Of Arsenic and Aliens

LakeMonoRumors have been swirling this week about a press conference NASA is starting right now. Some people have speculated that they’re going to announce evidence for life on another planet.

Well, not quite. Scientists have found a form of life that they claim bends the rules for life as we know it. But they didn’t need to go to another planet to find it. They just had to go to California.

The search for alien life has long been plagued by a philosophical question: what is life? Why is this so vexing? Well, let’s say that you’re hunting for change under your couch so that your four-year-old son can buy an ice cream cone from a truck that’s pulled up outside your house. Your son offers to help.

“What is change?” he asks.

“It’s…” You trail off, realizing that you’re about to get into a full-blown discussion of economics with a sugar-crazed four-year-old. So, instead, you open up your hand and show him a penny, a nickel, a dime. “It’s things like this.”

“Oh–okay!” your son says. He digs away happily. The two of you find lots of interesting things–paper clips, doll shoes, some sort of cracker–which you set aside in a little pile. But you’ve only found seventeen cents in change when the ice cream truck pulls away. Tears ensue.

As you’re tossing the pile of debris into the trash, you notice that there’s a dollar bill in the mix.

“Did you find this?” you ask.

“Yes,” your son sobs.

“Well, why didn’t you tell me?”

“It’s not change. Change is metal. That’s paper.”

Scientists have proposed hundreds of definitions for life, none of which has emerged as the winner. (For more on this quest, see “The Meaning of Life,” a cover story I wrote for SEED.) NASA, which would like to find life elsewhere in the universe, has taken a very practical approach to the question, simply asking what sort of definition of life should would be the best guide for their search. Traditionally, they’ve put a priority on life as we know it. All life on Earth uses DNA or RNA to encode genes; all life on Earth uses the same basic genetic code to translate genes into proteins; all life uses water as a solvent. One reason that NASA has put so much emphasis on looking for life on Mars is that it’s plausible that life as we know it might have existed on Mars back when the planet was warm and watery. And besides, how are we supposed to look for a form of life we’ve never seen before?

But in 2007 a National Academies of Science panel urged that we take a broader view of life, so that we wouldn’t miss the dollar bill in the couch. Other kinds of life were at least imaginable–such as organisms that used different backbones for their genes, or perhaps might swim through liquid methane like fish swim in water. (Here’s my write-up in the Times.) Some of the panelists–most notably, Steven Benner of the Foundation for Appllied Molecular Evolution–even endorsed a more radical notion. As I described in this feature for Discover, Benner and others speculate that maybe alien life is here on Earth.

A lot of evidence, for example, suggests that the first forms of life used RNA as both genes and enzymes. Later, double-stranded DNA evolved and DNA-based life wiped out RNA life. But perhaps RNA life still clings to existence in places where DNA-based life can’t drive them extinct. Benner suggests tiny pores in rocks that would be too small for bacteria.

No one has found RNA life yet, nor have they found any all-natural alien on Earth. But as I point out in Microcosm, there are definitely aliens among us.

They’re called E. coli.

Or, rather, they are laboratory stocks of E. coli that scientists have transformed so that they use new genetic codes or even use new nucleotides, the “letters” of DNA. No life that we know of has ever lived this way.

NASA’s press conference concerns another nearly-alien kind of life on our own planet. NASA has sponsored many expeditions to the toughest places on Earth for life to survive, from glaciers to deserts to acid-drenched mines. One of these expeditions was to Mono Lake, a practically toxic body of water, an extreme environment. It’s very salty, very alkaline, and is steeped in arsenic. The “weird life” report singled out arsenic-based life as one topic worth investigating, so Felisa Wolfe-Simon of the NASA Astrobiology Institute and her colleagues isolated a strain of bacteria and brought it back to the lab to study its growth.

As I mentioned earlier, life as we know it uses DNA for its genes (except for some viruses that use RNA). DNA has a backbone made of two alternating units: sugar and phosphate. Phosphate is one phosphorus atom and four oxygen atoms. It just so happens that arsenic–despite being a poison–has a lot of chemical properties similar to phosophorus. In fact, one arsenic atom and four oxygen atoms combine to form a molecule called aresenate that behaves a lot like phosphate.

Wolfe-Simon and her colleagues reared the bacteria in their lab, initially feeding them a typical diet of essential nutrients, including phosphate. But then they gradually reduced the phosphate in their diet and replaced it with arsenate. Before long, as they report today in Science, the bacteria were growing nicely on an all-arsenate diet, without a speck of added phosphate. The scientists then probed the DNA of the bacteria and concluded that they were sticking the arsenate into the DNA in place of phosphate. Phosphate is also vital for other molecules, such as proteins, and the scientists found arsenate in them as well. In other words–arsenic-based life.

Or…maybe not. In Science, reporter Elizabeth Pennisi writes that some scientists are skeptical, seeing other explanations for the results. One possible alternative is that the bacteria are actually stuffing away the arsenic in shielded bubbles in huge amounts.

I got in touch with Benner, who also proved to be a skeptic. “I do not see any simple explanation for the reported results that is broadly consistent with other information well known to chemistry,” he says. He pointed out that phosphate compounds are incredibly durable in water, but arsenate compounds fall apart quickly. It was possible that arsenate was being stabilized by yet another molecule, but that was just speculation. Benner didn’t dismiss the experiment out of hand, though, saying that it would be straightforward to do more tests on the alleged arsenic-DNA molecules to see if that’s what they really are. “The result will have sweeping consequences,” he said.

If Wolfe-Simon can satisfy the critics, this will be research to watch. The Mono Lake bacteria probably don’t actually exist in an arsenic-based form in nature, since they grow much faster on phosophorus. They’re aliens, but aliens in the same way unnatural E. coli are, thanks to our intervention. But Wolfe-Simon’s results suggest that life based on arsenic is at least possible. It might even exist naturally in places on Earth where arsenic levels are very high and phosphorus is very scarce.

Such a discovery would indeed be huge news–although not as huge as a similar discovery on another planet. For now, we will have to content ourselves with arsenic-laced dreams.

(PS: You should be able to watch the press conference live starting at 2pm Thursday 12/2 here.)

Reference: Wolfe-Simon et al, “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus” Science, 10.1126/science.1197258

[Image of Mono Lake by .Bala via Flickr, under Creative Commons License]

[Update: Fixed Wolfe-Simon’s name. Now I am left with images of wolf salmon roaming in packs.]

[Update: Fellow Discover bloggers Ed Yong and Phil Plait are on the case, too.]

[Update: I’ve been adding in various corrections pointed out by astute readers. Importantly, the researchers raised the bacteria with no *added* phosphate. But the medium did have a little phosphate in it anyway. More about this on Monday!]

[Upate: Well, Monday became Tuesday, but better late than never: Here’s my new article on the arsenic backlash at Slate.]

44 thoughts on “Of Arsenic and Aliens

  1. It’s Wolfe-Simon, not Wolf-Salmon!

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

    [CZ: Thanks!]

  2. In other words–arsenic-based life.

    I think it would be exceedingly misleading to refer to “ordinary” life as ‘phosphorus-based’.

    Seems to me the spin is out of hand on this. Even if these bacteria can sub-in arsenic for phosphorus when forced to, this would represent an interesting adaptaion of bacteria to high-arsenic environments, nothing more. We already have a large catalog of bacterial adaptations to other seemingly harsh chemical environments, and one more isn’t worth a hyped NASA presser. IMO.

  3. Often times I wonder if the definitions of life were all wrong. Why do the rhythms of life has to be driven by our colored view? Me thinks that NASA is looking to find some hyping to keep from losing funding

  4. “Phosphate is also vital for other molecules, such as proteins, and the scientists found phosphate in them as well. In other words–arsenic-based life.”
    Shouldn’t that be
    “Phosphate is also vital for other molecules, such as proteins, and the scientists found ARSENATE in them as well. In other words–arsenic-based life.”

    [CZ: Indeed! Thanks.]

  5. I’m not a scientist, just an avid armchair follower of most sciences, at least until I get to the Wonderland gate and find myself way over my head. I know that there as been speculation for decades about silicon-based life, but arsenic-based is a new one on me, unless I’ve simply forgotten about it ( easily possible, given my memory!).

    It would be encouraging to learn that life based on another element, since it would greatly broaden the possibility of discovering *some* form of life elsewhere, even if merely bacterial life (as opposed to aliens with rays guns and space ships that slip back and forth across several dimensions). And just a day or two ago I read that astronomers are re-thinking the theoretical number of stars in the Universe, and now speculate there may be as many as three times more stars than they previously though — hence, that many more possibilities of finding habitable planets. Even if carbon-based life turns out to be the only kind possible, it’s hard to believe there isn’t *some* sort of life elsewhere, which I say partly because the 500 or so exoplanets we’ve discovered so far seem to pretty strongly indicate that there are a fair number of planets orbiting their stars in the Goldilocks Zone (though most aren’t truly Earth-like, to be sure, at least not so far).

    Fascinating “maybe-a-breakthrough-discovery,” and great article!

    Minerva Smelibut said on December 2nd, 2010 at 5:36 pm, in part, ” Me thinks that NASA is looking to find some hyping to keep from losing funding.”

    C’mon, Minerva — surely not every single scientist on the planet sells his or her soul. What you wrote is akin to saying anyone who joins the Marines does so for the chance to visit faraway, perhaps even exotic places, meet fascinating people — then kill them.

    @Richard Prins “foreign coins.” THAT brought a smile! Thanks! 😉

  6. What I would like to see is a x-ray diffraction spectrum. By replacing P with As the double helix structure should be changed. That would be totally unambiguous.

  7. Salt lakes are a fairly common Western United States phenomena. Many of these features cycle between being lakes, mushy brines, or hard salt flats depending on climate swings. But Mono Lake in particular has been very affected by water diversions by the City of Los Angeles starting abruptly in 1941. See: http://www.monolake.org/about/story.

    Have non-Mono Lake bacteria been tested? How would a “normal” bacterial strain cope with increasing As?

    At any rate, it seems to me that the fact the chemistry of the lake has not been consistent over time would be relevant.

  8. My naive non-Biologist questions are:

    If I were raising something in captivity in my laboratory, I think I would attempt to feed it what I thought it wanted to eat. Why did the researchers start out with pure phosphate rather than arsenate or an exact match to the Mono Lake brine if these bacteria are supposed to be arsenic based life?

    If I wanted to compare how the Mono Lake bacteria handled arsenate differently than normal strains, I think I might start both strains on phosphate and increase the arsenate. Can the non Mono Lake bacteria adapt? Or, at that point where the normal bacteria were near death, what was different with the way the Mono Lake bacteria were incorporating the As? Do normal bacteria end up with As distributed throughout? Wouldn’t this help answer the sequestration vs assimilation question raised above?

    [CZ: Here is my non-biologist answer: These bacteria are not, despite some news reports this week, arsenic-based life. On Mono Lake, they are ordinary, phosphate-based life. But, perhaps due to their high tolerance for arsenic, they can swap arsenic for phosphate in an experiment–at least according to the scientists. As for your second question, arsenic is toxic to most organisms, including bacteria, and they have mechanisms to get rid of it from their system. Some have better mechanisms than others. And some bacteria at Mono Lake can even feed on arsenic: http://www.ncbi.nlm.nih.gov/pubmed/20511421. The bacteria in this paper were not dying off from arsenic poisoning–they were growing on pure arsenic and no phosphate (assuming there was no contamination).]

  9. From a non living system perspective, I think that in high As, brine-y solutions that the relevant chemical equibria would be driven to extremes such that normal ideas as to what was or wasn’t stable “in water” would not apply. So substituting arsenic for phosphorus in chemical molecules under these conditions doesn’t strike me as necessarily all that impressive.

    It seems to me that the amazing thing is that the bacteria stay alive under these conditions.

    That was my thought behind my question: “at that point where the normal bacteria were (would be) near death, what was different with the way the Mono Lake bacteria were (would be) incorporating the As?”

  10. Thanks for well-written and entertaining post. Your story about a four-year-old son, loose change, and scrambling to buy ice cream was perfect.

    I would like to clarify one point you make about Mono Lake:

    “One of these expeditions was to Mono Lake, a practically toxic body of water. It’s very salty, very alkaline, and is steeped in arsenic.”

    Arsenic exists in many forms, and not all are equally toxic to all life, nor are the type and/or concentrations in the water column such that inhibit an astonishingly productive ecosystem. Mono’s (pronounced Moe’-no) average annual primary productivity is 686 gC/m2-yr, and it often exceeds 1000 gC/m2-yr. The lake supports not only algae but trillions of brine shrimp and a massive population of alkali flies, in turn supporting millions of migratory and resident birds.

    The lake’s microbial life has only recently received attention since about the time NASA first used the lake as a test bed for robotic Mars missions in 1995. The bacterium and viruses in the lake, in its seeps and springs, in its anoxic depths, and around brackish lagoons, present a great frontier of weird and unknown. It’s a micro-wilderness.

    As Dr. Wolfe-Simon pointed out, the story is not about Mono Lake, but I did want to clarify that Mono is far from being a toxic body of water.

    [CZ: Thanks! I’ll revise that part of the post.]

  11. Yeah; I have to pitch in with Benner, having read the paper but not the supplement: the element fractions depends on the extraction procedure, and it doesn’t seem to be checked but “standard”. For example, the DNA gel wash is supposed to remove small RNA (mostly) fragments, but what about proteins. (Which can be used for sequestering.)

    @ Mehkong Kurt:

    there as been speculation for decades about silicon-based life

    Perhaps in scifi; SiO2 being solid pretty much torpedoes the idea among scientists AFAIU.

  12. “SiO2 being solid pretty much torpedoes the idea among scientists AFAIU”

    How does this rule out silicon-based life? (I say this as a complete non-biologist.) We had life on Earth long before any significant amount of atmospheric oxygen, so I would assume such life didn’t need much CO2 transport.

  13. “Before long, as they report today in Science, the bacteria were growing nicely on an all-arsenate diet, without a speck of phosphate.”

    This is wrong. The bacteria were always grown in phosphate — the “non-phosphate” media had 3 uM phosphate contamination, as the authors acknowledge in the text. This phosphate contamination is one reason why many scientists do not believe this paper at all.

    The microbiologist Rosie Redfield has published a devastating critique of this paper:


    [CZ: Thanks–I will rein in the figurative language. And I highly recommend Redfield’s post.]

  14. “The Mono Lake bacteria probably don’t actually exist in an arsenic-based form in nature, since they grow much faster on phosophorus.”
    I can’t agree with this statement at all, to rebate it with an analogy, many facultative anaerobic microorganisms can grow faster with enough oxygen or other external electron acceptors but this doesn’t mean they don’t actually exist in anaerobic fermentative form in nature.
    Likewise, GFAJ-1 could be adapted to thrive with either phosphorous or arsenic depending on the specific surrounding availability of both. An evolutionary adaptation to incorporate arsenic when phosphorous is scarce could better explain why these bacteria are capable to grow under phosphorous deprivation replacing it with arsenic.
    Alternatively, perhaps it is energetically more advantageous to directly incorporate arsenic into biomolecules than spend energy trying to get rid of it under conditions in which the combined effect of arsenic concentration and arsenic-phosphorous ratio is above certain threshold level.

  15. Two editorial notes:

    “Benner suggests tiny pores in rocks that would be too big for bacteria.” Don’t you mean, “…too small for bacteria”?

    You might want to correct spelling in this sentence: “One possibile alternative is that…”

    [CZ: Thanks, thanks–fixed, fixed]

  16. for a great read, i recommend “Origins of Life” by Freeman Dyson, 1985 with a 2nd edition in 1999. then there’s James Lovelock’s great treatment in “Ages of Gaia” of the Oklo algal mat in Gabon that evolved its own nuclear reactor. life is OPPORTUNISTIC, and just because it’s harder to use As than P doesn’t make it impossible…call me an As-hole if you want to. i just hope there are bacteria out there that can use selenium instead of sulfur, to clean up all the Bureau of Reclamation’s water projects that have caused so many bird and amphibian deaths and deformities in the Pacific Flyway (yeah, also read “Death in the Marsh” by Tom Harris.)

  17. Intelligent Bacteria: Cells are Incredibly Smart
    For years I just sort of assumed that cells were self-reproducing blobs of protein. Maybe you did too. Turns out they’re way smarter than that. You will be amazed at this video. Dr. Bonnie Bassler from Princeton University presents a beautiful TED talk on how bacteria communicate with each other by forming words out of simple molecules.
    She also explains…

    How bacteria strategize together on how to ‘take down’ their host
    Elegant systems of bioluminescence
    Symbiotic relationships between organisms
    Cells speak multiple languages
    Enjoy this remarkable presentation. And a sincere thanks to Patrik Beno for sharing it with me.
    Perry Marshall

    This is really incredible. Where did the proposed bacterial molecular codes come from?

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