December 28, 2010

Does NASA 'new' life form signal multiple evolutionary tracks

Update, Dec. 28: Here's a lot more on how NASA had motive to fluff this bad science. Read the whole thing, to be sure, but this image ought to say it all:
Inside NASA, some employees have taken to wearing T-shirts emblazoned with the letters "WWED," which stands for "What Would Elon Do?" — a reference to SpaceX founder and Chief Executive Elon Musk, the Internet tycoon who invested his own fortune in pursuit of his dream of sending humans into space.
That's an agency hugely afraid for its future, and probably thinking it needs all the fluffery it can get, or do.

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As reported in the New York Times and plenty of places elsewhere, NASA today unveiled the "discovery" of a new bacterium in which arsenic appears to substitute for phosphorus in both DNA and ATP.

First, before getting to the meat of the header, let's explain the scare quote first, then the italics.

The New York Times notes this bacterium was CULTIVATED to substitute arsenic for phosphorus; it wasn't "discovered."
The bacterium, scraped from the bottom of Mono Lake in California and grown for months in a lab mixture containing arsenic, gradually swapped out atoms of phosphorus in its little body for atoms of arsenic.

OK, so that would leave us a bit skeptical about how relevant this is to multiple evolutionary tracks.

Second, also from the NYT ... the DNA claims haven't fully tested out yet, so this might also be rushed science:
By labeling the arsenic with radioactivity, the researchers were able to conclude that arsenic atoms had taken up position in the microbe’s DNA as well as in other molecules within it. Dr. Joyce, however, said that the experimenters had yet to provide a “smoking gun” that there was arsenic in the backbone of working DNA.

That addresses the appears to replace phosphorus.

Now, let's get to the meat of the header.

A notable sidebar to this story, as written up in detail by Greg Laden, is whether this doesn't open the window to multiple lines of evolution.

I think that's unlikely, even though theoretically possible. Here's why.

Per Nature News, the arsenic-based bacteria were just 60 percent as efficient in growth rate as their original kin. That's a pretty huge efficiency difference. Given that few places on earth, if any, have significantly higher arsenic concentrations than Mono Lake, it would be hard for such bacteria to find an extremophilic location that exempted them from phosphorus-based competition.

Nature News has more on that line of thought:
For example, if phosphate in ATP was exchanged for arsenate, would the energy-transfer reaction that powers a cell be as efficient? In metabolic processes in which arsenate would bind with glucose, would the bonds it forms — weaker than those of phosphate — be as effective? And phosphate groups bind to proteins modify their function, but would arsenate work as well?

All good questions.

And, there's yet more skepticism from Nature News.

First, exactly how is the arsenic working?
To be truly convincing, however, the researchers must show the presence of arsenic not just in the microbial cells, but in specific biomolecules within them, says Barry Rosen, a biochemist at Florida International University, Miami. "It would be good if they could demonstrate that the arsenic in the DNA is actually in the backbone," he said.

Also, he says, the picture is still missing an understanding of what exactly the arsenic–phosphorus switch means for a cell, says Rosen. "What we really need to know is which molecules in the cell have arsenic in them, and whether these molecules are active and functional," he says.

And, how do the arsenic compounds avoid breaking down?
"It remains to be established that this bacterium uses arsenate as a replacement for phosphate in its DNA or in any other biomolecule found in 'standard' terran biology," says Steven Benner, who studies origin-of-life chemistry at the Foundation for Applied Molecular Evolution in Gainesville, Florida.

Arsenate forms much weaker bonds in water than phosphate, that break apart on the order of minutes, he says, and though there might be other molecules stabilizing these bonds, the researchers would need to explain this discrepancy for the hypothesis to stand. Still, the discovery is "just phenomenal" if it holds up after further chemical analysis, Benner adds. "It means that many, many things are wrong in terms of how we view molecules in the biological system."

That then said, per the specifics of how arsenic is poisonous to multicellular life, as (gasp, I'm referencing it again) Wikipedia's arsenic article notes, while this theoretically opens the door to multiple evolutionary pathways, in reality, I can't see that there's a great likelihood of it, at least this particular pathway.

So, this needs a LOT more research. It ain't Pons-Fleischmann trotting out cold fusion, no, but, it does seem ... sketchy, so far. (That said, I'll admit that Wikipedia's article on cold fusion is iffy itself.)

That said, I'm boosting part of my response to Greg into the body of the post here.

First, I am by no means the only person who has said he or she thought the paper, etc., was rushed. To analogize: Bite size chunks can be undercooked and, IMO, this chunk needed more time on the grill.

Second, per me, PZ Myers and many others, there's disagreement on how "spectacular" the trick is, especially given that this was a trick induced in a controlled environment. Again, I note: Mono Lake already has a high arsenic level, and (so far at least) no similar arsenophilic bacteria have been found in the natural environment of the lake. Add in the relative weakness of arsenic bond to phosphorus ones in water, and, at least on Earth, that leaves open the question of just how likely it is.

Now, tying that to exobiology. I don't know what difference, if any, Mars has from Earth in As/P ratios. Given the fact that wasn't mentioned in the presser, the answer is either "little difference" or else "oops, big NASA error." But, short of something like that, a talk of environmental differences, NASA erred again, or "fluffed/hyped," in making the exobiology link.

Oh, and a final note for Greg the commenter - possibly Greg Laden?

From a commenter at Pharyngula:
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. ...

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. ...

6) It’s been known that arseno-ADP, the ATP analog, is not stable in water. ... How do you get to arseno-DNA without arsenic analogs of ATP?

So, sorry, Greg, nice try but you're flogging a dead horse.

Update, Dec. 6: If shoddy research controls and mechanics make an experiment bad science, then this looks to pretty officially be bad science. Note to Greg Laden and other "fluffers" - why continue flogging this? Let's see some more posting at Science Blogs and Discover about how this baby ever saw the light of day, instead.

Update, Dec. 9:More yet on the NASA fluffery angle:

Here's proof of the fluffery - the hed on NASA's annoucement:
"Get Your Biology Textbook...and an Eraser!"

Fact is, as P.Z. Myers, Wikipedia and many other sites noted, arsenic replacing phosphorus in organic compounds, albeit much simpler ones than DNA, isn't even new. As for it actually doing so in DNA, well, the trumpeted NASA experiment doesn't necessarily prove that.

And, NASA's PR machine is still going, in this wire story that connects the iffy experiment to discovery of more habitable planets and more stares:

Meanwhile, more motive for NASA to trumpet itself? Perhaps worries about the successful orbital flight of SpaceX's Dragon. though NASA was kind enough to offer congratulations.

Remember, getting back to the budgetary motive angle, Obama has talked about leaning more on private services to head to the space station.

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Update, Dec. 20:Arsenic exobiology researcher Felisa Wolfe-Simon is dismissive, and in a wrongly, fudging, sense, concerns about hydrolysis of the arsenic compounds in DNA. Seriously, this has gone beyond breathless; this is indeed bad science.

Per Wikipedia's article on alternative life chemistry, linked below, the hydrolysis issue caught y attention the day of the announcement. Obviously, it caught the attention of science professionals, too, and Ms. Wolfe-Simon is left without explanation, so she bloviates.

4 comments:

Greg said...

Just to be clear: This organism (the Mono lake bacterium) itself is an ordinary bacterium that can do a rather spectacular trick. It is the trick it self, as it were, that opens up our thinking into parallel origins on earth as well as refines our thinking for what might be possible on other planets/moons.

Greg said...

Regarding this:

So, this needs a LOT more research. It ain't Pons-Fleischmann trotting out cold fusion, no, but, it does seem ... sketchy, so far.

What you need to understand is this: Research works this way these days. The simple easy discoveries, where a few facts can be quickly uncovered and reported are long over. Research is always published in bite size chunks. There are no papers that come out and answer all the questions for a brand new line of research. Rather, one bit comes out at a time, and each bit justifies further research for the next (via funding) and at the same time exposed what is going on in the data, the reasoning, etc. for critique and development of ideas.

Gadfly said...

Greg, addressing your second comment first: What you need to understand is this: Research works this way these days. The simple easy discoveries, where a few facts can be quickly uncovered and reported are long over.
I am by no means the only person who has said he or she thought the paper, etc., was rushed. To analogize: Bite size chunks can be undercooked and, IMO, this chunk needed more time on the grill.

Then, your first statement: This organism (the Mono lake bacterium) itself is an ordinary bacterium that can do a rather spectacular trick.
Oh, I got that from the start. But, per me, PZ Myers and many others, there's disagreement on how "spectacular" the trick is, especially given that this was a trick induced in a controlled environment. Again, I note: Mono Lake already has a high arsenic level, and (so far at least) no similar arsenophilic bacteria have been found in the natural environment of the lake. Add in the relative weakness of arsenic bond to phosphorus ones in water, and, at least on Earth, that leaves open the question of just how likely it is.

Now, tying that to exobiology. I don't know what difference, if any, Mars has from Earth in As/P ratios. Given the fact that wasn't mentioned in the presser, the answer is either "little difference" or else "oops, big NASA error." But, short of something like that, a talk of environmental differences, NASA erred again, or "fluffed/hyped," in making the exobiology link.

Greg said...

I am by no means the only person who has said he or she thought the paper, etc., was rushed. To analogize: Bite size chunks can be undercooked and, IMO, this chunk needed more time on the grill.

Considering that most of what people have said about this even by your claim is BS, you have no safety in numbers. How cooked a research project is can always be questioned. There is no proper amount. It is always true that a project could have been taken further or published earlier. Post hoc quarterbacking on that aspect is a waste of time.

I'm pretty sure there are A+/P- envoronments in the universe.

Mono lake is not a complete enigma. It is a research site even for people at the LRC (where I was a faculty member for a few years). I'm pretty sure that the research there has been interesting but spotty . If a grad student came to me and said "We have a good handle on the bacterial flora here" I'd make them do pushups.