Mono Lake bacteria build their DNA using arsenic (and no, this isn't about aliens)

By Ed Yong | December 2, 2010 12:28 pm

Mono_lake_arsenic_bacteria

Note: Serious concerns have been raised about the conclusions of this study. I’ve written a summary of the backlash in a separate post.

Arsenic isn’t exactly something you want to eat. It has a deserved reputation as a powerful poison. It has been used as a murder weapon and it contaminates the drinking water of millions of people. It’s about as antagonistic to life as a chemical can get. But in California’s Mono Lake, Felisa Wolfe-Simon has discovered bacteria that not only shrug off arsenic’s toxic effects, but positively thrive on it. They can even incorporate the poisonous element into their proteins and DNA, using it in place of phosphorus.

Out of the hundred-plus elements in existence, life is mostly made up of just six: carbon, hydrogen, oxygen, nitrogen, sulphur and phosphorus. This elite clique is meant to be irreplaceable. But the Mono Lake bacteria may have broken their dependence on one of the group – phosphorus – by swapping it for arsenic. If that’s right, they would be the only known living things to do this.

The discovery is amazing, but it’s easy to go overboard with it. For example, this breathlessly hyperbolic piece, published last year, suggests that finding such bacteria would be “one of the most significant scientific discoveries of all time”. It would imply that “Mono Lake was home to a form of life biologically distinct from all other known life on Earth” and “strongly suggest that life got started on our planet not once, but at least twice”.

The results do nothing of the sort. For a start, the bacteria – a strain known as GFAJ-1 – don’t depend on arsenic. They still contain detectable levels of phosphorus in their molecules and they actually grow better on phosphorus if given the chance. It’s just that they might be able to do without this typically essential element – an extreme and impressive ability in itself.

Nor do the bacteria belong to a second branch of life on Earth – the so-called “shadow biosphere” that Wolfe-Simon talked about a year ago. When she studied the genes of these arsenic-lovers, she found that they belong to a group called the Oceanospirillales. They are no stranger to difficult diets. Bacteria from the same order are munching away at the oil that was spilled into the Gulf of Mexico earlier this year. They aren’t a parallel branch of life; they’re very much part of the same tree that the rest of us belong to.

That doesn’t, however, make them any less extraordinary.

Phosphorus helps to form the backbone of DNA and it’s a crucial part of ATP, the molecule that acts as a cell’s energy currency. Arsenic sits just below phosphorus in the periodic table. The two elements have such similar properties that arsenic can usurp the place of phosphorus in many chemical reactions. But arsenic is a poor understudy – when it stands in for phosphorus, it produces similar but less stable products. This partially explains why the element is so toxic. But the bacteria of Mono Lake have clearly found a way to cope with this.

They have every reason to do so. Mono Lake sits in a sealed basin close to California’s Yosemite National Park. With no outlet connecting it to other bodies of water, any chemicals flowing into the lake tend to stay there. As a result, the lake has built up some of the highest concentrations of arsenic on the planet. To survive here, bacteria have to be able to cope with the poison.

In 2008, Ronald Oremland (who was also involved in the latest study) discovered bacteria in Mono Lake that can fuel themselves on arsenic. Like plants, they can photosynthesise, creating their own food using the power of the sun. But where plants use water in this reaction, the bacteria used arsenic. Wolfe-Simon has taken these discoveries a step further, by showing that the bacteria are actually incorporating arsenic into their most important of molecules.

She took sediment from Mono Lake and added it to Petri dishes containing a soup of vitamins and other nutrients, but not a trace of phosphorus. She took samples from these dishes and added them to fresh ones, gradually diluting them to remove any phosphorus that might have stowed away onboard. And all the while, she added more and more arsenic.

Amazingly, bacteria still grew in the dishes. Wolfe-Simon isolated one of these arsenic-lovers – a strain called GFAJ-1. Using an extremely sensitive technique called ICP-MS that measures the concentrations of different elements, she showed that the cells of these bacteria did indeed contain large amounts of arsenic.

By giving the bacteria a mildly radioactive form of arsenic, Wolfe-Simon could also track where the element ended up in the cells. The answer: everywhere. There was arsenic in the bacteria’s proteins and in their fat molecules. It had replaced phosphorus in many important molecules including ATP and glucose (a sugar). It was even in their DNA, a conclusion that Wolfe-Simon backed up with a number of other techniques. All other life uses phosphorus to create the backbone of the famous double helix, but GFAJ-1’s DNA had a spine of arsenic.

It’s an amazing result, but even here, there is room for doubt. As mentioned, Wolfe-Simon still found a smidgen of phosphorus in the bacteria by the end of the experiment. The levels were so low that the bacteria shouldn’t have been able to grow but it’s still not clear how important this phosphorus fraction is. Would the bacteria have genuinely been able to survive if there was no phosphorus at all?

Nor is it clear if the arsenic-based molecules are part of the bacteria’s natural portfolio. Bear in mind that Wolfe-Simon cultured these extreme microbes using ever-increasing levels of arsenic. In doing so, she might have artificially selected for bacteria that can use arsenic in place of phosphorus, causing the denizens of Mono Lake to evolve new abilities (or overplay existing ones) under the extreme conditions of the experiment.

Other species can cope with arsenic too. Some switch on genes that give them resistance to arsenic poisoning, while others can even “breathe” using arsenate. But GFAJ-1 uses the element to an even greater extent. How does it manage?

Under the microscope, the bacteria become around 50% larger if they grow on arsenic compared to phosphorus, and they develop large internal compartments called vacuoles. These might be the key to their success. Wolfe-Simon thinks that the vacuoles could act as a safe haven for unstable arsenic-based molecules – they might contain chemicals that steady the molecules, and they might keep out water that would hasten their breakdown.

These are questions for future research. In the mean time, the angle being used to sell the story is that this might have implications for alien life. Of course, the results have nothing to do with aliens. If anything, they expand the possibilities of what alien life might look like. If bacteria on Earth can exist using a biochemistry that’s very different to that of other microbes, it stands to reason that aliens could do the same.

That hasn’t stopped the hype machine from rolling forward, fuelled by a public announcement from NASA, teasing a press conference about an “astrobiology discovery”. It’s a shame. In teasing their own press conference two days ahead of time, and refusing to budge on the embargo when the first information trickled in, NASA effectively muzzled everyone who knew about the actual story while allowing speculation to build to fever pitch.

That may, of course, be their intention. However, I can’t help but feel that the result will be a lot of disappointed people, who’ve been robbed of an opportunity to be excited about a genuinely interesting discovery.

Update: John Sutherland from the MRC Laboratory of Molecular Biology at Cambridge adds to the skepticism. He notes that arsenic-based compounds are “not sufficiently stable in water for the phosphorus to arsenic substitution implied in this paper to be functional” and the arsenic-phosphorus swap hasn’t been demonstrated by the study’s experiments in a “chemically rigorous manner”. For Sutherland, the acid test would be actually synthesising a double helix of arsenic-based DNA and characterising its structure in detail. You could then use the data from that analysis “as a reference point” to examine the DNA from the Lake Mono bacteria. “This has not been done,” he notes, and even if it were, the existing evidence suggests that the molecule would break apart when it’s exposed to water.

Update 2: Rosie Redfield has published a devastating critique of the paper, describing it as “lots of flim-flam, but very little reliable information.” It’s an incredibly technical post, recommended for everyone but probably only suitable for those with a scientific background. Likewise, Alex Bradley has a critique of his own. And David Dobbs asks if science journalists could have done better. I know I could have.

Update 3: The updates are coming thick and fast on this story and I’m struggling to keep up with them. For the moment, check out the Guardian’s story tracker for a comprehensive look at the coverage, responses, and counter-responses.

Update 4: I’ve summarised the last week of responses to this study in a new post.

Reference: Science http://dx.doi.org/10.1126/science.1197258

My other take on this story

More on extreme bacteria:

If the citation link isn’t working, read why here
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CATEGORIZED UNDER: Bacteria, Molecular biology

Comments (47)

  1. rpg

    Meantime the DOI isn’t resolving so I can’t actually read the paper…

  2. Thank you for the concise post on this.
    It really is a shame. My labmate and I were excited from the hype…then it just became less and less. It’s a shame that NASA had to pull out the drama.

    All that said, it is a really amazing discovery. Microorganisms always have amazing tricks to show us.

  3. Jenny Morber

    Thank you, once again, for a clear and reasoned explanation. I must admit that I am a little sad that the news does not announce the discovery of hitch-hiking alien bacteria on an asteroid in the desert. Aliens on the cover of Time would be a nice end for the creationists.

  4. I guess NASA is having a hard time getting funded, that’s the reason behind this hype. Good piece!
    If I am allowed to extend the polemic even further, frankly I don’t see how can astrobiology be considered a proper science. Since no alien form of life has been discovered yet (conspiracy theorists might disagree), as of now it can be purely speculative. Not even theoretical, as long as we use the word “theory” as it should be in science (at least biological science) – just speculative. It’s still fascinating and worth thinking about, but I’d rather consider it an extension of some other, more robust field of biology (e.g. study of extremophiles) and not a field on its own, as apparently some do. If there is some astrobiologist friend out there: sorry but that’s what I think, can you show I’m wrong?

  5. Great post, as usual, Ed. Also loved the Posterous!

    You’re right to be irritated with a certain agency’s PR department. This is going to lead to a swarm of mouth-breathers yelling about ANOTHER NASA HOAX!!!1!, I’m afraid.

  6. Simon

    Paul Davies has been talking about this ‘Shadow Biosphere’ for quite some time and the research at Mono Lake had been very promising so it’s no shock to me.

  7. Tina

    Just a note……….Mono Lake is not within Yosemite National Park. It is actually 12-13 miles east of Yosemite.

  8. “Mono Lake sits in a sealed basin within California’s Yosemite National Park.”

    Ah, no. Mono Lake is near, but not within, Yosemite National Park. Mono Lake lies within Inyo National Forest.

    [Fixed. Cheers - Ed]

  9. Jung Choi

    Great, lucid explanation. Tremendously exciting, no need for the hyperbole as you point out. Any idea if this strain and the parent are being sequenced?

  10. @Simon – It’s not a Shadow Biosphere. As I understand it, that concept refers to a second branch of life that evolved independently from everything we know. That’s not what was found. These bacteria are part of the same tree we’re on. They do occasionally and mostly have different biochemistry.

  11. As cool as this is, arsenic is not a good substitute for phosphorus and so this is likely to be an isolated example. Part of the reason is basic chemistry; compared to the phosphate esters in DNA, arsenate esters are very unstable and are hydrolyzed remarkably fast. That makes this finding even more impressive, but it also precludes extensive substitution of arsenic for phosphorus in DNA-like genetic material.

    The Harvard chemist Frank Westheimer wrote a memorable paper explaining “why nature chose phosphates” which can be found here. It explains based on basic principles of chemistry why phosphates rather than arsenates or silicates have been chosen by life. Must read for those who think alternative life-forms could be common.

    [Indeed. I did mention the point about stability in the post. Must've been a doozy of a selection pressure to overcome that - Ed]

  12. Matt

    Blogger Yong states: “It had replaced phosphorus in many important molecules including ATP and glucose (a sugar)”

    Last I checked glucose does not contain phosporus in the first place.

    Hmmm…..

    [Crap crap crap. Stupid mistake. Misread a sentence in the paper, but I really should have spotted that. Cheers Matt. Fixed - Ed]

  13. Bigby

    Since Wolfe-Simon took samples and diluted them she was, in effect, creating a very powerful homeopathic remedy. And since the bactieria thrived in this culture that’s proof that homeopathy works…right?

  14. Caleb

    When did glucose start having phosphorus in it?? (Thanks for fixing that)

    Also, are we to assume that sulpholipids are exclusively being used in the membranes of this organism?

  15. dshizuka

    Thanks for the most insightful and hyperbole-free take on this story I’ve seen. You asked all the questions I wanted to ask and then some. There are a lot of amazing stuff in this study and it’s nice to separate out the solid stuff from the fluff.

  16. Georg

    First,
    we need to know, why arsenic is rather toxic to higher
    animals (non-toxicity to single-cell units is not so
    remarkable, this is quite common)
    Second arsenic was consumed by men formerly,
    the Austrian writer Peter Rosegger (mid 19th century)
    writes about “arsenik eaters” in his mountain home.
    The mineral water of Baden-Baden (in use for about
    2000 years) contains a lot of arsenic. Such small doses
    make you gain weight and give a “lively” teint.
    The image of arsenic is much exaggerated by its criminal
    past, that is the main base of the hype.
    Georg

  17. Torbjörn Larsson, OM

    If there is some astrobiologist friend out there: sorry but that’s what I think, can you show I’m wrong?

    I’m not astrobiologist, but I’m currently studying in such a university course.

    And you are simply wrong, astrobiologists have found life among the stars – we are it. The course, as well as most books, use Earth as a case study against the processes of planetary system formation, probiotic & protobiotic chemistry et cetera. This work shows how alive that first leg of astrobiology is.

    Also, as a second leg we have started to look at planetary bodies with similar imbalances as our biosphere has made, Mars (methane) and Titan (hydrogen, acetylene, carbon isotope ratio) are among them.

    Finally, the finds of exoplanets, now on the order of 1 k planets, is the third leg. Composition of atmospheres is a beginning study object. (As an example, this week another atmosphere, the first super-Earth AFAIU, was beginning to be constrained.) And if and when we find biospheres among them, their distribution will help characterize likely pathways to life, ours among them.

  18. em

    Great article, informative and free of any sensationalism.
    For those who want to see the article here is the direct link to science(access to science required), not sure why the DOI link does not work.
    http://www.sciencemag.org/content/early/2010/12/01/science.1197258.abstract

  19. Sven DiMilo

    Thanks for a reasoned and properly skeptical take on this wildly over-hyped story.
    Even your post title goes too far:
    Mono Lake bacteria ^may be able to^ build their DNA using arsenic ^when forced to do so in the lab^

  20. These bacteria are also reported to do quite well on Iocane powder. (Sorry, couldn’t resist!)

  21. Chris

    Certainly an exciting result, and a good write up Ed. But having looked over the paper at Science Express, I’m not convinced yet. There are some strange standard error values quoted (e.g. dry mass of arsenic in As grown cells being 0.19 +/- 0.25%). Maybe someone who knows about the technical details of these measurements can offer an opinion. They report that variation as being perhaps due to the sample preparation methods used, but with that much variation, I’d like to see them back up their assay with another technique.
    And as far as I can tell, they did not show the presence of adenosine tri-arsenate. They show that most of the As was found in the sub-cellular fraction containing small molecular weight metabolites which would normally include ATP.
    On the other hand, the evidence for incorporation of arsenate into the nucleic acid backbone seems convincing to me.
    On the whole: fascinating, and I await more research with baited breath!

  22. ld

    OK, so glucose alone does not have phosphorus in it, but glucose phosphates form critical steps in sugar metabolism. And the authors do state they find arsenylated glucose molecules in the bacteria.

    If you really insist on being picky about this, protein doesn’t have phosphorus “in” it either.

  23. Laura Rodgers

    The initial innoculation was into liquid media, but that’s a really minor point. The inaccuracy I take more issue with is “vitamins and other nutrients, but not a trace of phosphorus.” There was still phosphorus in the mainly-arsenic condition, and more than a trace amount.

    [I think that's a case of unclear communication rather than inaccurate. You'll note that later I said that there were detectable levels of phosphorus. I meant that there wasn't any phosphorus in the media they used. Also I knew they used liquid media, which is why I said "soup". I'm not sure "media" is a widely understood term in the context of "growth media". - Ed]

  24. Ed hits a point every other article on this news item missed:

    “Nor is it clear if the arsenic-based molecules are part of the bacteria’s natural portfolio. Bear in mind that Wolfe-Simon cultured these extreme microbes using ever-increasing levels of arsenic. ”

    Good for him. Of course, the bacteria was only cultured over a matter of days, not years, so they’re unlikely to have evolved anything drastically novel in a matter of a couple dozen generations. Whether their capability to utilize arsenic actually happens in the wild requires more science (and maybe even better situations with low phosphorus and high arsenic).

    I disagree with Ed on astrobiology potential though. This result tells us not to give up on the (hypothetical) environments that have lots of arsenic and little phosphorus.

    [Cheers Brian. I'm not really naysaying the astrobiology potential though. I did say, "If anything, they expand the possibilities of what alien life might look like," which I think sort of covers the point you made. - Ed]

  25. Frankly, I wonder if NASA ginned up at least some of this PR for budget/fiscal reasons, for “planetary research” reasons. This could be a way to push for more Mars exploration money.

    Beyond that, arsenic substitution in other organic compounds, such as arsenic “sugars,” is already documented.

    http://socraticgadfly.blogspot.com/2010/12/bad-or-at-least-breathless-science-by.html

  26. @ Torbjörn Larsson, OM:
    > And you are simply wrong, astrobiologists have found life among the stars – we are it.
    True indeed, but should we call the study of such life… astrobiology? You could do with, you know, *biology*. Otherwise we should say also astrogeology, astrogeography, etc. etc….
    > This work shows how alive that first leg of astrobiology is
    You call it “first leg of astrobiology”, i call it simply biochemistry ;)
    > Also, as a second leg we have started to look at planetary bodies with similar imbalances as our biosphere has made, Mars (methane) and Titan (hydrogen, acetylene, carbon isotope ratio) are among them [...]
    Ok, but as of now we are only studying the ABIOTIC factors. If I set a study in the Amazon rainforest and measure only, say, atmospheric variables – temperature, moisture, whatever – but not anything directly related to living things, I’m not doing biology, astro- or not astro-
    Thus I don’t see how I was wrong, sorry…

  27. Aleksandar Kuktin

    Fascinating.

    Since the inclusion of As creates unstable molecules, I believe this fact can be reexpressed as “the inclusion of As instead of P reduces the half-life of cell’s molecular component parts”.

    The important thing with this, IMHO, is that such a handicap can be fought against by increasing the turnover of such component parts. One’s cybernetical profile, however, would have to be reasonably robust to do that. IOW: maybe they have simpler gene interdependencies? Less gene interactions? Less protein interactions?

    Wonder how would one measure that…. And if there is some threshold?

    And, most critically: what are the competitive (evolutionary) (dis)advantages of that? Beside capability to live in an arsenic soup, ofc.

  28. Raptor

    @ Walter S.

    You’re pretty much equating searching for life on other worlds than our own to searching for the invisible pink unicorn. While we know the invisible pink unicorn does not exist, the only way to know if life on other planets does exist, is to search for it. And, we know that it most likely exists, because it exists here and we are one planet out of many trillions. And, to sum up what you are saying is this ‘we shouldn’t search for X because we haven’t found it yet and so it shouldn’t be a legitimate field of science.’ If we applied that to everything, nothing would be discovered. I mean, you could have said that 30 years ago (give or take) about exoplanets. “We shouldn’t search for exoplanets because we haven’t found any yet and the search for them isn’t a viable research field.” Or about chemistry, we could still be doing alchemy, you know ‘No one’s found an element, so we shouldn’t search for them and chemistry isn’t a valid field because we have alchemy.’ The only way we’re going to find other life is to study different forms of life here, and how to detect them, and then apply that knowledge to looking at other planets. Sorry, but you don’t get to decide what a specialization in a field is or what it’s called. The people working in it, studying it, doing actual science, however, do. And so yes, this is a very narrow field of study (as is most things. You know how huge biology is and that most people who study biology don’t have phd’s in biology?) Astrobiologist is exactly what it is says it is. It is using knowledge from astronomy and biology to do science… and that gets it’s own field every time.

  29. Naoko from Japan

    I read about the newly found creature that can be an alien. Main papers in Japan largely covered the story. Honestly, I was disappointed to know facts from your post. NASA, I think, is really want to show its reason d’etre among this long lasting economic recession. Thank you for giving these informations.

  30. If I’m reading the paper right, there’s plenty of reason to be skeptical.

    1) Funny numbers.

    From Table S1 of the supplementary materials, a) The authors found comparable As concentrations in *both* the +As/-P and -As/+P phenol extracts (~3,600 ppb for P-fed, 4,700 ppb for As-fed). b) The concentration of As in the As-fed DNA/RNA extract was <20 ppb (below the threshold of measurement? but the threshold is given as 1 ppb in the discussion and elsewhere in the table) vs. 118 ppb in the P-fed. Neither number suggests meaningful As uptake into anything. (The data do indicate that P was severely depleted in the As-fed sample – by as much as 99%, but I don't see any data to indicate where more than a very tiny fraction of that might have been replaced by As.)

    2) A striking omission.

    Most telling to me: As was found in the P-fed bacteria (at ppb levels on the same order of magnitude as in the As-fed bacteria), and the bacteria are from an As-rich environment, so isn't it plausible that *both* As-fed and P-fed bacteria contained a smattering of As in some of their biomolecules? Certainly there's no reason for the researchers to ignore that possibility right? So why did they run the critical synchrotron X-ray analysis *only* on the As-fed sample? For that sample, the data were consistent with the hypothesis that As was in the DNA.

    Isn't it a basic scientific principle to *compare* (and they did compare P-fed vs. As-fed in other analyses)? Maybe because if they had (I can't help wonder that they might have in fact done and suppressed the analysis) found As in the DNA of the P-fed sample, well, poof goes the press conference – it's barely newsworthy. This is only exciting if As is *not* in the DNA of the P-fed sample – that is, if the As-fed sample in fact *incorporated* As into its DNA (and is using As-substituted biochemistry, which remains to be studied).

    Am I missing something, or is there little evidence of As-based biochemistry, and next to none to indicate that the As-feeding aspect of the experiment showed anything except that depriving these bacteria of phosphorus causes them to lose phosphorus and become very bloated?

  31. Waclaw Szybalski

    Over half century ago we have been replacing methyl groups in DNA with bromine or iodine. We have proved that such chemically different DNA is functional. Also viruses and cells with halogenated DNA were alive. For ultimate proofs we were separated halogenated DNA or viruses using CsCl or Cs2SO4 gradients.
    Present authors should also separate the As-DNA from P-DNA using CsCl or Cs2SO4 gradients and
    determine their biological activity by a transformation or transfection assay.
    Good luck. (See in Google: Litman and Szybalski, BBRC 1963 pp:473-481)

  32. @ Raptor:
    No, I’m not. As I said:
    “I’d rather consider it an extension of some other, more robust field of biology (e.g. study of extremophiles)”
    … which is very different than saying:
    > ‘we shouldn’t search for X because we haven’t found it yet and so it shouldn’t be a legitimate field of science
    What I’m trying to say is just that, imho, it cannot (yet) considered a proper branch of biology in its own right, such as microbiology or plant pathology or acarology etc. I don’t rule out the possibility that it eventually will become – but for that to happen, we must first find this non-Earthly life (at least indirectly – say, traces of biotic activities on Mars’ surface). Until then, we can only build the context for it. Meaning that all which goes under the name “astrobiology” for now belongs to one well-established field or the other, and it’s still not practical to consider astrobiology a discipline in its own right. Be free to differ, but please don’t attribute to me things I never meant to say…
    And – to go back to the Mono Lake bacteria story – I find quite irritating that some people try to bring astrobiology in, and with a red carpet indeed, when there’s really little or no room for it
    (speaking of which, this time someone grasped the takehome message even better than you Ed ;) http://scienceblogs.com/pharyngula/2010/12/its_not_an_arsenic-based_life.php )

  33. Josh

    Saying “arsenic based” is incorrect. This is still carbon based life. Also I highly doubt that Arsenic is used in proteins, unless it is also substituting for Nitrogen instead of just Phosphorus. That would truly be amazing, but I think you need to check your sources.

  34. (note: this originally got marked as spam when I included a link to an ASM blog post. Don’t know why. So, please ignore the previous entries.)

    Well that was fun, no?

    This story seems to have split in to two (ignoring confirmation of and/or building on these findings)…

    * Does this bug really suggest anything new in terms of what form a life might have in world unconnected to ours (esp one with very different percentages of starting materials, climate, etc)
    and
    * The “NEW LIFE” angle.

    At first blush, what this does suggest (if it’s proven true) is that there are alternatives for known macromolecule synthesis that uses alternate elements. (Presumably in this case As might be used wherever it’s family-mate P is normally). That is good to know. I’d be more jazzed if they found that a DNA analogue, perfectly functional, had a truly radically different structure. Doesn’t sound to be the case.
    Beyond that, I’m not sure what astrobiology significance this has.

    As for the parallel life angle. Man! This should have been dropped before it even got said.

    There has always been an assumption of something like this: if two prongs of evolution began, say, soon after the founding of some form replicating nucleic acid variants – one form of evidence of this *could* be a significantly different codon usage table. Although this wouldn’t be conclusive either – enough microbes with slight shifts to make late divergence possible as well.

    Regardless, a finding like that, of a *vastly* different codon table, would certainly be major news and freaking off the hook exciting.

    (Though, oddly, just yesterday on Small Things Considered (my old dept. Chairman’s blog), there’s a post reviewing some computational approaches suggesting our particular code is one of the most resistant to bad effects from point mutations. So… )

    BUT, as you point out, you didn’t need to really know the codon usage table once you read that the genes are the same (don’t get access to sci papers: I assume extremely high homology? Near identical?)

    Once you know that – and you know who it’s closest relative is, I can’t see where anyone gets the parallel life aspect.

  35. Doesn’t Figure S2 show that the bacteria contain 100-fold more P than A even after culture in medium with no added P? I think they’re growing on the 3 µM P in this medium, and perhaps incorporating traces of the A.

    p.s. I’d pay close attention to anything Waclaw Szybalski says (@#31) – he knows his microbiology!

  36. Thanks to everyone for the valuable comments.

    @Josh – I agree on “arsenic-based” which is now gone. The bit about proteins – they mean post-translational modifications rather than the amino acids themselves but I’ve used “proteins” as a short-hand because (a) the piece was getting complicated enough as it was for a general audience and (b) they use a similar short-hand in the paper.

    @Scott – You write “I can’t see where anyoen gets the parallel life aspect.” Quite. And here’s the thing – you get it by not reading the paper and relying on earlier speculation (like the article I linked to in an early paragraph).

  37. Georg

    In the 50ties
    up to early 60ties there was a “cause celebre” in France. A woman
    (Marie Besnard) was accused to have murdered a dozen (?) of her
    realtives using arsenic.
    After several trials she was released, because the origin of the arsenic
    in the bodys on the graveyard was not clear.
    There was arsenic outside in the soil in instances, but not with other
    corpses. The most recent science was used then, (neutron activation)
    but the question of mobilisation /immobilisation of arsenic in the soil
    in the end was not answered.
    I would look for bakteria in that graveyards with modern analytic tools.
    Georg

  38. I hadn’t realized some of the speculation was coming, in part, from the authors – in public communication – not the paper, I think.

    There’s even a clip of Wolfe-Simon on a BBC documentary at least implying that these could be from a separate origin of life.

    But, as it states in the paper, the ribosomal sequencing puts it in the class of Gamma proteobacteria (and I’m no longer in science, so while I er… illicitly… got the Sci article, I can’t see the supplemental, but I assume it’s shown there).

    Once that’s said, then it looks like it’s in the same large grouping (proteobacteria) as helicobacter (the ulcer-bug) and freaking gonorrhea. In theory, this should end the ‘parallel’ discussion at the source.

    It’s too bad cause there’s totally (pending continued study) something interesting here. I mean, proof that life can naturally find a way to (sort of) restructure the core macromolecules of life *is* a big deal. It *could* contribute to thinking about how life could form under different environmental circumstances. But the discussion prompted by the coverage is not really valid.

    Which is frustrating when, at the same time, average folks got excited about it.

  39. Schenck

    As far as the press release, the researchers that made this discovery were, as far as I understand, already part of NASA’s astrobiology group (or one of its groups), the paper’s lead author is listed as that (amoung others).

    So you have, in effect, astrobiologists, doing research on a grant that was awarded because it would advance astrobiology, making a /huge/ discovery, and so, yeah, NASA’s press release was totally correct, its an astrobiological discovery that has big implications for the search for evidence of extraterrestrial life. Its not NASA’s fault that a bunch of lunatics thought that would mean ‘we found alien life’.

    If NASA finds alien life, it won’t be announced by a couple of researchers on NASATV, the President of the United States will interrupt prime time programming on /every/ tv and radio channel to tell us.

  40. Gaythia

    @Schenck – If someone interrupts prime time programing on TV and radio some of us won’t hear/see a thing. Hopefully, Ed Yong will be around online to explain to us what is going on.

    @ Ed, this is an excellent, clearly written post. Too bad that NASA didn’t understand that clearly explained real science would be better than going for the hype.

    I think that we ought to take up a collection so that you can take a field trip and see Yosemite and Mono Lake first hand!

  41. Torbjörn Larsson, OM

    Now I’ve read the paper, and I have to agree with Steve Kass, there’s plenty of reasons to be skeptical.

    Adding to Kass, my layman take was that the separating washes and gel treatments weren’t characterized. For example, the gel separation I’m reading as removing small RNA (for example) fragments, but not characterized for removing proteins (say). And if the organism has trouble with arsenic, it should use proteins to sequester it.

    there wasn’t any phosphorus in the media they used.

    Yes there was, but a minimal amount.

  42. Torbjörn Larsson, OM

    @ Walter S. Andriuzzi:

    Since I already motivated why astrobiology is considered a specific area, I don’t see the point to argue your contentions. Especially since you in other comments seem dead set to make astrobiology “not a subject”.

    Nevertheless, in the spirit of “bystanders may learn”:

    > And you are simply wrong, astrobiologists have found life among the stars – we are it.
    True indeed, but should we call the study of such life… astrobiology? You could do with, you know, *biology*. Otherwise we should say also astrogeology, astrogeography, etc. etc….

    Yes, we should, since the idea is to look for characteristics of environments and putative life elsewhere. Which in turn can inform and be informed by biology in our own environment.

    i call it simply biochemistry ;)

    Chemistry of young star systems, interplanetary dust particles, comets and moons are quite different from biochemistry on Earth. Before studying, no one knew it was biochemistry btw.

    Ok, but as of now we are only studying the ABIOTIC factors.

    No, we are also studying habitability. You can look up Mendez work to see how Earth habitability corresponds to exoplanet habitability.

  43. I’ve now posted a thorough analysis of the microbiology and molecular biology in the Science paper. Click on my name for the link to my blog (RRResearch). Bottom line: bad science, no good evidence for arsenic incorporation.

  44. Luke

    Aliens? Haven’t you all figured it out yet? WE ARE THE ALIENS.

    Either our home planet filled up and we shifted here or we are test subjects and have been placed here to be observed.

    But we are the aliens to this planet.

  45. Hi this is kind of of off topic but I was wondering if blogs use WYSIWYG editors or if you have to manually code with HTML. I’m starting a blog soon but have no coding knowledge so I wanted to get guidance from someone with experience. Any help would be enormously appreciated!

  46. dent

    Radiotelescopy revealed hydrocarbons on titan some time ago. methane etc….
    thomas gold speculated that with the action of archaea present in substrata- consuming hydrocarbons, methane or methane hydrates would result indicating the russian abiogenic theory to be correct and that life does exist on other planet environments.
    If archaea existed during the formation of a cold planet that gradually heated from the core as gold posits then extraterrestrial life began in the earth before the swirling dust clouds and gases settled out allowing photosynthesis. Life that surrounds deep ocean heat vents have a multitude of forms – it seems more reasonable that life moved from within the planet outwards as conditions outside the planet became more useable, ultimately the debris that created the planet in the first place contained the originating archaea.
    This theory would imply that life is of extraterrestrial origins and has innate adaptability.

  47. Jeremy

    As a biotechnologist I agree 300% with John Sutherland and others who critique this story to expose its flaws. In the experiment it states there were small amounts of phosphorus present after the repeated dilutions, and with arsenic being unstable in the presence of water it seems like it still needs a level of phosphorus present to form a stable trellis for DNA. I don’t believe a complete arsenic backbone would be biologically viable at all. Synthesize it, slap it in a chromosome, and prove it.

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