Classic case of evolution refuted

[Loudmouth]

You just agreed with me natural selection didn't have a role here.

If I go to a desert and observe that erosion by water is not occurring in a 40 acre area can I draw the conclusion that no water erosion is occurring anywhere on Earth?

And this is from the paper:
"The signature of adaptive evolution in the ADH coding sequence is not caused by substitutions on the D. melanogaster lineage. "

Yes. One gene in one lineage.

It's as if nobody knows (or is willing to admit) what appealing historical narriative they're talking about.

The appealing historical narrative is statistical signals of selection in a protein that reacts with ethanol. The coding region for ADH isn't the only sequence that directly interacts with alcohol, nor is the coding region of ADH the only possible target for evolution in the ADH gene. The researchers also stated that changes in the promoter region may prove to be important in alcohol tolerance.

Darwin? never heard of him.

Honesty? I guess you never heard of it.

 

[Loudmouth]

List it here.

What was that hypothesis? Let's see if you can get it right this time.

 

[Squeegee Beckenheim]

Testing natural selection was their premise. They expected there would be a difference in fitness, giving selection something to work with. Instead there was no difference, evolution proceeded just fine without Darwin. Which is why they cautioned against believing such appealing historical narriatives.

I've asked you to substantiate statements such as these more than once before. Could you please go back and read post #50 and do what I request of you there?

 

[Squeegee Beckenheim]

They plainly stated their reasons:
"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."
And if you still think this is only about one particular fruit fly:
"This strategy of engineering 'ancestralized animals' could be applied to many evolutionary questions," Thornton said.
Hoping they are talking about some other well known appealing historical hypothesis out there is childish. Everyone knows when they say classic causes of evolution they mean natural selection working on random mutations.

This has nothing to do with the request in post #50. Could you address that, please?

 

[Vaccine]

Note what they say elsewhere in the paper: "Advances in genetic mapping, experimental studies of molecular function and transgenic engineering have allowed hypotheses of molecular adaptation between recently diverged populations to be tested with increasing rigour 11,12,13,14,15,16". Those numbers are references to studies in which researchers confirmed hypotheses about natural selection driving particular molecular changes. There have been other cases where more detailed studies have refuted similar hypotheses. This paper falls into the latter class. It's good, solid work, but it says nothing at all about the overall role of natural selection in molecular evolution.

They also said this in the paper:
"Rigorously testing hypotheses in this area has been a major challenge."

So which is it, has it been rigorously tested or not? The press release had this to say about the recently developed methods:
"The evidence from this approach is only circumstantial, however, because genes can evolve quickly for many reasons, such as chance, fluctuations in population size, or selection for functions unrelated to the environmental conditions to which the organism is thought to have adapted"

New methods is certainly increasing rigour but circumstantial isn't confirmed. Why are would say confirmed when they said increasing rigour?
Yes, how bizzare to think natural selection has a role in testing causes of adaptation. Or that some classic, well-known, intuitive, appealing, historical hypothesis of adaptation isn't Darwinian.

 

[Vaccine]

They were only testing ONE gene in ONE species of fruit fly. How are you not getting this or are you being deliberately dense?

"This strategy of engineering 'ancestralized animals' could be applied to many evolutionary questions," Thornton said.
One of the guys who wrote the paper said it was about more than one particular fruit fly. The ones insisting otherwise are basically saying they know more about the paper than the ones who wrote it. It's obvious people don't like the caution issued and are going to act dense.

 

[Warden_of_the_Storm]

"This strategy of engineering 'ancestralized animals' could be applied to many evolutionary questions," Thornton said.
One of the guys who wrote the paper said it was about more than one particular fruit fly. The ones insisting otherwise are basically saying they know more about the paper than the ones who wrote it. It's obvious people don't like the caution issued and are going to act dense.

No, they more about the paper than YOU do and don't like you straight up lying about what the paper and the link says.

 

[sfs]

They also said this in the paper:
"Rigorously testing hypotheses in this area has been a major challenge."

So which is it, has it been rigorously tested or not?

Yes, it has been rigorously test. Have you not read the paper? Here's what they're saying: Rigorously testing hypotheses about historical selection has been a major challenge. Recent developments have made it possible to meet that challenge for differences between closely related populations, but not for differences between species. Now, thanks to our cleverness, we can meet it for different species as well.

The press release had this to say about the recently developed methods:
"The evidence from this approach is only circumstantial, however, because genes can evolve quickly for many reasons, such as chance, fluctuations in population size, or selection for functions unrelated to the environmental conditions to which the organism is thought to have adapted"

Nope, that's wrong again. The circumstantial evidence comes from identifying "signatures of selection". The methods of "increasing rigor" are the recently developed ones, and are not circumstantial: "Advances in genetic mapping, experimental studies of molecular function and transgenic engineering" is the list they give in the paper.

 

[sfs]

"This strategy of engineering 'ancestralized animals' could be applied to many evolutionary questions,"

I should hope so.

One of the guys who wrote the paper said it was about more than one particular fruit fly. The ones insisting otherwise are basically saying they know more about the paper than the ones who wrote it.

Sorry, but we understand the paper quite well (in fact, the paper cites a paper I'm an author of). This method could be used to test more hypotheses. That "could" there -- that's a marker in English for the subjunctive mood. It indicates a hypothetical or contrary-to-fact statement. This method could be used to test more hypotheses, but so far it's only been used to test one. It hasn't been used to test any sweeping generalizations about selection; it's been used to test one particular hypothesis about selection for at one gene in one species.

 

[Squeegee Beckenheim]

Vaccine, could you please answer post #50?

 

[Loudmouth]

They also said this in the paper:
"Rigorously testing hypotheses in this area has been a major challenge."

What are those hypotheses and in what area are they talking?

"The evidence from this approach is only circumstantial, however, because genes can evolve quickly for many reasons, such as chance, fluctuations in population size, or selection for functions unrelated to the environmental conditions to which the organism is thought to have adapted"

The evidence from what approach?

Yes, how bizzare to think natural selection has a role in testing causes of adaptation. Or that some classic, well-known, intuitive, appealing, historical hypothesis of adaptation isn't Darwinian.

How bizarre that would continue to misrepresent the science.

 

[Loudmouth]

One of the guys who wrote the paper said it was about more than one particular fruit fly.

Just as NASA is about more than just one rocket launch. You don't claim that it is impossible to fly to Mars because the very first launch failed to get there.

So far they have used this technique once for one gene in one species. They are saying that this same technique can be applied to any gene in any species, BUT THEY HAVEN'T DONE IT YET!!! What is so hard to understand?

How in the world can you claim that random mutation and natural selection have been falsified because one mutation in one gene in one species was not preserved due to positive selection?

The ones insisting otherwise are basically saying they know more about the paper than the ones who wrote it. It's obvious people don't like the caution issued and are going to act dense.

We know way more about the paper THAN YOU DO.

 

[Vaccine]

I should hope so.

Sorry, but we understand the paper quite well (in fact, the paper cites a paper I'm an author of). This method could be used to test more hypotheses. That "could" there -- that's a marker in English for the subjunctive mood. It indicates a hypothetical or contrary-to-fact statement. This method could be used to test more hypotheses, but so far it's only been used to test one. It hasn't been used to test any sweeping generalizations about selection; it's been used to test one particular hypothesis about selection for at one gene in one species.

Congrats on being cited.
So why the caution about accepting intuitively appealing accounts of historical molecular adaptation that are based on correlative evidence?
Why don't you consider that a sweeping statement?

 

[KCfromNC]

"This strategy of engineering 'ancestralized animals' could be applied to many evolutionary questions," Thornton said.
One of the guys who wrote the paper said it was about more than one particular fruit fly.

Where? Your quote says it could be applied to other research. Which papers show that it has been and that the results demonstrate a non-materialistic cause for the diversity of species like you've been claiming?

 

[KCfromNC]

What was that hypothesis? Let's see if you can get it right this time.

And, crickets. Any surprise?

 

[Loudmouth]

Congrats on being cited.
So why the caution about accepting intuitively appealing accounts of historical molecular adaptation that are based on correlative evidence?

The thing you keep getting wrong is that the correlative data is not coming from their ancestralization of genes. There are two separate methods that biologists are using, and you keep conflating the two.

The method used prior to the paper was the comparison of genome sequences. They applied statistical tests and found that changes in the D. melanogaster ADH gene were consistent with positive selection. Because the ADH gene metabolizes ethanol they correlated this statistical positive test to alcohol tolerance.

The problem is that the statistical method is prone to false positives. The same signal of positive evidence can also be produced by genetic drift and population dynamics. This is the "correlative evidence" that they are talking about, and geneticists have long known that this method can be prone to false positives.

What the paper under discussion is offering is a direct way of testing the candidates for positive selection that the statistical method has found. What they found in one single example is that the statistical method does indeed produce false positives, which isn't a major surprise. It could also be that the mutations they looked at in the study are under positive selection, but not with respect to alcohol tolerance. What the authors are saying is that people shouldn't fall in love with the statistical method for detecting positive selection because it can produce false positives.

 

[Squeegee Beckenheim]

Vaccine, could you please answer post #50? It would be very instructive to know what you believe the actual tested hypothesis to be.

 

[Mike Lane]

An old joke:
A man arrives at the gates of heaven. St. Peter asks, "Religion?"
The man says, "Methodist."
St. Peter looks down his list and says, "Go to Room 24, but be very quiet as you pass Room 8."
Another man arrives at the gates of heaven. "Religion?"
"Lutheran."
"Go to Room 18, but be very quiet as you pass Room 8."
A third man arrives at the gates. "Religion?"
"Presbyterian."
"Go to Room 11, but be very quiet as you pass Room 8."
The man says, "I can understand there being different rooms for different denominations, but why must I be quiet when I pass Room 8?"
St. Peter tells him, "Well, the Baptists are in Room 8, and they think they're the only ones here."

An even older joke,
A rich man was on his knees in church praying for God to help him get over a difficult problem he was having with a business deal when a ragged old man knelt beside him and asked God for $10 so he could buy himself a meal and a bed for the night, the rich man put his hand in his pocket and took out a $10 bill and gave it to the man, the old man left and the rich man got back on his knees and said, "Now Lord concentrate on me".

 

[Warden_of_the_Storm]

Vaccine, could you please answer post #50? It would be very instructive to know what you believe the actual tested hypothesis to be.

I think that we can safely assume that Vaccine has fled this thread.