Talk:Evolution of snake venom/GA1

GA Review
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Reviewer: I'll take on this interesting article. Chiswick Chap (talk · contribs) 22:36, 16 March 2017 (UTC)


 * My apologies, Chiswick Chap, I've been busy, and will continue to be busy for another couple of days, after which I hope to address your more substantive points. Vanamonde (talk) 13:29, 19 March 2017 (UTC)

General comments

 * I notice that there are a lot of photos of snakes, but only one illustration of a molecule (and no evolutionary diagrams of any sort). Perhaps something is awry here, or perhaps it shows something of the state of knowledge. If it were possible, more on the molecular side, and at least alternative conjectures for the evolutionary state of play would be of interest: these could be cladograms, perhaps, annotated with names of venom molecules or 'source' molecules later adapted (exapted?) for venoms (or coloured squares each representing a named molecule) in different parts of the evolutionary tree ... I wonder. Chiswick Chap (talk) 22:44, 16 March 2017 (UTC)
 * This is a good point, and I'll see what I can do. Proteins being what they are, all diagrams thereof tend not to look very different to the layman...this, for instance, is a metalloproteinase, which we could reasonably include in the section about tenderizing prey; but does it add very much? Not sure. The phylogeny is tricky for a different reason; that there is no authoritative phylogeny, and indeed strong disagreement about the evolutionary history. The way around this, I suppose, would be to present a phylogeny from one particular study, and describing it as such...so I'll work on finding a good one, which is both substantive and understandable. Vanamonde (talk) 05:43, 17 March 2017 (UTC)


 * The phylogeny has two parts: that of the snakes themselves, which seems to be reliable and is depicted in Snake; and of the venoms, which might have one or many origins, which could be marked on a copy of the cladogram; ditto that of lizards + snakes.


 * Further, the snake images could perfectly well be used as small thumbnails to label the relevant parts of the cladogram(s), so we'd see, for instance, that Crotalus rattlesnakes are in the Viperidae. This would give a visual clue to "where" each example fits in the bigger picture, which is what I was missing at first reading.
 * I think all cladogram issues are sorted out, right?
 * Yes. We haven't entirely got rid of the long-list-of-snake-pics-down-right-hand-side but it's certainly within GA parameters now.


 * It would (also) be helpful to gloss each example, such as Crotalus, with its family, like "(Viperidae)", but this would supplement not substitute for a phylogenetic (cladogram) view. Chiswick Chap (talk) 07:29, 17 March 2017 (UTC)
 * done, I believe


 * On the similarity of all protein models :) you can turn this to your advantage by showing side-by-side a protein supposed to be the origin of a toxin and the toxin itself (you have Phospholipase A2, would be ideal to have the matching venom version also). (There's a small mystery about the File:PDB_1rm8_EBI.jpg image you mention: it says it's used in MMP16, but the protein (enzyme) shown there does not have the small stick-molecule (the enzyme's substrate that it digests???), I can't work out how that is possible given Wikipedia's linking mechanisms.) Still, the fact that here is a digestive enzyme with substrate, and it's also a component of a venom, is well worth illustrating and discussing. Chiswick Chap (talk) 08:42, 17 March 2017 (UTC)
 * I've added the image of the enzyme. I'm not sure the side-by-side idea is practical at the moment, simply because the images do not exist, and I haven't the ability to produce them. Vanamonde (talk) 06:07, 22 March 2017 (UTC)


 * Throughout the article, it would be helpful to gloss taxonomic names to show where they fit in; for example Agkistrodon could be glossed "Agkistrodon, another pit viper,".
 * done a few; let me know if more are needed.
 * Much improved, I've added a couple more. Chiswick Chap (talk) 13:47, 19 March 2017 (UTC)

Specific comments

 * Lead image: nice photo, but the article is lacking an image of a snake with its prey, which would more directly represent the subject, such as this rattlesnake. See also Category:Serpentes eating - there are egg-eating snakes too, which could be useful in your discussion of reduced toxicity as eggs don't run away, and photos of constrictors such as this rainbow boa, again illustrating the loss of toxicity. Chiswick Chap (talk) 09:06, 17 March 2017 (UTC)
 * I've switched the first image. The trouble with that category is that a) they are mostly non-venomous snakes, and we really only have place for one of those, and b) they are aesthetically not the best images. Nonetheless, I've also replaced the sea snake image with that of an egg-eating snake eating an egg.
 * Well, the effect is far more convincing. Chiswick Chap (talk) 06:50, 22 March 2017 (UTC)


 * Pre-digestion of prey: wikilink homeostasis, platelet, cell membrane (and remove hyphen), hemorrhage, necrosis.
 * done


 * Tracking bitten prey: how exactly do disintegrins assist tracking? Sounds as if it might be smell?
 * yep, smell. clarified.


 * Tracking bitten prey: why not consider using images of an integrin alongside (see Template:Multiple image) a disintegrin? We know that disintegrins interact with (aka royally foul up) integrin receptors. Did they perhaps evolve from integrins? Whether they did or didn't, the two images side by side would say clearly that these toxins work by mimicking the shape and binding of integrins.
 * Honestly I think this is rather too complicated, because the activity of the disintegrin has not been linked to its use in tracking; this might be a discussion more suited to the Snake venom page.
 * Eh? You say "The study concluded that these disintegrin proteins were responsible for allowing the snakes to track their prey, by changing the odor of the bitten animal.[14]", so why the contradiction? Chiswick Chap (talk) 06:50, 22 March 2017 (UTC)
 * True: but their actions upon integrin receptors are not discussed here. I'd be okay with just the picture of a disintegrin, if you think that would be helpful? Vanamonde (talk) 07:22, 22 March 2017 (UTC)
 * Yes. But I think the pair of images should be side-by-side (as should the pair above); could be either a 2-image gallery or a multi, horizontal. Chiswick Chap (talk) 07:55, 22 March 2017 (UTC)
 * Okay, I've added the disintegrin image, and made the above pair horizontal as well.


 * Mechanisms of evolution: this gets pretty technical in the first paragraph. Suggest wikilink inflammation, lipase, allele;
 * done: linked homologous recombination instead, will work on the explanation when I'm back.


 * please explain what non-allelic homologous recombination is and how it helps.
 * Given this a shot, take a look


 * Selection pressure: wikilink coevolution, evolutionary arms race.
 * coevolution is already linked, linked the other term.


 * Selection pressure: what do you mean by "is likely to evolve via adaptive evolution." Needs rewording.
 * reworded: is this better?


 * Selection pressure: "neutral processes" - presumably need to wikilink genetic drift, if not to say so explicitly.
 * well it isn't just genetic drift, though, is it. If anything genetic drift is a minor part of this: mostly it's random mutation.
 * Ah, that misled me, so please say 'mutation and genetic drift' or something of that sort.
 * I've already linked neutral evolutionary processes above, but I've added the links in a parenthesis.

Summary
There is very little wrong with this article, and it should be a worthy GA very shortly. Apart from the need to manage technicality in a few places, my main concern is the repetitive nature of the illustrations, which should be replaced by something more explanatory, and I've made suggestions for how that might be achieved. Chiswick Chap (talk) 09:36, 17 March 2017 (UTC)
 * I think that's everything, but for the issue of the duplicate phylogeny, which I'm uncertain about. Thoughts? Vanamonde (talk) 06:38, 22 March 2017 (UTC)

There remains scope for a more detailed cladogram of (part of) the Colubroidea to show events more precisely, but we have covered the main points adequately.
 * Just one item open on the disintegrin question. :Chiswick Chap (talk) 06:57, 22 March 2017 (UTC)
 * All done, and a worthy GA. I think the article is clearer now, with more impact, and I hope you find it so also. As research proceeds I'm sure that many more extraordinary details will be revealed on this topic at molecular level. Chiswick Chap (talk) 09:33, 22 March 2017 (UTC)