…and this is a 
Oh, great. I get to be the wet blanket.
There's a lot of news going around right now about this NASA press release and paper in Science — before anyone had read the paper, there was some real crazy-eyed speculation out there. I was even sent some rather loony odds from a bookmaker that looked like this:
WHAT WILL NASA ANNOUNCE?
NASA HAS DISCOVERED A LIFE FORM ON MARS +200 33%
DISCOVERED EVIDENCE OF LIFE ON ONE OF SATURNS MOON +110 47%
ANNOUNCES A NEW MODEL FOR THE EXISTENCE OF LIFE -5000 98%
UNVEILS IMAGES OF A RECOVERED ALIEN SPACECRAFT +300 25%
CONFESSES THAT AREA 51 WAS USED FOR THE ALIEN STUDIES +500 16%[The +/- Indicates the Return on the Wager. The percentage is the likelihood that response will occur. For Example: Betting on the candidate least likely to win would earn the most amount of money, should that happen.]
I think the bookie cleaned up on anyone goofy enough to make a bet on that.
Then the stories calmed down, and instead it was that they had discovered an earthly life form that used a radically different chemistry. I was dubious, even at that. And then I finally got the paper from Science, and I'm sorry to let you all down, but it's none of the above. It's an extremophile bacterium that can be coaxed into substiting arsenic for phosphorus in some of its basic biochemistry. It's perfectly reasonable and interesting work in its own right, but it's not radical, it's not particularly surprising, and it's especially not extraterrestrial. It's the kind of thing that will get a sentence or three in biochemistry textbooks in the future.
Here's the story. Life on earth uses six elements heavily in its chemistry: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur, also known as CHNOPS . There are other elements used in small amounts for specialized functions, too: zinc, for instance, is incorporated as a catalyst in certain enzymes. We also use significant quantities of some ions, specifically of sodium, potassium, calcium, and chloride, for osmotic balance and they also play a role in nervous system function and regulation; calcium, obviously, is heavily used in making the matrix of our skeletons. But for the most part, biochemistry is all about CHNOPS.
Here's part of the periodic table just to remind you of where these atoms are. You should recall from freshman chemistry that the table isn't just an arbitrary arrangement — it actually is ordered by the properties of the elements, and, for instance, atoms in a column exhibit similar properties. There's CHNOPS, and notice, just below phosphorous, there's another atom, arsenic. You'd predict just from looking at the table that arsenic ought to have some chemical similarities to phosphorus, and you'd be right. Arsenic can substitute for phosphorus in many chemical reactions.
This is, in fact, one of the reasons arsenic is toxic. It's similar, but not identical, to phosphorus, and can take its place in chemical reactions fundamental to life, for instance in the glycolytic pathway of basic metabolism. That it's not identical, though, means that it actually gums up the process and brings it to a halt, blocking respiration and killing the cell by starving it of ATP.
Got it? Arsenic already participates in earthly chemistry, badly. It's just off enough from phosphorus to bollix up the biology, so it's generally bad for us to have it around.
What did the NASA paper do? Scientists started out the project with extremophile bacteria from Mono Lake in California. This is not a pleasant place for most living creatures: it's an alkali lake with a pH of close to 10, and it also has high concentrations of arsenic (high being about 200 µM) dissolved in it. The bacteria living there were already adapted to tolerate the presence of arsenic, and the mechanism of that would be really interesting to know…but this work didn't address that.
Next, what they did was culture the bacteria in the lab, and artificially jacked up the arsenic concentration, replacing all the phosphate (PO43-) with arsenate (AsO43-). The cells weren't happy, growing at a much slower rate on arsenate than phosphate, but they still lived and they still grew. These are tough critters.
They also look different in these conditions. Below, the bacteria in (C) were grown on arsenate with no phosphate, while those in (D) grew on phosphate with no arsenate. The arsenate bacteria are bigger, but thin sections through them reveal that they are actually bloated with large vacuoles. What are they doing building up these fluid-filled spaces inside them? We don't know, but it may be because some arsenate-containing molecules are less stable in water than their phosphate analogs, so they're coping by generating internal partitions that exclude water.
What they also found, and this is the cool part, is that they incorporated the arsenate into familiar compounds*. DNA has a backbone of sugars linked together by phosphate bonds, for instance; in these baceria, some of those phosphates were replaced by arsenate. Some amino acids, serine, tyrosine, and threonine, can be modified by phosphates, and arsenate was substituted there, too. What this tells us is that the machinery of these cells is tolerant enough of the differences between phosphate and arsenate that it can keep on working to some degree no matter which one is present.
So what does it all mean? It means that researchers have found that some earthly bacteria that live in literally poisonous environments are adapted to find the presence of arsenic dramatically less lethal, and that they can even incorporate arsenic into their routine, familiar chemistry.
It doesn't say a lot about evolutionary history, I'm afraid. These are derived forms of bacteria that are adapting to artificially stringent environmental conditions, and they were found in a geologically young lake — so no, this is not the bacterium primeval. This lake also happens to be on Earth, not Saturn, although maybe being in California gives them extra weirdness points, so I don't know that it can even say much about extraterrestrial life. It does say that life can survive in a surprisingly broad range of conditions, but we already knew that.
So it's nice work, a small piece of the story of life, but not quite the earthshaking news the bookmakers were predicting.
*I've had it pointed out to me that they actually didn't fully demonstrate even this. What they showed was that, in the bacteria raised in arsenates, the proportion of arsenic rose and the proportion of phosphorus fell, which suggests indirectly that there could have been a replacement of the phosphorus by arsenic.
Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PCW, Anbar AD, Oremland RS (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science DOI: 10.1126/science.1197258.
Life Science
Physical Science
Comments
Posted by: menckensghost
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December 2, 2010 5:44 PM
Thanks for this, Dr. Myers. Vy helpful.
Klaatu barada nikto anyway.
Posted by: rditmars
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December 2, 2010 5:45 PM
Now, how about Si substituting for C?
"I'm a doctor, not a bricklayer!"
http://en.wikipedia.org/wiki/The_Devil_in_the_Dark
Posted by: Cor (formerly evil)
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December 2, 2010 5:45 PM
This wouldn't be a case of new "information" creeping into the gene pool, would it? Specifically, "information" about how to incorporate aresenic into your metabolism? If it is, somebody might want to clue in Banana Man.
Then get him to try some arsenic himself.
Posted by: louis14
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December 2, 2010 5:46 PM
I don't know enough biology to know whether this announcement rightfully earned its notoriety. What impressed me when I watched the press conference was the comments of some of the guests.
One commented that 'extraordinary claims require extraordinary evidence'. Another (who said he has worked in phosphate chemistry all his life) wanted to thank the scientist who presented the study for possibly pulling the rug from under his feet.
A nice blend of excitement, sobriety and lack of dogmatism. Go science!
Posted by: Cosmic Snark
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December 2, 2010 5:47 PM
The Fox News anti-science types will look at all the wild media speculation on what would be said at the press conference, and then blame NASA for rumor-mongering in an attempt to drum up publicity when it turns out that the discovery is much more mundane than said wild media speculation.
I can hear it already: "Why are we wasting so much money on NASA when there are potholes that need to be filled?"
Posted by: billygutter01
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December 2, 2010 5:49 PM
So there won't be a host of alien, arsenic based femme fatales arriving to poison us with kisses of death?
Pity.
Posted by: Glen Davidson
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December 2, 2010 5:49 PM
I thought they'd already found an archaeal organism that substituted arsenic for phosphorus in at least some cases.
I think what's thought to be interesting (if not actually worthy of all the hype) is that arsenic apparently can be incorporated into DNA by these organisms. At least it expands the possibililities for life, although it's clearly not earthshaking (it was always obvious that arsenic could replace phosphorus in most cases, with a few tweaks).
I'm glad to see it getting some attention, but I hope that the hype doesn't backfire on them.
Glen Davidson
Posted by: louis14
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December 2, 2010 5:50 PM
Or rather, while there are tax-breaks for the obscenely rich to be preserved.
Posted by: buckyball60
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December 2, 2010 5:51 PM
Thank you as always. My first thought was to come here and get a realistic analysis.
Posted by: Glen Davidson
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December 2, 2010 5:53 PM
Here's a source noting previously-known use of arsenic in microbial metabolism:
http://www.microbemagazine.org/index.php/02-2010-home/1358-microbial-arsenic-metabolism-new-twists-on-an-old-poison
It was already fairly extensive. The new stuff is interesting, but only incremental.
Glen Davidson
Posted by: rystefn
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December 2, 2010 5:53 PM
It's still pretty cool... but I think that about a lot of biology. Fascinating stuff.
Posted by: billygutter01
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December 2, 2010 5:56 PM
@6 Perhaps that should read Kisses Of DeathTM
Posted by: ted.strauss
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December 2, 2010 5:57 PM
Thanks for providing some concise and useful information about this breaking science news.
Posted by: Dhorvath, OM
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December 2, 2010 5:57 PM
Phooey, no poison based life afterall.
Posted by: steverino63
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December 2, 2010 5:58 PM
NASA hugely overfluffed this. As PZ notes, with arsenic, it's already been found in "sugars." Wiki actually has a good section on arsenic biology here: http://en.wikipedia.org/wiki/Hypothetical_types_of_biochemistry
Beyond that, I wonder if NASA's fluff isn't in part an attempt to sell Congresscritters on the need for more Mars landers or something.
More thoughts here:
http://socraticgadfly.blogspot.com/2010/12/bad-or-at-least-breathless-science-by.html
Posted by: Glen Davidson
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December 2, 2010 5:59 PM
Doubts about the claims of arsenic being incorporated into the DNA:
Good questions. If arsenate is being stabilized by unknown means, so much the better. If not, the most interesting aspect of this research would be gone.
Glen Davidson
Posted by: https://www.google.com/accounts/o8/id?id=AItOawk2LVR_QSh35qR3yXcKxxWjyFavdT6LDHQ
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December 2, 2010 6:00 PM
O come on PZ, don't spoil the fun! These are really Aliens, admit it!
:-)
Why can't I login using openID with my blogger? I get an error 0o
http://stateofflabbergastedness.blogspot.com/
Posted by: Brian
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December 2, 2010 6:00 PM
Maybe not, but it's still much more interesting than what I was actually expecting.
Extrapolating backwards from the hype, I was figuring it was going to be a paper about how arsenic-based life could possibly exist, in theory, based on this here computer simulation.
Posted by: Glen Davidson
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December 2, 2010 6:01 PM
Link for the source I used in #16:
http://www.csmonitor.com/Science/2010/1202/How-does-an-arsenic-based-life-form-work-exactly
Glen Davidson
Posted by: hje
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December 2, 2010 6:03 PM
Good review (below) that discusses the issues associated with the chemistry of arsenic, including the possibility of stable incorporation into backbone of polynucleotides. At the very least, the citations are good places to go for more relevant experimental data.
http://cosmos.asu.edu/publications/papers/WolfeSimon_etal_IJA2009.pdf
Posted by: Naked Bunny with a Whip
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December 2, 2010 6:03 PM
But how will all your fancy-schmamcy science talk affect my new arsenic-yogurt business plan?
Posted by: casecob
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December 2, 2010 6:05 PM
It would be cool to either transcriptionally profile and/or sequence these guys and look for closely related species to do the same thing with.
One could then try to infer ancestral state and determine if these guys adapted to the arsenate-rich environment or if the ancestor would more likely to utilize phosphate.
*sigh*
I'm a one-trick pony... these are the questions I always ask.
Posted by: Arnold T Pants
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December 2, 2010 6:07 PM
This is cool research, but I cringe every time a journal publication is immediately accompanied by a press conference. It's pretty much always a mistake.
Posted by: michael.g.sternberg
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December 2, 2010 6:09 PM
Bingo - perfect loophole for a sequel to Evolution - http://www.imdb.com/title/tt0251075/
(Not that this movie needs any more loopholes, but it's goofy enough for popcorn.)
Posted by: Rev. BigDumbChimp
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December 2, 2010 6:09 PM
I for one welcome our Arsenic based yada yada yada
Posted by: maarten.jan
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December 2, 2010 6:10 PM
What I interpreted first from the media is that they discovered life completely unrelated to anything else. When I watched the nasa stream I quickly realised it wasn't that spectacular.
It IS an interesting discovery, but not for most people. I experienced it rather as an anticlimax watching the vid. Turned it off after 10 minutes.
Posted by: Glen Davidson
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December 2, 2010 6:13 PM
As far as extraterrestrial life goes, I doubt that arsenic makes much of a difference. Phosphorous is far more common than is arsenic (arsenic is less common than uranium in our crust, although uranium is more common than most people realize), and I doubt that anything is likely to cause arsenic to be more available than phosphorus is, other than in exceptional spots within environments that are otherwise rather more rich in phosphorous.
So again, this may be reasonably interesting, but what does it really have to do with finding life on other planets, moons, etc.?
Glen Davidson
Posted by: 'Tis Himself, OM
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December 2, 2010 6:13 PM
Thank you, PROFESSOR Myers, for explaining why arsenic is poisonous.
Posted by: Menyambal: Making sambal (it isn't dragon magic).
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December 2, 2010 6:16 PM
Thanks for the explanation, PZ, I knew you'd discuss this, and I knew you'd make it clear and appropriate to its importance.
Yeah, it was over-hyped. I dunno if NASA meant for it to be, but speculation was rampant. Why not just announce it, instead of announcing that they were going to announce it?
Bacteria using arsenic has been known about a few years, and these guys are just a variation of a well-known strain, not something that has been distinct from the dawn of time.
By the way, old horse-traders back in the 1800s used to feed arsenic to scrawny horses. They'd start off with a small dose, and work up. The horses would swell up, and eat up, and wind up looking pretty good. The trick was to sell them before they burnt up.
Lake Mono is the place with all those weird formations sticking up. Those formed underwater, and the lake level was lowered by humans.
Posted by: Steve LaBonne
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December 2, 2010 6:21 PM
It's some really cool biochemistry and yet another demonstration of the amazing metabolic versatility of bacteria. That's good enough for me.
Posted by: dabada
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December 2, 2010 6:25 PM
That's not right, none of these amino acids contain phosphorus. Their molecular formulas are:
serine C3H7NO3
tyrosine C9H11NO3
threonine C4H9NO3
If I remember biochemistry right, none of the amino acids contains P, and that was one of the key facts that lead to the discovery that DNA and proteins are two distinct things: (some) proteins contain sulfur but no phosphorus and DNA contains P but no S.
Maybe PZ meant that proteins that have a high percentage of those amino acids usually also contain phosphates or something else but didn't explain himself well?
Posted by: finkel.avi
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December 2, 2010 6:28 PM
Everybody knows it's not CHNOPS, it's SPONCH.
Posted by: Steve LaBonne
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December 2, 2010 6:29 PM
dabada, those are the aa's that can be and often are phosphorylated, by the enzymes called protein kinases. This is an important biochemical control mechanism.
Posted by: Sven DiMilo
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December 2, 2010 6:32 PM
Those three amino acids are the most common sites for phosphorylation of proteins; presumably PZ meant that some phosphorylated proteins were arsenicated instead. I agree it's baffling as written.
Posted by: BEG
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December 2, 2010 6:35 PM
This was also a pretty good explanation in layperson terms: http://www.astrobio.net/exclusive/3698/thriving-on-arsenic
I coudln't understand all the wild speculation until I took a look at *those* announcments. Whups :)
#17 -- I can't log in using open id, either. Drives me nuts. Typepad was the only thing that seemed to work (no twitter option, and I won't use facebook for *anythign* but facebook) and I don't care for it, but...
Posted by: Gordon
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December 2, 2010 6:35 PM
If there's one flaw in saying "we'll make an announcement in 2 days about exobiology" it is that anything less than an alien mothership will fall short of the hype...
Posted by: Sven DiMilo
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December 2, 2010 6:36 PM
"I'm a doctor, not a bricklayer!"
heh. now that's exobiology!
Posted by: dabada
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December 2, 2010 6:41 PM
Thanks Steve LaBonne and Sven DiMilo. Yeah, the way he wrote it sounded wrong to someone without much biochem knowledge and I figured that he probably meant something else, but I couldn't guess what. Now it makes a lot more sense.
Posted by: joelion
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December 2, 2010 6:41 PM
PZ - the NASA release says Mono Lake has been isolated for 50 years
http://www.nasa.gov/topics/universe/features/astrobiology_toxic_chemical.html
Does the Science article mention if they think this behavior has evolved in the past 50 years? If so, does this make it any more remarkable? Or is that a reasonable amount of time for bacteria to evolve such a trait?
Posted by: geralcorasjo
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December 2, 2010 6:41 PM
I watched the conference live online and I thought that exact thing too. My skeptical bull shit-o-meter went off. Before I stick my neck out there, let me say I support NASA and I want to see them get more funding but..
The woman who was the face of this event was young, attractive, and enthusiastic. I loved that a young woman is in the light for this but I feel for NASA she will be a convenient poster girl for funding. Repeatedly she referenced how she was 'early in her career' and had '15-20 years' ahead of her where she was going to pursue this subject. The panelists did not hesitate to offer what this discovery meant in the search for ET, all the funding dollars they're going to need, all the discoveries this will create.
All I heard during this conference was "We're still relevant. Please stay tuned and continue to fund us."
Posted by: Blattafrax
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December 2, 2010 6:42 PM
@dabada
The amino acids PZ mentions can have a phosphate (PO42-) attached - or not. Its a convenient way to change the charge and size of the amino acid. In changing this, the structure and therefore function of the protein containing that amino acid changes.
There are proteins in cells that add (kinases) or remove (phosphatases) phosphates on other proteins - catalytic enzymes, cell surface receptors, kinases/phosphatases themselves, etc. It's a very convenient way to regulate the work of these proteins. With kinases acting on kinases (acting on other kianses) though, it can create _extremely_ complex networks of interactions that are usually not well understood. Which makes it much more interesting.
Posted by: evilDoug
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December 2, 2010 6:43 PM
"geologically young lake"
Oh Greek letter #23! So much for the opportunity to made reference to Arsenic and Old Lakes.
~~~~
Casecob @ #22 - just the sort of thing I was thinking about. Lots of opportunity for lots of additonal research.
It may only be one trick, but it is a good one.
~~~~
I wonder how long it will be before the woo merchants will jump on this and start marketing the bacterium as some sort of cure-all. Maybe blend it with A. flos-aquae from Oregon.
In the mean time, we could use some here. Just feed the trolls a little each time they show up.
Posted by: Barbara3
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December 2, 2010 6:43 PM
Sorry to be off topic, but murderous fossil cephalopods are worth a moment's thought.
http://pygs.lyellcollection.org/content/58/2/81.abstract
Posted by: Randomfactor
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December 2, 2010 6:52 PM
...the biologist looked disappointed, and God said, "hey, I sent you an Antarctic Martian meteorite and an arsenophile bacterium..."
Posted by: Westcoaster
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December 2, 2010 6:54 PM
I think NASA badly bungled this story. There are stories all over the internet about how they'd found an organism with a totally new biochemistry. Those stories are still up, even though they are incorrect. I listened to the press conference expecting to hear evidence of a totally separate origin of life on earth, which would be fantastic. Instead we got a modification of known biochemistry, possibly quite interesting, but not remotely in the same league as a separate origin for life. I was very disappointed.
The problem could easily have been avoided if the announcement of the press conference had included a brief summary of the story. Instead NASA opted to build suspense and hype by being secretive about it.
Posted by: potsdamsc
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December 2, 2010 6:55 PM
No love for histidine? ;_;
Especially considering how important it is for bacterial two-component signaling...
Aside from that, it's a magnificent article as always.
Posted by: dabada
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December 2, 2010 6:57 PM
Thanks for the explanation, Blattafrax. I understand what he meant now. I probably wouldn't have thought twice about it if the sentence had been worded differently, like "these amino acids are often phosphorylated". The "contain" made me think too literally and it puzzled me.
Posted by: gregorycolby
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December 2, 2010 7:07 PM
Even the much-reduced-from-pre-announcement-speculation hype by NASA has me scratching my head. I'm with PZ: this is very cool, but it's cool-if-you're-into-microbiology-or-biochemistry-cool, not changes-the-way-we-think-about-life cool. NASA is talking this up as though it should transform our expectations of what extraterrestrial life might be like, but I don't see how that could be. This is an example of an entirely familiar form of life that has the remarkable ability to survive, not thrive, with As standing in for P in much of its biochemistry. There are lots of directions to take this in, but looking for extraterrestrial life or even shadow biospheres on earth? Color me unconvinced.
It's not as though speculation about alternate chemistries for life is anything new, either; people have been talking up silicon as a replacement for carbon for decades. This is admittedly less of a dramatic (and much less improbable) study, but it doesn't give us sufficient reason yet to think that we're missing something.
But then, I'm one of those boring, cranky biologists who thought that we had done all the testing for life on Mars that we needed to when we got the answer back for "Liquid water: Y/N?"
Posted by: Greg Laden
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December 2, 2010 7:08 PM
Well, no, it is earthshaking and exciting and important. This is really really cool science.
It's rather a shame that the hype ... that real live living life stuff was found on some moon or planet, or that an organism heretofore unknown on earth was discovered in a swamp in California ... has caused the need for a wet blanket (and that does require the wet blanket, of course) but the find itself is very, very cool.
Posted by: BEG
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December 2, 2010 7:09 PM
Oh hey, those billboards?
NY Drivers Caught in Christmas Billboard Feud
Pretty amusing.
Posted by: Jaycubed
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December 2, 2010 7:12 PM
I've already had several people ask me about the "extraterrestrial arsenic lifeform" after seeing some teasers from NASA fans. I told them I would want to wait & see. Not a surprise it's nothing of the sort.
Thanks PZ for the clear explanation of what was actually discovered. I'll be able to enlighten some friends and bum out some of my more ET hopeful acquaintances.
Posted by: David Marjanović
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December 2, 2010 7:18 PM
Liar !! Everyone knows it's CHONSP.
Leads to magic formulas like "Ras – Raf – MEK – ERK!"* and to things like the MAPKKK (matrix-associated protein kinase kinase kinases).
* I once had to learn that signaling pathway by heart. *sigh*
QFT!
Posted by: kelseymh
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December 2, 2010 7:18 PM
See the supplemental material from the paper in Science. Figure S1 shows the phylogenetic tree for GFAJ-1 based on 16S ribosomal RNA.
Posted by: Andrew G.
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December 2, 2010 7:19 PM
@17, regarding openid and blogger:
There's a bug somewhere (in MT?) that causes it to get the openid server page for blogger wrong. You can work around this (as I demonstrate here) by, when you get the error message page, changing the url from "openid-login" to "openid-server" (leaving all the rest of the url the same) and hitting enter.
Posted by: Turdus
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December 2, 2010 7:24 PM
My first thought was that I hope the migratory birds that stop at Mono Lake are not getting dosed with arsenic from accidentally ingesting these bacteria.
@ #42: Arsenic & Old Lakes indeed!!!!!
Posted by: Josh Andrews
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December 2, 2010 7:27 PM
Wasn't arsenic used by some athletes, before steroids came on to the scene, to boost performance. If they took a small enough amount they would win the race. Too much and they die. Given that this shouldn't be much of a surprise.
Posted by: Nerd of Redhead, OM
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December 2, 2010 7:27 PM
The size difference between a row 2 element and a row 3 element is greater than for a row 3 element and a row 4 element. Silanes (Si-Si bonds) only form short chains before becoming unstable. Phosphates and arsenates are much closer in size.I remember that quote from the show back from the 60's when that was first used for patching up the Horta.Posted by: =8)-DX
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December 2, 2010 7:29 PM
Thanks for this post... my local(CZ) web news site showed up an article on this (with exactly the information you debunked) and I thought: lets check Pharyngula (and immediately though Oh! PZ may have other more important things to deal with, he might not have seen the news yet!) and I was pleasantly surprised to get a scientist's view on the matter so quickly..
Even so, interesting new discoveries make for interesting mind-boggling!
Posted by: Hank Fox
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December 2, 2010 7:37 PM
A couple of the early stories on the event referred to Mono (pronounced MOW-know and not MON-o) Lake as "deadly poisonous," which it is not.
True, the lake water is so alkaline as to be undrinkable, but the lake is full of algae, trillions of tiny brine shrimp (sea monkeys!), and swarms of alkali flies. As a result, it's one of the richest migratory bird sanctuaries in North America, playing host to something like 2 MILLION waterbirds, including 35 species of shorebirds. (Check the Wikipedia entry for Mono Lake for more.)
The lake takes its name, in case anyone wonders, from that of a Native American tribe that once lived in the area.
If you ever get to visit Yosemite National Park in California (a half day's drive from San Francisco), Mono Lake is about 12 miles east of the park's eastern portal.
It’s also weirdly beautiful.
Posted by: Hank Fox
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December 2, 2010 7:41 PM
Huh. My "weirdly beautiful" link didn't work.
I'll try it this way:
http://www.google.com/images?q=mono+lake&oe=utf-8&rls=org.mozilla:en-US:official&client=firefox-a&um=1&ie=UTF-8&source=og&sa=N&hl=en&tab=wi&biw=1244&bih=837
Posted by: Rey Fox, Bird Caller Guy
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December 2, 2010 8:24 PM
But is it true that you can catch mono from swimming in there?
Posted by: Jadehawk, cascadeuse féministe
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December 2, 2010 8:27 PM
a science post? I thought this was an atheist blog? I really used to like reading this blog for all it's beautiful insights into the follies of religion, but now I'm gonna have to find a new atheist blog that isn't littered with all this biology and science stuff.
Posted by: Rorschach
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December 2, 2010 8:28 PM
That and bacteria making babies every 20 minutes would have given selection plenty to work on, I assume.So how is this different than what happened to Lenski's E.Coli, and not just evolution in action, rather then a de novo way of building lifeforms ?
Posted by: Tim, not my real name.
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December 2, 2010 8:33 PM
Buzzkill PZ. I was so hoping this was how the rapture begins, and I really wanted to get excited about bacteria.
Thanks for explaining this. Once I saw Faux news was onto the story, ironically that's when I started to pay attention.
Posted by: First Approximation, L'esprit de l'escalier
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December 2, 2010 8:43 PM
Interesting, but definitely over-hyped.
Posted by: wyogold
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December 2, 2010 9:25 PM
This is worthless science by press conference.
Their method to purify the DNA is laughable. *Any* halfway modern lab would use a cheap kit, which would yield far more pure DNA than a post-phenol chloroform fraction. Then (a restiction digest of) the DNA should be analyzed by a southern blot, which should reveal radiation originating from the As73 in the DNA.
Seriously, this should never have been published.
Posted by: wyogold
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December 2, 2010 9:32 PM
This is worthless science by press conference.
Their method to purify the DNA is laughable. *Any* halfway modern lab would use a cheap kit, which would yield far more pure DNA than a post-phenol chloroform fraction. Then (a restiction digest of) the DNA should be analyzed by a southern blot, which should reveal radiation originating from the As73 in the DNA.
Seriously, this should never have been published.
Posted by: Sven DiMilo
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December 2, 2010 9:42 PM
The correct headline, as I opined @ Yong's, would be something like:
Mono Lake bacteria may be able to build their DNA using arsenic instead of phosphorus when forced to do so in the lab.
Posted by: Ike
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December 2, 2010 9:47 PM
Hey, i think having arsenic instead of phosphorous in the backbone of DNA is absolutly mindblowing. We all now life is tough and can endure in the most extreme conditions. But this is the first time something else rather than the usual chemicals is found in the makeup of vital biomolecules (and what's more vital than DNA?)
PZ Myers says:
"Arsenic already participates in earthly chemistry, badly. It's just off enough from phosphorus to bollix up the biology, so it's generally bad for us to have it around."
OK, so what? Nobody said it wasn't an adaptation and that it's easy to imagine a mechanism to how it came to be. But the thing is, it's still quite unique. Maybe it's no so easy to substitute one of CHNOPS from the the backbone of the DNA (the molecule that fails with the slightest mistake). And this shows not only that life is hard (we know this already) but that is can be made of other chemicals at it's most basic level. And this is HUGE. No?
Posted by: elzoog
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December 2, 2010 9:54 PM
In other words, somebody lied. The fact that the bacteria is unremarkable is forgivable, but to tell people that it was extraterrestrial was a lie.
Whoever it was that lied should be called out on it.
Posted by: Ike
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December 2, 2010 9:56 PM
Jesus, some of the comments here are full of venon (arsenic?).
Posted by: ColonelZen
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December 2, 2010 10:15 PM
From the hype in the nerd press, I was expecting them to roll out a dissecting table with ET broken down on it (slight exaggeration).
The real message, I suspect, was "there are attractive women in science, doing interesting and important things". A good message overall, methinks.
The undying cynic in me wonders plaintively, having a daughter in grad school and knowing somewhat of the story about how grad students and post-doc researchers are used as virtual slave labor in many institutions, if this isn't a subtle, "keep wearing those chains! You too can hit the research lottery to a tenure track position someday" message.
While it may have been worth a press release contemporaneous with the paper's publication, and an orbit or two around the seminar circuit with local publicity for Dr. Wolfe-Simon, and maybe a TED talk or two - it *is* important work, if not - to the lay public - earth shattering. Now from a biological and biochemical point of view, if not for the tone of our host's post, I would have thought (though not myself a scientist) that it would be worth a bit of excitement. Dr. M are there other oddities in life *this* significant? I got the definite hint from the conference that FWS thinks but cannot yet prove that the phosphorous-arsenic transposed DNA is taking part in active reproduction of the bacteria. That, I would think is worth a shot or two of the good stuff.
-- TWZ
-- TWZ
Posted by: Sven DiMilo
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December 2, 2010 10:16 PM
For comparison, radioactive Rubidium isotopes have long (> 50y) been used as biochemical Potassium tracers. Any pair of element-and-next-heaviest-element of a Periodic-Table Group has such similar chemo-electrical properties that many enzymes treat them similarly. It's just chemistry.
That tolerance for a heavier neighbor-element can evolve, under strong selection pressure for tolerance, is, in the end, NOT THAT BIG A DEAL.
I really think that's what we have here; another extremophile.
*SHRUG*
Posted by: philosopher.animal
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December 2, 2010 10:23 PM
It is true that it isn't arsenic based in the way that people mean "carbon based" (and, science fiction only, "silicon based"). But phosphates are pretty important to us too, I'd think, and these - from what I read in the "podcast transcript" on the Science website at least - was that these bacteria were now arsenate creatures. I don't have access to the original article so I don't know if this means the equivalent of ATP is replaced, or what precisely, however.
I think it is a big deal, and I'm just a philosopher-animal, not a biochemist. I do agree however that the hype (not by NASA itself, as far as I can tell) was ridiculous ...
Posted by: grizzlybaker
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December 2, 2010 10:51 PM
One wonders if the bacteria are particularly susceptible to Head & Shoulders.
Posted by: Ctenotrish
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December 2, 2010 11:58 PM
"Arsenic and Old Lakes" - y'all are awesome! I am pretty sure we need a T-shirt. So funny :)
Posted by: MadScientist
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December 3, 2010 12:49 AM
I'd like to know how the animals in that lake (and other alkali lakes) tolerate the harsh alkaline conditions. You wouldn't need soap to wash your hands in that lake - just put your hands in and rub - the oils in your skin (and lipids in cell membranes) will be converted to soap. You'll need a lot of fresh water to rinse your hands afterward though.
Posted by: Rosie Redfield
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December 3, 2010 12:59 AM
From the Supplementary Material Fig. S2 it looks like the cells grown in medium with arsenic but no added phosphorus nevertheless contained 100 times as much phosphorus as arsenic. This suggests that the cells were growing, very slowly, on the 3.1 µM phosphate in the 'no-added-phosphorus' medium, and PERHAPS incorporating small amounts of arsenic into various phosphorus-containing molecules.
Posted by: heygetthis
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December 3, 2010 1:07 AM
A question about the formation of additional vacuoles - is energetic favorability the mechanism for increasing surface:volume ratio to deal with the water instability of arsenates? Does it represent a phase transition subject to threshold effect, such that lesser arsenic concentration would be insufficient to result in the requisite surface:volume ratio for viability?
Posted by: drhozmail
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December 3, 2010 1:11 AM
So arsenate lifeforms weren't found on Uranus? pity...
Posted by: MidChaos
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December 3, 2010 1:21 AM
Rather than just take Mr. Myers word as gospel, wonderful though he so often is, I did what I imagine he’d rather I do in most cases, and I actually went to an expert scientist - and actual microbiologist - and asked for a breakdown of all of this. She was not in agreement with Mr. Myers’ blog post, to put it mildly. She said that he is tremendously downplaying the importance of this discovery, if not indeed misunderstanding it; she elaborated on this at length, more than I could follow, in fact, but the following is what I managed to get her to specifically put down for further consideration.
First, she directed me to one of the articles the actual experts were passing around today in the labs - http://www.nature.com/news/2010/101202/full/news.2010.645.html - that also appears to have more to say about the impressiveness of this discovery. That article included this bit she wanted to stress: “The culture did not grow at all when deprived of both arsenate and phosphate.” It goes on: “When the researchers added radio-labelled arsenate to the solution to track its distribution, they found that arsenic was present in the cellular fractions containing 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.”
She then explained: “It’s not that they tolerated the aresenate, but that they used it. This has never happened before.” She added: “By labeling the arsenate, they can actually see where the arsenate goes, specifically. Otherwise, the cell could theoretically have had a mechanism to just tolerate, not use, the arsenate. We have techniques that have been around for decades that are used to separate various cell components (DNA extraction, lipid extraction, etc.) in order to study these fractions.”
She pointed out this section from the Nature article also: “The team used two different mass-spectrometry techniques to confirm that the bacterium's DNA contained arsenic, implying - although not directly proving - that the element had taken on phosphate's role in holding together the DNA backbone. 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.”
She further explained the significance of this, and it is beyond what Mr. Myers apparently underplays: “Until they grow DNA crystals with arsenic, they will not really be able to ‘prove’ that this is happening. Scientists often have a hard time speaking in absolutes and say things are ‘suggested’ when in fact they are all but proved. In this case, arsenic has NEVER been part of DNA fractions, so finding it as part of this organism’s elemental nucleic-acid make-up shows that the arsenic is present, which ‘implies’ that it is being used to replace the phosphorus in the backbone (due to its absence). Yes, I’m looking forward to seeing how this effects the DNA because of size considerations of the arsenic, but it’s still quite a discovery.”
This is in fact a major discovery in terms of the search for ET life as well. Derrick Pitts, chief astronomer and planetarium director for the Franklin Institute, was just talking about this on Keith Olbermann’s show. He elaborated on the further importance of this discovery: “We’ve been able to determine that the six basic building blocks for life are not actually cast in stone, so the model that we set up for ourselves to look for life in other environments, say in other planets and other things like that, really now can expand itself, and that in turn expands the possibilities for finding different kinds of life in different environments, so we’ve upped our chances of being able to discover life.” You can see the full interview here: http://www.msnbc.msn.com/id/3036677/ns/msnbc_tv-countdown_with_keith_olbermann/#40483819.
Posted by: Ryan
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December 3, 2010 2:25 AM
Well I can't comment really not being a scientist but I did see a show on Discovery about finding extra terrestrial life on earth. Coincidentally it was a couple of months ago. The guys kept refering to a "Shadow biospere." A different tree of life. Normally I'm really skeptical of anything on Discovery especially when they dramatize the whole issue. Still it's really interesting. As for what it really means I don't know. PZ seems to take the opposite tack of the scientists in the program.... Going to have to read up some more I guess. Sigh.
Posted by: SheepdogB
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December 3, 2010 2:41 AM
I knew this would be one of the best places to come for reliable input on this. NASA's PR department is sounding desperate for attention. Tabloid science reporting-whew!
The one thing I like seeing is that scientists are arguing about this-historically that's quite often been the circumstance when really interesting science is done and seriously cool discoveries are made.
Posted by: steverino63
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December 3, 2010 2:59 AM
@geralcorasjo: I didn't have a chance to see the presser; thanks for confirmation of what I suspected.
@GregLaden ... Sorry, not earthshaking. Nor, per NASA's presumed budget push, is it Mars-shaking. As for multiple evolutionary paths, not likely, either: http://socraticgadfly.blogspot.com/2010/12/does-nasa-new-life-form-signal-multiple.html
@glenndavidson ... that's why it has nothing to do with the search for extraterrestrial life, other than NASA budget-fluffing
@Menyambal ... arsenic is in turkeys today for similar reasons. Yep, our overregulating socialist gummint still allows that
@wyogold ... that's probably part of why some of the skeptics are skeptical
@midchaos ... obviously neither you nor your friend read the multiple skeptical comments near the end of the Nature article
And:
@Ike ... like midchaos, you were apparently blinded by the fluffery
Posted by: Octopug
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December 3, 2010 3:03 AM
When I read the news this morning I figured Pharyngula would be the only place to find whether this really was something amazing or not. It's good to see the science laid-out in (relatively) simple terms without all the hoo-ha.
That said, I for one welcome our new arsenic-eating Overlords.
Posted by: Blattafrax
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December 3, 2010 3:18 AM
Sigh. The BBC had this labelled as 'a new form of life'. It isn't. As many have commented.
The paper looks to me like a rush-job. Science accepted it with only half the work done, probably to stop Nature getting it instead. As with steverino63's Barry Rosen* quote above (#84), the experiment that should be in there is purification of the DNA or a phosphoprotein and a proper elemental analysis. This isn't that difficult if the bacteria can be cultured in liquid medium. But what _I_ really want to see is crystal structures.
And talking about crystal structures: This quote from the paper
is just not right. Crystallographers have been replacing sulphur with selenium in proteins for years. OK, not making obligate selenophiles and only 'artificially' replacing sulphur by raising the medium concentration of selenium and lowering the sulphur. Oh... That's what this paper describes.
*Barry Rosen is one of those people who knows a _lot_ about molecular biology. You can trust him to be wise, if not always right.
Posted by: Blattafrax
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December 3, 2010 3:21 AM
Arggh. Submitted too soon.
Having said all that. I don't mean it isn't interesting. It is. Very.
Posted by: Sitly
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December 3, 2010 3:21 AM
Honestly, this is not anything that mindblowing or new, frankly.
A few years back an organism (a marine diatom) was discovered that can metabolize cadmium and put it into carbonic anhydrase, whereas the wildtype enzyme used zinc. So, when researchers grew this organism in conditions with low zinc concentrations but high cadmium concentrations, the organisms were able to survive, whereas other organisms would be poisoned by the cadmium.
It is interesting that in this case arsenic could replace phosphorus in DNA, but it's nothing new. Chemically similar elements performing similar functions--enzymologists have been doing this for ages by trying things like substituting the metal in an enzyme for a different metal and comparing its activity to the wildtype enzyme.
Reference for those interested: Lane, T.; Saito, M. A.; George, G. N.; Pickering, I. J.; Prince, R. C.; Morel, F. F. M. "Isolation and Preliminary Characterization of a Cadmium Carbonic Anhydrase from a Marine Diatom" Nature, 2005, 435, 42.
Posted by: flowgisto
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December 3, 2010 3:23 AM
Everybody is talking about the structural significance, but if it's true that arsenic has been incorporated in the metabolic processes, the thermodynamic implications are huge. Yes, it's cool to have DNA with arsenic, but don't forget that the energy stored in phosphate bonds is the primary way that our metabolism has to transfer energy. Change the element and you change the enthalpy of those reactions, and if the organisms were able to adapt the ridiculously fine tuned network of reactions, I for one would be impressed. Just think of the implications for protein phosphorylation!
Posted by: Bill
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December 3, 2010 3:32 AM
Thanks for this PZ. I deflated some balloons on Facebook this morning, noting that what they had demonstrated was adaptation (a pretty cool one, too), not a 'shadow biosphere', then went on a rant about how the media (and some scientists) will sensationalise these sorts of things.
Glad to know I was right - given I was just working off the media reports (which did have the truth in there, you just had to search it out).
What is does show is that life on this planet is pretty freaking awesome.
Posted by: akshay
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December 3, 2010 3:39 AM
Science is observational only,and this research gives new perspective to look at what popularly known as Life .Please give time to go through last para ,where I tried to talk to you regarding this blog.
Arsenic wants us to redefine LIFE
Posted by: Blattafrax
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December 3, 2010 3:47 AM
#91
Arsenic is a poor substitute for phosphorus in the same design as has been used on Earth for the last 4.5 billion years. It is as relevant to astrobiology as fitting a wooden leg to an amputee.
Posted by: John Morales
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December 3, 2010 4:23 AM
(Meanwhile, in a in a galaxy far far away, Flattabrax comments: "Phosphorus is a poor substitute for arsenic in the same design as has been used on Terreh for the last 5.4 billion years. It is as relevant to astrobiology as fitting a chitin pedipalp to an amputee.")
Posted by: Al B. Quirky
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December 3, 2010 5:15 AM
Root me dead .. Science .. actual Science (which implies Chemistry of course) on Pharyngula. If Captain Feathersword keeps this up, you'll never get rid of me.
Posted by: John Morales
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December 3, 2010 5:21 AM
[meta]
I'll say this, ABQ: Compared to you, yanshen is interesting.
Posted by: https://www.google.com/accounts/o8/id?id=AItOawnG39uMFt69kwCKZ8DoxtmMCvmzr5chx94
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December 3, 2010 5:21 AM
Excellent post! Thank you PZ Myers.
(And I not one of your usual fans.)
Posted by: MidChaos
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December 3, 2010 5:50 AM
@steverino63: I wasn't "blinded by the fluffery." I asked an actual microbiologist who spent the day talking with other actual microbiologists about this entire study - not a regular biologist, and not a chemist as the "skeptic" who wheeled out there was. In fact, it doesn't sound to me like you read what this microbiologist was pointing out well, nor does it sound like you read the several ways in which the conference skeptic himself said earlier that he could be wrong, and indeed ways in which he pointed out that arsenate could work better in certain environments.
But this isn't my field - I admit that - so that's why I conferred with people who do actually carry out this work. You can come here and swallow things whole hog if you want to, even when they are beyond the specific area of scientific work of the blogger, and even when they are demonstrably incorrect assessments in some cases, but I will continue to ask my questions of the actual microbiology experts.
And might I add, you sir are a jerk - there was no excuse for your sorry tone. If losing readers is what Myers wants, then allowing commenters like you to skulk around to bully people who offer a dissenting view is 100-percent the way to go. It is indeed rather a scientific faux pas for Myers to belittle the discovery of scientists in another field, and it's quite a rude move of you to belittle visitors here - people who simply try to elaborate on and further discuss the subject at hand - the way you did to me and some of the other commenters. But you have fun attacking guests as long as the party lasts; I'm done with this for good.
Posted by: Blattafrax
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December 3, 2010 6:00 AM
@John Morales: I laughed...
But I think you make my point for me - granted in a much more entertaining manner. Our biology is adapted over billions of years to deal with the interesting chemistry of the P-O-P bond. Squeezing As into this instead of P is possible, but the original design is still earth-bound.
A life-form with arsenic-based chemistry is entirely possible and might be more useful where the environment is not dominated by water. But it either has i) very different chemistry from us or ii) is a modified phosphate-based beast.
In the first case, this bug has no interest, in the second, it gives useful information. In both it's "as relevant as fitting a wooden leg to an amputee". For the latter, it might not be very well adapted, but at least you have some insight into how a tree feels.
Posted by: Blattafrax
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December 3, 2010 6:12 AM
@MidChaos.
Don't be such a wuss. You made a very sensible comment and someone thought you overplayed the significance. If you think that was rude, then perhaps this isn't the place for you. Or perhaps people should be less rude. Whatever. Pharyngula is Pharyngula - adapt.
This is a "political" paper on some interesting science. Published to boost Science's readership, but just a trailer for the real information, which will be fascinating. I'm pretty excited about it personally, but it's not the discovery of a new life-form or of any relevance to other life-sustaining chemsitries.
Posted by: John Morales
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December 3, 2010 6:21 AM
Blattafrax, thanks.
Your good humour is appreciated.
ceteris paribus is not a good null hypothesis. The bounds of what constitutes "life as we know it" have been expanded. And yet, we make so many (implicit) assumptions.
So, yes, there's merit to the claim that this "impacts" (ugly word, that) exobiology, though maybe not so much astrobiology.
Posted by: Blattafrax
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December 3, 2010 6:37 AM
In the same way that artificial limbs do?But point taken (and has anyone got another horse? This one wearing out.)
Posted by: PenguinFactory
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December 3, 2010 6:46 AM
This is yet another case where relying on the mainstream media for your science information is a bad idea. Early reports made it sound like these bacteria were naturally using arsenic instead of phosphate for their entire DNA backbone, constituting a genuine shadow biosphere seperate from everything else on Earth.
Still, the fact that anything can do this at all is very interesting.
Posted by: lucky_luc
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December 3, 2010 6:50 AM
http://imgs.xkcd.com/comics/arsenic_based_life.png
Posted by: pilcrow
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December 3, 2010 7:01 AM
It's still cool, if a bit less life-changing than the mainstream media would have us believe.
Posted by: semopcoes
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December 3, 2010 8:35 AM
Hooray for natural selection, a phrase conspicuously missing from the news reports I saw. Kudos to the NASA scientists who thought up the neat prediction and experiment to test it. And once again, a big, fat raspberry to clueless science journalism.
Posted by: stripey_cat
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December 3, 2010 9:19 AM
My personal metric for how cool some release is is how long I burble about it. This one got a couple of hours (on and off) between me and the boyfriend, and will probably be resurrected tomorrow when we've got a biochemist friend round to dinner. So not totally earth-shattering, but still pretty damn cool.
And, after all, as a layman, cool science is really what I'm looking for!
Posted by: https://me.yahoo.com/a/AKp_B_gSkpRDRUl5yBtgnnB0OHZG#94c23
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December 3, 2010 9:53 AM
I can see why this isn't really a big deal. I mean, it's just your basic lake...
*ducks*
Posted by: Schenck
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December 3, 2010 10:09 AM
I for one was totally blown away by this announcement. This is a species of bacteria that uses Arsenic to build its DNA. DNA is a pretty darned conservative molecule, swapping out components of its backbone /should/ be a big no no. The science textbooks /did/ get re-written on this one, you can have genetic molecules that don't use something as universal as phosphorous.
As far as some people saying that this never should've been published, I just feel that that is totally wrong. This is a BIG discovery. Describe the structure of DNA. Now you have to us Arsenic (true, its very limited).
And yes, maybe the NASA researchers are just a bunch of dummies who had no idea what they were doing and they totally screwed up the analysis, future work can confirm or deny that. Regardless, this paper was the /announcement/ of the finding.
I am really glad that they did this in a press conference, it was exciting. Luckily it was running during a class I was teaching, so my students and I talked about it, and then we watched the announcement and talked about it (we stopped class in the middle to do this).
They got to find out about this major discovery (again, its a /genetic material built out of a different material/) at the same time that most other scientists did. They also got to see that a scientist can follow an idea straight through to completion, from conception to collection to testing, and they got to see that just because NASA scientists made the announcement, doesn't mean that everyone accepts it, because there were researchers that absolutely disagreed about the findings at the conference, and they even argued about it for a bit. This was also really good because my class is an Oceanography class, and some of these researchers were oceanographers, it shows how interdisciplinary science has become.
Press Conferences are for the general public, this was /everything/ that science literacy and outreach should be. The /only/ issue was that people were expecting an announcement of the discovery of extraterrestrial life, but what could NASA do, it was a discovery by their astrobiology workers, and it has big implications for astrobiology. They /probably/ should've added to their initial press release that 'no one is going to be announcing the discovery of extraterrestrial life at this press conference', but that's really just a quibble.
Now, having said that, its really unfortunate that the press has decided to report this as "Arsenic eating bacteria', I don't recall if anyone actually claimed that these bacteria:
(1) can perform Arsenic-based chemosythesis (which apparently was already discovered a while ago)
nor
(2) specialize in Arsenic-ameliorating chemistry (which apparently many organisms do, and this one probably does also)
So the way that this press conference is being mis-reported, it just underlines the need for these sorts of things. When one of the researchers was talking about /d/ and /p/ orbitals, I think most of the world's eyes glazed over,but that's something someone learns about in basic organic chemistry (and that was him trying to /not/ be too technical). We definitely have a science literacy problem on this planet, and poo-pooing 'science by press conference', when its /good/ science like this, isn't helping.
Posted by: cardamomo14
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December 3, 2010 10:13 AM
Well done dear Pharyngula boy...
We already suspected it was a cloud of smoke around WikiLeaks, didn´t we?
Cheers...
Posted by: Jake666
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December 3, 2010 10:31 AM
This article is not revolutionary, but PZ didn't mention the most interesting thing about the results. Bacteria grew on As-/P+ medium, they grew on As+/P- medium (although poorly). They did not however grow on As-/P-. This strongly suggest (even if we consider small contaminations of each medium by phosphorus), that arsenic did partly substitute phosphorus in some crucial biological function. Obviously, this would be nothing more than a side-effect of extreme resistance to arsenic (these bacteria had plenty of phosphorus available in their natural evironment). But apparently the mechanisms for arsenic resistance not only include neutralisation of arsenic that enters the cell, but also increasing its stability when it become incorporated in biomolecules. Also, the article itself doesn't say anything about life on other planets. In fact, it plainly states that the isolated strain belongs to a group of gammaproteobacteria, which is known to contain many arsenic-resistant species.
Posted by: mswzebo
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December 3, 2010 10:53 AM
I’m a microbial ecologist. Years ago (sigh – a decade and a half ago), I was on the island of Tortola with my wife and her PhD advisor, repainting his house after a big storm (and snorkeling, drinking medicinal gin and tonics, and generally marveling at the wonderfulness of life). No radio, no tv, no newspapers (because of some arcane strike or nonpayment problem or some other island thing). One day at a restaurant we found an abandoned island newspaper with an editorial that started with “Now that NASA has discovered life on Mars…” – which of course set us on fire. What did they find? Of course it had to be (will be?) microbial. DNA? Lipids? Amino acids with a particular stereochemistry? Dipicolinic acid (indicative of spores)? What could it have been? It turned out to be the “microbial fossils” which were too small to even contain a lipid-enveloped ribosome, so were clearly non-living - as far as we understand life.
A year later, I interviewed with NASA for a postdoc position. They were trying to design a MARS expedition, and when I heard that I said “Wow – what kind of molecules are you going to look for?” ….and their response was – “We don’t know – what do you think we should look for?” …which was encouraging and vindicating in a sense for a hardworking, passionate, poor academic but also I was hoping they had a great idea that I didn’t know about….
My Thoughts: the research itself is pretty cool. I also applaud them for the press release; I don’t interpret this as self-promotion so much as I think it is scientists reaching out to the public. We all need to do more of this!
Is the research paradigm-changing? Well, I’m in the field, and I have a very hard time believing it’s real, so therefore I guess the answer is yes, it’s paradigm-changing. Not long ago, we didn’t know about ribozymes, or riboswitches, or RNAi…maybe this really is a new window into fundamental biological processes. This may uncover some important fundamental biological processes here on earth that we didn’t know about before. Maybe trace amounts of arsenic are important to many living things.
There are some corollaries, such as membrane lipids that are not phospholipids. These have recently been shown to be common in marine ecosystems (http://www.ncbi.nlm.nih.gov/pubmed/19182781) but weren’t recognized until recently.
I’m a little concerned about the gel in Figure two, though. The +As lane shows a nice tight genomic band, and no RNA. The –As lane is a) grossly overloaded, b) the genomic DNA migrated to a different spot than in the +As lane (not because of supercoiling, as the lead author mentioned during the press conference –this looks way more like high salt concentration…i.e. suggesting that the two protocols for isolateing DNA were different? Unclear – but something weird there.) and c) lots of rRNA is present. If the rRNA were present in +As this might suggest that RNA with As incorporated isn’t susceptible to the RNAse they used during isolation (a cool possibility maybe conferring some selective advantage) but here they show the opposite – the RNA is only present –As. What gives?
Posted by: Schenck
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December 3, 2010 10:58 AM
It also seems like this is one of those great times in science where a study that is REALLY worthy of doing is attempted replication of the original authors results. The bacteria live in a lake inside the US that US scientists wanting to confirm/refute these finds probably can get pretty good access to. Hopefully there's a few labs and researchers out there who are planning out new research in this vein right now.
Posted by: octopod
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December 3, 2010 11:25 AM
PZ, I'm not qualified to opine on the quality of the gels, but I do take issue with your comments about this not illuminating anything in the past. Arsenic solubility is highly dependent on redox state: in modern oceans it is not terribly soluble but in an Archean ocean, with its very low redox state, it was one or two orders of magnitude more soluble, and therefore more available. I don't know about the solubility or redox state of P in pre-oxic oceans, but this does suggest that there might have been some advantage to being able to use As instead of P back then, and this could be a metabolic relic. Possibly not of a whole lot of interest to most people, but I'm very interested in the whole early biosphere thing, and this is quite informative for that.
Posted by: https://me.yahoo.com/a/RpPKBqEQlcJ5XQRljBAUIFZjux1j.QmOoidH#f5707
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December 3, 2010 12:07 PM
I think one thing that needs to be noted here is that these bacteria originally developed in a much less hostile environment, so while they prove that bacteria can survive in a poisonous environment, it does not prove that they can evolve in a poisonous environment. As PZ says, this really has nothing to do with evolutionary development.
Posted by: https://me.yahoo.com/a/RpPKBqEQlcJ5XQRljBAUIFZjux1j.QmOoidH#f5707
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December 3, 2010 12:51 PM
I think one thing that needs to be noted here is that these bacteria originally developed in a much less hostile environment, so while they prove that bacteria can survive in a poisonous environment, it does not prove that they can evolve in a poisonous environment. As PZ says, this really has nothing to do with evolutionary development.
Posted by: hillaryrettig
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December 3, 2010 12:57 PM
Joan Slonczewski's The Children Star is a terrific sf novel about an encounter with a planet full of arsenic-based life forms. (She's my favorite!)
Posted by: Sven DiMilo
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December 3, 2010 1:00 PM
MidChaos@#81 & #97: Your microbiologist correspondent said nothing that Dr. Myers did not (except for pointing out the important negative control treatment.) The only difference was in the judgmental conclusion: this is very cool and important vs. this is pretty cool but not that important.
You bought the spin. This is meaningless rhetoric. Unless the plan* was to completely write off high-arsenic environments as impossible for (presumably independently originated) extraterrestrial life, then this changes nothing. Nothing!
Totally speculative. Zero evidence.
Agreed. It reports an apparently unusual phenomenon, but includes few detailed analyses and no plausible mechanism.
Like what? If arsenate has identical electrical properties to phosphate, why would a protein react diferently to arsenophylation than phosphorylation?
A sucker for credentialism and the argument from authority. Dude. The argument is about biochemistry, not microbiology.
Please specifically identify one (1).
You're a fool. The discovery itself is still rather dubious, and in any case it was nowhere belittled. What was belittled was the ridiculous game of exobiological telephone that resulted from NASA's non-announcement.
No, this has not been shown. At best, it is a species of bacteria that can use arsenic to connect nucleotides when forced to do so under laboratory conditions.
*and I doubt this was the plan; it would have been a mighty stupid one
Posted by: puf-almighty
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December 3, 2010 2:06 PM
That says, to me, that nothing interesting happened here. If there wasn't an analysis that showed, for instance, that the phospholipids had become arsenolipids, then why should we expect that the arsenic was included in the biochemistry at all? Why not just assume, parsimoniously, that they were sequestering the Arsenic in those big vacuoles?
Posted by: Sal Bro
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December 3, 2010 2:23 PM
puf-almighty,
I was wondering the same thing. I think Jake666 partly answered it in #110:
It doesn't rule out the possibility that As was being sequestered in vacuoles, too, but it does suggest that the cells were using As in other ways.
Posted by: nicholas.bauer
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December 3, 2010 3:51 PM
I've only read some of the later comments, and a couple other aspects of the paper are not being mentioned correctly.
Also, yes this paper was rushed. The disclaimer for ScienceExpress articles is that they are not the final, published version.
Also, she also has more results toward a second paper which she hopes to have submitted in a year or so, which she claims allows her to be more certain of the findings of this first paper.
The paper also found that in phenol-extracted fractions (where essentially only DNA should be present), mass spec analysis demonstrated that the As:P ratio was ~1:1. Either way arsenic was strongly associated with the DNA.
The paper also found that As X-ray spectra was consistent with As-O and As-O-C covalent bonds.
Finally, this is an important discovery for the search for life and understanding the requirements for life and the origin of life. If we saw a planet high in arsenic and low in phosphorous (can't do all that much analysis from this distance), we probably would have written it off.
What this work does is show that there are some conditions in which arsenic can take the place of phosphorous. The reason why so many are skeptical is that, according to what we know, something like this just shouldn't happen at all. If further research confirms these results, it provides another possible avenue to explore for the origin of life and extends our understanding of what life can look like, not just what we might imagine or hypothesize it to look like.
No, it isn't THAT exciting. But it is that exciting.
Posted by: Schenck
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December 3, 2010 4:14 PM
I really think that the researchers on this paper need to be given more credit than they've gotten so far. They are (obviously) aware that elements can substitute for one another in biomolecules, they are aware (obviously) that Arsenic is a weaker link than Phosphorus, and all the other reasons why this sort of thing /should not/ happen. BUT, they theorized, it can and it does, and a great way to test that is to go out to the types of environments that could contain such critters. Lo and behold, they find them.
If this is a 'non-meainginful, expected result', then, please, anyone, collect samples of bacteria from places where there are normal levels of Arsenic, grow bacteria in an Arsenic rich medium, and show that they incorporate Arsenic into their genetic material. One of the /really/ great things about this research is that it /should not/ have been done, a sober, serious scientist would probably say, like so many (but not all of those who disagree with this research), that Arsenic can't substitute into an organisms genetic material, anymore than silicon can replace carbon. The paper authors should absolutely be congratulated for going against the scientific orthodoxy on the subject. NO ONE predicted that there are bacteria out there that incorporate Arsenic into their genetic material, DESPITE there being plenty of research on Arsenic biochemistry.
Sven DiMilo: "At best, it is a species of bacteria that can use arsenic to connect nucleotides when forced to do so under laboratory conditions."
This means that its a species of bacteria that uses Arsenic instead of Phosphorus to build its DNA, a totally unexpected, practically unbelievable discovery. And it is rather disingenuous to suggest that these bacteria were forced to do this: that they don't do it 'naturally', its not a coincidence that the only time anyone has shown Arsenic substituting for Phosphorous in genetic material /just happened/ to be with a species of bacteria that coincidentally lives in an Arsenic contaminated environment; this happens in nature. These researchers theorized, despite what practically anyone would have previously thought, that Arsenic can substitute for Phosphorus, they figured out where such organisms might occur, and they found them, they did not just happen to induce this ability to have Arsenic in the genetic material in their experiments.
Posted by: Ike
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December 3, 2010 4:43 PM
steverino63 - Post 83
@Ike ... like midchaos, you were apparently blinded by the fluffery
Sorry, i work with microbes. I get exicted like a kid with these things. Anyway... i'll wait for confirmation (i'm sure the critics are already rushing for an epic debunking of NASA claims about this). DNA in the backbone of DNA, in organism living is some natural niche, would be a huge find. I hope this gets confirmation.
Posted by: Ike
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December 3, 2010 4:45 PM
Where you read "DNA in the backbone of DNA", plese read arsenic in the backbone of DNA.
Posted by: flutterdrew
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December 3, 2010 5:32 PM
This blog is great. It brings me back to my undergraduate, pre-med years.. Thanks for your perspective. I've shares a link to this blog with the community at http://bleditor.com with a few other blogs on this discovery.
Check it out at http://bleditor.com/bledit.php?bleditID=15466
PS - I love the headline of this blog: "Evolution, development, and random biological ejaculations from a godless liberal"
Posted by: stevekass
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December 3, 2010 6:43 PM
Regarding what nicholas.bauer said in particular:
Yes, the As:P ratio was high in the phenol extract of the +As/-P sample. But, the ppb values given in Table S1 (supplementary materials) seem to indicate that the reason was a drop in phosphorus (by 99%), but no particular uptake of As due to the arsenic "diet."
In the -As/+P phenol: ~250000ppm P and 3700ppm As
In the +As/-P phenol: ~4500ppm P and 4600ppm As
Same order of magnitude of arsenic levels in both phenol samples. Worse yet (though I suspect I'm misreading something, because I don't understand the <20ppb figure. The text mentions 1ppb detection and "<1" appears below), the DNA/RNA extract of +As/-P shows no measurable arsenic, while +As/+P has 118ppb.
Adding to my skepticism, the authors report X-ray analysis only for the +As/-P sample. This makes little sense. If they hypothesized that +As/-P was unlike -As/+P, why didn't they run this key test on both samples? Why is -As/+P missing from Figure 3, despite appearing alongside +As/-P in Figure 2 (and as data in Figure 1)? Could it be that its "Figure 3" would have appeared indistinguishable (except for the P panel) from +As/-P ?
If I had to guess, and I think I have reason to be cynical, what this research finds is that there's a slight bit of arsenic in some biochemicals of some bacteria that grow where there's a lot of arsenic. If you take away phosphate and give them arsenate instead, they get bloated and sick (Fig. 1), their phosphorus gets depleted (Fig. 2), and maybe there's just a tiny bit more arsenic in some places it already was (Fig. 2 and Table S1).
Posted by: nicholas.bauer
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December 3, 2010 9:00 PM
@stevekass: I realized after posting that I might have misread the table. They could have been a little more clear/organized with it. I'm thinking they got the +As/-P and -As/+P DNA extract values swapped. Even then, of course, that's much less As than I thought it was saying.
As for the X-ray graph, I thought about why there wasn't a comparison, and I think its because you'd only get any kind of signal if you had arsenic in the first place because phosphorous, as they state, doesn't respond to x-rays in that way, so that figure was meant more to indicate what types of bonds the As was involved in more than anything else.
Still, if the media lacks phosphorous, it does then require arsenic to grow, and it can grow without arsenic just fine. So the arsenic is replacing phosphorous in *some* capacity.
We don't necessarily know if that is "sick" for the cells. It is possible that the vacuoles reduce the water content and that could contribute to the stability of the arsenate esters. But that's just speculation.
Posted by: nicholas.bauer
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December 3, 2010 9:08 PM
Scratch that about swapping values. If As was as low as it is in the -As/+P, and assuming it didn't change, it would be well below the lower detection limit given.
Posted by: As-hole Skeptic
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December 3, 2010 10:24 PM
Things to worry about:
1) The best As:P ratio they got was 7.3:1 in dry cell weight. They are using media with phosphate contaminants (~3 uM). The extremely slow growth rate (20-fold in six days; compared to E. coli roughly 20-fold in 90 min) suggests limited growth that is occurring from phosphate salvage.
2) Their As measurements are unconvincing for ICP-MS. The dry weight of As was measured at 0.19% +/- 0.25 % over eight measurements. The error is bigger than the data. There are numerical fubars obvious in the paper – the ratio of As to P calculated from 0.19/0.019 (Table 1) should not be 7.3.
3) There is no evidence that As is incorporated into functional DNA or RNA and that such As-nucleotide is competent in replication/translation. They have evidence that As is incorporated into nucleic acids. That’s a major leap from there to functionally competent DNA/RNA.
4) Arsenate diesters are unstable in water. The hydrolysis rates for arsenate esters are 10,000 – 1,000,000 times faster than the corresponding phosphate esters. No stability; no genetic information. The notion that water is kept away is curious at best and the hallmark of pathological science at worst.
5) The available redox potentials for As can cause problems as As(III) and As(V) can cycle under physiological conditions… for example, anoxic lake bed sediment. Only As(V) has the tetrahedral geometry needed to mimic phosphate.
6) It’s been known that arseno-ADP, the ATP analog, is not stable in water. Hydrolysis rates have been estimated at 70 min-1. To put that into context, the study of enzyme kinetics using arseno-ADP is challenging as the straightforward water hydrolysis reaction is far faster than any enzymic reaction. How do you get to arseno-DNA without arsenic analogs of ATP?
7) Arsenic accumulation by plants and bacteria has been known for a long time. The organisms have been genetically engineered to sequester high levels of arsenic with the hopes that they can be used in bioremediation. Bacteria are known to generate polymeric material to sequester arsenic.
It would be poor of me to bash this work so harshly without giving an alternate theory, so here goes. There is no As incorporation into canonical, functional DNA. The organism is generating garbage nucleic acid to sequester the arsenic and avoid the toxicity. The garbage nucleic acid is being partitioned into vacuoles and, thus, the cells get bigger. This theory fits the data presented without rewriting any biochemistry. Much as I would love this result to be true I can’t just throw out a whole bunch of very well established chemistry. In support of the authors, the Science paper is fairly muted and only really claims As incorporation into ‘biomolecules.’ The press conference, the media frenzy and the breathless acceptance of As-based life on the other hand… stink.
Posted by: steverino63
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December 4, 2010 3:06 AM
@As-hole 128: Thanks for the additional detail on things like As diesters' and ATP analog's problems with water. I had read general info on that elsewhere, but had not sceen details.
Can you tell Greg Laden, still frothing at the mouth over this, Point No. 1?
Posted by: mswzebo
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December 4, 2010 11:45 AM
w/ regard to As-hole skeptic's post
your #1 - the growth rate reported is not particularly slow for environmental isolates; comparing it to laboratory-grown E.coli under optimum growth conditions is not a reasonable thing to do - like saying cars don't work for transportation because they aren't as fast as jet fighters. Even E. coli grows a lot slower in minimal media or colder temperatures.
#1 continued...your point that they could be scavenging P seems to be contradicted by the fact that they don't grow in -P/-As media. However, the As might serve another role rather than a functional one. For example, the As could induce gene expression of some transporter that was required for scavenging P (maybe?)....thus growth would only occur +As.
@stevekass
you said"the ppb values given in Table S1 (supplementary materials) seem to indicate that the reason was a drop in phosphorus (by 99%), but no particular uptake of As due to the arsenic "diet.""
If you look at the gel in figure two, there are some differences in the DNA extract in lane 2(+As) and lane 3 (-As). One of those differences is that the genomic DNA (uppermost band) migrates slower in lane 3. This can be caused by a high salt concentration or by a high protein concentration. Running a gel takes a few hours ; why didn't they re-run that gel after cleaning the DNA? It may be that the proteins/salts associated with the -As DNA sample are high in P, which would depress the As/P ratio. Also, there is RNA still present in the -As DNA but not in the +As DNA? Why wasn't the DNA RNAsed? I'm not trying to be picky, but I would expect a senior undergraduate to look at that gel and say, "I need to clean up my -As sample and run a lower concentration. I'll send you the new gel picture tonight".
@ As-hole your point #3 - excellent point. - a duplicate, 'faulty' RNA polymerase that sequestered As into junk RNA seems like it would have a selective advantage for an organism living in a +As environment...similarly, polyphosphates are frequently accumulated into vacuoles and these enzymes might evolve to cope with As.
Finally, I disagree that the press conference was junk. Our culture is dominated by scientifically illiterate (and innumerate) people. That isn't going to change unless we try to engage people in the results and the process of science. NASA assembled a team of a)an articulate, young scientist perhaps worthy of emulation, who strove to frame her results and speculate about big picture ideas), b) a high level NASA administrator who was also articulate and did not overstate or politicize the findings as you might have expected her to, c) a contrasting point of view guy(!!!!)- who does this but scientists?!! Guy c) gave the press conference an entirely different feel for me, and it led to discussions about the culture and process of science that were real and had to be worthwhile for young people watching. Intelligent kids disenchanted with political partisan bickering had to find that part compelling.
I was disappointed by the questions afterward - "USA today - we're disappointed you didn't produce a walking, talking alien- do you have a comment on that?" and Brazil somethinsomethin - "What are the practical human applications of this finding?" but hey - we live in a culture where exactly one network covered the conference live, and that network cut off the (articulate, intelligent plain-spoken and interesting) lead researcher mid-sentence to get Bill Nye's take on the findings.
I sure wouldn't want to be the one up on the podium, but hey, I applaud those people up there for trying to educate and inspire. I give them full credit.
Posted by: Sven DiMilo
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December 4, 2010 3:48 PM
Good comment As_hole Skeptic.
Interesting hypothesis.
Posted by: Sven DiMilo
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December 4, 2010 6:42 PM
As for why you might care about Dr. Laden's deep thoughts on this, remember that he's a biological anthropologist.
Posted by: Rosie Redfield
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December 5, 2010 7:11 AM
I've now posted a detailed microbiology/molecular biology critique of their experiments at RRResearch. Basically, they don't have any good evidence of arsenic incorporation into DNA.
Posted by: wasmek
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December 5, 2010 9:47 AM
Yes i agree
http://www.points2shop.com/?ref=uin1286040814
Posted by: billnut
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December 5, 2010 11:09 AM
"Why not just announce it, instead of announcing that they were going to announce it?"
Because they wanted somebody in the room when they announced it.
"In other words, somebody lied. The fact that the bacteria is unremarkable is forgivable, but to tell people that it was extraterrestrial was a lie."
Did anyone at nasa say it was extraterrestrial? I doubt it. Please provide your reference? Sounds more like confussed media speculation. Still pretty remarkable IMO.
"MAPKKK (matrix-associated protein kinase kinase kinases)."
I thought is was mitogen-activated-PKKK. PZ?
Posted by: Bill Door
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December 5, 2010 11:15 PM
PZ, when discussing the elemental composition of lifeforms you did not mention iron. We heme biochemists will not tolerate this; we curse you to having all your Fe-protoporphyrin IX replaced with Zn-protoporphyrin IX. That'll fix you.
Posted by: SkepticCanary
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December 6, 2010 8:29 AM
While I think this discovery is fascinating, it's not exactly earth-shattering. Like any good science, it was predictable.
http://www.skepticcanary.com/2010/12/06/arsenic-eating-bacteria-fascinating-but-not-that-surprising/
Posted by: Cannabinaceae
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December 6, 2010 9:24 PM
This blog entry has a joke at the end of the first (and only, when I looked) comment that I personally think is kind of funny, and relevant to this discussion.