Arsenic-incorporating bacterium: Why all the controversy?

[Fanghur]

OK, I'm pretty sure many of you have heard about the bacteria discovered by NASA which is allegedly able to incorporate arsenic into its DNA in place of phosphorous. I cannot for the life of me understand why this claim is proving so difficult to prove or disprove. I mean I've got a Biotechnology diploma from college and am currently working on my Undergrad in Microbiology at the University of Guelph, so I know about various DNA-probing techniques.

 

However it strikes me that the easiest method to definitively prove (or disprove) that the bacterium incorporates arsenic into its DNA would be to grow a sample of the bacterium in an environment starved of phosphorous and rich in arsenic; and also another sample of the bacterium in ordinary phosphorous-rich medium with no arsenic as a control. Then isolate and purify the DNA of both samples, and then run both of them through a mass spec to see whether its DNA has a peak corresponding to arsenic.

 

Any college or university lab could run this experiment, so why the heck is there so much controversy over this bacterium? Am I overlooking some fundamental problem here?

[CharonY]

This has been discussed in two other threads. The controversy is more that it got published as it is, rather than due to the difficulties to demonstrate it. Several have proposed that looking for mass-shifts in MS spectra would be a far better indicator than the indirect measurements in the article. The author was actually asked pretty much the same. I am pretty sure there have been some requests for the DNA by now.

[Fanghur]

But Charon; that's exactly my point. Why would NASA have published when they did, in a way which even I admit makes the evidence seem circumstantial at best, when they could have easily proved it beyond questionable doubt using mass spectroscopy? Probably in less than a day, I might add?

 

They must have known that a claim this groundbreaking would be highly controversial, and yet they didn't have the sense that an undergrad has to verify it first? The only explanations I can think of off-hand are; either they're idiots, or they were up to something. The fact that they hailed this as a breakthrough in the field of Astrobiology and peaked the whole planet's interest tends to suggest the latter.

[Mr Skeptic]

I wonder if they're abusing the idea that "all press is good press"? The controversy will ensure this issue gets revived often, until it gets proved one way or the other.

[CharonY]

There are a lot of things involved. First of all, getting into science is an incredible incentive to publish things quickly, especially if one is more junior (as the corresponding author). Secondly, it is something that the reviewers should have picked up, but did not. It is quite possible that the authors pushed it out quickly with the intention to add more data, if the reviewers requested them. Apparently, they did not.It is not clear, for instance, what background the respective reviewers had. Also note that the article had a lot of senior authors (including e.g. theoretical physicists), whose contribution to the work is not clear to me.

 

Also note that NASA did not publish it per se, but the work was funded by them. They do not have a great track record when it comes to microbiological findings.

So there is likely the combination of lack of expertise in specific areas, the desire to publish high, and being funded by a high-profile agency and the juniority (is that a word?) of the corresponding author. Plus probably a lot more that I have no direct insight into.

 

There is a reason why in many specific areas Science and Nature are not regarded as high-quality in terms of data. They like to publish cool and interesting things, rather than meticulous work. Though of course the cynic could argue that it is easier to spot errors in these highly visible journals.

[Rip:20]

There are a lot of things involved. First of all, getting into science is an incredible incentive to publish things quickly, especially if one is more junior (as the corresponding author). Secondly, it is something that the reviewers should have picked up, but did not. It is quite possible that the authors pushed it out quickly with the intention to add more data, if the reviewers requested them. Apparently, they did not.It is not clear, for instance, what background the respective reviewers had. Also note that the article had a lot of senior authors (including e.g. theoretical physicists), whose contribution to the work is not clear to me.

 

Also note that NASA did not publish it per se, but the work was funded by them. They do not have a great track record when it comes to microbiological findings.

So there is likely the combination of lack of expertise in specific areas, the desire to publish high, and being funded by a high-profile agency and the juniority (is that a word?) of the corresponding author. Plus probably a lot more that I have no direct insight into.

 

There is a reason why in many specific areas Science and Nature are not regarded as high-quality in terms of data. They like to publish cool and interesting things, rather than meticulous work. Though of course the cynic could argue that it is easier to spot errors in these highly visible journals.

 

Hehe. They're struggling in the rocket dept. too.

 

Fail

Edited March 16, 2011 by Rip:20

[steevey]

However it strikes me that the easiest method to definitively prove (or disprove) that the bacterium incorporates arsenic into its DNA would be to grow a sample of the bacterium in an environment starved of phosphorous and rich in arsenic; and also another sample of the bacterium in ordinary phosphorous-rich medium with no arsenic as a control. Then isolate and purify the DNA of both samples, and then run both of them through a mass spec to see whether its DNA has a peak corresponding to arsenic.

 

 

 

Why not just use chemical testing on the said bacteria? If NASA or someone hasn't done that, how else would they even suspect arsenic is actually incorporated into the bacterium DNA?

 

So what if arsenic is in the water, bacterium could develop a resistance to it which would have likely been NASA's or anyone's first assumption, but that's not what they are saying now, they moved on from that. They find bacterium living in sulfuric acid but they don't say sulfur is in that bacterias DNA, because its not. There must be some test to determine it which a web designer didn't put in. It's not like just anyone can view every test that the Fermi-Lab has done, not even the ones that claim to discover new particles like charm quarks, even though its widely accepted by physicists that those particles exist.

 

Just so everyone is clear:

Not every piece of information in the world is on the internet yet, not even all the books in the world are on the internet yet, and I bet there's tons of files pertaining to debates here that have been tested and documented but the universities just never bothered to hire a web designer to put them up, or the head scientists didn't care or think to put them on the internet.

Edited March 17, 2011 by steevey

[SMF]

Just a thought. Perhaps those persons who have not actually read the study under question should refrain from commenting about it. http://scholar.google.com/scholar?start=0&hl=en&as_sdt=0,5&cluster=12247241756468139397

SM

[Marat]

There is also the fact that everyone is profoundly uncomfortable with the notion of toxins being integrated into life processes without disrupting or destroying them, and this background gives the whole effort to demonstrate the presence of arsenic here a particular edge. For example, I know many otherwise highly educated scientists who have refused to believe my true statement that appleseeds contain enough cyanide to kill a small child if eaten in a bunch all at once, but this is something every physician learns.

[CharonY]

Except from a microbial standpoint the toxin argument does not matter as what counts as toxins for us often can be considered food to them. The major issue is the chemical instability of arsenic bonds and the biological importance of phosphate bonds. A simple exchange would be incredibly tricky physiologically.

 

Regarding appleseeds, unless crushed only a limited amount of cyanide will be released from the seeds during normal digestion. While technically correct, it would take quite a bit to be lethal. A few other food sources would be more efficient. It is somewhat well-known that rosaceae produce cyanide compounds, btw.