#Arseniclife reviews: Missing the forest for the trees

In this year's ScienceOnline conference I co-moderated a productive session on peer review in which I pointed out how overly conservative or agenda-driven peer reviews can prevent the publication of legitimate science. Now here's a case where the opposite seems to have occurred; highly questionable science making it through the filter of peer review as easily as particles of dust would make it through a sieve with penny-sized holes.

Thanks to the Freedom of Information Act, USA Today and a couple of other scientists got their hands on the reviews of the infamous #arseniclife paper. There were three reviewers of the study, and all of them approved the paper for publication.

What's interesting is how effortlessly the reviewers miss the forest for the trees. We of course have the benefit of hindsight here, but it's still striking how all three reviews simply swallow the flawed paper's basic and potentially textbook-changing paradigm - the substitution of arsenic for phosphorus - right off the bat. Once they accept this basic premise, all their other objections can simply be seen as nitpicking and window dressing. Only one reviewer asks questions that come close to questioning the absence of phosphorus in the medium, but even he or she quickly veers off course. Another calls the paper a "rare pleasure" to read, seemingly unaware that the pleasure which the paper has provided comes from an extraordinarily ambitious claim that needs to be vetted as closely as possible.

In fact the reviewers ask good questions about vacuoles seen in the bacterium, about better standards for some of the experiments, about better methods to quantify arsenic in its various forms. They even ask a few very chemical questions regarding bond distances. But all these questions are somewhat beside the point since they flow from a fundamentally flawed belief.

When I was in graduate school, the most important thing that my advisor taught me was to always question the assumptions behind a study. If you don't do this, it's easy to be seduced by the technical details of the experiment and to let these details convince you that the basic premise is validated. That's what seems to me to have happened here. All the reviewers seem to have been sucked into legitimate and interesting questions about minutiae. But all the time they forget that what really needs to be questioned is the giant assumption from which all the minutiae have been derived, an assumption that we now know does not stand up to scrutiny. There's an important lesson here.

"Arsenic bacteria": Coffin, meet nails

For those dogged souls still following the whole debacle of arsenic-eating bacteria, it seems that Science has published what should be close to the death knell for "arsenic life". I already mentioned the report by Rosy Redfield and there's another one by Tobias Erb's group at ETH. The title of the paper is "GFAJ-1 is an arsenate-resistant, phosphate-dependent organism".

It's worth reflecting on that title again; "arsenate-resistant, phosphate-dependent". Yes, that description applies to GFAJ-1. It also applies to me, Shamu the killer whale, E. coli 0157 and Francis Bacon. In fact it applies to all the normal life forms that we know. So basically the title says that GFAJ-1 is not much different in this respect from any other bacterium that you may happen to find in a thimbleful of mud scooped up from your backyard.

The paper goes on to analyze the behavior of the bacterium in the presence and absence of phosphorus and arsenate. The bacterium seems to survive in tiny concentrations of phosphate, a concentration that was interestingly deemed as an "impurity" in the original Wolfe-Simon studies. It also does not survive on arsenate but starts dividing as soon as trace amounts of phosphorus are added. The authors' conclusion is clear: "We conclude that cultures in the previous study might have grown on trace amounts of phosphate rather than arsenate". This is what several experts had suspected since the beginning. Their suspicion was based on life's extraordinarily resilience and its ability to zealously guard and use every single atom of precious growth nutrients.

The authors also analyze the composition of the biomolecules (nucleotides, sugars etc.) in GFAJ-1 in the presence and absence of arsenate. They find only phosphate incorporated in the organism's essential machinery. While this does not necessarily argue against the use of arsenate, it demonstrates that when given a choice GFAJ-1 clearly prefers phosphate.

That observation is however not as striking as the next one where they find some metabolites containing arsenate, specifically sugars with arsenate appended to them. The question then is, are these metabolites formed biogenically or abiotically? To try to distinguish between these possibilities, the authors ran mock experiments where they treated glucose medium with arsenates. The purported metabolites showed up in the products and their formation is also supported by simple thermodynamic arguments which favor the attachment of arsenates to sugars. Thus it seems that simple chemistry rather than complex biology is sufficient for explaining the small amounts of arsenated metabolites. The scientists further resort to careful experiments to rule out the existence of other arsenated biomolecules.

The sum total of these experiments says that GFAJ-1 can grow in the presence of phosphate, that it cannot grown in arsenate, and that it can grow in high concentrations of arsenate only when supplemented with limiting concentrations of phosphate. Taken together with the other paper by Rosy Redfield, this is as good a case against arsenic-based life that we can make right now.

The papers are good examples of the conservative yet decisive style that scientists are accustomed to pitching their results in. Unfortunately the original authors have not reacted as conservatively. If anything their responses are transparently shallow and unconvincing. When asked about the results, Felisa-Wolfe Simon said that:

"There is nothing in the data of these new papers that contradicts our published data."

That reply almost convinces me that denial is the most sincere form of self-deception.

A current collaborator of Wolfe-Simon had even more remarkable things to say:

“There are many reasons not to find things — I don’t find my keys some mornings,” he said. “That doesn’t mean they don’t exist. The absence of a finding is not definitive.”

To which I might add that there is a possibility that disgruntled unicorns with chemistry PhDs looking for jobs may well exist, since we haven't found any yet.


Update: Paul@Chembark nicely weighs in.

"Arsenic bacteria": If you hadn't nailed 'im to the perch 'e'd be pushing up the daisies

Rosie Redfield (who blogs on this network) has just published an official, careful and decisive rebuttal to the "arsenic bacteria" fiasco in collaboration with a group at Princeton. The paper which will appear in Science is under embargo for now, but there is a copy available at that bastion of free publication arXiv. Readers may remember Redfield as the scientist who offered the most meticulous preliminary criticism of the original paper by Felisa Wolfe-Simon and others. Wolfe-Simon and the rest of the arsenic group refused to engage in debate with Redfield and other critics at the time, citing the "non-official" nature of the offered criticism and asking for publication in a more formal venue. Looks like they finally got their wish.

The abstract could not be clearer:

"A strain of Halomonas bacteria, GFAJ-1, has been reported to be able to use arsenate as a nutrient when phosphate is limiting, and to specifically incorporate arsenic into its DNA in place of phosphorus. However, we have found that arsenate does not contribute to growth of GFAJ-1 when phosphate is limiting and that DNA purified from cells grown with limiting phosphate and abundant arsenate does not exhibit the spontaneous hydrolysis expected of arsenate ester bonds. Furthermore, mass spectrometry showed that this DNA contains only trace amounts of free arsenate and no detectable covalently bound arsenate."

It's a fairly short paper but there are many observations in it which quite directly contradict the earlier results. The strain of bacteria that was claimed to grow only when arsenic was added to the medium was found to not grow at all. In fact it did not budge even when some phosphate was added, growing only after the addition of other nutrients. Trace element analysis using several techniques detected no arsenate in DNA monomers and polymers. This is about as definitive an argument as can be published indicating that the claims about the bacteria using arsenic instead of phosphorus in their essential biomolecules were simply incorrect. Much credit goes to Redfield who patiently and probingly pursued the counterargument, undoubtedly at the expense of other research in her lab. In addition she did open-science a great service and described all the ongoing research on the blog. She sets a standard for how science should be done, and we should hope to see more of this in the future.

Sociologically the episode is a treasure trove of lessons on how science should not be done. It checks off some standard "don'ts" in the practice of science. Don't fall prey to wishful thinking and confirmation bias that tells you exactly what you wanted to hear for years. Don't carry out science by press conference and then refuse to engage in debate in public venues. And of course, don't fail in providing extraordinary evidence when making extraordinary claims. If the original paper had been published cautiously and without hullabaloo, it would have become part of the standard scientific tradition of argument and counterargument. As it turned out, the publicity accompanying the paper made it a prime candidate for demolition by blogs and websites. If nothing it provided a taste of how one needs to be extra careful in this age of instant online dissemination. There's also some "do's" that deserve to be mentioned. The researchers did reply to criticism later and make their bacterial strains available to everyone who wanted to study them in a gesture of cooperation, but their earlier behavior left a bad taste in everyone's mouth and detracted from these later acts.

When the original paper came out, many of us were left gaping with eyes wide open at visions of DNA, ATP, phosphorylated proteins and lipids swirling around in a soup of arsenic, carrying out the exact same crucial biological processes that they were carrying out before without skipping a heartbeat. We just had a gut feeling that this couldn't be quite right, mainly because of the sheer magnitude of the biochemical gymnastics an organism would have to undergo in order to retool for this drastically different environment. Gut feelings are often wrong in science, but in this case it seems they made perfect sense.

What next? As often happens in science, I suspect that the defenders of the original paper will not outright capitulate but will fight a rearguard retreat until the whole episode drops off everyone's radar. But this paper here, it clinches the case for normal biochemistry as well as anything could. Good old phosphorus is still one of life's essential elements, and arsenic is not.

Phosphorus beats arsenic...by a factor of seventeen powers of ten

For all the implications about little green men and alien bacteria, the real question at the heart of the great arsenic controversy was essentially chemical: Can arsenic substitute phosphorus in the key biomolecules and metabolic processes of life and especially those in the GFAJ-1 bacteria? I and others referred to a classic paper published many decades ago by the eminent Harvard chemist Frank Westheimer which pointed out the instability of arsenates compared to phosphates. This is still the central chemistry-based question in everyone's minds. In a just accepted article in the journal ACS Chemical Biology, researchers in Missouri and Cairo provide a nice overview of the great challenges associated with substituting As in place of P in the backbone of DNA.

They start off by pointing to the similarities between the two elements; similar atomic size, pkA values (which would allow similar acid-base behavior) and electronegativities. These similarities would lead us to believe in the ready replacement of P by As, but that's where they end. From here on the devil is in the details.

Experiments have been conducted with model compounds approximating the phosphate diester backbone in DNA and its putative As counterpart. Firstly the authors note that the phosphodiester backbone is really stable to hydrolysis (the cleavage of the bonds by water), so stable in fact that it's difficult to measure its rate of hydrolysis in DNA because of the slow rate of the reaction. This has led to many studies performed on model compounds where the two linkages to sugars in the DNA backbone have been replaced by suitable alkyl groups. These studies have measured the half-life of the phosphate diester linkage. The half-life of a reaction measures the time taken for half the reaction to finish and is a very convenient tool for quantifying its rate; in case of the phosphate diester compounds, it turns out to be a whopping 30,000,000 years. This is a huge achievement if you consider the very high concentration of water in cells which is 55 M. As the authors say, this means that only two out of the 3 billion base pairs in the DNA from a human cell are expected to undergo spontaneous, uncatalyzed hydrolysis per week. It is a testament to the amazing power of catalytic enzymes that this reaction is brought within reasonable time frames in biological systems. While the results from the model system constitute an extrapolation to DNA, it's a reasonable one since the accessibility of the P to attack by water in the model compounds is similar to that in DNA.

The corresponding arsenic diesters present a scenario that's out of the ballpark. The half-life of the model arsenate diesters is no more than 0.06 seconds which corresponds to a difference of a factor of 10¹⁷ between the two. This is an absurdly large number; as just one comparison, it exceeds the number of cells in the typical human body by a factor of ten thousand. Error bars will do nothing to change it. In fact the hydrolysis of arsenate diesters is so fast that this fact has been used productively by scientists who want to study the kinetics of phosphate containing molecules but who are thwarted by the extremely slow nature of the reaction; substitute the P with As and you get a system which will otherwise be similar but which will transform itself rapidly into the desired products. What biology abhors, chemists can adore.

The magnitude of the problem is driven home by the calculation that with this rate of hydrolysis, half of all the arsenodiester linkages in the DNA of the GFAJ-1 bacterium would be cleaved in less than a tenth of a second. In addition there are other problems with As. As the authors note, As can also change its oxidation states more easily compared to P. The oxidation state of As and P in the DNA backbone is +5. But unlike P, As can undergo ready enzymatic conversion to a +3 oxidation state. Compounds containing As +3 are even more unstable than those containing As +5.

Now does this mean that organisms substituting As for P cannot exist? No. But as basic chemistry demonstrates, this would present very great challenges of stability. As indicated, there could be possible solutions to this problem such as dehydrating conditions containing very little water or the presence of special proteins that stabilize DNA and shield it from water. But it's clear that any such extremely novel ideas would be speculative at best until supported by evidence.

I hate quoting Carl Sagan all the time but his statement about extraordinary claims requiring extraordinary evidence is a cliche because it's true.

Fekry, M., Tipton, P., & Gates, K. (2011). Kinetic Consequences of Replacing the Internucleotide Phosphorus Atoms in DNA with Arsenic ACS Chemical Biology DOI: 10.1021/cb2000023

Aliens, arsenic and alternative peer-review: Has science publishing become too conservative?

In 1959, physicists Philip Morrison and Giuseppe Cocconi advanced a hypothesis about how we could detect signals from extraterrestrial civilizations. The two suggested monitoring microwave signals from outer space at the frequency of 1420 MHz. This frequency is the frequency of neutral hydrogen, the most abundant element in the universe and one which aliens would likely harness for communication. The paper marked the beginning of serious interest in searching for extraterrestrial life. A year later, Freeman Dyson followed up on this suggestion with an even more fanciful idea. He conjectured that a sufficiently advanced civilization might be able to actually disassemble a planet the size of Jupiter and use its parts to create a shell of material that would surround the parent planet’s solar system. This sphere would capture solar energy and allow civilizations to make the most efficient use of all such energy. The most telling signature of such an advanced habitat would be an intense infrared signal coming from the sphere. Thus Dyson recommended looking for infrared signals in addition to radio signals if we were to search for aliens. The sphere came to be known as a ‘Dyson sphere’ and became fodder for a generation of science fiction enthusiasts and Star Trek fans.

These two ideas and especially the second one sound outrageous and highly speculative to say the least. Can you guess where both were published? In the two most prestigious science journals in the world; the Morrison paper was published in Nature while Dyson published his report in Science. This was in 1960. I can say in a heartbeat that I don’t see similar ideas being published in these journals today, and this is a situation which we all should regret.

I bring up this issue because I think it indicates the significant changes in attitude about publishing novel scientific ideas that have occurred from 1960 to the present. In 1960 even serious journals like Nature and Science were open to publishing fanciful speculation, provided it was clearly enumerated. Now the demands for publishing have become more stringent, but also more narrowly defined. While this may have led to the publishing of more ‘concrete’ science, it has also dissuaded researchers from venturing out into novel territory. Most importantly, it has led the scientific community to put an unnecessarily high premium on ideas being right rather than interesting.

Science progresses not by being right or wrong but by being interesting. Most scientific ideas in their infancy are tentative, unsubstantiated and incomplete. Yet modern scientific publishing and peer review largely discourage the presentation of these ideas by insisting on convincing evidence that they are right. In most cases this emphasis on accuracy and complete validation is necessary to save science from itself; we have seen all too many cases of pseudoscience that looked superficially plausible but which turned out to be full of holes. Science usually plays it safe by insisting on unimpeachable evidence. But in my opinion this stringent self-correcting process has gone too far, and in our desire to err on the safer side we have erred on the extreme side. This is having a negative impact on what we can call creative science. The insistence on foolproof data and the public censure that researchers would face if they don’t provide it is deterring many scientists from publishing provocative results that are still in the early stages of gestation. Demands for conservative presentation are also accompanied by conservative peer review since reviewers fear backlash as much as authors. All this is unfortunate and is to the detriment of the very core of scientific progress, since it’s only when provocative ideas are published can other researchers validate, verify and refute them.

The furor about the recent paper on “arsenic-based” life brings these issues into sharp focus. Much of the hailstorm of criticism would have been avoided if the standards and formats of scientific publishing allowed the presentation of ideas that may not be fully substantiated but which are nonetheless interesting. By now we are all familiar with the torrent of criticism about the paper that has come from all quarters, from blog posts to opinions from well-known experts. What is clear is that the experiments done were shoddy and controls were lacking. But the criticism is detracting from the potential value of the paper. Irrespective of whether the claims of arsenic actually being incorporated in the bacterium’s replicative and metabolic machinery are true, the paper is undoubtedly interesting, if only as an example of a hitherto unknown novel extremophile. Yet it is in danger of simply being forgotten as one of the uglier episodes in the history of science publishing.

There is in fact a solution to this problem, one which I have been in favor of for a long time. What if there was a separate section specifically devoted to relatively far-fetched ideas and this paper had been published in that section? The paper would then likely have been taken much less seriously and its tenets would have been accepted simply as thought-provoking observations pointing to further experimentation rather than established facts. So here’s my suggestion; let the top scientific journals have a separate section entitled ‘Speculation’ (or perhaps ‘Imaginings’) which allows the presentation of ideas that are fanciful and speculative. The ideas proposed could range from purely theoretical constructs to the documentation and interpretation of unusual experimental observations. The only requirement is that they should be unorthodox and interesting, backed up by more or less known scientific principles, clearly defined and enumerated and contain testable hypotheses. Let there be a second type of peer-review process for these ideas, one which is as honest as the primary process but more forgiving of the lack of foolproof evidence.

The idea about Dyson spheres would fit in nicely in such a section. Another example that comes to my mind is an idea proposed by the biophysicist Luca Turin. Turin conjectured that we may smell molecules based not on their shape but on the vibrations of their bonds. The history of this idea is interesting since others had already proposed it earlier in respectable journals. Turin actually wrote it up and sent it to Nature. Nature deliberated for an entire year and rejected the paper. In this case Nature should at least be commended for taking so long and presumably giving careful consideration to the idea, but the point is that they wouldn’t have had a problem publishing it in a ‘Speculation’ section right away. Turin’s idea was interesting, novel, highly interdisciplinary, enumerated in great detail and backed up by well-known principles of chemistry and spectroscopy. It satisfied all the criteria of a novel scientific idea that may or may not be right. Turin finally published in a journal which only specialists read, thus precluding the concept from being appreciated by an interdisciplinary cross-section of scientists. There is now at least some evidence that his ideas may be right.

Interestingly, there is at least one entire journal devoted to the publication of interesting hypotheses. This is the journal ‘Medical Hypotheses’. Medical Hypotheses prominently lacks peer review (although they have instituted some peer review recently) and has occasionally come under fire for publishing highly questionable papers, such as those criticizing the link between HIV and AIDS. But it has also served as a playground for the interaction of many interesting ideas. The editorial board of Medical Hypotheses features highly respected scientists like the neurologist V S Ramachandran and the Nobel Prize winning neuroscientist Arvid Carlsson. Ramachandran himself has iterated the need for such a journal. Science and Nature merely have to devote a small section in each issue to the kinds of ideas that are published in Medical Hypotheses, perhaps with a higher standard.

It’s worth reiterating Thomas Kuhn’s notions of paradigm shifts in science here. Scientific paradigms rarely change by playing it safe. Most scientific revolutions have been initiated by bold and heretical ideas from maverick individuals, whether it was Darwin’s ideas about natural selection, Einstein’s thoughts about the constancy of the speed of light, Wegener’s ideas about continental shift or Bohr’s construction of the quantum atom. Not a single one of these ideas was validated by foolproof evidence when it was proposed. Many of them sounded outright bizarre and counter-intuitive. But it was still paramount to bring these ideas to a greater audience. Only time would tell whether they were right or wrong, but they were undoubtedly supremely novel and interesting. And almost all of them were published by leading journals. It was the willingness to entertain interesting ideas that made possible the scientific revolutions of the twentieth century. It seems to be a strange historical anomaly to find journals much more prone to publishing speculative ideas a hundred years ago than today. Today we seem to worship the safety of truth at the expense of the uncertain but bold reaches of novelty.

Of course, the existence of a second-tier of publication and peer review would undoubtedly have to be carefully monitored. There is after all a thin line between reasonable speculation and pseudoscience. The reviewers in this tier would have to pay even more careful attention than they usually do to ensure that they are not pushing baseless fantasies. But as we have seen in the case of the vibrational theory of smell and the case of arsenic-loving bacteria, it’s not that hard to separate legitimate science with uncertain truth value from mere storytelling.

Once the ground rules are established and the initial obstacles are overcome, the second tier of peer review would have many advantages apart from encouraging the publication of speculation. It would also make reviewers more comfortable in recommending publication; since the ideas are speculative anyway, they would not insist on complete verification and would not fear backlash if the ideas they had reviewed turn out to be wrong. Journal editors would similarly find it easier to approve publication. And the scientific community at large perhaps would not be as critical as it has been in the case of the recent paper because it too would accept the proposed ideas not as declarations of truth but as tentative exploration. But the greatest beneficiaries of the improved system would undoubtedly be the publishing scientists. Their minds would be much freer to dream and they would fear much less retaliation from the community for daring to do this. Most importantly, unlike the recent case, they would not be under pressure to make statements whose implications exceed the objective factual implications of their claims, and they would be happy to just present the claims as interesting observations that point the way towards further experiments.

Science progresses by being the ultimate free-market of ideas; this has led to it being a highly social process where scientists build on each other’s work. But for this social process to work the ideas must be liberated from their initial nebulous beginnings. Ideas in the scientific marketplace come in different flavors, from boring and established to interesting and maverick. The current scientific publication and peer-review process imposes a straitjacket that ideas have to fit in in order to be ‘pre-selected’ for entry into this market. This keeps out some of the most interesting ideas and more importantly, dissuades thinkers from even pursuing them in the first place. The straitjacket does serve the valuable purpose of filtering flotsam but it is also filtering out too many other interesting things. Science is too haphazard and full of unexpected twists and turns to be entrusted to rigid rules of review and publication. We need to accept the liability of occasionally having a dubious idea published in order to keep open the possibility of also giving novel beginnings a public platform; the beauty of science is that the bonafide dubious ideas automatically get weeded out through scrutiny and so we should not have to worry about too many of them going on extended rampages. But the potentially good ideas can only be fleshed out by other scientists when they are allowed to be exposed to criticism, appreciation and ridicule. Even if the ideas themselves ultimately sink, they may serve as spores which lead to the germination of other ideas. And it is the germination of these other ideas that gets transformed into trees of scientific discovery.

We are all sheltered, invigorated and inspired by the branches of these trees. Let’s give them an opportunity to grow.

Medicine! Poison! Arsenic! Life itself!

A few months back when the Nobel Prize for chemistry was announced, a few observers lamented that unlike physics and biology, perhaps chemistry does not have any 'big' questions to answer. So here's a question for these skeptics. What branch of science has the biggest bearing on the discovery of an organism that utilizes arsenic instead of phosphorus? If you say "biology" or "geology" you would be wrong. The essential explanation underlying today's headline about an arsenic-guzzling bacterium is at the chemical level. The real question to ask is about the key molecular mechanisms in which arsenic substitutes phosphorus. What molecular level events enable this novel organism to survive, metabolize and reproduce? Of course the discovery is significant for all kinds of scientists including biologists, geologists, astronomers and perhaps even philosophers, but the essential unraveling of the puzzle will undoubtedly be at the level of the molecule.

Many years back I read a classic paper by the late Harvard chemist Frank Westheimer called "Why Nature Chose Phosphates". In simple and elegant terms, Westheimer explained why arsenic cannot replace phosphorus and silicon cannot replace carbon in the basic chemistry of life. In a nutshell, phosphates have the right kind of acid-base behavior at physiological pH. The single negative charge in phosphates in DNA hinders nucleophilic attack by water and hydrolysis without making the system so stable that it loses its dynamic nature. Arsenates, simply put, are too unstable. So are silicates.

And yet we have an arsenate-metabolizing bacterium here. Arsenic, the same stuff that was used in outrageous amounts in Middle-Age medicines and which later turned into the diabolical murderer's patent weapon of choice makes a new appearance now as a sustainer of life. First of all let's be clear on what this is not. It's not an indication that "life arose twice", it does not suddenly promise penetrating insight into extraterrestrial life, it probably won't win its discoverers a Nobel Prize and in fact it's not even technically speaking an 'arsenic-based life form'. The bacteria were found in a highly saline and alkaline lake with a relatively high concentration of arsenic where they were happily using conventional phosphorus-based chemistry. The fun started when they were gradually exposed to increasing concentrations of arsenic and increasing dilutions of phosphorus. The hardy little creatures still continued to grow.

But the real surprise was when the cellular components were analyzed and found to contain a lot of arsenic and very little phosphorus, certainly too less to sustain the metabolic machinery of life. If true this is a significant discovery, although not too surprising. Chemistry deals with improbabilities, not impossibilities. Life forms utilizing arsenates were conjectured to exist for some time, but such total substitution of arsenic for phosphorus was not anticipated.

If validated the work raises fascinating questions, not about extraterrestrial life or even about life's origins, but more mundane and yet probing ones about the basic chemistry of life. I haven't read the original paper in detail yet, but here are a few thoughts whose confirmation would lead to new territory:

1. The best thing would be to get a crystal structure of arsenic-based DNA. That would be a slam dunk and would really catapult the discovery to the front ranks of novelty. The second-best thing would be to do experiments involving labeled phosphorus and arsenic, to find out the exact proportion of arsenic getting incorporated. Which brings us to the next point.

2. How much of the cellular components are trading phosphorus for arsenic? Life's molecules are crucially dependent on phosphate. Not just DNA but signaling molecules like kinases and AMP are phosphorus-based. And of course there's ATP. What is fascinating to ponder is whether all of these key molecules traded phosphorus for arsenic. Perhaps some of them like DNA are using arsenic while others keep on using phosphorus. Checking the numbers and concentrations left over would certainly help to decide this.

One thing that should be confirmed and re-confirmed beyond the slightest shade of doubt is that there is absolutely no phosphorus hanging around which would be sufficient to sustain basic life processes; the entire conclusion depends on this fact. Traces of phosphorus can come from virtually anywhere; from the media (no, not the journalists, although it could come from them too), from human bodies, from laboratory equipment. A rough analogy from chemistry comes to mind; we have seen in the past how 'transition metal-free' reactions turned out to be catalyzed by traces of transition metals. If life is pushed to the brink by decreasing the phosphorus levels in its environment, the first thing we would expect it to do would not be to use arsenic but to scavenge the tiniest amounts of vital phosphorus from its environment with fanatic efficiency. It's interesting to note that the phosphorus concentrations being measured are in femtograms, which means that the error bars need to be zealously monitored. If it turns out that there is enough phosphorus to sustain a core cycle of essential processes while others are utilizing arsenic, the conclusions drawn would still be interesting but not as revolutionary as the current ones, and we probably won't be calling it an 'arsenic-based' life form then. In any case, my guess is that the utilization of phosphorus was selective and not ubiquitous. Organisms rarely utilize all-or-none principles and usually do their best under the circumstances.

If arsenic is truly substituting phosphorus in all these signaling, genetic and structural components, that would really be something because it would create more questions. By what pathways does arsenic enter these molecules? How does it affect the kinetics of reactions involving them? And most important are questions about molecular recognition. There are hundreds of proteins that recognize phosphorylated protein residues and similar other molecules. Do all these proteins recognize their arsenic containing counterparts? If so, is this the result of mutations in most of these proteins?; it seems hard to imagine that simultaneous mutations in so many biomolecules to make them recognize arsenic would result in viable living organisms. A more conservative explanation is that most of these molecules don't mutate but still recognize arsenic, albeit with different specificities and affinities that are nonetheless feasible for keeping life's engine chugging. The molecules of life are exquisitely specific but they are also flexible and amenable to changing circumstances. They have to be so.

3. And finally of course, how does the protein expression systems of the bacteria cope with arsenic-based DNA? As mentioned above, arsenates are unstable. To counter this instability does DNA expression simply get ramped up? How do proteins control the unpacking, packing, duplication and transcription of this unusual form of DNA? For starters, how does DNA polymerase zip together arsenated nucleotides for instance? How does the whole thing essentially hold together?

There are of course more questions. Whatever the implications, this is an interesting discovery that would keep scientists busy for a long time. Like all truly interesting scientific discoveries it asks more questions than it answers. But ultimately it should come as no surprise. The wonders of chemistry combined with those of Darwinian evolution have allowed life to conquer unbelievably diverse niches, from methane-riddled environments to hot springs to sub-zero temperatures. In one way this discovery would only add one more feather into the cap of a robust and abiding belief- that life is tough. It survives.

Selenium for sulfur should be next (but I wouldn't wait around for silicon...)

Update: Two first-rate rebuttals to the paper. One is an outstanding and meticulously detailed piece by University of British Columbia microbiologt Rosie Redfield. The other one is a Scienceblogs post. Basically the question keeps coming back to whether there could have enough phosphorus for survival. It's worth noting the application of Occam's Razor here. If bacteria which normally metabolize phosphorus were challenged with an arsenic-rich and phosphorus-poor environment, what would they first do? Start incorporating arsenic in their basic biochemistry or intensely adapt their life processes so that they zealously start sequestering and utilizing the smallest traces of the vital phosphorus? Occam's Razor and everything that we know about evolution suggests the latter.

Wolfe-Simon, F., Blum, J., Kulp, T., Gordon, G., Hoeft, S., Pett-Ridge, J., Stolz, J., Webb, S., Weber, P., Davies, P., Anbar, A., & Oremland, R. (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus Science DOI: 10.1126/science.1197258

Score for the British

"Using a small nuclear reactor at Pavia, in northern Italy, the researchers subjected hairs said to have been taken from Napoleon at different stages in his life to eight hours of irradiation. They found arsenic levels even higher than previously suggested; "a hundred times the average found in hair today," said Adalberto Piazzoli, who led the study.

But by testing other samples, including locks of hair taken from Napoleon's wife, Joséphine, the team discovered that such levels were normal. "The environment in which people were immersed at the start of the 19th century evidently led to the ingestion of quantities of arsenic that we would consider dangerous today," Piazzoli said. Possible sources included "dyes, glues and the smoke from wood fires," Angela Santagostino, a toxicologist, told the daily La Stampa."

Ok, one French blow to British character retracted. But what about Napoleon's own trusted friend Marquis De Montholon who was also a prime suspect? The story of Napoleon's possible assassination by arsenic was one of the tales that got me interested in science. Sten Forshufvud, the Swedish dentist who investigated this did some classic and absolutely fascinating detective work that was described in The Murder of Napoleon. I need to go back to his book; it seems unlikely that he didn't think of running others' hair through a mass spec as a control.