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It isn't an assumption; the null hypothesis here is that that doesn't happen. Genes coding for cryoprotective proteins have indeed, as you suggest, evolved inde

It isn't an assumption; the null hypothesis here is that that doesn't happen. Genes coding for cryoprotective proteins have indeed, as you suggest, evolved independently among various species. The resulting genes, despite all producing proteins similar enough to do the necessary job, are "radically different" and "highly diverse." [1] What's different in this case is that, in three otherwise very distantly related species of fish, we find their antifreeze proteins are coded for by the same genes: > But, the isolated occurrence of three very similar type II AFPs in three distantly related species (herring, smelt and sea raven) cannot be explained by this mechanism. These globular, lectin-like AFPs have a unique disulfide-bonding pattern, and share up to 85% identity in their amino acid sequences, with regions of even higher identity in their genes. A thorough search of current databases failed to find a homolog in any other species with greater than 40% amino acid sequence identity. [1] In light of the fact that all other genes known to code for these proteins are very distinct both from this one and from one another, 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, i.e., that horizontal gene transfer has occurred among these vertebrates. [1] https://pubmed.ncbi.nlm.nih.gov/18612417/ https://pubmed.ncbi.nlm.nih.gov/18612417/

erdewit 5y ago
Also, the article mentions that the introns - the "junk" DNA around the DNA that encodes the actual protein - is 95% similar.
teachingassist 5y ago
> 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 5y ago
  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 5y ago
    > 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 5y ago
      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 https://en.m.wikipedia.org/wiki/Antifreeze_protein

erdewit 5y ago

Also, the article mentions that the introns - the "junk" DNA around the DNA that encodes the actual protein - is 95% similar.

teachingassist 5y ago

> 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 5y ago
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 5y ago
  > 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 5y ago
    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 https://en.m.wikipedia.org/wiki/Antifreeze_protein