Bacteria eat arsenic -- and survive!

The next test for these bacteria will be to see if they can survive in elderberry wine.

I thought the real significance was that they used arsenic in their DNA in place of phosphorus, not that they ate it per se.

I recall Isaac Asimov's essay(s) on the potential for biologies based on combinations of chemicals other than those we prefer to use. In particular, silicon was a reasonable alternative to carbon because of its structural similarities. The news from NASA and USGS is exciting and interesting, but not exactly a new idea to longtime sf readers.

My wife is reading a review from 2003 about metabolism of arsenic by bacteria in the same lake.

The paper has also been taken apart by Rosie Redfield.

I thought the real significance was that they used arsenic in their DNA in place of phosphorus, not that they ate it per se.

Most astounding of all is that when you magnify the bacteria they look like old lace.

@Doc Bill,

The black gaps in the lace are the bacteria, and the big white blobs inside them are the granules of what is probably the energy-storage molecule polyhydroxybutyrate.

I thought the real significance was that they used arsenic in their DNA in place of phosphorus, not that they ate it per se.

I just skimmed Professor Redfield's article, and it was largely Greek to me. Can you synthesize it in 25 words or less for those of us who have no idea what OD₆₀₀ and cfu are? Where I come from, OD is your right eye. OK, OK, you may have more than 25 words.

Based on the Rosie Redfield link, even what I described above may include a lot of very premature conclusions.

I do think that the adaptation of extremophiles to at a minimum tolerate fairly high concentrations of arsenic is interesting in itself.

Bob O'H said: The paper has also been taken apart by Rosie Redfield.

Matt Young -

I will step back and let the real experts get started, but cfu = "colony forming units" and OD600 = optical density of a solution for a 600 nm wavelength of visible light. They are both, in this context, ways of estimating the density of bacteria per unit volume of a solution.

Can you synthesize it in 25 words or less for those of us who have no idea what OD₆₀₀ and cfu are?

IANAB either, but I note that biologists Jef Huisman and Hans Matthijs of the University of Amsterdam are pretty unimpressed by this paper. According to this weekend's NRC Handelsblad (up-market Dutch newspaper) they say that the evidence presented fails to demonstrate that phosphorus has been replaced by arsenic in the DNA.

but cfu = "colony forming units" and OD600 = optical density of a solution for a 600 nm wavelength of visible light. They are both, in this context, ways of estimating the density of bacteria per unit volume of a solution.

As I understand it, Silicon bonds are quite rigid, in contrast to Carbon bonds, which are flexible and allow Carbon based molecules to bend and wiggle; a necessity for life as we know it. If so, life as we know it could not be Silicon based. Not a chemist, so I am open to correction.

I assume these colonies were nurtured at pretty much the same temperature.

I am curious about the temperatures at which these “arsenic and phosphorus forms” are most viable.

Just looking at the difference in ionization potentials suggests that dropping the temperature for the arsenic form may make it more viable than the phosphorus form.

This doesn’t give any indication of what the bacteria actually “do” with the arsenic, but if it is temperature dependent, that may give some idea about where it is incorporated.

Mike Elzinga -

Yes, you are correct on all counts.

The colonies were probably nurtured at temperatures that are similar to those in the lake, which, given its geographic location, are probably not very extreme (the fact that other "extremophiles" are adapted to temperature, rather than chemical, extremes, notwithstanding).

One source of contention seems to be physical chemistry related - whether it's even possible for nucleotide triphosphate structure to include one or more arsenic atoms in place of phosphorus atoms, and be stable, under reasonable conditions. I'm not sure whether this has been resolved, although it would seem to be an easily resolvable issue.

At "worst", these bacteria merely have a very high tolerance for environmental arsenic (ironically, high ability to exclude arsenic from "substituting" for phosphorus would be one conceivable mechanism of achieving this). At "best", they actually can sometimes use arsenic as an imperfect substitute for phosphorus, exploiting the atomic similarities that would cause poisoning for other lineages. Either of these is pretty damn interesting on its own. The latter could be said to be peripherally related to ideas about life in extra-terrestrial environments, if such environments were conjectured to be much like earth, but with more arsenic and less phosphorus (although that seems odd given the amounts of each of those elements in the universe).

The media claims have been silly. This finding is very neat, but is not in any way directly related to origin of life research, nor does it have any resemblance to a discovery of life with a different genetic code or fundamentally different biochemistry from the rest of life on earth.

As I understand it, Silicon bonds are quite rigid, in contrast to Carbon bonds, which are flexible and allow Carbon based molecules to bend and wiggle; a necessity for life as we know it. If so, life as we know it could not be Silicon based.

Doc Bill said: Most astounding of all is that when you magnify the bacteria they look like old lace.

Jim Thomerson said: As I understand it, Silicon bonds are quite rigid, in contrast to Carbon bonds, which are flexible and allow Carbon based molecules to bend and wiggle; a necessity for life as we know it. If so, life as we know it could not be Silicon based. Not a chemist, so I am open to correction.

Life on earth is predominantly based on C, H, O, N, S and P, with ions of Na, Ca, Cl, K, and Mg playing important roles, and requirements for small amounts of some other metalic elements, most obviously Fe in metazoans that use a hemoglobin system, but other things as well.

If you just tried to substitute Si for the C, without making any other changes, it probably wouldn't work, to say the least.

Whether an entire similar system, based on heavier elements from the same columns (many of which are highly toxic to much of life on earth precisely because they can partly "mimic" similar but smaller atoms), could originate, and get to the point of individual reproducing cells enclosed in some kind of membrane, or something recognizably similar, is an interesting conjecture.

Of course, we still have a massive amount to learn about how life originated here on earth. (And as I noted above, the bacterial lineage under discussion here is not likely to be any more related to that question than any other bacterial lineage.)

harold said: The media claims have been silly. This finding is very neat, but is not in any way directly related to origin of life research, nor does it have any resemblance to a discovery of life with a different genetic code or fundamentally different biochemistry from the rest of life on earth.

Dale Husband said:

Jim Thomerson said: As I understand it, Silicon bonds are quite rigid, in contrast to Carbon bonds, which are flexible and allow Carbon based molecules to bend and wiggle; a necessity for life as we know it. If so, life as we know it could not be Silicon based. Not a chemist, so I am open to correction.

Sounds about right. Also, due to the heavier weight of the silicon atoms, anything made from them would have a higher melting or boiling point than similar molecules made from carbon atoms. That would explain why in science fiction, silicon based life forms are usually in extremely hot environments.

Whether a life form *could* be based on arsenic rather than phosphorus is separate from the question of whether one would arise on it's own in a replay of the onset of life. And that is a separate question of whether a life form based on phosphorus could evolve to one based on arsenic. I suspect the answer to the latter two questions would be no. It's unlikely to start out the arsenic way because, although they are chemically similar, phosphorus is present in the universe at levels that are several thousand times higher than arsenic.

And given that life as we know it is now so critically dependent on phosphate, is likely that a particular strain of bacteria could, at this point, only develop a tolerance for arsenate, not switch completely. And my gut tells me it’s more likely to respond to the presence of arsenate by developing an ability to better discriminate against it, rather than developing the ability to interchangeably substitute arsenate for phosphate. That is, its more likely that natural selection would enhance an organisms ability to prevent arsenic from interfering with normal biochemistry via selection for phosphate-processing enzymes that are even more selective for phosphate over arsenate.

It would be an interesting experiment to do long term evolution studies to see how good enzymes could get.

Divalent,

I think life has more evolutionary potential than you give it credit for. Already on our own planet we see life forms capable of adapting to an extraordinary array of environments. Once upon a time oxygen was a waste product that caused horrendous chemical damage inside cells, now it is an essential element for almost all of the Eukarya and many of the Bacteria and Archea.

Actually, I should have said that oxygen is still a waste product that causes damage to cells, but it is now also essential to many organisms.

Today’s (Dec. 6, 2010) Astronomy Picture of the Day has a picture of Lake Mono with an inset of the bacteria.

Doc Bill said: Most astounding of all is that when you magnify the bacteria they look like old lace.

People show quite a range of reaction to arsenic exposure (a common water contaminant in parts of the Indian subcontitnent)

There is a significant inter-individual variability in susceptibility to progression from arsenic exposure to clinical manifestations of arsenic toxicity (e.g. skin, lung, liver and bladder cancers). Several observational as well as biochemical studies have led to a prevalent hypothesis that nutritional status may account for a substantial portion of this variability, though no controlled clinical studies have addressed this important hypothesis. http://www.mailman.columbia.edu/our-faculty/profile?uni=mvg7

Wheels' points of SiO2 stability and lack of varied silicon chemistry are pretty big hurdles to overcome. The chances of silicon based life seem pretty slim.

I love the post title. There was an actual Enquirer (I think) headline back in the '80's that read "Man Cuts Off His Head With Chainsaw And Lives!".

[NASA] trumpeted the discovery as “an astrobiology finding that will impact the search for evidence of extraterrestrial life.”

Unfortunately, Science and Nature are all too prone to publish sensational-sounding results without delving too much into their actual merit. Anyone who's ever had a paper rejected by either should feel simultaneous annoyance and schadenfreude over the reaction. I know I do.

John Harshman said: Unfortunately, Science and Nature are all too prone to publish sensational-sounding results without delving too much into their actual merit. Anyone who's ever had a paper rejected by either should feel simultaneous annoyance and schadenfreude over the reaction. I know I do.

John Harshman said: Unfortunately, Science and Nature are all too prone to publish sensational-sounding results without delving too much into their actual merit. Anyone who's ever had a paper rejected by either should feel simultaneous annoyance and schadenfreude over the reaction. I know I do.

The research was featured at the recent teleconferecne by the NASA Astrobiology Institute. We tried to host a post-conference discussion here at PT. The conference organizers, even announced this to the conference members, and some did try to respond to questions.

All (almost all) of the presentations were available on line, including Felisa's. It still is- "Alternative Biochemistry and Arsenic, or Life as We Might Not Expect It," Felisa Wolfe-Simon, US Geological Survey.

You all could have been weeks ahead of the newspapers, and broadcasts.

I'm an old guy, so I have no idea what this means

"Well, as they say on the Web, IANAB,..."

Sorry.

By the way, I've been wondering why your header illustration with the words "Panda's Thumb" in big letters has a photograph of a panda's head. Please show a photograph of a panda's thumb, which I've never seen.

I'm an old guy,

so I have no idea what this means "Well, as they say on the Web, IANAB,..."

Please show a photograph of a panda's thumb, which I've never seen.

John Kwok -

I hope that this is an over-hyped but very worthwhile discovery.

At worse, it seems to be a bacterial lineage with a very interesting adaptation to an environmental compound that is toxic to most life. That's true even if it's just an arsenic-tolerating extremophile, and even more true if it can utilize arsenic as a substitute for phosphorus under limited conditions. Figuring out the mechanism of tolerance will be of great interest, and it could even have applications.

It's unfortunate that all of this "Arsenic-based Invaders From Uranus" type publicity (the authors' own fault, and so is the preliminary nature of the data and the possibility of some claims that may not stand up) got started, but the discovery itself may still turn out to be of great interest.

Gary Hurd -

Yes, there was some interesting stuff discussed here with respect to that conference. Mostly OOL stuff (this bacterial strain is an adaptation of unequivocal standard terrestrial cellular life, of course).

I think that this particular discovery has very, very limited implications for either OOL or extraterrestrial life, but on the other hand, it seems cool.

Doing biological research in extreme terrestrial environments seems like a perfectly good thing for NASA to do.

harold said: It's unfortunate that all of this "Arsenic-based Invaders From Uranus" type publicity (the authors' own fault, and so is the preliminary nature of the data and the possibility of some claims that may not stand up) got started, but the discovery itself may still turn out to be of great interest.

Mike Elzinga said:

harold said: It's unfortunate that all of this "Arsenic-based Invaders From Uranus" type publicity (the authors' own fault, and so is the preliminary nature of the data and the possibility of some claims that may not stand up) got started, but the discovery itself may still turn out to be of great interest.

This has been a problem with reporters for as long as I can remember. I remember I and my colleagues cringing when a reporter got wing of our research and wanted to interview someone about it. Not one person I have ever worked with in my entire career with ever wanted to talk to a reporter. It was always the case that a reporter or his editor wanted to inject some catchy phrase or “human interest” paragraph that made the whole article look ridiculous. Most scientists know their results are subject to being overturned. They would rather have the crucible of peer-review and crosschecking by other scientist take care of this process rather than have it sensationalized with ludicrous science fiction mixed in.

harold said: John Kwok - I hope that this is an over-hyped but very worthwhile discovery. At worse, it seems to be a bacterial lineage with a very interesting adaptation to an environmental compound that is toxic to most life. That's true even if it's just an arsenic-tolerating extremophile, and even more true if it can utilize arsenic as a substitute for phosphorus under limited conditions. Figuring out the mechanism of tolerance will be of great interest, and it could even have applications.

Mike Elzinga said:

harold said: It's unfortunate that all of this "Arsenic-based Invaders From Uranus" type publicity (the authors' own fault, and so is the preliminary nature of the data and the possibility of some claims that may not stand up) got started, but the discovery itself may still turn out to be of great interest.

This has been a problem with reporters for as long as I can remember. I remember I and my colleagues cringing when a reporter got wing of our research and wanted to interview someone about it. Not one person I have ever worked with in my entire career with ever wanted to talk to a reporter. It was always the case that a reporter or his editor wanted to inject some catchy phrase or “human interest” paragraph that made the whole article look ridiculous. Most scientists know their results are subject to being overturned. They would rather have the crucible of peer-review and crosschecking by other scientist take care of this process rather than have it sensationalized with ludicrous science fiction mixed in.

John Kwok said: But NASA bears some of the blame for playing this up too:

John Harshman said: Unfortunately, Science and Nature are all too prone to publish sensational-sounding results without delving too much into their actual merit. Anyone who's ever had a paper rejected by either should feel simultaneous annoyance and schadenfreude over the reaction. I know I do.

I've been fortunate to be able to review and edit press releases about my work.

I watched the presentation on TV and thought it very poorly done. There were two reporters shown in sidebars and it was clear that neither had any idea what was going on. The station soon switched to another topic.

I don't get the graph scale discussion, Rosie seems to me to have it right.

Absorbance is already log so that an exponential decreasing intensity with a thicker or denser sample becomes a linear measure of same.

Then it must be wrong to compare that linear density measure on a linear scale with a semilog scale for another linear density measure (# cells/volume)!?

I am wondering if how much of the results were due to accidental contamination by arsenic.

John Kwok -

I'm not a microbiologist but I have spent a lot of time in clinical microbiology labs, and cultured a lot of E. coli back in the old days. I also have a pretty good background in biochemistry and molecular biology.

It will massively surprise me if the bacteria do not turn out to be adapted to a high arsenic environment. That alone is a worthwhile finding. It's possible that even this is wrong, but that's unlikely.

The claims of arsenic substituting for phosphorus have some rationale behind them. They may or may not stand up to more rigorous testing, but they weren't just made out of thin air.

The Pons-Fleishman cold fusion claims had no steps to bounce down. It was either cold fusion, or it wasn't, and it wasn't.

Here the circumstance is a bit different. It's true that the "Arsenic-eating killer tomatoes from Uranus" reports are incorrect.

I would say it is overwhelmingly likely that these are bacteria that can tolerate a fairly high environmental concentration of arsenic, which alone is of interest and a great model for further study. The entire technique of PCR, which has revolutionized molecular genetics research, was massively accelerated by study of an obscure extremophile bacterial strain.

I am pretty skeptical of the "arsenic in the DNA" claims, but some kind of ability to exploit arsenic may well be found. That would make it even more interesting.

Doc Bill -

Just FYI, Stuyvessant High is an enriched PUBLIC school in NYC, where a lot of smart kids from humble backgrounds get their education. It's academically one of the best schools in the country, but it's no Andover. And there's nothing George W. Bush could have done to get into Stuyvessant. Not even if John Kwok wanted him to.

Harold, my old buddy, and fellow Delta Pi Gamma president-for-life, I'm sure Kwok came from Humble, Tx, to attend Stuyvessant where he learned to drop names faster than I dropped calculus (twice).

All of which makes me suspicious of the idiotic comment attributed to my great friend and Klingon aficionado Kwok. Should I be proved wrong, however, I shall unfriend him (again) from my Facebook and teach the moron a great lesson. So there.

John Kwok: The entire technique of PCR, which has revolutionized molecular genetics research, was massively accelerated by study of an obscure extremophile bacterial strain.

Doc Bill said:

I am wondering if how much of the results were due to accidental contamination by arsenic.

You must be a Kwok impersonator! First, the real Kwok wouldn't write something that stupid. Second, the real Kwok would quote at least two classmates from his fancy, dancy New York high school. And, third, the real Kwok would point out the importance of arsenic in Klingon cosmology. So, impostor, you didn't fool us at all. Better luck next time!

harold said: Doc Bill - Just FYI, Stuyvessant High is an enriched PUBLIC school in NYC, where a lot of smart kids from humble backgrounds get their education. It's academically one of the best schools in the country, but it's no Andover. And there's nothing George W. Bush could have done to get into Stuyvessant. Not even if John Kwok wanted him to.

Doc Bill said:

I am wondering if how much of the results were due to accidental contamination by arsenic.

You must be a Kwok impersonator! First, the real Kwok wouldn't write something that stupid. Second, the real Kwok would quote at least two classmates from his fancy, dancy New York high school. And, third, the real Kwok would point out the importance of arsenic in Klingon cosmology. So, impostor, you didn't fool us at all. Better luck next time!

Why the attempted discussion was less successful than I had hoped is that a cluster of barnacles are affixed to the PT hull. They are the "commentators" who are still in this thread pontificating about a paper they have not read, and research that they are apparently unable to understand.

I don't get the graph scale discussion, Rosie seems to me to have it right.

I think your comments would have more credibility if you removed the ones that suggest what the author's motives are. It is difficult to distinguish between evil and incompetence. Just stick to the facts and leave out the personal jabs.

Please stop feeding the Kwok troll. I realize that he is mostly on the right side and he frequently makes sense, but anyone who publishes 3, 4, and 5 comments in a row is a troll. Please do not bait him any more; I do not think I can tolerate reading "mendacious intellectual pornographer" one more time. Indeed, just dictating the phrase is enough to make anyone neurotic.

Gary Hurd said: Why the attempted discussion was less successful than I had hoped is that a cluster of barnacles are affixed to the PT hull. They are the "commentators" who are still in this thread pontificating about a paper they have not read, and research that they are apparently unable to understand.

Matt Young said: Please stop feeding the Kwok troll. I realize that he is mostly on the right side and he frequently makes sense, but anyone who publishes 3, 4, and 5 comments in a row is a troll. Please do not bait him any more; I do not think I can tolerate reading "mendacious intellectual pornographer" one more time. Indeed, just dictating the phrase is enough to make anyone neurotic.

Matt (and others)-

The discussion on OD600 is a bit confused. Yes, optical density is the log of the inverse of transmittance ( OD = log(I0/I) ). But transmittance is not proportional to concentration, OD is. This is Beer's law, OD = e * l * c, where e is extinction coefficient, l is path length, and c is concentration. I refer you to the wikipedia entries on absorbance and beer's law:
http://en.wikipedia.org/wiki/Optical_density
http://en.wikipedia.org/wiki/Beer%27s_law

Now, it is true that OD600 of cells is not measuring absorbance proper, but scattering, so it only obeys beer's law when OD is low (and thus secondary scattering effects are negligible). Fortunately, this is generally true for OD600 less than 0.5 or so, right in the range of maximum sensitivity for most commercial spectrophotometers. See the following, and links therein for details:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC170707/pdf/aem00013-0282.pdf

So in most cases, including the arsenic paper, OD600 is proportional to cell density, not log cell density. As for Rosie's point, I think she's being a little harsh, for this particular point (her other criticisms are spot on, as is her point that these problems should have been caught in review). OD600 is normally presented on a linear scale (mainly b/c the dynamic range is only about a log or so), while cell density is often presented on a log scale; so the respective scales for each figure are fine. Nevertheless, Rosie is correct to point out that these two graphs cannot be compared directly, without correcting for scale.

Oops. amend the above:
forgot the minus sign in absorbance: OD = - log(I0/I) (where I is detected intensity, I0 is input intensity, and I/I0 is transmittance)

also, for the reference about OD of cells, "links therein" should have been references therein; the paper predates the interwebs.

So in most cases, including the arsenic paper, OD600 is proportional to cell density, not log cell density. As for Rosie’s point, I think she’s being a little harsh, for this particular point (her other criticisms are spot on, as is her point that these problems should have been caught in review). OD600 is normally presented on a linear scale (mainly b/c the dynamic range is only about a log or so), while cell density is often presented on a log scale; so the respective scales for each figure are fine. Nevertheless, Rosie is correct to point out that these two graphs cannot be compared directly, without correcting for scale.

This is Beer's law,...

Matt-
I of course encourage you to check my claims and correct me if I'm wrong. It's also refreshing to have someone consider points rationally and adjust their views when warranted; I've probably spent too much time arguing with creationists, to be impressed with this, but so it goes.

I agree with you that there's no evidence of underhandedness here, and it's a bit unfair to claim so. However, naivete and wishful thinking probably did come in to play, and I'm not the only one to think so. Check out Carl Zimmer's article in slate:
http://www.slate.com/id/2276919/

harold-
I agree, it's a minor point, and not central to the most controversial claims. I encourage you to check out Carl's article, too, I'm mostly in agreement with many of the others mentioned there.

David said: Matt- I of course encourage you to check my claims and correct me if I'm wrong. It's also refreshing to have someone consider points rationally and adjust their views when warranted; I've probably spent too much time arguing with creationists, to be impressed with this, but so it goes. I agree with you that there's no evidence of underhandedness here, and it's a bit unfair to claim so. However, naivete and wishful thinking probably did come in to play, and I'm not the only one to think so. Check out Carl Zimmer's article in slate: http://www.slate.com/id/2276919/ harold- I agree, it's a minor point, and not central to the most controversial claims. I encourage you to check out Carl's article, too, I'm mostly in agreement with many of the others mentioned there.

John Kwok said: Not only that David, but Carl Zimmer has (no surprise) done his homework and shown that there are other scientists who are skeptical not only of the results, but how the NASA team's analysis was carried out:

David said: Matt- I of course encourage you to check my claims and correct me if I'm wrong. It's also refreshing to have someone consider points rationally and adjust their views when warranted; I've probably spent too much time arguing with creationists, to be impressed with this, but so it goes. I agree with you that there's no evidence of underhandedness here, and it's a bit unfair to claim so. However, naivete and wishful thinking probably did come in to play, and I'm not the only one to think so. Check out Carl Zimmer's article in slate: http://www.slate.com/id/2276919/ harold- I agree, it's a minor point, and not central to the most controversial claims. I encourage you to check out Carl's article, too, I'm mostly in agreement with many of the others mentioned there.

Thanks for the link, David.

The Carl Zimmer article is pretty much right in sync with everything else I have heard.

My conclusions -

1) It's honest research but possibly hasty.

2) It's pretty damn likely that these bacteria tolerate high levels of arsenic in their environment. That's a very cool feature, one with potential applications, and one that shouldn't be dismissed if everything else doesn't pan out.

3) The claim that they incorporate it into DNA was not completely without rationale, but that claim is highly controversial and contamination rather than incorporation might be the explanation. The physical chemistry arguments about the stability of arsenic in aqueous solution are perhaps the most worrisome. Still, I will reserve judgement until others attempt to replicate this more rigorously.

4) In no way shape or form does this research have strong implications for OOL, or, likely, seriously unusual biochemistry. These are earthly bacteria with an adaptation.

I'm late to this party, but I think Redfield makes a pretty devastating argument against As in the DNA. The expected instability of DNA containing AsO4 in place of PO4 has been noted above. But Redfield also analyzes the authors' data on the amount of As in gel purified DNA. The result is only sufficient to account for about 1 As for every 5000 base pairs. The other 9,999 backbone links are presumably standard PO4.

1 modification per 5000 bp is quite a low level. Even if it's true, it might simply be the equivalent of 'damaged DNA' that the cell hasn't (yet) repaired. It's certainly not consistent with the claim that these cells are "using" As in their DNA.

quetzal -

I just happened to post this on another blog -

There are four basic possibilities with regard to incorporation of arsenic into DNA in this bacterial strain. Incidentally, although the toxicity of arsenic is multi-factorial, it is mainly due to its interference with ATP as the fundamental unit of energy exchange.

1) The idea that they require or utilize arsenic in a way analogous to the use of phosphorous in other life ("arsenic based life form") can be dismissed out of hand; the paper makes no such claim, media reports notwithstanding, and shows that the bacteria do better on a high P low As medium.

2) The paper does suggest that, when environmental P is low, they may use As as a substitute, at least in some ways. That is a very controversial suggestion and it should be viewed with skepticism. Nevertheless, it probably warrants further study.

3) It's possible that they somehow can tolerate the incorporation of some amount of As into structural DNA or other crucial cell biochemicals, at least at low ratio to P.

4) Or they might actually be extremely effective at excluding As from biochemical reactions, and As found in the DNA fraction, as purified, might be a contaminant. "3)" and "4)" are not necessarily mutually exclusive. There could be tolerance for low level incorporation and and some contamination.

I am, of course, taking it for granted that the bacteria do tolerate high As concentration in the external environment, which I think has been show adequately enough that the onus is on those who would challenge that.

"Researchers said that the bacterium was trained to grow without phosphorus..."

Uh, How exactly do you TRAIN a bacterium to grow without phosphorus? Wouldn't a random mutation that just happened to be successful for this particular environment be more likely? Or are we trying not to upset the creationist crowd?

Uh, How exactly do you TRAIN a bacterium to grow without phosphorus?

David has the right of it on absorbance being proportional to cell density, in his Dec. 7 1:05am comment. I regret claiming this proportionality for transmittance in Rosie's thread. (Old guy... slaps self.)

I remember the great lengths some researchers had to go in order to show the some bacteria could grow without elements like iron. The task of demonstrating that their apparatus and media were free of trace iron was huge. What this paper shows is that one shouldn't skimp on the controls...

Given the short format of Science papers, one would hope the online, supplementary data provides more detail.

Aside: I noticed that John Roth and Norm Pace provide skeptical comments in the Zimmer article. That's not good.

Matt Young said:

I don't get the graph scale discussion, Rosie seems to me to have it right.

No, she does not. A commenter, AMac, explained it correctly on her blog at 9:41 today. I responded to that commenter, saying that I thought he got it exactly correct, but my comment has since disappeared. Very briefly, the optical transmittance is proportional to the concentration of cells in suspension (at least presuming that the suspension is optically thin).

Matt Young said: Please stop feeding the Kwok troll.

And now I *know* you are rushing it, *I* didn't answer the Kwok. :-D

With regard to OD, please see my comment at the top of this page.

It is important to understand it and get it right, but it is, in this routine application, a measure of bacterial survival and growth. It is a very, very, very time-tested and routine technique. It is highly intuitive that bacteria make a broth solution "cloudy" when they reproduce in it. That part of the paper is very uncontroversial. The bacteria were isolated from an arsenic contaminated lake; anyone who claims that they don't even have a tolerance for a high arsenic environment is making an unusually obsessive criticism, and the onus is on them to demonstrate how that result is fundamentally wrong, and how there are bacteria in the lake if it is.

Mere efforts to fine tune or correct the precise growth rate would be constructive and potentially important, but at a high level of specialized detail, and would not conflict with the observed result that the bacteria in question are unusually tolerant of environmental arsenic.

The controversy revolves around whether the bacteria are merely resistant to arsenic, or whether they can utilize it as a less good substitute for phosphorus; the authors imply the latter, but the former is likely to be more correct, and that's true even if they have and tolerate some low level incorporation of arsenic into their biochemistry when grown on high arsenic low phosphorus media. However, further testing will resolve this to a greater degree of rigor.

The ludicrous idea that they preferentially utilize or require arsenic instead of phosphorus ("arsenic based life form") is in no way, shape, or form supported by the reported results, media claims notwithstanding.

I will note that these bacteria could be said to "prefer" high arsenic environments in a more mundane sense.

They grew better in low arsenic medium in the lab, but in non-lab environments like that, they would likely be out-competed by other bacteria. High arsenic gives them a relative competitive advantage.

Here are some questions I am left with - some of them may well be answered in the paper, and my apologies if they are...

1) What other bacteria are they related to? They sort of look like cocci in the electron micrographs. I don't even know if they are gram negative or gram positive.

2) I doubt that they need arsenic as a nutrient, even a trace one, but have they been grown on truly arsenic free media?

3) How did their growth rate on low arsenic, high phosphorus media compare with the growth rate of common environmental bacteria?

harold said: I will note that these bacteria could be said to "prefer" high arsenic environments in a more mundane sense. They grew better in low arsenic medium in the lab, but in non-lab environments like that, they would likely be out-competed by other bacteria. High arsenic gives them a relative competitive advantage. Here are some questions I am left with - some of them may well be answered in the paper, and my apologies if they are... 1) What other bacteria are they related to? They sort of look like cocci in the electron micrographs. I don't even know if they are gram negative or gram positive. 2) I doubt that they need arsenic as a nutrient, even a trace one, but have they been grown on truly arsenic free media? 3) How did their growth rate on low arsenic, high phosphorus media compare with the growth rate of common environmental bacteria?

John Kwok said: Before you consider these questions, harold, I would suggest reading Carl Zimmer's Slate piece first. In light of what I have read there, I think these questions are now moot:

harold said: I will note that these bacteria could be said to "prefer" high arsenic environments in a more mundane sense. They grew better in low arsenic medium in the lab, but in non-lab environments like that, they would likely be out-competed by other bacteria. High arsenic gives them a relative competitive advantage. Here are some questions I am left with - some of them may well be answered in the paper, and my apologies if they are... 1) What other bacteria are they related to? They sort of look like cocci in the electron micrographs. I don't even know if they are gram negative or gram positive. 2) I doubt that they need arsenic as a nutrient, even a trace one, but have they been grown on truly arsenic free media? 3) How did their growth rate on low arsenic, high phosphorus media compare with the growth rate of common environmental bacteria?

I don't interpret the Zimmer summary that way.

Arsenic resistance is fairly rare and itself of interest. (This is not necessarily the only instance of it, but it is unusual and of interest.)

One could simply attach an arbitrary exaggerated claim to any discovery, and then say that the valid parts of the discovery shouldn't even be discussed because an exaggerated claim was made. However, that would be most silly.

I suppose it's true that research on the mechanism of arsenic resistance will be inappropriately inhibited by the backlash against the publicity, but that's unfortunate.

And that will be my final comment on the thread, as no-one seems to have much interest in this topic beyond refuting the exaggerated media claims.