Arsenic and Old News - Evolution News & Views

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Arsenic and Old News

The media has been buzzing about NASA's claim that scientists that have discovered "life as we do not know it" (MSNBC)--purportedly finding bacteria that can use arsenic instead of phosphorous in its DNA. David Klinghoffer already blogged about this story here, interviewing astronomer Guillermo Gonzalez (who has conducted research on astrobiology) on the find.

The public first became aware of this story last week when NASA announced it would be holding a press conference that would reveal "an astrobiology finding that will impact the search for evidence of extraterrestrial life." NASA's announcement inspired a chorus of speculative excitement among materialists and UFO true-believers alike, who stated things like:

NASA is holding a press conference on Thursday to make an announcement. According to NASA, they will "discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life."

The Internet is abuzz with all types of "guesses" as to what exactly will be revealed. These include: Extraterrestrial life has been discovered on another planet, a microbe that thrives in arsenic has been discovered, life on Saturn's moon Rhea has been verified, among others. ... For those of you who are hoping for a major announcement of the finding of "little green men," don't hold your breath.

The Wall Street Journal reported that "[s]o great was the media stampede that even the White House and members of Congress were calling on NASA to clarify." As USA Today noted, "Mary Voytek, head of NASA's Astrobiology Program, said 'I'm sorry if they are disappointed' for anyone expecting NASA to produce evidence of alien life."

As we've seen, scientific discoveries that could impact questions about origins are often overhyped. Not only were those hoping for "little green men" sorely disappointed by NASA's announcement, but those hoping for any form of "completely alien" life, or even merely an earth-based microbe "that thrives in arsenic" should have been disappointed by the actual facts. We've been receiving questions about this find and thought it would be worth reviewing what was actually found, what critical scientists are saying, and what this episode really means.

What is being claimed in the media?

If you believe what you read in the media, then you'll hear that scientists discovered "a bacteria whose DNA is completely alien to what we know today" (Wired) or even that this "bacteria is made of arsenic" (Wired) which is "capable of using arsenic to build its DNA, RNA, proteins, and cell membranes" (Gizmodo). Another tech website called it "arsenic-based life" which is "very alien in terms of how it's put together" and claimed, "NASA has, in a very real sense, discovered a form of alien life" (io9). Even a Nature news article suggests "you can potentially cross phosphorus off the list of elements required for life."

Of course, the punchline is that this discovery "redefines 'life as we know it'" (Yahoo), and if life can exist in forms radically different from normal life on Earth, then this might demonstrate, as another site put it, "a 'proof of concept' for alien life." And as materialist thinking goes, if life evolved elsewhere on earth, then it could have evolved here. But...

What has really been discovered?

No one at NASA reported the discovery of extraterrestrial life. In fact, the scientists didn't even discover alien life on planet Earth. In most respects it doesn't appear highly different from bacteria we already know -- it's not even a new type of bacteria, as it's a member of a known bacterial phylum, Gammaproteobacteria. This type of bacterium is known to naturally uptake arsenic, which makes it a bit less surprising that the investigators were able to experimentally induce the bacterium in the lab to grow in an arsenic-rich environment.

In fact, it isn't clear that the bacterium is using arsenic in its DNA or even in its other biomolecules. As the New York Times reported:

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.
Similarly, even Science reported severe skepticism of this research:
[Barry Rosen, a biochemist at Florida International University in Miami] says he still has lingering concerns that the arsenic is simply concentrated in the bacterial cell's extensive vacuoles and not incorporated into its biochemistry. He would like to see Wolfe-Simon's team demonstrate a functional arsenic-containing enzyme, for example. Steven Benner, an astrobiologist at the Foundation for Applied Molecular Evolution in Gainesville, Florida, is more skeptical: That GFAJ-1 uses arsenic as a replacement for phosphorus, 'is, in my opinion, not established by this work,' he says." (Elizabeth Pennisi, "What Poison? Bacterium Uses Arsenic To Build DNA and Other Molecules," Science, Vol. 330:1302 (December 3, 2010).)
Likewise, Rosie Redfield, a microbiologist at the University of British Columbia strongly critiqued the paper by writing that "it doesn't present ANY convincing evidence that arsenic has been incorporated into DNA (or any other biological molecule)." She identified several aspects of the experiment which might cause the bugs' DNA to artificially appear rich in arsenate, writing:
The two atoms have very similar chemical properties, but bonds with arsenic are known to be much less stable than those with phosphate, so most researchers think that biological molecules containing arsenic rather than phosphorus would be too unstable to support life. ...

The Methods describes a standard ethanol precipitation with no washing (and no column purification which would have included washing), so I think some arsenate could easily have been carried over with the DNA, especially if it is not very soluble in 70% ethanol. Would this arsenate have left the DNA during the gel purification? Maybe not - the methods don't say that the DNA was purified away from the agarose gel matrix before being analyzed. This step is certainly standard, but if it was omitted then any contaminating arsenic might have been carried over into the elemental analysis.

.... Bottom line: Lots of flim-flam, but very little reliable information. The mass spec measurements may be very well done (I lack expertise here), but their value is severely compromised by the poor quality of the inputs. If this data was presented by a PhD student at their committee meeting, I'd send them back to the bench to do more cleanup and controls.

There's a difference between controls done to genuinely test your hypothesis and those done when you just want to show that your hypothesis is true. The authors have done some of the latter, but not the former. They should have mixed pregrown E. coli or other cells with the arsenate supplemented medium and then done the same purifications. They should have thoroughly washed their DNA preps (a column cleanup is ridiculously easy), and maybe incubated it with phosphate buffer to displace any associated arsenate before doing the elemental analysis. They should have mixed E. coli DNA with arsenate and then gel-purified it. They should have tested whether their arsenic-containing DNA could be used as a template by normal DNA polymerases. They should have noticed all the discrepancies in their data and done experiments to find the causes.

Redfield wasn't the only scientist who felt that the procedures used in the experiment might have been flawed. Carl Zimmer reports at Slate that while the scientists he spoke with admitted the possibility that arsenic-using bacteria might exist, they did not feel this research demonstrated that they did:
But almost to a person, they felt that the NASA team had failed to take some basic precautions to avoid misleading results.

When the NASA scientists took the DNA out of the bacteria, for example, they ought to have taken extra steps to wash away any other kinds of molecules. Without these precautions, arsenic could have simply glommed to the DNA, like gum on a shoe. "It is pretty trivial to do a much better job," said Rohwer.

In fact, says Harvard microbiologist Alex Bradley, the NASA scientists unknowingly demonstrated the flaws in their own experiment. They immersed the DNA in water as they analyzed it, he points out. Arsenic compounds fall apart quickly in water, so if it really was in the microbe's genes, it should have broken into fragments, Bradley wrote Sunday in a guest post on the blog We, Beasties. But the DNA remained in large chunks--presumably because it was made of durable phosphate. Bradley got his Ph.D. under MIT professor Roger Summons, a professor at MIT who co-authored the 2007 weird-life report. Summons backs his former student's critique.

Another fact that differs from some media accounts is that these bacteria grow much better on standard phosphate than arsenic. The research paper in Science reported: "GFAJ-1 is not an obligate arsenophile and it grew considerably better when provided with P." Since arsenic and phosphate are in the same column (group) in the periodic table, the two elements have similar properties and it isn't overly surprising that if you starve this bacterium of phosphate, it will uptake arsenic. Likewise the NY Times reported:
Despite this taste for arsenic, the authors also reported, the GFAJ-1 strain grew considerably better when provided with phosphorus, so in some ways they still prefer a phosphorus diet. Dr. Joyce, from his reading of the paper, concurred, pointing out that there was still some phosphorus in the bacterium even after all its force-feeding with arsenic. He described it as "clinging to every last phosphate molecule, and really living on the edge."

Dr. Joyce added, "I was feeling sorry for the bugs."

An excellent blog by a scientist at Townhall.com provides further analysis, explaining why arsenic-based DNA would be much less efficient than phosphorous-based DNA:
DNA uses phosphorus as the critical bond between "rungs" of the double helix. If you think of a ladder as made of two rails and many rungs, then phosphorus is the atom that permits three connections--an up-rail, a down-rail, and a rung. This is the backbone of the DNA molecule, and when you combine two strands of DNA in a double helix, you have two rails like a railroad, twisting through space. Many of the molecular motors that copy DNA, repair DNA, make RNA, modify transcription of RNA etc, run up and down on these rails. And because this is such a long molecule, they have to move fast.

But the size of the phosphorus +5 ion is about 34 picometers, whereas the size of the replacement arsenic +5 ion is 47 picometers. This is a change in size of 38%. Replacing the phosphorus in these rails (black dots in graphic) with arsenic is like changing the gauge of the railroad. And if you hit that change of gauge at 30 mph, there's going to be a train wreck. None of the critical DNA machinery is going to like swapping out even one phosphorus atom, much less all of them! ... [I]t would be my educated guess, that it has the same DNA code, the same ATP shape as normal Earth life, only switching to arsenic when it has to. In other words, I think we are seeing highly adapted Earth life, and not alien extraterrestrial life.

In fact, Carl Zimmer reports that it's possible that the bacteria in the experiment did have access to phosphorous:
But how could the bacteria be using phosphate when they weren't getting any in the lab? That was the point of the experiment, after all. It turns out the NASA scientists were feeding the bacteria salts which they freely admit were contaminated with a tiny amount of phosphate. It's possible, the critics argue, that the bacteria eked out a living on that scarce supply. As Bradley notes, the Sargasso Sea supports plenty of microbes while containing 300 times less phosphate than was present in the lab cultures.

"Low levels of phosphate in growth media, naive investigators and bad reviewers are the stories here," said Norman Pace of the University of Colorado, a pioneer of identifying exotic microbes by analyzing their DNA, who was another co-author on the weird-life report.

So this bacterium isn't really all that different than other known life after all. Even Paul Davies of NASA and Arizona State University admits the bacterium is not a new life form: "It can grow with either phosphorous or arsenic. That makes it very peculiar, though it falls short of being some form of truly 'alien' life belonging to a different tree of life with a separate origin."

It seems there's some pretty strong criticism of the claim that these bacteria have arsenic-based DNA, or even that they're using arsenic in any important biochemical way. The one thing that seems clear is that when you starve this particular type of bacterium of phosphate and give it a lot of arsenic, it will uptake arsenic. Beyond that, there's much controversy.

I don't think it's safe at present to cross phosphate off the list of elements required for life, nor is this "proof of concept of alien life," or even "life as we do not know it."

What does it mean?

All skepticism aside, this appears to be a potentially fascinating discovery which certainly would greatly add to our knowledge of life's diversity. Bacteria are incredibly diverse and are found in virtually every environment we look for them on Earth, and this research expands that knowledge. But no one found alien life, and it's not clear if this could even tell us anything about alien life. More work must be done to determine whether these bugs have actually incorporated arsenic into their DNA and other biomolecules. And at base it really says nothing about the origin of life. So why all the hype?

Before I return to this commentary, let me first say that I'm a huge supporter of NASA and space exploration. As a young kid, I wanted nothing more than to be an astronaut. I still think space travel is mankind's greatest technical accomplishment, and I cringe when politicians and bureaucrats spend untold trillions on bailouts, military projects, and social services, but are unwilling to give a comparative pittance to NASA to further space exploration.

That being said, it's no secret that NASA is a bit worried about budget issues in the present economy. Perhaps it was feeling like it needed some attention and thus tried to make a big deal about an interesting, but ultimately quite modest, discovery of a weird bacterium. Seth Shostak analyzes NASA's behavior thusly:

Interesting news, but not everyone felt that the story justified NASA's pre-release publicity, which suggested that the new research was a major milepost in the search for alien life.

Indeed, many thought that the agency's advance notice had wandered beyond the misty borders of "tantalizing" into the dangerous land of "hype." On the day before the press conference, my in-box bulged with dozens of inquiries about the upcoming revelations, asking whether NASA was about to tell us they had finally found proof of extraterrestrials. After all, if the research to be disclosed at the press event was not at least this dramatic, then why was the publicity overture so seductively coy?

Rosie Redfield concludes: "I don't know whether the authors are just bad scientists or whether they're unscrupulously pushing NASA's 'There's life in outer space!' agenda. I hesitate to blame the reviewers, as their objections are likely to have been overruled by Science's editors in their eagerness to score such a high-impact publication." Likewise, Carl Zimmer writes:

Some scientists are left wondering why NASA made such a big deal over a paper with so many flaws. "I suspect that NASA may be so desperate for a positive story that they didn't look for any serious advice from DNA or even microbiology people," says John Roth of UC-Davis. The experience reminded some of another press conference NASA held in 1996. Scientists unveiled a meteorite from Mars in which they said there were microscopic fossils. A number of critics condemned the report (also published in Science) for making claims it couldn't back up. And today many scientists think that all of the alleged signs of life in the rocks could have just as easily been made on a lifeless planet.
Space exploration should be supported even if the search for extraterrestrial life is stalling out. Perhaps if we funded NASA sufficiently to continue to explore other planets in our solar system, then it wouldn't need to push moderate discoveries with ideologically-driven hype in order to justify its continued existence.


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