12 ms·

Microbes use arsenic in their DNA: Proves phosphorus is not required for life

208 points by roadnottaken 16y ago

RiderOfGiraffes 16y ago
Choose your news source for this story: http://news.ycombinator.com/item?id=1962894 http://news.ycombinator.com/item?id=1962894 - go.com http://news.ycombinator.com/item?id=1962893 http://news.ycombinator.com/item?id=1962893 - nytimes.com http://news.ycombinator.com/item?id=1962846 http://news.ycombinator.com/item?id=1962846 - nature.com http://news.ycombinator.com/item?id=1962696 http://news.ycombinator.com/item?id=1962696 - longislandpress.com http://news.ycombinator.com/item?id=1962386 http://news.ycombinator.com/item?id=1962386 - gizmodo.com http://news.ycombinator.com/item?id=1962200 http://news.ycombinator.com/item?id=1962200 - gizmodo.com http://news.ycombinator.com/item?id=1962110 http://news.ycombinator.com/item?id=1962110 - google.com http://news.ycombinator.com/item?id=1957823 http://news.ycombinator.com/item?id=1957823 - skymania.com http://news.ycombinator.com/item?id=1953228 http://news.ycombinator.com/item?id=1953228 - kottke.org
civilian 16y ago
Huh! Biochemistry major here... So I guess that the bacteria just rarely uses Sulphur-Sulphur (thiol) bonds in it's proteins, since Arsenic has a high affinity for it (and that's what causes arsenic toxicity in everything else). http://en.wikipedia.org/wiki/Arsenic#Biochemical_basis_of_arsenic_toxicity http://en.wikipedia.org/wiki/Arsenic#Biochemical_basis_of_ar... "suggesting the possibility of a biochemistry very different from the one we know" Seems like a bit of an exaggeration, but news will be news. Thiols are important for the structure & enzymatic activity, but this bacteria is proof that there are ways around it. Besides that difference, I'm guessing they're the same.
- jaysonelliot 16y ago
  You don't think that the discovery of the first organism to use a different element than phosphorous is a big deal? Cynicism is cool and all that, but this sure sounds like big news to me.
  - sandipc 16y ago
    it's a really big deal... provided the arsenic is actually incorporated into nucleic acids, and the bacteria aren't just surviving on background levels of phosphate. it will be interesting to read the original paper when it comes out in Science later today, and not just accounts of the paper from other sources
  - deleted 16y ago
    [deleted]
  - dnautics 16y ago
    *you don't think the discovery of the first organism to use a different element than sulfur was a big deal? Oh wait, we all do it. http://en.wikipedia.org/wiki/Selenocysteine http://en.wikipedia.org/wiki/Selenocysteine
  - dotBen 16y ago
    it would be a much bigger deal if that element was a replacement for carbon :P
- paraschopra 16y ago
  I'm sure DNA physical structure (angles, bends, etc.) with Arsenic instead of Phosphorous won't be exactly same. Arsenic has same tetrahedral structure as Phosphorous but the atom is sure bigger in size and at DNA scales, size would play a large role in determining shape of molecule. I'm sure you realize that physical interactions play a great role in a cell.
  - dnautics 16y ago
    you would think, but there's also: http://en.wikipedia.org/wiki/XDNA http://en.wikipedia.org/wiki/XDNA It's true that the subtle loss of a hydroxyl group leads to all sorts of differences between RNA and DNA (RNA likes to be single-stranded more than DNA does) but there's TNAs (unfortunate acronyms) and PNAs (not to be confused with PNAS) and other things that basically work and look like DNA with fairly un-subtle changes. Furthermore, Arsenic really isn't THAT much bigger than Phosphorus (vdw radius 1.85 vs 1.80; covalent radius 1.19 vs 1.06).
- crocowhile 16y ago
  Yes, beside the fact that they found a way to change the structure of their DNA, RNA, and a few hundreds enzymes involved in energy metabolism they are the same... This is so huge that my money go into a mistake: I bet these bacteria just found a way to either get rid of arsenic or to neutralize its allosteric toxicity by maskerading or something. The paper is not out yet so I cannot give my opinon on the experimental data but from what I read there is no evidence that DNA actually contains arsenic and until that arrives I believe it's a red herring.
  - mechanical_fish 16y ago
    It does seem overwhelmingly likely to be a mistake. But an exciting one! Biochemistry sports fans like myself will watch with interest. EDIT: Hey, my upvote voted you down by mistake! Somebody upvote the parent, please.
  - roadnottaken 16y ago
    "from what I read there is no evidence that DNA actually contains arsenic" FTFA: "When the researchers added radio-labelled arsenate to the solution to track its distribution, they found that arsenic was present in the bacterium's proteins, lipids and metabolites such as ATP and glucose, as well as in the nucleic acids that made up its DNA and RNA. The amounts of arsenate detected were similar to those expected of phosphate in normal cell biochemistry, suggesting that the compound was being used in the same way by the cell. The team used two different mass-spectrometry techniques to confirm that the bacterium's DNA contained arsenic... Analysis with laser-like X-rays from a synchrotron particle accelerator indicated that this arsenic took the form of arsenate, and made bonds with carbon and oxygen in much the same way as phosphate." It sounds like there IS some evidence...
    - crocowhile 16y ago
      The author themselves are tyring to explain to you that "Our data are strongly suggestive of arsenic replacing phosphorus". Where suggestive =!= evidence. Plus, read the paragraph "A world of possibilities" to see why so(FTFA). There is no evidence. There are results that are compatible with that and other scenarios. Science is not so easy as you wish it was.
jaysonelliot 16y ago
Felisa Wolfe-Simon's name is going to end up in the history books along with Leeuwenhoek and Darwin. Talk about a life-changing discovery!
- spot 16y ago
  Maybe but not for this work. This wasn't the 2nd origin of life story that was predicted.
  - mechanical_fish 16y ago
    Yes, the touchstone of everyone's work should be how well it compares to the figments of one's imagination. Poor Einstein! If only he'd discovered warp drive, he'd be as famous as Zephraim Cochrane!
    - TheSOB88 16y ago
      I think it's more that this isn't very game-changing. Einstein revolutionized physics with relativity; Darwin revolutionized biology. What does this discovery revolutionize? Biochemistry perhaps, but it seems a bit too specific to have far-reaching impacts.
    - badkungfu 16y ago
      Wow, snarky. I had the same impression. This sounds really, really cool but it's still an organism that uses DNA, and we're still related to it. As a layperson, I don't see why this says a lot more about the potential for life elsewhere. If it's not a wholly new occurrence of life, then it's something that "did life" the same way we do until it happened to need this really cool adaptation. I understand that my lack of biology training probably contributes to my not getting it, but that's where most people are coming from. A lot of time has been spent explaining the significance of Einstein's work and most people still don't "get it", we may need the same here. So, instead of snarking...explain again/better/differently than others have.
      - cryptoz 16y ago
frisco 16y ago
This seems silly. Phosphorous not being required for life seems obvious to me: ok, maybe it's believed to be used in all Earth-originated, carbon-based life, but why would we believe a priori that it's an absolutely necessary component of any biological life anywhere (which seems to be what's implied by NASA and the relation of this to exobiology)? If we develop silicon-based artificial intelligence (how do you define life, anyway? That matters when you're talking about astrobiology), would we run a headline, "Researchers prove carbon not required for life"? I've always thought the scientific community stated that alien life may use a totally different biochemistry from us? Edit: so, in some senses this is like P!=NP being proven, except less important, since it's only one component (phosphorus). It's scientifically a big deal but doesn't change the world because it's largely what we've always expected (the metaphor breaks down that this doesn't have the major secondary consequences like N=NP would).
- davidsiems 16y ago
  http://lesswrong.com/lw/im/hindsight_devalues_science/ http://lesswrong.com/lw/im/hindsight_devalues_science/
  - frisco 16y ago
    I don't think this is hindsight bias though. As a scientist (not in biochemistry or astrobiology, though) I understand this had to be specifically shown, but this is one of those things that most people I talk to and I have always just casually treated as obvious. The confirmation is important scientifically, but shouldn't change our viewpoint, since it's what we've always expected. Am I wrong here? Any computational biologists or biochemists want to tell me this wasn't expected at all?
    - varjag 16y ago
      You can argue that possibility of alien life is also quite a common idea. Yet a confirmation of that would be considered a major scientific breakthrough.
      - 16y ago
sorbus 16y ago
"The researchers isolated the organism and found that when cultured in arsenate solution it grew 60% as fast as it did in phosphate solution — not as well, but still robustly. The culture did not grow at all when deprived of both arsenate and phosphate."
akharris 16y ago
Two weeks ago: antimatter contained long enough to be studied. This week: life without phosphorous. Next week: flying skateboards?
- cryptoz 16y ago
  I think the first artificial, human directed production of antimatter was by CERN in 1995. I'm not sure what you mean by "two weeks ago", but antimatter has been around a lot longer than that.
  - akharris 16y ago
    Two weeks ago, CERN made the announcement that they had contained antimatter long enough (at LHC) to study it properly. First time it's ever been done that well. Pretty stunning accomplishment.
    - cryptoz 16y ago
      Ah, right! Thanks
- prawn 16y ago
  On flying skateboards, we were wondering the other day in the office about Parrot-style drones that you could hang from: http://www.blogcdn.com/www.engadget.com/media/2010/01/parrot-ar-drone-03.jpg http://www.blogcdn.com/www.engadget.com/media/2010/01/parrot... Risky, but I'd try it!
TheSOB88 16y ago
Why people constantly stick to the idea that all possible organisms must have similar biochemistry to us is beyond me. Think about it: Out of the humongous search space of chemicals, the ones we use happened to work for us. A combination of randomness and building on what worked before got us to where we are. Why should life not be able to use chemistry in completely different ways in order to replicate itself? Why are we so arrogant as to think that our design is the only design? Edit: My point is that our ratio of "shit we know" to "shit we don't know we don't know" is infinitesimally small in the field of possible lifeforms' biochemistry. That is, we only know stuff very close to us on a cosmic scale; we effectively have blinders to all other possibilities. And there's already a lot of biochemical variation on Earth: To give some small examples, viruses don't even have DNA, and plants use less amino acids than animals. The self-similarity of what we have so far can be explained, I think, by evolution. We all started out from the same point, so there's very little incentive to "reinvent the wheel" as it were. Only under extreme conditions like we have here, or the geothermal vents underwater, do we observe marked differences.
- cryptoz 16y ago
  > Why are we so arrogant as to think that our design is the only design? We're not. Nobody is. The reason scientists don't look for life on other planets that is made of other chemicals is that we may not be able to recognize that as life. It's much better - read, scientific - to look for something we can recognize. Also, there are chemical properties of the elements that make up life on Earth that allow for fast reactions, bonding, etc. Most of the rest of the elements in the periodic table react more slowly in normal conditions, making the process for life less likely. Not impossible. Just less likely. We think. So we focus on looking for what we know about. That's the best way to do it. Nobody worth their degree will ever claim that our "design" (bad word choice, by the way) is the only one.
  - TheSOB88 16y ago
    I wasn't trying to address any bearing this has on finding alien life, just speaking theoretically - we shouldn't assume that everything should be like us. If it hasn't been your experience that most people think that way, then I must have misjudged. I agree on the second paragraph, but especially the last sentence. I know "design" is used by IDers, but what other word can adequately reference the incredibly complicated way our cells and bodies work? Thanks for the response.
dnautics 16y ago
I don't know. You would think, but you can autoclave a solution of "deionized ultrafiltered water" which should have "no" carbon in it at all, and bacteria will find a way to grow in it if you get it contaminated, they will concentrate the trace trace trace amounts of carbon. How carefully did they prep their DNA? These days nobody is careful and they use these crap kits which are good enough, convenient enough to get molecular biology done. The other day in lab I suggested someone isolate DNA using caesium chloride gradient ultracentifugation and the only people who knew what I was talking about were the two old (70+) year old senior scientists but they agreed that it was the way to go.
drcode 16y ago
OK, this news is very interesting, but it does not prove much about extraterrestrial life. We know that organisms can adapt to their environment. Incorporating some fraction of arsenic into a cell's dna is an example of such adaptation. The question that really matters is "has life originated more than once in the universe?" This experiment has no bearing on that: They took a standard terrestrial cell, with a carbon-based history, and simply subjected it to some new conditions. This is NOT a new life form that originated from a novel environment and using a different chemistry. However, NASA is getting awfully close to selling it as such in their press conference, which is misleading.
- jpwagner 16y ago
  I think this finding deserves a bit more respect. Of course it does not answer ALL of our questions, but it proves DNA does not need phosphorus! AMAZING!
  - Archaeum 16y ago
    I agree that this is remarkable, but I think it's valid to criticize publicizing the finding as an astrobiology discovery, which is exactly what NASA (or its public relations department, at any rate) is calling it--and which it is not, despite its implications for astrobiology. If we care about engaging the public, we should be concerned about sensationalism that detracts from the solid work of the scientists. If you cause people to think you're going to show them extraterrestrial life, fairly or not, you run the risk of them tuning out when the reality is less flashy, even if it's groundbreaking.
    - jpwagner 16y ago
      I couldn't disagree more. Astrobiology researchers made this finding. If you think it's not astrobiology take it up with NASA.
      - Archaeum 16y ago
        I'm surprised by the strong objection. I understand that the lead scientist is with the NASA Astrobiology Institute, but I still think that despite the important implications for astrobiology, calling it astrobiology is questionable. If neither NASA nor any astrobiologists had been involved, exactly the same results could have been obtained, and the astrobiology connection (though it might be played up because it is an interesting angle) would more clearly be incidental. In other words, I don't think you lose any accuracy or diminish the finding by referring to it as biological rather than astrobiological. That said, I'm not sure I really want to get caught up on "biology" versus "astrobiology" as terms. I think the greater point (or at least the point I was trying to make) is about communicating clearly and managing expectations. When you say astrobiology or exobiology, invariably some people are going to cry, "What, no aliens? You tricked me!" If that indignance prevents them from trying to understand the importance of the story, should we even bother trying to cater to them? I don't have a good answer for that. Without raising the idea of extraterrestrial life, they might not have been engaged at all. It's just something for those involved in public outreach to be aware of.
RiderOfGiraffes 16y ago
Official announcement: http://news.ycombinator.com/item?id=1963296 http://news.ycombinator.com/item?id=1963296
bradfordw 16y ago
It has its own twitter account! https://twitter.com/#!/ArsenicBacteria https://twitter.com/#!/ArsenicBacteria
- cryptoz 16y ago
  s/it's/its
cstross 16y ago
As Mono Lake is of volcanic origin and formed around 760,000 years ago (per Wikipedia) I'd be astonished if the arsenophile(?) evolved there in that short a time span. Which leaves open the question of where it came from, and whether arsenic tolerance is present but dormant in other extremophiles. Other points of note: never mind the cellular DNA integrating arsenate, the whole respiration cycle seems to be affected, presumably running on ATA rather than ATP. Which implies huge amounts of molecular booty in the shape of enzymes that are powered by a different reduction gradient (ATA-AMA rather than ATP-AMP). Possible down to earth applications? Lest we forget, Pakistan has a monstrous problem with arsenic-contaminated wells ( http://www.irc.nl/page/16331 http://www.irc.nl/page/16331 ) and a bacterial culture that thrives on arsenic could offer new approaches to arsenic sequestration. And that's just off the top of my head. (My biochemistry is, alas, too rusty to go much further without a refresher course. Hmm ...)
- jacquesm 16y ago
  If a bacterium consumes the arsenic from a contaminated well the well is now contaminated with the corpses of bacteria that are rich in arsenic. You'd have to add another pass to get rid of the bacterial residue (possibly easier, but still).
  - enjo 16y ago
    Doesn't that depend on the byproduct produced by the respiration cycle?
    - jacquesm 16y ago
      Apparently they accumulate it.
  - sudont 16y ago
    Possibly a small sludge pond that would filter the water through as per a sewage treatment plant? I'm thinking that if it's in the wells, it's due to the solvent action of water on the rocks, and cleaning out the wells would only be a temporary solution.
roadnottaken 16y ago
Here's the article from Science: http://www.scribd.com/doc/44550217/Science-2010-Wolfe-Simon-Science-1197258 http://www.scribd.com/doc/44550217/Science-2010-Wolfe-Simon-...
stavrianos 16y ago
bicycle discovered constructed entirely from wood: proves metal not required for transportation http://www.leevalley.com/newsletters/woodworking/2/3/article1-1.jpg http://www.leevalley.com/newsletters/woodworking/2/3/article...
- anigbrowl 16y ago
  We already knew that because we have had wooden boats, carts, and planes (gliders).
  - jjs 16y ago
    You're missing the point—this is the single greatest discovery in exobicyclology since E.T.!
    - anigbrowl 16y ago
      Tee-hee - it's true that these NASA announcements are often a bit of an anticlimax, but I suppose that's the price of having so much science-fiction to enjoy. Oddly enough,the first bicycles were actually made out of wood - they were called velocipedes and today we call them balance bikes. Like scooters, they were powered by pushing feet along the ground. I was going to link to an amusing site about these, but while looking it up I was surprised to discover that there are in fact modern bicycles mostly made from wood, although they're quite expensive: http://www.renovobikes.com/ http://www.renovobikes.com/ ...so I wasn't as well well-informed as I thought I was.
bld 16y ago
Here's the press conference in three ~10 minute parts: Part 1: http://www.youtube.com/watch?v=hu5dXnCUs7I http://www.youtube.com/watch?v=hu5dXnCUs7I Part 2: http://www.youtube.com/watch?v=0LsihAsX4z8 http://www.youtube.com/watch?v=0LsihAsX4z8 Part 3: http://www.youtube.com/watch?v=Nu0VvxuicLw http://www.youtube.com/watch?v=Nu0VvxuicLw The lead author gives a talk at 2:26 in Part 1 that I thought was an excellent example of how to communicate science (or other technical subject) and implications to a general audience.
olalonde 16y ago
Most theories[1] agree to say that replicating life predates DNA. Wouldn't that mean that we could still have a common ancestor with this life form? [1] http://en.wikipedia.org/wiki/Abiogenesis#Other_models http://en.wikipedia.org/wiki/Abiogenesis#Other_models
- joelburget 16y ago
  We not only could have a common ancestor, it seems to me to be almost certain. What are the chances that some other life has evolved with DNA completely independently
  - olalonde 16y ago
    I second, but that's what the first article posted on HN seemed to suggest. http://skymania.com/wp/2010/11/alien-life-form-is-here-on-earth.html/ http://skymania.com/wp/2010/11/alien-life-form-is-here-on-ea...
  - yread 16y ago
    Why do you consider it certain? It could have just died off being much less efficient than us.
    - joelburget 16y ago
      Well, DNA is fairly complex. Of all the elements and compounds life could involve it seems rather unlikely that DNA evolved in two places completely separately. Not impossible, but very unlikely.
      - dnautics 16y ago
        actually, no. DNA/RNA are in fact, just about the simplest chemical choices that can perform replication. Ribose, for example is the lowest energy pentafuranose, which means in a random mix of sugars you'll find ribose in the highest concentration. The funny thing is that the KSS principle seems to hold in nature, we've tried in the lab to design alternatives to DNA/RNA, and none of them seem to work quite so well. http://www.sciencemag.org/content/284/5423/2118.short http://www.sciencemag.org/content/284/5423/2118.short
joelburget 16y ago
Perhaps NASA should be more cautious about holding a press on astrobiology, and with a Science embargo. Clearly everyone will immediately think of aliens, and for good reason. It's NASA, it's about astrobiology, and it's something big enough to embargo Science. They're just asking for all the alien stories. And let's be clear, these are not aliens.
- ugh 16y ago
  Holding a press conference for this pretty sweet discovery was completely justified. The language in the press release made it clear ahead of time that Nasa didn’t make any discovery related to life on other worlds, only a few overly eager bloggers spun crazy theories like that. Whoever is disappointed by this and claims that Nasa hyped too much doesn’t have her or his head screwed on right.
  - joelburget 16y ago
    I agree that it's an amazing discovery. Admittedly I didn't read the actual press release so you're probably right that they acted correctly. I only read second hand accounts of what they were going to announce.
dnautics 16y ago
high resolution Mass spec is such a shitty technique and is completely non-quantitative. How do you know that arsenic isn't associated with, say, a protein that makes the DNA resistant to being taken apart chemically. I will believe this result when they stain the DNA and run samples of the DNA down a density gradient ultracentrifugation and show that arsenic content in the media correlates with increased density of DNA, as you would expect if the arsenic is replacing phosphorus. If you don't know what i'm talking about, it's this classical experiment: http://en.wikipedia.org/wiki/Semiconservative_replication#Biophysical_evidence http://en.wikipedia.org/wiki/Semiconservative_replication#Bi... Here is my personal scientific experience speaking: If you see it everywhere, then it's likely to be an artefact. Clean up your technique, clean your instruments, and go back to an old school technique. Remember how the physicists who discovered CMB cleaned out the pigeon scat from their microwave horn telescope before they started to believe what they saw.
EGreg 16y ago
Don't mean to get all religious on ya, but I wanted to ask here... Is there any evidence of macro-evolution having ever taken place in recorded history? I'm asking this with no agenda, but curious. As far as I know, no new species have ever been produced, despite natural or unnatural selection. So what makes us say that there is no other force or process that causes speciation? How are scientists so convinced that mutation and natural selection is all that is required, despite never having observed a single instance of speciation? To be scientific, a theory has to make some potentially falsifiable, non-obvious predictions. Then we can test those predictions, and if our experiments confirm them then the theory survives. I totally agree that the hypothesis "natural selection occurs" has been proven in ample ways (ok, maybe the white->dark->white butterflies was a bad one, but bacteria and their resistance to antibiotics is proof enough). But to form a completely new species... Species is defined as "as a group of organisms capable of interbreeding and producing fertile offspring" according to Wikipedia. Two animals are of different species if none of their offspring have ever been observed to be fertile. At least, that's a good working definition. It bothers me that scientists have been interbreeding literally thousands of generations of fruit flies and despite all selection pressures, artificial or not, were never able to produce a single new species. Sure, it's hard to try and mate every fruit fly with every other fruit fly, so maybe there were divergent species, but after a few generations, this should have revealed itself. If this is really the case, then how come we take it for granted that humans, homo erectus, neanderthals etc. were all divergent species that had a common ancestor something like 50,000 years ago? Am I way off? If you take the fruit fly lifetimes and human lifetimes, in those 50,000 years we had about as many generations as the fruit fly generations. And we got all this speciation supposedly, using nothing more than mutation and natural selection. But where is the proof? I'm not necessary arguing that one of the religions is right and there is another force. But are scientists being biased here when they simply assume there isn't any other force? It's as if I was looking at cars from the 1920s all the way up until now, and I saw gradual change, and based on this I decided that there was no designer of these cars. I don't think that follows at all. Just curious if someone knows links that can resolve this for me :)
- dnautics 16y ago
  http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment http://en.wikipedia.org/wiki/E._coli_long-term_evolution_exp...
gort 16y ago
If you have access (i.e. from university or whatnot) the actual paper is now online at: http://www.sciencemag.org/content/early/2010/12/01/science.1197258.full.pdf http://www.sciencemag.org/content/early/2010/12/01/science.1...
vibragiel 16y ago
"It's not arsenic-based life" http://scienceblogs.com/pharyngula/2010/12/its_not_an_arsenic-based_life.php http://scienceblogs.com/pharyngula/2010/12/its_not_an_arseni...

208 points by roadnottaken 16y ago

Choose your news source for this story: http://news.ycombinator.com/item?id=1962894 http://news.ycombinator.com/item?id=1962894 - go.com http://news.ycombinator.com/item?id=1962893 http://news.ycombinator.com/item?id=1962893 - nytimes.com http://news.ycombinator.com/item?id=1962846 http://news.ycombinator.com/item?id=1962846 - nature.com http://news.ycombinator.com/item?id=1962696 http://news.ycombinator.com/item?id=1962696 - longislandpress.com http://news.ycombinator.com/item?id=1962386 http://news.ycombinator.com/item?id=1962386 - gizmodo.com http://news.ycombinator.com/item?id=1962200 http://news.ycombinator.com/item?id=1962200 - gizmodo.com http://news.ycombinator.com/item?id=1962110 http://news.ycombinator.com/item?id=1962110 - google.com http://news.ycombinator.com/item?id=1957823 http://news.ycombinator.com/item?id=1957823 - skymania.com http://news.ycombinator.com/item?id=1953228 http://news.ycombinator.com/item?id=1953228 - kottke.org

civilian 16y ago

Huh! Biochemistry major here... So I guess that the bacteria just rarely uses Sulphur-Sulphur (thiol) bonds in it's proteins, since Arsenic has a high affinity for it (and that's what causes arsenic toxicity in everything else). http://en.wikipedia.org/wiki/Arsenic#Biochemical_basis_of_arsenic_toxicity http://en.wikipedia.org/wiki/Arsenic#Biochemical_basis_of_ar... "suggesting the possibility of a biochemistry very different from the one we know" Seems like a bit of an exaggeration, but news will be news. Thiols are important for the structure & enzymatic activity, but this bacteria is proof that there are ways around it. Besides that difference, I'm guessing they're the same.

jaysonelliot 16y ago
You don't think that the discovery of the first organism to use a different element than phosphorous is a big deal? Cynicism is cool and all that, but this sure sounds like big news to me.
- sandipc 16y ago
  it's a really big deal... provided the arsenic is actually incorporated into nucleic acids, and the bacteria aren't just surviving on background levels of phosphate. it will be interesting to read the original paper when it comes out in Science later today, and not just accounts of the paper from other sources
- deleted 16y ago
  [deleted]
- dnautics 16y ago
  *you don't think the discovery of the first organism to use a different element than sulfur was a big deal? Oh wait, we all do it. http://en.wikipedia.org/wiki/Selenocysteine http://en.wikipedia.org/wiki/Selenocysteine
- dotBen 16y ago
  it would be a much bigger deal if that element was a replacement for carbon :P
paraschopra 16y ago
I'm sure DNA physical structure (angles, bends, etc.) with Arsenic instead of Phosphorous won't be exactly same. Arsenic has same tetrahedral structure as Phosphorous but the atom is sure bigger in size and at DNA scales, size would play a large role in determining shape of molecule. I'm sure you realize that physical interactions play a great role in a cell.
- dnautics 16y ago
  you would think, but there's also: http://en.wikipedia.org/wiki/XDNA http://en.wikipedia.org/wiki/XDNA It's true that the subtle loss of a hydroxyl group leads to all sorts of differences between RNA and DNA (RNA likes to be single-stranded more than DNA does) but there's TNAs (unfortunate acronyms) and PNAs (not to be confused with PNAS) and other things that basically work and look like DNA with fairly un-subtle changes. Furthermore, Arsenic really isn't THAT much bigger than Phosphorus (vdw radius 1.85 vs 1.80; covalent radius 1.19 vs 1.06).
crocowhile 16y ago
Yes, beside the fact that they found a way to change the structure of their DNA, RNA, and a few hundreds enzymes involved in energy metabolism they are the same... This is so huge that my money go into a mistake: I bet these bacteria just found a way to either get rid of arsenic or to neutralize its allosteric toxicity by maskerading or something. The paper is not out yet so I cannot give my opinon on the experimental data but from what I read there is no evidence that DNA actually contains arsenic and until that arrives I believe it's a red herring.
- mechanical_fish 16y ago
  It does seem overwhelmingly likely to be a mistake. But an exciting one! Biochemistry sports fans like myself will watch with interest. EDIT: Hey, my upvote voted you down by mistake! Somebody upvote the parent, please.
- roadnottaken 16y ago
  "from what I read there is no evidence that DNA actually contains arsenic" FTFA: "When the researchers added radio-labelled arsenate to the solution to track its distribution, they found that arsenic was present in the bacterium's proteins, lipids and metabolites such as ATP and glucose, as well as in the nucleic acids that made up its DNA and RNA. The amounts of arsenate detected were similar to those expected of phosphate in normal cell biochemistry, suggesting that the compound was being used in the same way by the cell. The team used two different mass-spectrometry techniques to confirm that the bacterium's DNA contained arsenic... Analysis with laser-like X-rays from a synchrotron particle accelerator indicated that this arsenic took the form of arsenate, and made bonds with carbon and oxygen in much the same way as phosphate." It sounds like there IS some evidence...
  - crocowhile 16y ago
    The author themselves are tyring to explain to you that "Our data are strongly suggestive of arsenic replacing phosphorus". Where suggestive =!= evidence. Plus, read the paragraph "A world of possibilities" to see why so(FTFA). There is no evidence. There are results that are compatible with that and other scenarios. Science is not so easy as you wish it was.

jaysonelliot 16y ago

Felisa Wolfe-Simon's name is going to end up in the history books along with Leeuwenhoek and Darwin. Talk about a life-changing discovery!

spot 16y ago
Maybe but not for this work. This wasn't the 2nd origin of life story that was predicted.
- mechanical_fish 16y ago
  Yes, the touchstone of everyone's work should be how well it compares to the figments of one's imagination. Poor Einstein! If only he'd discovered warp drive, he'd be as famous as Zephraim Cochrane!
  - TheSOB88 16y ago
    I think it's more that this isn't very game-changing. Einstein revolutionized physics with relativity; Darwin revolutionized biology. What does this discovery revolutionize? Biochemistry perhaps, but it seems a bit too specific to have far-reaching impacts.
  - badkungfu 16y ago
    Wow, snarky. I had the same impression. This sounds really, really cool but it's still an organism that uses DNA, and we're still related to it. As a layperson, I don't see why this says a lot more about the potential for life elsewhere. If it's not a wholly new occurrence of life, then it's something that "did life" the same way we do until it happened to need this really cool adaptation. I understand that my lack of biology training probably contributes to my not getting it, but that's where most people are coming from. A lot of time has been spent explaining the significance of Einstein's work and most people still don't "get it", we may need the same here. So, instead of snarking...explain again/better/differently than others have.
    - cryptoz 16y ago

frisco 16y ago

This seems silly. Phosphorous not being required for life seems obvious to me: ok, maybe it's believed to be used in all Earth-originated, carbon-based life, but why would we believe a priori that it's an absolutely necessary component of any biological life anywhere (which seems to be what's implied by NASA and the relation of this to exobiology)? If we develop silicon-based artificial intelligence (how do you define life, anyway? That matters when you're talking about astrobiology), would we run a headline, "Researchers prove carbon not required for life"? I've always thought the scientific community stated that alien life may use a totally different biochemistry from us? Edit: so, in some senses this is like P!=NP being proven, except less important, since it's only one component (phosphorus). It's scientifically a big deal but doesn't change the world because it's largely what we've always expected (the metaphor breaks down that this doesn't have the major secondary consequences like N=NP would).

davidsiems 16y ago
http://lesswrong.com/lw/im/hindsight_devalues_science/ http://lesswrong.com/lw/im/hindsight_devalues_science/
- frisco 16y ago
  I don't think this is hindsight bias though. As a scientist (not in biochemistry or astrobiology, though) I understand this had to be specifically shown, but this is one of those things that most people I talk to and I have always just casually treated as obvious. The confirmation is important scientifically, but shouldn't change our viewpoint, since it's what we've always expected. Am I wrong here? Any computational biologists or biochemists want to tell me this wasn't expected at all?
  - varjag 16y ago
    You can argue that possibility of alien life is also quite a common idea. Yet a confirmation of that would be considered a major scientific breakthrough.
    - 16y ago

sorbus 16y ago

"The researchers isolated the organism and found that when cultured in arsenate solution it grew 60% as fast as it did in phosphate solution — not as well, but still robustly. The culture did not grow at all when deprived of both arsenate and phosphate."

akharris 16y ago

Two weeks ago: antimatter contained long enough to be studied. This week: life without phosphorous. Next week: flying skateboards?

cryptoz 16y ago
I think the first artificial, human directed production of antimatter was by CERN in 1995. I'm not sure what you mean by "two weeks ago", but antimatter has been around a lot longer than that.
- akharris 16y ago
  Two weeks ago, CERN made the announcement that they had contained antimatter long enough (at LHC) to study it properly. First time it's ever been done that well. Pretty stunning accomplishment.
  - cryptoz 16y ago
    Ah, right! Thanks
prawn 16y ago
On flying skateboards, we were wondering the other day in the office about Parrot-style drones that you could hang from: http://www.blogcdn.com/www.engadget.com/media/2010/01/parrot-ar-drone-03.jpg http://www.blogcdn.com/www.engadget.com/media/2010/01/parrot... Risky, but I'd try it!

TheSOB88 16y ago

Why people constantly stick to the idea that all possible organisms must have similar biochemistry to us is beyond me. Think about it: Out of the humongous search space of chemicals, the ones we use happened to work for us. A combination of randomness and building on what worked before got us to where we are. Why should life not be able to use chemistry in completely different ways in order to replicate itself? Why are we so arrogant as to think that our design is the only design? Edit: My point is that our ratio of "shit we know" to "shit we don't know we don't know" is infinitesimally small in the field of possible lifeforms' biochemistry. That is, we only know stuff very close to us on a cosmic scale; we effectively have blinders to all other possibilities. And there's already a lot of biochemical variation on Earth: To give some small examples, viruses don't even have DNA, and plants use less amino acids than animals. The self-similarity of what we have so far can be explained, I think, by evolution. We all started out from the same point, so there's very little incentive to "reinvent the wheel" as it were. Only under extreme conditions like we have here, or the geothermal vents underwater, do we observe marked differences.

cryptoz 16y ago
> Why are we so arrogant as to think that our design is the only design? We're not. Nobody is. The reason scientists don't look for life on other planets that is made of other chemicals is that we may not be able to recognize that as life. It's much better - read, scientific - to look for something we can recognize. Also, there are chemical properties of the elements that make up life on Earth that allow for fast reactions, bonding, etc. Most of the rest of the elements in the periodic table react more slowly in normal conditions, making the process for life less likely. Not impossible. Just less likely. We think. So we focus on looking for what we know about. That's the best way to do it. Nobody worth their degree will ever claim that our "design" (bad word choice, by the way) is the only one.
- TheSOB88 16y ago
  I wasn't trying to address any bearing this has on finding alien life, just speaking theoretically - we shouldn't assume that everything should be like us. If it hasn't been your experience that most people think that way, then I must have misjudged. I agree on the second paragraph, but especially the last sentence. I know "design" is used by IDers, but what other word can adequately reference the incredibly complicated way our cells and bodies work? Thanks for the response.

dnautics 16y ago

I don't know. You would think, but you can autoclave a solution of "deionized ultrafiltered water" which should have "no" carbon in it at all, and bacteria will find a way to grow in it if you get it contaminated, they will concentrate the trace trace trace amounts of carbon. How carefully did they prep their DNA? These days nobody is careful and they use these crap kits which are good enough, convenient enough to get molecular biology done. The other day in lab I suggested someone isolate DNA using caesium chloride gradient ultracentifugation and the only people who knew what I was talking about were the two old (70+) year old senior scientists but they agreed that it was the way to go.

drcode 16y ago

OK, this news is very interesting, but it does not prove much about extraterrestrial life. We know that organisms can adapt to their environment. Incorporating some fraction of arsenic into a cell's dna is an example of such adaptation. The question that really matters is "has life originated more than once in the universe?" This experiment has no bearing on that: They took a standard terrestrial cell, with a carbon-based history, and simply subjected it to some new conditions. This is NOT a new life form that originated from a novel environment and using a different chemistry. However, NASA is getting awfully close to selling it as such in their press conference, which is misleading.

jpwagner 16y ago
I think this finding deserves a bit more respect. Of course it does not answer ALL of our questions, but it proves DNA does not need phosphorus! AMAZING!
- Archaeum 16y ago
  I agree that this is remarkable, but I think it's valid to criticize publicizing the finding as an astrobiology discovery, which is exactly what NASA (or its public relations department, at any rate) is calling it--and which it is not, despite its implications for astrobiology. If we care about engaging the public, we should be concerned about sensationalism that detracts from the solid work of the scientists. If you cause people to think you're going to show them extraterrestrial life, fairly or not, you run the risk of them tuning out when the reality is less flashy, even if it's groundbreaking.
  - jpwagner 16y ago
    I couldn't disagree more. Astrobiology researchers made this finding. If you think it's not astrobiology take it up with NASA.
    - Archaeum 16y ago
      I'm surprised by the strong objection. I understand that the lead scientist is with the NASA Astrobiology Institute, but I still think that despite the important implications for astrobiology, calling it astrobiology is questionable. If neither NASA nor any astrobiologists had been involved, exactly the same results could have been obtained, and the astrobiology connection (though it might be played up because it is an interesting angle) would more clearly be incidental. In other words, I don't think you lose any accuracy or diminish the finding by referring to it as biological rather than astrobiological. That said, I'm not sure I really want to get caught up on "biology" versus "astrobiology" as terms. I think the greater point (or at least the point I was trying to make) is about communicating clearly and managing expectations. When you say astrobiology or exobiology, invariably some people are going to cry, "What, no aliens? You tricked me!" If that indignance prevents them from trying to understand the importance of the story, should we even bother trying to cater to them? I don't have a good answer for that. Without raising the idea of extraterrestrial life, they might not have been engaged at all. It's just something for those involved in public outreach to be aware of.

RiderOfGiraffes 16y ago

Official announcement: http://news.ycombinator.com/item?id=1963296 http://news.ycombinator.com/item?id=1963296

bradfordw 16y ago

It has its own twitter account! https://twitter.com/#!/ArsenicBacteria https://twitter.com/#!/ArsenicBacteria

cryptoz 16y ago
s/it's/its

cstross 16y ago

As Mono Lake is of volcanic origin and formed around 760,000 years ago (per Wikipedia) I'd be astonished if the arsenophile(?) evolved there in that short a time span. Which leaves open the question of where it came from, and whether arsenic tolerance is present but dormant in other extremophiles. Other points of note: never mind the cellular DNA integrating arsenate, the whole respiration cycle seems to be affected, presumably running on ATA rather than ATP. Which implies huge amounts of molecular booty in the shape of enzymes that are powered by a different reduction gradient (ATA-AMA rather than ATP-AMP). Possible down to earth applications? Lest we forget, Pakistan has a monstrous problem with arsenic-contaminated wells ( http://www.irc.nl/page/16331 http://www.irc.nl/page/16331 ) and a bacterial culture that thrives on arsenic could offer new approaches to arsenic sequestration. And that's just off the top of my head. (My biochemistry is, alas, too rusty to go much further without a refresher course. Hmm ...)

jacquesm 16y ago
If a bacterium consumes the arsenic from a contaminated well the well is now contaminated with the corpses of bacteria that are rich in arsenic. You'd have to add another pass to get rid of the bacterial residue (possibly easier, but still).
- enjo 16y ago
  Doesn't that depend on the byproduct produced by the respiration cycle?
  - jacquesm 16y ago
    Apparently they accumulate it.
- sudont 16y ago
  Possibly a small sludge pond that would filter the water through as per a sewage treatment plant? I'm thinking that if it's in the wells, it's due to the solvent action of water on the rocks, and cleaning out the wells would only be a temporary solution.

roadnottaken 16y ago

Here's the article from Science: http://www.scribd.com/doc/44550217/Science-2010-Wolfe-Simon-Science-1197258 http://www.scribd.com/doc/44550217/Science-2010-Wolfe-Simon-...

stavrianos 16y ago

bicycle discovered constructed entirely from wood: proves metal not required for transportation http://www.leevalley.com/newsletters/woodworking/2/3/article1-1.jpg http://www.leevalley.com/newsletters/woodworking/2/3/article...

anigbrowl 16y ago
We already knew that because we have had wooden boats, carts, and planes (gliders).
- jjs 16y ago
  You're missing the point—this is the single greatest discovery in exobicyclology since E.T.!
  - anigbrowl 16y ago
    Tee-hee - it's true that these NASA announcements are often a bit of an anticlimax, but I suppose that's the price of having so much science-fiction to enjoy. Oddly enough,the first bicycles were actually made out of wood - they were called velocipedes and today we call them balance bikes. Like scooters, they were powered by pushing feet along the ground. I was going to link to an amusing site about these, but while looking it up I was surprised to discover that there are in fact modern bicycles mostly made from wood, although they're quite expensive: http://www.renovobikes.com/ http://www.renovobikes.com/ ...so I wasn't as well well-informed as I thought I was.

bld 16y ago

Here's the press conference in three ~10 minute parts: Part 1: http://www.youtube.com/watch?v=hu5dXnCUs7I http://www.youtube.com/watch?v=hu5dXnCUs7I Part 2: http://www.youtube.com/watch?v=0LsihAsX4z8 http://www.youtube.com/watch?v=0LsihAsX4z8 Part 3: http://www.youtube.com/watch?v=Nu0VvxuicLw http://www.youtube.com/watch?v=Nu0VvxuicLw The lead author gives a talk at 2:26 in Part 1 that I thought was an excellent example of how to communicate science (or other technical subject) and implications to a general audience.

olalonde 16y ago

Most theories[1] agree to say that replicating life predates DNA. Wouldn't that mean that we could still have a common ancestor with this life form? [1] http://en.wikipedia.org/wiki/Abiogenesis#Other_models http://en.wikipedia.org/wiki/Abiogenesis#Other_models

joelburget 16y ago
We not only could have a common ancestor, it seems to me to be almost certain. What are the chances that some other life has evolved with DNA completely independently
- olalonde 16y ago
  I second, but that's what the first article posted on HN seemed to suggest. http://skymania.com/wp/2010/11/alien-life-form-is-here-on-earth.html/ http://skymania.com/wp/2010/11/alien-life-form-is-here-on-ea...
- yread 16y ago
  Why do you consider it certain? It could have just died off being much less efficient than us.
  - joelburget 16y ago
    Well, DNA is fairly complex. Of all the elements and compounds life could involve it seems rather unlikely that DNA evolved in two places completely separately. Not impossible, but very unlikely.
    - dnautics 16y ago
      actually, no. DNA/RNA are in fact, just about the simplest chemical choices that can perform replication. Ribose, for example is the lowest energy pentafuranose, which means in a random mix of sugars you'll find ribose in the highest concentration. The funny thing is that the KSS principle seems to hold in nature, we've tried in the lab to design alternatives to DNA/RNA, and none of them seem to work quite so well. http://www.sciencemag.org/content/284/5423/2118.short http://www.sciencemag.org/content/284/5423/2118.short

joelburget 16y ago

Perhaps NASA should be more cautious about holding a press on astrobiology, and with a Science embargo. Clearly everyone will immediately think of aliens, and for good reason. It's NASA, it's about astrobiology, and it's something big enough to embargo Science. They're just asking for all the alien stories. And let's be clear, these are not aliens.

ugh 16y ago
Holding a press conference for this pretty sweet discovery was completely justified. The language in the press release made it clear ahead of time that Nasa didn’t make any discovery related to life on other worlds, only a few overly eager bloggers spun crazy theories like that. Whoever is disappointed by this and claims that Nasa hyped too much doesn’t have her or his head screwed on right.
- joelburget 16y ago
  I agree that it's an amazing discovery. Admittedly I didn't read the actual press release so you're probably right that they acted correctly. I only read second hand accounts of what they were going to announce.

dnautics 16y ago

high resolution Mass spec is such a shitty technique and is completely non-quantitative. How do you know that arsenic isn't associated with, say, a protein that makes the DNA resistant to being taken apart chemically. I will believe this result when they stain the DNA and run samples of the DNA down a density gradient ultracentrifugation and show that arsenic content in the media correlates with increased density of DNA, as you would expect if the arsenic is replacing phosphorus. If you don't know what i'm talking about, it's this classical experiment: http://en.wikipedia.org/wiki/Semiconservative_replication#Biophysical_evidence http://en.wikipedia.org/wiki/Semiconservative_replication#Bi... Here is my personal scientific experience speaking: If you see it everywhere, then it's likely to be an artefact. Clean up your technique, clean your instruments, and go back to an old school technique. Remember how the physicists who discovered CMB cleaned out the pigeon scat from their microwave horn telescope before they started to believe what they saw.

EGreg 16y ago

Don't mean to get all religious on ya, but I wanted to ask here... Is there any evidence of macro-evolution having ever taken place in recorded history? I'm asking this with no agenda, but curious. As far as I know, no new species have ever been produced, despite natural or unnatural selection. So what makes us say that there is no other force or process that causes speciation? How are scientists so convinced that mutation and natural selection is all that is required, despite never having observed a single instance of speciation? To be scientific, a theory has to make some potentially falsifiable, non-obvious predictions. Then we can test those predictions, and if our experiments confirm them then the theory survives. I totally agree that the hypothesis "natural selection occurs" has been proven in ample ways (ok, maybe the white->dark->white butterflies was a bad one, but bacteria and their resistance to antibiotics is proof enough). But to form a completely new species... Species is defined as "as a group of organisms capable of interbreeding and producing fertile offspring" according to Wikipedia. Two animals are of different species if none of their offspring have ever been observed to be fertile. At least, that's a good working definition. It bothers me that scientists have been interbreeding literally thousands of generations of fruit flies and despite all selection pressures, artificial or not, were never able to produce a single new species. Sure, it's hard to try and mate every fruit fly with every other fruit fly, so maybe there were divergent species, but after a few generations, this should have revealed itself. If this is really the case, then how come we take it for granted that humans, homo erectus, neanderthals etc. were all divergent species that had a common ancestor something like 50,000 years ago? Am I way off? If you take the fruit fly lifetimes and human lifetimes, in those 50,000 years we had about as many generations as the fruit fly generations. And we got all this speciation supposedly, using nothing more than mutation and natural selection. But where is the proof? I'm not necessary arguing that one of the religions is right and there is another force. But are scientists being biased here when they simply assume there isn't any other force? It's as if I was looking at cars from the 1920s all the way up until now, and I saw gradual change, and based on this I decided that there was no designer of these cars. I don't think that follows at all. Just curious if someone knows links that can resolve this for me :)

dnautics 16y ago
http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment http://en.wikipedia.org/wiki/E._coli_long-term_evolution_exp...

gort 16y ago

If you have access (i.e. from university or whatnot) the actual paper is now online at: http://www.sciencemag.org/content/early/2010/12/01/science.1197258.full.pdf http://www.sciencemag.org/content/early/2010/12/01/science.1...

vibragiel 16y ago

"It's not arsenic-based life" http://scienceblogs.com/pharyngula/2010/12/its_not_an_arsenic-based_life.php http://scienceblogs.com/pharyngula/2010/12/its_not_an_arseni...