[teachingassist]

> that three species should have a near-identical sequence coding for a near-identical protein suggests rather strongly that this version of the gene arose in one species and was then acquired by the other two

We'd strongly expect the amino acid sequence to be similar both by "convergent evolution" (each case evolved independently with the same motivation) and "lateral transfer" (one case evolved and then shared DNA across species), so this wouldn't typically distinguish those two cases.

The sibling answer about structure of introns and exons is a more convincing answer, in my opinion. I don't think we would expect to see that in convergent evolution, but we would in a copy-paste job.

[throwanem]

On what basis do you hold any such expectation? The paper explicitly contrasts its subject with several examples of convergent evolution producing functionally equivalent, but proteomically and genomically highly distinct, outcomes - which is typical of convergent evolution in general.

That said, I agree that the similarity of adjacent noncoding sequence is also a strong indicator that convergent evolution isn't causative here.

[teachingassist]

> On what basis do you hold any such expectation?... The paper explicitly contrasts its subject with several examples of convergent evolution producing functionally equivalent, but proteomically and genomically highly distinct, outcomes

On the basis that the protein is the function here. (antifreeze protein). There might only be one good, or best local maximum, solution for this problem at the protein level. So, we would expect natural selection might converge on that one solution. And, the results of two runs would not be nearly as different as they are in cases where natural selection is optimizing for a system process.

Obligatory coding comparison:

If I asked two programmers to code a webshop, I would expect the underlying code to look substantially different - if the code looked the same, I'd take it as evidence of copying.

If I asked two programmers to code "If A then B", I would expect the underlying code to look substantially the same, whether or not they copied.

A specific antifreeze protein is the second case: both the code and the outcome. It's not part of a system which would have more freedom of variation in its solutions.

[throwanem]

Preventing crystallization of water is the function. And again, on what basis so presume? Trivial literature review would have sufficed to reveal that there is a whole, mostly very nonhomologous, class of these proteins, not just the one. [1] It is precisely for this reason that near identity observed in the proteins used by these three unrelated fish species is surprising.

As I have already noted this morning, it is at best pointless to attempt to reason out genomics based on first principles drawn from computing. Thank you for taking the time to demonstrate the kind of error that invariably results!

[1] https://en.m.wikipedia.org/wiki/Antifreeze_protein

[teachingassist]

Even with all this 'trivial literature review', there still remains the possibility three fish might have randomly walked [or non-randomly walked] into the same solution with the same local maximum, which couldn't be distinguished from lateral transfer just by looking at the protein structure.

"A doesn't always happen this way" isn't evidence, at all, for B happening. Your logic is faulty.

Thank you for appreciating my sense of humour. As someone who has worked in a genomics lab, I think coding analogies are perfectly fine. The analogy is not in error.

[throwanem]

Happily, the paper does not only do that! Too, there are several comments peripheral to this thread which discuss the paper's findings outside the proteome.

Far be it from me to suggest that anyone in a Hacker News thread has failed to do even the most basic of reading in a field outside their own, but I will say that the paper is linked in one of my earlier comments, should you perhaps like to renew your acquaintance with its contents.

[teachingassist]

> Happily, the paper does not only do that!

Yes, happily! Since, as I was saying in my first comment: I didn't agree with this part of the paper's abstract being relevant evidence, or your take on it; but I agreed with it in other aspects.