Talk:Arsenic biochemistry

Revision of Jan 3 - Blog-like article in my humble opinion

In my very humble opinion, and not having contributed substantively very much, this article has become sort of bloggy, pushing the recent news on the possibility of As replacing P in some microorganisms. That news is very topical, but an encyclopedia article should emphasize more conventional material, i.e. real As-containing biomolecules (there are several As-natural products) and authenticated roles of As in biology (e.g. Arsenic#Biomethylation of arsenic). The problems that stick out to me are the following:

• about 40% of the article is overlaps heavily or is a concentrate Arsenic toxicity, i.e. most of the article is not new.
• excessive emphasis on astrobiology (fun stuff, but verging on synthesis and speculation), i.e. much of the remainder is speculative or fringey.
• not sure why the article discusses bond lengths of As-X vs P-X. IMHO, more relevant is redox potential and pKa's of various acids, but then it occured to me, why are is there any comparison As and P in an encyclopedic overview of bioAs chem (or why not As and Se, or other directions on the periodic table)? The reason is that well intentioned editors are pushing something that tickles their fancy vs describing the topic at hand (I plead guilty of the same crime in other articles!).

Sorry for my grumpy comments... I will try to add some content, which is more productive.--Smokefoot (talk) 01:19, 4 January 2011 (UTC)

Hello, this article is now a far cry from its original self. However it does have a lot of room for improvement. It was born from the GFA-1 discovery and so it relied heavily on it. Since the activity and interest in this article seems to have died down, I'd say go for it and do your best. Cheers, --BatteryIncluded (talk) 01:37, 4 January 2011 (UTC)

Okay, it takes some time to get the info. The astrobiology hobbyists really did a number on this article, and it is always difficult to rectify an article after it has been filled with specialized refs supporting someone's hobby/perspective. It's a recurring problem.--Smokefoot (talk) 13:58, 4 January 2011 (UTC)

I blame NASA. They went overbord this time. Cheers, --BatteryIncluded (talk) 14:43, 4 January 2011 (UTC)

It was not NASA that added references 21-34 to this general article, i.e. the role of As in microbiology and astrobiology. And now, when one tries to rebalance this article so that readers interested in the general topic of bioAs, I will get howls from these hobbyists if one of their pet references are removed. That nuisance recurs in Wikipedia, i.e. WP:UNDUE, when hobbyists become fascinated with a newsy item but dont know the basics. Oh well.--Smokefoot (talk) 14:09, 6 January 2011 (UTC)

The point of the article is the As biochemistry, so expect entries in microbiology. Regarding the astrobiology aspect, it was NASA's main punch line when presented GFAJ-1 bacterium, but it is covered in that rticle. Actually, there is no mention of astrobiology in this article, it only uses some references from astrobiology journals. Go ahead with your changes, after looking at your contributions elsewhere I do believe you are quite competent. Just keep it in the realm of biochemistry. If I can be of help please let me know. Cheers, --BatteryIncluded (talk) 20:33, 6 January 2011 (UTC)

Arsenic DNA redirects to this article, but I couldn't find a discussion of arsenic DNA the linking article was referring to, except for a brief technical mention at the start of a section with a rather opaque title. Seems to me there should either be a section on the arsenic DNA question, or—since you seem to have decided against that—perhaps Arsenic DNA should redirect to GFAJ-1. --MillingMachine (talk) 05:06, 31 July 2013 (UTC)

Great idea to redirect Arsenic DNA to GFAJ-1. This article at one time discussed discredited research purporting that As replaced P in DNA, but we are past that phase.--Smokefoot (talk) 07:43, 31 July 2013 (UTC)

Prebiotic = not biochemistry

The section on "prebiotic arsenic" has no business in an article on biochemistry, by definition. Otherwise the article invites essays on diverse arsenic minerals, Stellar nucleosynthesis etc. Probably this section might be better sited in arsenic. Anyway, as I have said above, the section comes close as original research (it is a fascinating subject).--Smokefoot (talk) 18:17, 9 January 2011 (UTC)

I agree. And you are doing a wonderful job. Cheers, --BatteryIncluded (talk) 18:35, 9 January 2011 (UTC)

Thanks for your collaboration. I will remove the expert tag. Best wishes, --Smokefoot (talk) 14:25, 10 January 2011 (UTC)

There are really two points in that section. A) That there are well-documented organisms today that respire arsenic (V), i.e. use it as an electron acceptor, and B) that arsenic may have been more available at some point in the distant past and/or on other planets. The first point is certainly important and relevant to a discussion of arsenic biochemistry (and isn't actually about "prebiotic" arsenic at all). The other point seems more speculative, and is presumably is meant to justify why "arsenic-based" biochemistry might have arisen in the first place. The recent rewrite removed much of the content about the potential for arsenate to substitute for phosphate (arsenic nucleic acids are still included, but the claims about GFAJ-1 and the prior papers on theoretical arsenic biochemistry weren't just about nuclei acids even though that got much of the press). The question of the historical availability of arsenic probably makes the most sense in the context of discussing its hypothetical ability to substitute for phosphorous in a more general way than is general surmised. Dragons flight (talk) 15:54, 10 January 2011 (UTC)

Good points. Yes, we need more info on the use of As(V) as an electron acceptor, how that works. Probably the events are like sulfate and other oxyanions. The "potential for arsenate to substitute for phosphate" approaches undue attention, certainly a minor point in the broad context of As biochemistry. The As for P theme is not discussed in the reviews (that I found) on As biochem. Biochem and Microbiology textbooks do not to discuss this speculative theme either. Tellingly, biochem books do not discuss Si for C, a venerable theme in science fiction. My own feeling is that readers who want to know about biochemistry of As are unlikely to be seeking analysis of As replacing P, or at least not much on that rather specialized point. Readers want to know about the "canon" of As biochem: which compounds are actually been identified and how these As compounds behave in living systems. Not so much: which compounds might exist and how they might behave and why they might have been selected. Otherwise every biochem article would get a section discussing the possible replacement of all sorts of elements. But these are only one editor's views.

Your suggestions do point to one important area of agreement: we need more on the pathway for reduction of As(V). It is mentioned in my microbook but few details. I looked at Sulfate-reducing bacteria, but it has no biochem in that article. I will address that gap, next weekend, perhaps. More suggestions are welcome. --Smokefoot (talk) 18:40, 10 January 2011 (UTC)

I will not modify that section in the next 2 weeks and will see what develops. Thanks guys. --BatteryIncluded (talk) 02:28, 12 January 2011 (UTC)

How about moving the prebiotic section to Organoarsenic chemistry? --BatteryIncluded (talk) 15:39, 28 January 2011 (UTC)

FWIW - yes, moving the prebiotic section to Organoarsenic chemistry seems like an ok idea to me at the moment.Drbogdan (talk) 14:49, 29 January 2011 (UTC)

Time to unwind the crap: Bio-arsenic debacle

A couple of years ago the article expanded with a lot of speculation that As could replace phosphate in all sorts of biological functions. The key paper has basically been killed off. So now is a good time to start unwinding this misleading content. My recommendation would be to contract the relevant articles rather than present a lot of hand-wringing. The two new articles in Science are mentioned in http://www.bbc.co.uk/news/science-environment-18770964. I hope that the contributing editors will prove as enthusiastic about completing their work. --Smokefoot (talk) 13:05, 10 July 2012 (UTC)

Is this a contribution? BatteryIncluded (talk) 13:16, 10 July 2012 (UTC)

Not sure what you mean, but my message is a reminder that hyped content that could mislead readers needs to be cleanup with the same vigor that it was added. This debunked content probably infects a variety of articles here. --Smokefoot (talk) 13:22, 10 July 2012 (UTC)

Looks like diligent scientific process brought up an update from robust skeptisicim to complete debunking of GFAJ-1, and I'll be happy to incorporate it in this article. Since you don't seem eager to work, could you please specify what is the "hyped content" that needs cleanup? Cheers, BatteryIncluded (talk) 14:39, 10 July 2012 (UTC)

Is methylation of arsenic detoxification?

Recent work has questioned whether methylation of arsenic detoxifies it, or whether it actually makes it more toxic. For example, Bergquist et. al. found that monomethylated arsenicIII was a more effective inhibitor of pyruvate dehydrogenase than inorganic AsIII, although dimethylated AsIII was less effective than either of them. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2685281/ The page on arsenic toxicity http://en.wikipedia.org/wiki/Arsenic_toxicity mentions some of these new findings. 163.11.224.111 (talk) 17:24, 30 November 2013 (UTC)

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backwards copy

A substantial portion of this article is reproduced (thinly disguised)in Sattar et al., 'Metabolism and toxicity of arsenicals in mammals,' Environmental Toxicology and Pharmacology, Vol. 48, 2016. KayemH (talk) 18:08, 2 December 2016 (UTC)