> 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 ...
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 ...
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.
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.
That said, I agree that the similarity of adjacent noncoding sequence is also a strong indicator that convergent evolution isn't causative here.
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.
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!
"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.
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.
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.
I'm not averse to the idea that I may be wrong on any of those points, but thus far I'm not seeing anything substantive to suspect I am likely to be so. These are just assertions that you're making, and while your reasoning itself is not unsound, the premises from which it follows as yet lack anything resembling substantiation, which is sorely needed given that those premises so contradict all available evidence.
...and, in response to your prior edit, this is coming from someone who has also worked in a genomics lab. Even if I hadn't, what point to claiming authority on that basis?
I apprehended it perfectly well; I'm still in disagreement, since my argument is unaffected.
> so contradict all available evidence
It doesn't, and that's what you have missed. What I said is logically harmonious with all available evidence.
By observing three fish with the same solution for antifreeze, we know that three fish have the same solution for antifreeze. This immediately contradicts any claim that all unrelated species have different solutions for antifreeze, which makes them worthy of study. It's a "black swan".
As such, whatever mechanism has caused this has not been seen to work this way elsewhere. Therefore, saying "this mechanism is not seen to work this way elsewhere" is not remarkable as evidence.
It's now a neutral statement which matches our expectation, and can't therefore be evidence against the mechanism. It's certainly not evidence for another mechanism.
I could just as well say "I have only observed horizontal transfer in N other cases, and this is not one of those N cases, therefore it is not horizontal transfer". That would be wrong, but has equal logical merit as your claim.
The paper doesn't claim causality either, but only argues, in my view pretty convincingly, that lateral gene transfer is a likelier explanation for the observed similarity than any other including convergent evolution. You haven't argued otherwise, but only that convergent evolution in this case is not implausible - which is true, but answers no claim that anyone is actually making.
There's no point in that that I can see, so if you want to keep on doing it, I'm afraid you'll need to do so in the absence of an interlocutor, or at least of an interlocutor who is me.
It is wildly unlikely that I should exist through the process of evolution, to waste my afternoon on this argument, and yet: here I am :) Have a nice day.
Oh, this was a direct response to the fact that you repeatedly implied that I was ignorant and hadn't done basic reading in the field. You were wrong about that as well.
Someone disagreeing with you is not always a sign of ignorance.
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.
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!)