Talk:GFAJ-1/Archive 1

Archive 1

Merger proposal

The following discussion is closed. Please do not modify it. Subsequent comments should be made in a new section.

I propose that Arsenic-based life be merged into GFAJ-1 (bacterium). I think that the content in the Arsenic-based life article can easily be explained in the context of GFAJ-1, and the GFAJ-1 article is of a reasonable size in which the merging of 'Arsenic-based life' will not cause any problems as far as article size or undue weight is concerned. BatteryIncluded (talk) 19:13, 2 December 2010 (UTC)

• Wait

Too soon. Give it a few days and see what the articles looks like. Knowitall (talk) 19:33, 2 December 2010 (UTC)

• Wait. My concern with the merge is the discovery of other specific bacterium (perhaps other life forms) that are arsenic-based. We can only speculate about what more (if anything) will be discovered, but limiting the topic solely to GFAJ-1 seems a bit closed-minded. I would rather see this specific bacteria listed an example on the Arsenic-based life article. The article needs more in-depth information, but considering the story was released to the media hours ago, more information will be added soon. Additionally, carbon-based life is its own article, do you propose that we merge it into every instance of carbon-based life? Seems a bit Carbon chauvinistic. 170.31.86.53 (talk) 19:44, 2 December 2010 (UTC)

• Wait

I completely agree. We shouldn't make synonym GFAJ-1 and Arsenic Based-life. They are different themes. This will open the scientific minds to think about what how the life can be create. So, if is rest a lot of phosphorus based organism, there's a big probability to find a bunch of arsenic based life. BlackReggae (talk) 19:51, 2 December 2010 (UTC)

• Merge or rename Arsenic-based life. Discovering an organism that replaces phosphorous with arsenic is significant. However, GFAJ-1 is NOT arsenic-based. It's still carbon based. Arsenic/phosphorous is a relatively small component of its overall atomic make-up. It's mostly water and carbon. We may find other organisms that can replace P with As, which would merit an article on these organisms collectively. But such an article should NOT be titled [Arsenic-based life]]. Is there any hypothetical speculation about possible extraterrestrial organisms that replace CARBON (not PHOSPHOROUS) with ARSENIC? That would be arsenic-based life. As the content of Arsenic-based life currently is about GFAJ-1, the article should be merged. If there is some well referenced speculation about the possibility of actually arsenic BASED life, it should go in that article. If other organisms turn up similar to GFAJ-1, they should be discussed collectively in an article perhaps to be titled something like Facultative incorporation of arsenic in place of phosphorous in terrestrial life-forms192.104.39.2 (talk) 20:37, 2 December 2010 (UTC)

• Strongly agree that Arsenic-based life should be renamed. You and I are carbon-based life that happens to also utilize a small amount of phosphorus. GFAJ-1 is carbon-based life that happens to also utilize a small amount of arsenic. (But only when it is grown in an artificial environment where it is starved of phosphorus.) There is no such thing as "arsenic-based life." 174.24.103.195 (talk) 06:25, 3 December 2010 (UTC)

• Comment. Somewhere Wolfe-Simon made the comment that she already has 14 other cultures from Mono Lake growing in arsenic. At present she doesn't know if any of these are different microbes than GFJA-1, but if they are then we would eventually need an article for the larger category of life. Dragons flight (talk) 20:42, 2 December 2010 (UTC)

• Rename Arsenic-based life I don't agree with the merge but I do agree with a name change, for the same reasons already stated here. 85.240.177.93 (talk) 20:47, 2 December 2010 (UTC)

• Merge or Rename Arsenic-based life. Like 192.104.39.2 up there said, the ability to substitute arsenic for phosphorous when starved does not make is arsenic-based. Since there is no known speculation for truly arsenic-based life (meaning, it utilizes arsenic in the same manner which known life uses carbon, which may not be chemically possible), there's no point in having an article with that title. Perhaps merge Arsenic-based life and add a redirect for people who search for the misnomer.65.182.82.248 (talk) 21:09, 2 December 2010 (UTC)

• Wait + Rename. Way too soon to merge. GFAJ-1 may not be the only organism that incorporates arsenic. However, the "arsenic-based life" article needs a more accurate title. --Thorwald (talk) 21:32, 2 December 2010 (UTC)

• Oppose merger proposal. It is entirely too soon to do such a merger. Arsenic-based life, or life based on non-phosphorous building blocks has now been suggested on the world scientific stage. It is my no means clear that GFAJ-1 is the only organism involved. N2e (talk) 00:22, 3 December 2010 (UTC)
• Oppose. This is not arsenic-based life, a counterpoint to carbon-based or silicon-based life! It's an extremophile that doesn't die in arsenic. Abductive (reasoning) 01:58, 3 December 2010 (UTC)

• Oppose. The bacteria uses arsenic in a new way--it is NOT arsenic-based life. Spinach Dip 09:01, 3 December 2010 (UTC)
• Oppose. Neither is arsenic-based life the same subject as GFAJ-1 (at most, the latter would be an instance of the former), nor is the GFAJ-1 an arsenic-based life form. In this organism, arsenic replaces phosphorus; not carbon. It is still an instance of a carbon-based life form; it just uses the abundant arsenic around it in place of phosphorus. 85.53.133.227 (talk) 10:39, 3 December 2010 (UTC)

• Proposal withdrawn- As the editor who first proposed the merger, I now withdraw the proposal. In the first few hours after the NASA press conference, both articles were almost the same, but the other article's title was Arsenic-based life. As time passed, both articles became more specific and certainly a merger now is certainly not granted.

As a final note, please believe me that there is no such thing as arsenic-based life nor arsenic-based DNA. GFAJ-1 is able to incorporate it to some degree and it remains a carbon-based microorganism. Cheers, --BatteryIncluded (talk) 14:47, 3 December 2010 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Define the acronym

If anyone knows what "GFAJ" stands for, please add the acronym definition to the article. Use of undefined acronyms is very bad practice... just because the NASA press release does it, doesn't mean WIkipedia should. 174.24.103.195 (talk) 06:52, 3 December 2010 (UTC)

Is the name GFAJ-1 really an acronym? I tried looking it up and every source I can find, even the non-NASA ones, just use it without hinting if it stands for something. DeeRD (talk) 15:29, 3 December 2010 (UTC)

Anecdotal evidence time! A member of the Something Awful forums who claims to know Felisa said that it stood for 'Give Felisa A Job'. Here's a link to the post, but obviously that doesn't prove anything. Hope that helps!! Gimmick Account (talk) 19:02, 3 December 2010 (UTC)

That's pretty funny, and if we can get a reliable source it should be included in the article. 174.24.103.195 (talk) 22:45, 4 December 2010 (UTC)

It's true, and here's a reliable source. --Hyqeom (talk) 04:54, 5 December 2010 (UTC)

Added that link to the External links section, it's to interesting to be left here. Feel free to move it up in the article. Johan G (talk) 15:07, 5 December 2010 (UTC)

I am fairly sure that GFAJ-1 is the name of this strain of bacteria, not an acronym standing for anything. I am a PhD student in molecular biology (with no connection to any arsenic bacteria work), however, I looked through the full published article online in Science as well as publicly available sequence information for this bacteria and nowhere is a name given. It is described as "Halomonadaceae bacterium strain GFAJ-1" (sequence info here: http://www.ncbi.nlm.nih.gov/nuccore/312284551) —Preceding unsigned comment added by 132.216.229.230 (talk) 21:38, 3 December 2010 (UTC)

Oh, it is the name of the bacterium, but as the poster in my link mentioned, scientists who discover a strain pretty much have free reign concerning its name. Unless someone knows of any similiarly-named organisms, it's probably the correct explanation for the acronym. Gimmick Account (talk) 22:03, 3 December 2010 (UTC)

Well, they may have not discovered a new species, hence the unimaginative strain name: when a new bacterium that cannot be grown is found it is called candidatus xxx yyy, when a new growable species is found it gets a gen. nov. sp nov. tag (and is submission to ATCC is optional, I think), here they don't give it a name, just a strain (hence not in italics) possibly because the species already has a name, but they are rightfully playing it safe (they are getting a lot of criticism). If you look at figure S1 it is in the Halomonas genus and if you Blast the sequence you get 99% identity to a bunch of bugs, the majority unclassified Halomonas (that is normal), a more variable marker should have been used to determine the correct species, but I reckon they are midway in assembling the genome, so in the next publication they will say. My two cent guess of the strain name, GFAJ-1 is Gwyneth W. Gordon, Felisa Wolfe-Simon, Ariel D. Anbar and Jodi Switzer Blum, but then on the other hand you can fit an acronym to anything, even beatles' songs... --Squidonius (talk) 01:01, 4 December 2010 (UTC)

How new?

Does this bacteria share a common ancestor with all other living things on Earth and just happens to be able to process arsenic, or is its ancestry convergent with ours? Basically, does this mean that life developed once or twice on Earth?65.182.82.248 (talk) 20:47, 2 December 2010 (UTC)

This bacteria shares an evolutionary history with all other life on Earth. Its DNA is normally just like that of any other organism. It just has the ability to incorporate some arsenic in place of some phosphorus under certain conditions. Otherwise, it is just a normal bacterium. -- Ed (Edgar181) 20:51, 2 December 2010 (UTC)

Agreed with above. If this were a completely distinct form of life from everything else, it almost certainly would not be using otherwise-normal DNA or ATP to begin with. - Drlight11 (talk) 20:58, 2 December 2010 (UTC)

That's what I thought, but with headlines like "NASA discovers all-new form of life!" I wasn't sure.65.182.82.248 (talk) 21:13, 2 December 2010 (UTC)

Also, AFAICT, these little guys use (and prefer) phosphorus when they can get it - so it's pretty clear that either:

1. These are descendants of a very primitive form of arsenic-only life that originated in an arsenic-rich environment which have learned to process phosphorous instead. That would suggest that all of the non-arsenic-loving phosphorous-based life is descended from GFAJ-1 or its close relatives.
2. These are a fairly standard phosphorous-based life form that has more recently evolved the ability to use arsenic instead when under extreme survival pressures.

I suspect the latter. But the idea that this is a case of parallel evolution - derived from a second abiogenesis event - seems astronomically unlikely because aside from this little arsenic trick - they seem to be biologically similar to all other life on Earth. If they were truly a second strand of life - you'd expect them to look amazingly different. Convergent evolution couldn't get to what we're seeing here. I think the NASA hoopla behind this is a little overrated. 70.112.128.105 (talk) 06:42, 3 December 2010 (UTC)

According to the article, this microbe is descended from the genus Halomonadaceae, which is a group of extremeophile bacteria. So GFAJ-1 does belong to the same tree of life as us, but is merely a form of life that has learned a couple neat new 'tricks'.

Actually, arsenate DNA can be compared to something like Pyrrolysine, which is an amino acid only present in a few methanogenic archea--utterly unique, yes, but not the proof (or result) of a whole new (undiscovered) tree of life. Spinach Dip 09:14, 3 December 2010 (UTC)

It shares a common ancestor with all other Proteobacteria. In the media, this story was overhyped with a lot of irresponsible speculation to the contrary. 174.24.103.195 (talk) 04:37, 5 December 2010 (UTC)

Important Clarification for the Ignorant

"Arsenic-based life" refers to something that is theoretical and probably nonsensical. (See: Carbon-based life.) The bacteria causing the recent sensation may utilize arsenic in place of phosphorous, in some capacity, but that is a very different thing than being "arsenic-based". The terminology is completely misguided, in the case of GFAJ-1.

I don't want to be a troll with that "Ignorant" crack, but the nonsense has to stop.216.254.111.34 (talk) 21:26, 2 December 2010 (UTC)

Language is a funny thing. If enough people use "arsenic-based life" to mean "life that incorporates arsenic into its core biomolecules" then that's what the phrase will ultimately mean. Of course "carbon-based life" means something stronger, but language has a way of developing lots of inconsistencies like that. Personally, I go by whatever the scientists are using. So far, it appears that the scientists have not been using "arsenic-based". Dragons flight (talk) 21:37, 2 December 2010 (UTC)

What Dragons flight said! Language is, at the end of the day, a descriptively determined phenomenon not a prescriptively described phenomenon based on what the root words, or similar word constructions, mean. N2e (talk) 00:25, 3 December 2010 (UTC)

The article has already been renamed Arsenic DNA. Abductive (reasoning) 08:48, 3 December 2010 (UTC)

Missing from the notes section

Note number 4: "^ a b Felisa Wolfe-Simon, et al. (2010). "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus". Science. doi:10.1126/science.1197258." Results in a DOI not found. SeanJA (talk) 00:37, 3 December 2010 (UTC)

The DOI appears to match what is on Science's website. My suspicion is that since the paper was only released today that the proper information has not yet found its way to the lookup database. Dragons flight (talk) 00:41, 3 December 2010 (UTC)

This takes some time and sometimes there is a typo somewhere in the database or a lazy science employee did not send it and than it will be a dead doi for some time .--Stone (talk) 08:37, 4 December 2010 (UTC)

Arsenic in Glucose?

"When the researchers added radiolabeled arsenate to the solution to track its distribution, they found that arsenic was present in the cellular fractions containing the bacterium's proteins, lipids and metabolites such as ATP and glucose,"

The other examples have phosphorus that can potentially be exchanged with arsenic. But I do not understand why glucose is there. 203.36.161.41 (talk) 04:22, 3 December 2010 (UTC)

Based on the paper, they broke the cellular constituents into four populations. Further, they found various amounts of arsenate in all four of these populations. One of those populations was the "small molecular weight metabolites", which includes substances like ATP, glucose, NADH, and acetyl-COA. Presumably the arsenate they observed in that population was bound to ATP or NADH analogs in place of the traditional phosphate. I think it is only coincidental that glucose also lives in the small molecular weight fraction, and not meant to indicate that arsenate is associated with glucose in any direct way. Dragons flight (talk) 05:07, 3 December 2010 (UTC)

Glucose 1-phosphate and glucose 6-phosphate are important metabolites, so in the absence of phosphate, formation of the arsenate analogs would be expected. WolfmanSF (talk) 05:18, 3 December 2010 (UTC)

I am grateful for the suggestion about the phosphorus in phosphorylated intermediates being replaced with arsenic, but can anyone tell me where the phosphorus would be found in the protein fraction? —Preceding unsigned comment added by Brivo1 (talk • contribs) 21:07, 5 December 2010 (UTC)

Proteins are routinely phosphorylated on amino acid side chains, so there is the potential for incorporation of arsenate there. -- Ed (Edgar181) 22:09, 5 December 2010 (UTC)

Arsenic-incorporating proteins aren't new either. Pjlmac (talk) 19:08, 12 December 2010 (UTC)

"Life can form in the absence of phosphorus"

The phrase: "It may indicate that life can form in the absence of large amounts of available phosphorus" is clearly a stretch. Life can survive in arsenic-rich environments but nobody can say if it can form in the absence of large amounts of available phosphorus. That's like saying that Polar Bears are the proof that mammals originated on the polar ice caps. 84.223.132.213 (talk) 14:22, 3 December 2010 (UTC) That's a great point. Did you already rephrase the sentence or should I? DeeRD (talk) 15:42, 3 December 2010 (UTC) Wait, I found the sentence, and I rephrase it to suggest that only some astrobiologists believe in this likelihood and that its not a sure thing as some might suggest in the media. DeeRD (talk) 15:44, 3 December 2010 (UTC)

Notice the wording, may indicate there. This is merely opening the door to an hypothesis, in case you felt compelled to keep it shut. -- 99.233.186.4 (talk) 23:24, 3 December 2010 (UTC)

Image

I have modified the image or DNA changing phosphate to arsenate, which may help the people who are not sure what is the phosphate part of DNA, however the fact that AsO4 acts as PO4 in GFAJ1 has not been proven in detail, so it a speculation. Can it still go in the namespace? --Squidonius (talk) 01:29, 4 December 2010 (UTC)

A 100% subsitution is not in the paper! The numbers suggest more like 10%. So this image is far from what is real. It might give the wrong impression to people not having read the publication.--Stone (talk) 08:35, 4 December 2010 (UTC)

No, the numbers show a 97% decline in phosphorus. You are probably confusing the observation that 10% of the bound arsenate was in DNA (with the rest in proteins and other things) with the assumption that only 10% of the DNA was changed. That's not true. Most of the arsenate was in other parts of the cell, but under normal conditions that would be true of phosphate as well since most of the phosphate in an ordinary cell is not associated with DNA. Dragons flight (talk) 22:56, 4 December 2010 (UTC)

I would prefer that this image be used on the Arsenic DNA page, since there is no evidence that GFAJ-1 is using arsenate in its DNA. Ideally, an Arsenate-backboned DNA image would show the changed 3D conformation of the helix. Abductive (reasoning) 23:02, 4 December 2010 (UTC)

There is plenty of evidence. There could still be better evidence, but there is no reason to discount the likely conclusion. PS. Have you read the paper yet? That would seem to be a prerequisite before arguing there is no evidence. Dragons flight (talk) 23:09, 4 December 2010 (UTC)

There is no proof in the paper, only speculation, that arsenic is incorporated into DNA. It is certainly plausible based on their data, but conclusive evidence is not there because they did isolate any pure DNA from the microorganism. I would guess that they are already working hard to determine exactly where and how the arsenic is incorporated and that these results will be published separately in the near future (maybe within a year or so). 96.227.89.95 (talk) 01:14, 5 December 2010 (UTC)

I believe this image is useful and illustrative to the layperson, even if the representation is not proven (yet) and/or whether or not a 0% or 100% substitution takes place. It clearly illustrates what all the fuss is about. I propose we add this image to both articles (GFAJ-1 and Arsenic DNA), but clearly note the caveats in the article caption. --Thorwald (talk) 00:31, 6 December 2010 (UTC)

I agree. --BatteryIncluded (talk) 00:34, 6 December 2010 (UTC)

I don't think it would be a good idea at all to add the image to this article. There is no discussion in the scientific literature surrounding GFAJ-1 which indicates this structure. Putting it in this article would infringe on Wikipedia's prohibition against original research. -- Ed (Edgar181) 00:54, 6 December 2010 (UTC)

I have removed the image from the article. I think there needs to be a reliable source proposing this structure before it can be added to the article. -- Ed (Edgar181) 01:08, 6 December 2010 (UTC)

Have you read the paper yet? This image depicts what is implied and illustrates the concept to the layperson. The image should be in the article. --Thorwald (talk) 02:29, 6 December 2010 (UTC)

Yes, I have read the paper, and they do not report a chemical structure. The image depicts a plausible interpretation of the findings, but unless there is a reliable source proposing this structure, I don't think we should include it. -- Ed (Edgar181) 13:49, 6 December 2010 (UTC)

This image is WP:OR, I'm afraid. Abductive (reasoning) 10:07, 6 December 2010 (UTC)

It's not OR, as this is clearly the idea being advanced by the paper (see: WP:OI). We should be careful in the caption to indicate that the degree of substitution, if any, is presently unverified. But there is no problem with presenting an image like this to show what the hypothesis entails. Might work better at (the somewhat misleadingly named) arsenic DNA article though, as this article is already a bit busy with images. Dragons flight (talk) 10:17, 6 December 2010 (UTC)

I agree with you, Dragons flight, that this image might work well at the arsenic DNA article. -- Ed (Edgar181) 13:49, 6 December 2010 (UTC)

Critics

There seems to be a few people out there having problems with the science article. In an interview a microbiologist claims that in the paper two experiments done months apart were inconsistent but never the less a average was made over both. He also claims that the small amount of phosphorous in the experiment might enough for the microbe to survive. --Stone (talk) 08:45, 4 December 2010 (UTC)

• I believe this is already noted in the article, in its own section. Abductive (reasoning) 12:36, 4 December 2010 (UTC)

Regarding genus Halomonas

The Science paper does not name a genus for GFAJ-1 (associating it only with family Halomonadaceae). In the supplemental material of the same paper, they give a genetic relationship tree based on 16S rRNA showing it was most closely related to the Halomonas genus. (Literally nestled between several Halomonas species.) Obviously, the authors had this information and yet they declined to assign GFAJ-1 to Halomonas in the main paper. It isn't obvious why they didn't, though perhaps they wanted a more complete genome first. Regardless, I think we shouldn't say GFAJ-1 is Halomonas since the paper doesn't actually say that it is. It would probably be fair to say that it is closely related to Halomonas, but I would prefer to wait on the definitive assignment until some set of scientists actually assign it to the genus, which they haven't done so far. Dragons flight (talk) 23:40, 4 December 2010 (UTC)

Agree. Have removed it, and added a cladogram so people can see for themselves how it's related to its phylogenetic neighbors. Sasata (talk) 00:14, 5 December 2010 (UTC)

Regarding that section, It has not been proven that the related species/strains can/cannot utilise arsenic nor do not commit that this is a even new species: I reckon that it should be noted that the paper talks about a new strain, not species (hence it is not followed by sp. nov nor are we waiting for the International Committee on Systematics of Prokaryotes to approve, see [1] for approved Halomonas) as mention in acronym section. On a side note (original research): the phylogeny is oddly done: they used RDB to get the alignment (which is correct so they know what they are doing), their sequence is of v. good quality (I checked it manually), but they make a ML tree with not only proteobacterian species, but Spirochaetes and Actinobacteria which are not the outgroup, but two epsilonbacteria end up as the root: I gave it a quick go using the ARB silva database as one can make the pipeline choose automatically up-to 40 neighbours and I got a clade Halomonas without any Chlorohalomonas, with good support to a bunch of unnamed species/strains [2], if the classic 97% identity threshold is used this is not a new species, but a strain of something nobody has even cared about enough give a name. --Squidonius (talk) 02:51, 5 December 2010 (UTC)

Good point about it being a strain, I've changed the lead to make that much more explicit; feel free to alter the article elsewhere as you see fit. About the phylogeny, it's not my speciality, so I'll take your word for it :) I imagine it won't be nameless for long. Sasata (talk) 03:21, 5 December 2010 (UTC)

The paper doesn't name a genus, but Henry Bortman, managing editor of Astrobiology Magazine, wrote "On the tree of life, according to the results of 16S rRNA sequencing, the rod-shaped GFAJ-1 nestles in among other salt-loving bacteria in the genus Halomonas." Seems like a reliable enough source to me. 174.24.103.195 (talk) 04:57, 5 December 2010 (UTC)

The Science paper also indicates this phylogenetic placement, but for whatever reason, does not explicitly say that this strain is in the genus (as Dragons flight points out above). Sasata (talk) 05:01, 5 December 2010 (UTC)

to further the mystery. I just remembered that RDP (they use) has an automated classifier and it automatically and unequivocally places it in Halomonas genus. I did some reading on the Halomonadacaea classification and expanded them, there used to be a lot of issues, but they seem to have been ironed out in 2002-2005, so it is not a "dodgy" family, like Bacillus and co.

Thanks Squidonius, that's pretty interesting; genomic technology sure has come a long way in recent years. Does RDP stand for Recombination Detection Program? Are you in favor of putting genus Halomonas back into the article? 174.24.103.195 (talk) 20:46, 5 December 2010 (UTC)

definitely and sorry for the crypticness, RDP, Ribosomal database project hosted at Michagan Uni and started by Woese and others, and ARB silva a collaboration between two german universities, are 16S databses with analysis pipelines (you give a fasta and they structurally align and find what it is), if you copy the sequence HQ449183 into the RDB classifier and set the confidence threshold upto 95% it is a Halomonas. The taxonomy is based on Bergey's Manual, so it is valid. There are 16S markers which define the genus which can be checked for Halomonadacaea (Dobson and Freeman, 1996), but this is unequovocably a Halomonas (over 95% confidence with ARB) and I believe the reference provided by 174.24.103.195 is sufficient. The problem arises in the species, the species/strain GTW from Guo, J.; Zhou, J.; Wang, D.; Tian, C.; Wang, P.; Uddin, M. S. (2007). "A novel moderately halophilic bacterium for decolorizing azo dye under high salt condition". Biodegradation. 19 (1): 15–19. doi:10.1007/s10532-007-9110-1. PMID 17347922. is over 99% identical and belongs in a nice clade of unnammed stuff as I am fairly sure M. meridiana MARC41 is mislabelled. Can someone else verify using the RDP classifier to have an adhoc peer-review? --Squidonius (talk) 23:16, 5 December 2010 (UTC)

"After identification of GFAJ-1 by 16S rRNA phylogeny (see below) as a member of the Halomonadaceae and closely related to microbes known to survive high arsenate concentrations, we tested..." (Reference). Cheers, --BatteryIncluded (talk) 23:19, 5 December 2010 (UTC)

Yes, we have all read the article, the problem that that information is incorrect by omission, it is a Halomonas based on the sequence, using litterally 5 action-worth of "original research" (open HQ449183, copy and paste in RDP classifier as they did, press submit and read. So the discussion here is: do we act dumb and copy paste or actually take it into account. --Squidonius (talk) 01:27, 6 December 2010 (UTC)

We follow Wikipedia policies and report what was actually in the sources. Sasata (talk) 01:33, 6 December 2010 (UTC)

Of course the authors are publishing their original research, and keep in mind that it was peer reviewed before being published. As for Wikipedia's purpose, we can only include what was published in the research paper(s). However, we could add the words "reported to likely be Halomonas" or something to that effect. Cheers, --BatteryIncluded (talk) 01:55, 6 December 2010 (UTC)

Ion structure diagrams removed

Comparison of phosphate (P) and arsenate (As) ions

   I removed the accompanying diagram. I don't claim a grasp of all the issues (so i didn't try to replace it), but a pair of independent diagrams does not constitute a comparison, nor in this case does it provide sufficient notable and relevant information on the topic to justify the clutter it introduces, distracting the reader's attention from material whose meaning is clear. I suspect that the editor had in mind causing the reader to say

Oh, yes, the two ions are comparable in every way, except that the two core atoms have different names and masses.

Some readers will not, however. (And since comparison but not contrast was mentioned, few who do will think

But the atoms are probably different in size, so maybe the ions will differ in size, and maybe even how they fit together with their environment.)

Specifically:

1. Most obviously, the differences in absolute type size and in the ratios between bond lengths and type could suggest the magnitude of the effective diameters of the ions (which IMO are unlikely to be as extreme as juxtaposition of the diagrams hints).
2. Some will not even imagine that the molecules might bear less resemblance to four-spoked wheels (with all atoms lying in the same plane) than to tetrahedral caltrops (by being 3-dimensional), and will imagine that measuring the angles shown in the diagrams would provide useful info.
3. I, for instance, know about the 3-dimensionality of the structures, and believe that the triply-ionized species represented nevertheless will (due quantum resonance between the two handednesses) fail to rotate the polarization of light even on a single-molecule scale. Still, i'm unwilling to rule out the differences between the diagrams in drawn bond angles reflecting each species having a different set of ratios between successive ionization energies (which i would expect to be in turn reflected by "richer" resonance in one, and differences in absorption spectra attributable to quantum effects).

    In this case, i suspect that the diagrams' different angles and apparent scales actually reflect the exigencies of fitting them into equal sized diagrams, and that the editor's point would be better made by a single image, with a lower-case "x" in place of P or As, and the caption

Conventional representation of common structure of phosphate and arsenate ions, where a phosporous atom (represented by "P") or an arsenic one (represented by "P") would replace the "x" shown

(absence of period intentional). That's provided (since it's dangerous to compare without also contrasting) that the adjacent paragraph goes into

The extra electron shell of arsenic causes the parallel structures of the two ions to differ in size and stability [, as follows] ....

or whatever the truth is.
--Jerzy•t 06:03, 6 December 2010 (UTC)

Fair enough, I've replaced them. Sasata (talk) 06:18, 6 December 2010 (UTC)

Rewording of ´implications´ sections.

Just after the ´Skepticism´ paragraph this one could use some weaseling: So title ´implications´ to ´possible implications´ and ´discovery of this microorganism´ to ´discovery of a microorganism´. ABMvandeBult (talk) 08:49, 6 December 2010 (UTC)

Link needs correcting

Reference 7 leads to the supporting material for the Wolfe-Simon paper, not the actual paper. This needs to be corrected. Wolfe-Simon is first author, but is she also the Principal Investigator? 96.54.32.44 (talk) 19:14, 6 December 2010 (UTC)

There are separate references for both the paper (#5) and the supporting material (#7). Sasata (talk) 19:26, 6 December 2010 (UTC)

Principal investigator in molbio papers (or generally - whereever authors are not listed alphabetically) is usually the last-listed author. Dysmorodrepanis (talk) 14:07, 8 December 2010 (UTC)

Further skepticism

There is growing skepticism about the scientific paper announcing GFAJ-1. "Almost unanimously, they [experts in the field] think the NASA scientists have failed to make their case." "This Paper Should Not Have Been Published": Scientists see fatal flaws in the NASA study of arsenic-based life. —Preceding unsigned comment added by 148.177.1.212 (talk) 18:57, 7 December 2010 (UTC)

See also here (German) - lack of control experiments, no mass spectrometry, the study is a methodological mess.

I am not sure about the interpretation of "GFAJ". It may be tongue-in-cheek in the cited source. As far as I can tell (being one myself), biologists (and other natural scienctists) are not really into making such jokes in public... in and by itself, it's totally biologists' humor, but it's very harsh, particularly since it concerns a young researcher.

But the original paper does not seem to give an explanation, and "GFAJ" does not appear to be a standard strain name (which would usually include either some reference to collection locality and/or the collection where first cultivated), and the "-1" is also intriguing (strains are usually numbered sequentially, as they are discovered or vouchered into collections). For example, I once worked with a cryptomonad strain named M.1875 - "Melkonian collection [= University of Cologne] strain number 1875" that is. Or the type strain of Hanusia phi, it is CCMP 325 - "[Bigelow] Culture Collection of Marine Phytoplankton strain number 325".

So, I'd rather like to see confirmation that the strain acronym indeed means what is is said to be, even though it does seem to be the most likely explanation. Dysmorodrepanis (talk) 14:02, 8 December 2010 (UTC)

I have outcommented the bit in the intro:

"The discovery of the microbe lends weight to the long-standing idea that extraterrestrial life could have a fundamentally different chemical makeup from life on Earth."

for the following reasons:

1. Not supported by the known data
2. No scholarly source; actual source was apparently the NASA press release (which is now known to have been a load of exaggerated PR bullshit and not in line with the facts)
3. No such claim can be made in any case, since GFAJ-1 evolved from normal terrestrial life by adaptation and is very closely related to normal terrestrial lifeforms. If anything on Earth has implications for astrobiology, it is extremophile Archaea (and possibly Deinococcus etc.), because these adapted to weird conditions right from the start and never had ancestors which lived under "normal" Earth conditions (see especially Methanogen#Methanogens_and_.28extreme.29_environments). The question of "fundamentally different chemical makeup" in astrobiology is a question of abiogenesis#Current models, not a question of how terrestrial life eventually adapts to environmental toxins after billions of years of the usual mode of life, and thus at present knowledge GFAJ-1 has nothing to do whatsoever with abiogenesis. (In a nutshell: without "normal life", GFAJ-1 would simply not exist; it could NEVER have evolved on a hypothetical planet where arsenic is far more abundant than phosphorus, even if such a planet would exist in this universe, which present knowledge suggests is not the case).

Essentially, GFAJ-1 has about as much significance for astrobiology as has any run-of-the-mill metallophyte. Which is to say "approximately zero". Dysmorodrepanis (talk) 14:29, 8 December 2010 (UTC)

Good. I'm not the only one who thought that sentence in the lead was bogus. Sasata (talk) 14:44, 8 December 2010 (UTC)

It is true that NASA sometimes resorts to BS press releases to help with their case to reduce funding cuts. The implications is what all the hoopla is about, so just find out what the authors or other scientists speculate are the "astrobiological implications" of this (potential) discovery, and then transcribe it here + refs. Cheers, --BatteryIncluded (talk) 17:01, 8 December 2010 (UTC)

Many methods commonly used to study DNA use water which hydrolyses Arsenic-DNA, so I'd suppose some methods cannot be done, is there any blog/editorial etc which discusses that? So this paper could be either wrong or rushed too much (nearly as much as the cloning of dolly which had a figure twice)... the paper took 2 month to be accepted (1 Sept to 8 Nov), so the reviewers probably did ask for some methods (btw, the sequence was deposited in October, so they were planning on not giving the 16S sequence out (hence getting away with the above mentioned drammatisation of ommitting the genus and that the 16S is 99% identical to another species and the inclusion of distant or unheard of species in their "zoomed-out" tree to make a proteobacterium sound alien). --Squidonius (talk) 20:59, 8 December 2010 (UTC)

Skepticism vs. Criticism

I don't think that the word "Skepticism" is adequate in this context, as skepticism is a normal characteristic of the Scientific Method in general and of the Peer-Review Process in particular. The correct wording should be "Criticism". Aldo L (talk) 06:14, 9 December 2010 (UTC)

• Please, go ahead and change it. Abductive (reasoning) 07:21, 9 December 2010 (UTC)
• Agree; criticism is more appropriate. GiftigerWunsch [TALK] 08:39, 9 December 2010 (UTC)

‐P/‐As media

Both the Fig. 1 caption in the paper and the "GFAJ-1 growth experiment" section in the supporting material clearly indicate that the ‐P/‐As medium used as a growth control contains glucose and vitamins. Note that "AML60 amended 10 mM glucose and vitamins" medium is defined as "pH 9.8 with the following constitution: 0.80 mM (NH4)2SO4, 0.20 mM MgSO4·7H2O, 1.0 M NaCl, 100 mM Na2CO3, 50 mM NaHCO3, 10 mM glucose, a full complement of vitamins (S2) and trace elements according to Widdel et al. (S3) with the addition of 45 nM Na2WO4·2H2O". In the "GFAJ-1 growth experiment" section the ‐P/‐As medium is explicitly defined as "AML60 amended 10 mM glucose and vitamins" with "no added AsO43- nor PO43-". Obviously, to test for microbial growth in a medium lacking a carbon source would be absurd. The "‐P/‐As media" described in Table S1 of the supporting material, if not a misprint, appears to be a special formulation designed to demonstrate the level of phosphate contamination of the salts added to the medium. WolfmanSF (talk) 11:32, 9 December 2010 (UTC)

The definition of the media used in the study seems a least to be confusing enough to cast doubt on the composition. As this is an important point, maybe this should be stated as such in the article, without stating either opinion as a fact. Having read the article myself, the various compositions given seem to me to be contradictory, so it is not possible to decide which one is correct until the authors themselves comment on it. Although Table S1 might well contain a misprint, I don't think it is valid to simply assume this, especially since it is not consistently misspelled throughout Table S1, but only for the two -As/-P repeats. — Preceding unsigned comment added by Rainbowwrasse (talk • contribs) 12:02, 9 December 2010 (UTC)

Since 1) leaving a carbon source out of the ‐P/‐As medium would defeat the purpose of a control experiment that is critical to the whole research project, and 2) none of the many critical commentators on the paper have flagged this as a problem, we are better off assuming that the description of the medium in the paper itself, and in the "GFAJ-1 growth experiment" section in the supporting material, is valid. WolfmanSF (talk) 18:27, 9 December 2010 (UTC)

It would be better not to assume anything and simply reporting the detail as they are presented by the authors themselves. This is particularly true if the details of the experiment are critical to the research. If we assume that the descriptions of the medium in the the paper itself are correct, we have to consider all descriptions, which leaves us with a contradiction. We cannot just pick a favourite. That no one has flagged this up as a criticism is irrelevant. It is not a criticism, but a statement of a fact. 129.67.76.170 (talk) 19:05, 9 December 2010 (UTC)

We have two verbal descriptions of the medium used in the growth control experiment, in both the paper and supporting material, which are explicit and unambiguous as indicating it lacked only phosphate and arsenate. Table S1 does not describe the control experiment; it is simply a listing of the samples analyzed by ICP-MS. Those samples don't have to be identical to the ones that were used in the growth control experiment. So, we have two statements whose interpretation is unambiguous, and a table whose interpretation is ambiguous. In such a case, one can employ a little common sense and go with the unambiguous information.

The fact that the critics have not flagged this as a problem is highly relevant. This is a high profile paper that has been scrutinized by many of the world's top biologists. Why would you would not want to take the scientific community's judgment on this matter into account? WolfmanSF (talk) 00:06, 12 December 2010 (UTC)

I agree with WolfmanSF that the description in Table S1 would not make biological sense, but because of that has to be mentioned when reporting the -As/-P data, which might be interpreted as a criticism within the Wikipedia article. I'm happy with the deletion. Rainbowwrasse (talk) 19:40, 9 December 2010 (UTC)

The deletion seriously weakens the whole article. The growth in the ‐P/‐As medium is a critical control experiment, and the paper could not have been published without it. It needs to be mentioned. WolfmanSF (talk) 00:06, 12 December 2010 (UTC)

In that case the contradictory statements on glucose content need to be mentioned as well. The precise composition is critical to the argument. Table S1 deals with the actual measured composition of the specific media used, rather than a general statement about media composition. It is common practice in microbiology to give the basic composition of media in the material and methods, and specify deviations from this within the text or results. We cannot just ignore the contradiction. If, as you assume 'Those samples don't have to be identical to the ones that were used in the growth control experiment', the whole point of the analysis and the validity of the experiment has to be called into question. It is completely irrelevant if anyone has had a problem with this or not, it is merely reporting the statements in the paper. Sorry. The paper may have been scrutinized by 'top biologists' (whatever those are), but if they did, they did not care to comment on the paper at length. The most detailed, and probably most cited, source of criticism that I have seen seems to be Rosie Redfield's blog. While I have the utmost respect for Dr Redfield, it would be a bit of a stretch to describe her as 'many of the world's top biologists'. For starters, she's only one person. We also know that the reviewers of the paper were not biochemists (http://www.latimes.com/news/science/la-sci-arsenic-bacteria-20101211,0,3642441.story). How do you know that 'the world's top biologists' have even looked at the paper? As things stand, there is no 'scientific community's judgment on this matter' to be taken into account. There is nothing to judge, just a fact to report. The statement that this paper could not have been published without the -As/-P control is pure conjecture; others have argued that other vital controls are also missing, and it was nevertheless published. Also, I do not agree that deletion of the -As/-P data seriously weakens the article, only the argument in favour of As utilisation. If it is included, the exact composition of the media has to be included to maintain an unbiased article. Leaving -As/-P out completely is a good compromise; I have no particular interest in either discrediting or validating the findings in this forum. Why are you so unwilling to compromise on this matter, and what do you propose to do to resolve it? Rainbowwrasse (talk) 11:49, 12 December 2010 (UTC)

My opinion is that unless the glucose content is a contested issue that has been published (and referenced), it may qualify as Original Research. Cheers, --BatteryIncluded (talk) 17:26, 12 December 2010 (UTC)

The study makes two different and mutually exclusive statements about the glucose content of the media, both of which are directly attributable to the published paper and supplemental material. No conclusions are drawn from stating this, so I do not believe that doing so qualifies as Original Research. It is equivalent to reporting any other detail of the methodology. On the other hand, stating that growth was limited in -As/-P medium makes the tacit assumption that the media were otherwise equivalent, which is directly refuted by one of the descriptions in the published material. If growth in -As/-P medium is mentioned, both media compositions presented in the original study have to be reported, precisely because not doing so would constitute an original analysis not supported by the presented data, even if this is not explicitly stated. However, reporting both compositions could be construed as a criticism, and I therefore think that any mention of the -As/-P experiment should be removed to preserve the neutrality of the article. Alternatively, a few people now seem to have picked up on this as a criticism (Rosie Redfield's blog), so perhaps it could be mentioned under 'criticisms'. I am not too happy with this option though, as it would put too much emphasis on the -glucose option. This seems unfair on the authors of the paper. I think -As/-P should be left out completely until the authors have had the change to address the criticisms levelled against them.Rainbowwrasse (talk) 20:35, 12 December 2010 (UTC)

The cell growth control is verbally described three times, twice in the paper:

1) "the fact that the level of PO43- impurities in the medium was insufficient to elicit growth in the control (-As/-P)" - this is just above the "Cellular stoichiometry and elemental distribution"" heading.

2) "Growth curves of GFAJ-1 grown on the defined synthetic medium amended with either 1.5 mM phosphate (solid circles), 40 mM arsenate (solid squares) or neither phosphate nor arsenate (open triangles)." - in the Fig 1. caption.

and once in the Supplementary Material:

3) "GFAJ-1 cells were grown in 10 ml total volume in 20-ml screw-top glass tubes in sterile AML60 amended 10 mM glucose and vitamins (as above) under three experimental conditions including +As/-P, 40 mM AsO43- with no added PO43; -As/+P, 1.5 mM PO43- with no added AsO43- and Control, no added AsO43- nor PO43-." - under the "GFAJ-1 growth experiment" heading.

These descriptions are all consistent with each other, and with the scientific rationale of the control experiment. But they appear inconsistent with the sample designations in Table S1, which is a list of samples analyzed by ICP-MS. Which is more likely: a) that when writing the paper, the authors forgot 3 times they they had left glucose out of the -As/-P medium, and also somehow during the entire period in which they worked on the project overlooked the fact that this omission destroyed the scientific value of their control experiment, or b) that they carelessly prepared Table S1 in a way that confused some readers? Common sense gives the answer. WolfmanSF (talk) 22:54, 12 December 2010 (UTC)

Invoking ‘common sense’ is rarely a valid argument. So called ‘common’ sense is hardly that, and is highly subjective and culturally variable. Your common sense may let you come to a completely different conclusion than that of others. The key word here is ‘conclusion’, i.e. the product of original thought. You ‘conclude’ that we can ‘assume’ that the authors were ‘more likely’ to have ‘meant’ to write ‘+10 mM glucose’, because everything else ‘wouldn’t make sense’, and that this is ‘obvious’ (I’m paraphrasing). I’m not saying that they did or did not add glucose, just that there are at least two different descriptions of the media used. That is not a synthesis or a conclusion, just a statement that can be directly attributed to the authors themselves, and I don’t need to make any assumptions. You are mistaken about the consistency of the description of the media in the paper and Supp Mat. The only description of the media that fits your assumption is this:

"GFAJ-1 cells were grown in 10 ml total volume in 20-ml screw-top glass tubes in sterile AML60 amended 10 mM glucose and vitamins (as above) under three experimental conditions including +As/-P, 40 mM AsO43- with no added PO43; -As/+P, 1.5 mM PO43- with no added AsO43- and Control, no added AsO43- nor PO43-.",

And even here the concentration of glucose in the medium could be either 10 or 20mM (see below). Your examples 1) and 2) make no mention of glucose, only of ‘defined synthetic medium’ at best. Although the authors give the general composition of their medium as

“…artificial defined Mono Lake medium (AML60; S1) at pH 9.8 with the following constitution: 0.80 mM (NH4)2SO4, 0.20 mM MgSO4•7H2O, 1.0 M NaCl, 100 mM Na2CO3, 50 mM NaHCO3, 10 mM glucose, a full complement of vitamins (S2) and trace elements according to Widdel et al. (S3) with the addition of 45 nM Na2WO4•2H2O”,

it is not explicitly stated if ‘defined synthetic medium’ and ‘AML60’ refer to medium including glucose, or only to the base salts medium. For example, if AML60 already includes glucose, why do the authors call it ‘AML60 amended 10 mM glucose’ in the description of the growth experiment? Does that then mean it was really 20mM glucose (10mM from AML60 and another 10mM added)?

Glucose is also listed as a separate ingredient throughout the paper in other contexts:

“Currently this isolate, strain GFAJ-1 identified by 16S rRNA sequence phylogeny as a member of the Halomonadaceae family of Gammaproteobacteria (see fig. S1) (11), is maintained aerobically with 40 mM AsO4 3-, 10 mM glucose and no added PO4 3- (+As/-P condition).”

“…cultures were then spread on plates containing AML60 1.5 % solid agar (10 mM glucose, 5 mM AsO4 3-, no PO4 3-).”

“Single colonies were picked and reintroduced into defined artificial liquid AML60 with 10 mM glucose, 5 mM AsO4 3-, and no PO4 3-.”

“We determined the +As/-P condition that elicited the best growth for GFAJ-1 was AML60 amended with 10 mM glucose, 40 mM AsO4 3-, no PO4 3- and incubated at 28°C.”

All these quotations may indicate that glucose was treated as an additive, rather than as part of the basic composition of the medium, but I never even claimed that. I just said that there is more than one description of the medium, and that the composition is not clear. You on the other hand have picked out one of the possible compositions and decreed it fact, based on your assumptions, and accused the authors of carelessness when they prepared Table S1. Is that a neutral point of view? Common sense gives the answer? ;-) Rainbowwrasse (talk) 14:20, 13 December 2010 (UTC)

Felisia W-S states that there was no glucose added to the media:

FAQ paper: http://ironlisa.com/gfaj/GFAJquestions_Response_16Dec2010.pdf

--BatteryIncluded (talk) 15:54, 17 December 2010 (UTC)

She states that glucose was not added to the medium used for the ICP-MS assays, but that it was added to the medium used for the -As/-P control experiment (showing that the cells needed either added phosphate or arsenate to grow), just as I interpreted the paper: "Then we added glucose and vitamins for all three treatments and either As for the +As treatments or P for the +P treatments" (emphasis added). WolfmanSF (talk) 20:47, 20 December 2010 (UTC)

Yes, the authors recognised that their previous statements were ambiguous (just as I have said all along, ahem) and have now clarified that the media indeed contained glucose. And sucrose: '...P measurements made on the medium after the addition of sucrose and vitamins...', (emphasis added). I'm glad they cleared that up... :-P Rainbowwrasse (talk) 15:57, 21 December 2010 (UTC)

...and now they changed it back to glucose... Maybe they are reading this discussion? If so: I'm sure you meant to say '...alkyl di-esters of arsenate...', not '... alkyl di-esters of arsenite...'. Either that, or Eqn. 2 is wrong. Cheers! ~ — Preceding unsigned comment added by Rainbowwrasse (talk • contribs) 17:58, 6 January 2011 (UTC)

Page views not dropping

Mycoplasma laboratorium, aka venter's so-called synthetic bug, is a nice example of news item in science which decreses in interest (here) and plateaus to 100-200 views per day. If a logical explanation is given, a decay/dampening exp(-t) +c, a diffussion exp(srt(t)+c, a powerlaw a**t+c or a logistic ect could be fitted (where c is the asymptote, aka constant number of readers). The first fits well and can be easily justified. In the case of GFAJ-1 fitting gives odd results (c=10k for decay, powerlaw fits well but is not a good model), meaning there could be a convoluted second trend (criticisms), so this article does not what to fade away anytime soon (should have been 600 views by now), so it will remain of high interest for another week, I am sorry to say to those that were hoping it would fade away (e.i. the unsolvable issues become of little importance). --Squidonius (talk) 21:23, 9 December 2010 (UTC)

Dropped to 4k and 1.1k, the constant number of readers will be under 200 if the last three data-points are taken in isolation (will resurge when the "FAQ" will be released), so matches mycoplasma laboratorium as mentioned. Oddly, it has been minimally vandalised (only 7 reversions over 444 edits). --Squidonius (talk) 03:16, 12 December 2010 (UTC)

Criticism on GFAJ-1 at the Felisa Wolfe-Simon article

A discussion on how the criticism on the GFAJ-1 discovery should be incorporated into the article on Felisa Wolfe-Simon is ongoing at Talk:Felisa Wolfe-Simon#Criticism on GFAJ-1. Some editors feel the criticism on her work would violate the biographies on living people policy, while others feel that failing to note the criticism violates the neutral point of view policy. Any input would be appreciated. —Ruud 22:24, 13 December 2010 (UTC)

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