and it is difficult to predict from sequence alone how genetic changes affect phenotypes and fitness 5,6,7,8 .

That sentence means that the markers that form one part of the data upon which the original hypothesis and hypotheses like it are based can be created by methods other than those that the hypotheses posit and, as such, data like that is not a good basis upon which to form a hypothesis.

 

[Bugeyedcreepy]

Your guess would be wrong.
Peer reviewed articles are very carefully worded. When they say "decisively refuted", they mean it.

As has been pointed out already, a particular evolutionary pathway for a particular enzyme in a particular species of fruit fly was the "decisively refuted" thing. From the article you've quoted,

"There is no doubt that D. melanogaster did adapt to high-alcohol food sources during its evolution, but not because of changes in the Adh enzyme. "The Adh story was accepted because the ecology, physiology, and the statistical signature of selection all pointed in the same direction. But three lines of circumstantial evidence don't make an airtight case," Thornton said. "That's why we wanted to test the hypothesis directly, now that we finally have the means to do so."​

They clearly state that evolution carried on just fine, so all the mechanisms of the Theory of Evolution are left perfectly in tact.

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.

Again, to correct your understanding, the "molecular causes of the flies' evolution", being the Adh enzyme pathway was the "simply wrong" bit, the pathway that evolutionary change occurred in is somewhere else in this fly's genome, just not where they had that close look. In no way were they stating that the flies' genome didn't change at all, or that evolution is wrong by any stretch!

Nowhere did I conclude this refutes the theory of evolution. Species evolve and adapt over time, duh. Their results refute the "accepted wisdom" about molecular adaptation. They said "The Adh story was accepted because the ecology, physiology, and the statistical signature of selection all pointed in the same direction. But three lines of circumstantial evidence don't make an airtight case,"
So all the people who think natural selection acting on random mutations is an "airtight case" to explain everything are simply wrong.

Again, wrong as stated above. Natural selection acting on random mutation is Exactly an "airtight case".

What exactly do you think I'm implying?
It isn't just about fruit flies.
"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."

No, as stated earlier, the accepted science regarding one evolutionary pathway of one particular enzyme in one particular species of fruit fly was examined in great detail, and was found to be wrong. They accept it happened via evolutionary mechanisms and even say this, just not in the way that it was thought to have happened.

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

Nope, again, one particular evolutionary pathway of one particular enzyme in one particular species of fruit fly was examined in great detail, and found to be wrong.

Considering you accused me of blasphemy for doubting Darwinism, 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."

Intuition can be as unreliable at findings of fact as faith is. Intuition should therefore always be applied sparingly, if at all, and only where absolutely unavoidable. Always seek to verify correlation with experimentation to be absolutely sure, and this is an excellent method to do so.

my contribution to this thread's Point Refuted A Thousand Times.... anyone keeping count?

 

[Papias]

Honestly, I thought people would actuallly read the articles ....

You didn't answer my question. I'll happily answer your question if you want to have an actual discussion, and that means answering my question to you first.

I asked you:

So you are saying that you had absolutely no intention of casting doubt on evolution in any way with this thread, Vaccine? Is that your honest answer? Would tell Jesus that?

Well?

In Christ-

Papias

 

[KCfromNC]

What exactly do you think I'm implying?

This, for starters :

simply pointing out random mutations and natural selection aren't the creative force behind genes people think they are.

 

[Vaccine]

As has been pointed out already, a particular evolutionary pathway for a particular enzyme in a particular species of fruit fly was the "decisively refuted" thing. From the article you've quoted,

"There is no doubt that D. melanogaster did adapt to high-alcohol food sources during its evolution, but not because of changes in the Adh enzyme. "The Adh story was accepted because the ecology, physiology, and the statistical signature of selection all pointed in the same direction. But three lines of circumstantial evidence don't make an airtight case," Thornton said. "That's why we wanted to test the hypothesis directly, now that we finally have the means to do so."​

They clearly state that evolution carried on just fine, so all the mechanisms of the Theory of Evolution are left perfectly in tact.

Nowhere did I say it refutes evolution in general or the theory. I've said all along it was about testing a cause. That isn't correct too say 'All the mechanisms' were left perfextly in tact. They "caution against accepting intuitively appealing accounts of historical molecular adaptation that are based on correlative evidence."

Again, to correct your understanding, the "molecular causes of the flies' evolution", being the Adh enzyme pathway was the "simply wrong" bit, the pathway that evolutionary change occurred in is somewhere else in this fly's genome, just not where they had that close look. In no way were they stating that the flies' genome didn't change at all, or that evolution is wrong by any stretch!

There wasn't anything to correct. I didn't say the flies genome didn't change or evolution in general didn't happen. It probably will turn out to be a case of directed evolution. It's absurd to think it was only about a fruit fly enzyme pathway. They are testing the evolutionary effects of genetic change and this is just their first test case.

Again, wrong as stated above. Natural selection acting on random mutation is Exactly an "airtight case".

They are testing the whole 'forged by chance' hypothesis and after only 1 test case are issuing a caution. Random mutations as a vehicle for molecular change is being tested, and found to be wanting.

No, as stated earlier, the accepted science regarding one evolutionary pathway of one particular enzyme in one particular species of fruit fly was examined in great detail, and was found to be wrong. They accept it happened via evolutionary mechanisms and even say this, just not in the way that it was thought to have happened.

Makes perfect sense to decisively refute something then just issue a caution, because that narriative about that one specific pathway, of that one specific enzyme, in that one specific species is just so darn appealing that some silly scientist can't help but propose it again.

Nope, again, one particular evolutionary pathway of one particular enzyme in one particular species of fruit fly was examined in great detail, and found to be wrong.

Intuition can be as unreliable at findings of fact as faith is. Intuition should therefore always be applied sparingly, if at all, and only where absolutely unavoidable. Always seek to verify correlation with experimentation to be absolutely sure, and this is an excellent method to do so.

my contribution to this thread's Point Refuted A Thousand Times.... anyone keeping count?

Speaking of PRATT:
"This strategy has yielded major insights into the mechanisms by which biochemical functions evolve"
They certainly thought it more than just about one pathway, one enzyme, or one species.

 

[Squeegee Beckenheim]

I've said all along it was about testing a cause.

It was not about "testing a cause". The experiment tested one specific hypothesis about whether one specific protein caused one specific adaptation in one specific species of fruit fly.

That isn't correct too say 'All the mechanisms' were left perfextly in tact. They "caution against accepting intuitively appealing accounts of historical molecular adaptation that are based on correlative evidence."

That sentence is cautioning against using correlative data to form hypotheses.

It's absurd to think it was only about a fruit fly enzyme pathway.

The paper quite explicitly states that the experiment it describes was testing one specific hypothesis about whether one specific protein caused one specific adaptation in one specific species of fruit fly.

They are testing the evolutionary effects of genetic change and this is just their first test case.

No, they have tested one specific hypothesis, and they will in the future test other hypotheses. The hypothesis they have tested is not "the evolutionary effects of genetic change".

They are testing the whole 'forged by chance' hypothesis and after only 1 test case are issuing a caution.

"Forged by chance" is not part of the hypothesis they tested. They used that expression to describe one of the potential causes for the data upon which the hypothesis they were testing was based. The "caution" they issued was against using correlative data to form hypotheses.

Random mutations as a vehicle for molecular change is being tested, and found to be wanting.

Not at all. To deal with the latter half of that sentence first - the paper itself suggests other causes for the adaptation in that fruit fly, one of which is exactly the same as the hypothesis that was tested, except pertaining to a different part of the genome. As for the first part of that sentence, that's just completely wrong. They tested whether one specific protein was the cause of one specific adaptation in one specific species of fruit fly. They didn't address the cause of the mutation they were testing at all, but they did suggest that the signature of change that the hypothesis they were testing on may have taken come about through random chance.

Makes perfect sense to decisively refute something then just issue a caution, because that narriative about that one specific pathway, of that one specific enzyme, in that one specific species is just so darn appealing that some silly scientist can't help but propose it again.

They didn't caution against proposing that specific hypothesis again, they cautioned against the methods that were used to generate that hypothesis.

Speaking of PRATT:
"This strategy has yielded major insights into the mechanisms by which biochemical functions evolve"
They certainly thought it more than just about one pathway, one enzyme, or one species.

That quote concerns one of the two methodologies that they combined in order to create the flies that they used in the experiment. It is not talking about the results of the experiment.

 

[Squeegee Beckenheim]

Here's an experiment - Vaccine, you seem to have your own ideas what the hypothesis the experiment was testing was. Why not read the paper that I linked on page 2 and quote the particular part of that paper that you think outlines what the hypothesis they are testing is?

I'll get you started:

We tested a widely held hypothesis of molecular adaptation—that changes in the alcohol dehydrogenase protein (ADH) along the lineage leading to Drosophila melanogaster increased the catalytic activity of the enzyme and thereby contributed to the ethanol tolerance and adaptation of the species to its ethanol-rich ecological niche.

I think that, quite clearly, sets out what the hypothesis they tested was. The sentence starts by saying that they tested a specific hypothesis, and then goes on to detail that hypothesis. What it says the hypothesis is is that one specific protein was responsible for one specific adaptation in one specific species of fruit fly.

Now please read the paper and quote what part of it you believe outlines what hypothesis they are testing. The portion you quote should contain the words "we tested the hypothesis", or something similar, and then detail the hypothesis they tested.

 

[Warden_of_the_Storm]

Nowhere did I say it refutes evolution in general or the theory.

And you are blatantly backpedaling now. Especially since the title of this thread, that YOU created, reads: "Classic case of evolution refuted."
If you didn't want to suggest that evolution was refuted, why did you use that word then?

 

[Vaccine]

You didn't answer my question. I'll happily answer your question if you want to have an actual discussion, and that means answering my question to you first.

I asked you:


Well?

In Christ-

Papias

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.

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.

 

[Subduction Zone]

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

Yes, evolution is change over time. There is no doubt that life as we know it is the product of evolution.

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.

Good, since you would be flooded with examples of that happening.

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.

But you didn't. You cited a paper that supported evolution. The paper that you linked was about only one particular pathway being shown to be wrong and nothing more. In fact it states how the technique that they used could be used elsewhere to confirm or refute particular pathways.

 

[Squeegee Beckenheim]

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.

You cited an article about a peer-reviewed source, which cautioned against basing hypotheses on correlative data.

 

[sfs]

You cited an article about a peer-reviewed source, which cautioned against basing hypotheses on correlative data.

That's an overstatement. They did not caution against basing hypotheses on correlative data; there is no problem with such hypotheses. They're cautioning against drawing conclusions from such data without functional followup. A hypothesis is fine, as long as you remember it's a hypothesis and find a way to test it.

(Note: as the paper points out, plenty of similar hypotheses about the molecular basis of adaptive evolution have been confirmed with additional testing.)

 

[Squeegee Beckenheim]

That's an overstatement.

True. I was trying to keep it simple, but perhaps I ought not have.

 

[KCfromNC]

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.

Where does the paper advocate for non-naturalistic explanations?

 

[Vaccine]

No, it seems to be about testing one particular proposed molecular pathway. And finding it wanting.

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.

 

[sfs]

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.

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.

 

[Vaccine]

Where does the paper advocate for non-naturalistic explanations?

The purpose for doing the experiment was to test causes of molecular adaptation, not propose alternative explanations. 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. There was some other cause. I'm perfectly justified pointing out random mutations isn't the creative vehicle atheists think it is.