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> But it is very surprising, even weird, that both fish do so with the same AFP gene Maybe that constellation of a gene is the "obvoius solution" and both fish

> But it is very surprising, even weird, that both fish do so with the same AFP gene Maybe that constellation of a gene is the "obvoius solution" and both fish will likely develop it by chance? Why assume the genes jump over ...

permo-w 5y ago
Do you think these scientists are stupid?
- foxhop 5y ago
  Part of science is questioning other peoples hypothesis, results, and analysis. This is how science works.
  - snakeboy 5y ago
    Yes, but speculation about the most obvious questions from someone who hasn't done any work to investigate whether it's already been addressed doesn't progress science either. Here's the 2nd paragraph from the linked article (which is already a source someone created to help non-experts understand the main ideas): > It isn’t surprising, then, that herrings and smelts, two groups of fish that commonly roam the northernmost reaches of the Atlantic and Pacific Oceans, both make AFPs. But it is very surprising, even weird, that both fish do so with the same AFP gene — particularly since their ancestors diverged more than 250 million years ago and the gene is absent from all the other fish species related to them. edit: I am more sympathetic to this behavior when the topic is more politically contentious, since it may be unreasonably difficult for a layman to know the biases of the authors and the source may indeed be trying to slide something under the rug. But here we're talking about fish genetics. There's no culture war or red vs. blue divide here (I hope!)
    - odyssey7 5y ago
      I can’t see the scientists being harmed by a layperson’s curious engagement. Every scientist was once a curious layperson.
      - snakeboy 5y ago
        I didn't say it harms scientists. I said this example doesn't progress science. Curious laypersons are well and good. I would recommend they start by reading the linked Quanta article :)
    - vlovich123 5y ago
      Not my field but another seemingly plausible explanation, at least to me, exists. The common ancestor did have this gene and most other descendants lost the gene because it wasn’t needed and was selected against.
  - permo-w 5y ago
    It is, but this is pretty much the first thing the article asks, and the first thing anyone would ask. The comment is almost acting like the scientists haven’t considered that hypothesis
- garmaine 5y ago
  Do you think this comment was helpful?
  - permo-w 5y ago
    Yes
throwanem 5y ago
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.
nerdychristie 5y ago
There are a few reasons convergent evolution is really unlikely here. 1) This particular gene isn't the obvious solution - there are many, highly diverse antifreeze proteins, not to mention other mechanisms of freeze resistance (glycerol production, for example). 2) Even if it were, the genetic code is redundant, meaning that there are often several 3-base codons that code for a given amino acid. So even if the exact amino acid sequence is what mattered, the odds of using the exact same coding to obtain that sequence is unlikely. 3) The similarity extends beyond the coding region. It includes stretches of DNA in between and flanking the gene's code itself. These are stretches of DNA that normally mutate at a much higher rate than the coding region itself, and they aren't under the selective pressure of making a working protein, so there's no real evolutionary explanation for how they'd end up so similar.

permo-w 5y ago

Do you think these scientists are stupid?

foxhop 5y ago
Part of science is questioning other peoples hypothesis, results, and analysis. This is how science works.
- snakeboy 5y ago
  Yes, but speculation about the most obvious questions from someone who hasn't done any work to investigate whether it's already been addressed doesn't progress science either. Here's the 2nd paragraph from the linked article (which is already a source someone created to help non-experts understand the main ideas): > It isn’t surprising, then, that herrings and smelts, two groups of fish that commonly roam the northernmost reaches of the Atlantic and Pacific Oceans, both make AFPs. But it is very surprising, even weird, that both fish do so with the same AFP gene — particularly since their ancestors diverged more than 250 million years ago and the gene is absent from all the other fish species related to them. edit: I am more sympathetic to this behavior when the topic is more politically contentious, since it may be unreasonably difficult for a layman to know the biases of the authors and the source may indeed be trying to slide something under the rug. But here we're talking about fish genetics. There's no culture war or red vs. blue divide here (I hope!)
  - odyssey7 5y ago
    I can’t see the scientists being harmed by a layperson’s curious engagement. Every scientist was once a curious layperson.
    - snakeboy 5y ago
      I didn't say it harms scientists. I said this example doesn't progress science. Curious laypersons are well and good. I would recommend they start by reading the linked Quanta article :)
  - vlovich123 5y ago
    Not my field but another seemingly plausible explanation, at least to me, exists. The common ancestor did have this gene and most other descendants lost the gene because it wasn’t needed and was selected against.
- permo-w 5y ago
  It is, but this is pretty much the first thing the article asks, and the first thing anyone would ask. The comment is almost acting like the scientists haven’t considered that hypothesis
garmaine 5y ago
Do you think this comment was helpful?
- permo-w 5y ago
  Yes

throwanem 5y ago

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.

nerdychristie 5y ago

There are a few reasons convergent evolution is really unlikely here. 1) This particular gene isn't the obvious solution - there are many, highly diverse antifreeze proteins, not to mention other mechanisms of freeze resistance (glycerol production, for example). 2) Even if it were, the genetic code is redundant, meaning that there are often several 3-base codons that code for a given amino acid. So even if the exact amino acid sequence is what mattered, the odds of using the exact same coding to obtain that sequence is unlikely. 3) The similarity extends beyond the coding region. It includes stretches of DNA in between and flanking the gene's code itself. These are stretches of DNA that normally mutate at a much higher rate than the coding region itself, and they aren't under the selective pressure of making a working protein, so there's no real evolutionary explanation for how they'd end up so similar.