December 29, 2010

Bad, or at least breathless, science, by NASA?

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.


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.

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. 7: The Guardian has an excellent roundup of NASA's dissing of all the skeptics and naysayers. Again, fluffers ... more skepticism!

Update, Dec. 8: Slate has an excellent article about how NASA has sponsored not-so-good science AND blown the media coverage issues. And, at least one professor says NASA had motive for this fluffery. But, because of the reason for that motive, it could well backfire:
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.

I didn't think so much about that as budgetary motives, but it makes sense. No big news from Mars probes for a while. Obama announces budget cuts and mission changes. The next planned shuttle flight keeps getting shoved back.

Yep, that's motive.

First, contra the breathlessness, at Gizmodo AND elsewhere (see below) — don't tell me that just because Gizmodo isn't a science site, that NASA had nothing to do with "framing." The evidence for that is becoming more and more clear, despite someone like Greg Laden at Scienceblogs, an unrepentant fluffer here and here. That said, Greg's definitely lost credibility in my eyes over this issue.

But, per the first of his linked blog posts:
I've asked for specific critiques of the NASA press release and have received one, which makes a good suggestion but hardly demonstrates that NASA lied or cheated or flim flamed.

You, on the other hand, are quickly making it onto my list.

I never said, myself, that NASA "lied or cheated." I didn't use the phrase "flim flamed" [sic] for its fluffery, either. But, if that's what you think fluff PR for apparently shoddy science should be called, OK!

The New York Times and Phil Plait both also, among others, seem to have gotten a bit breathless.

Second, it's simply untrue that it "doesn't share the biological building blocks of anything currently living in planet Earth." As this Wikipedia page points out, arsenic substitution in some "sugars" in some bacteria is well-known. And, for readers who criticize Wiki, before this story, the three footnotes on the arsenic section prior to this story come from the University of Minnesota, NIH, and New Scientist. Got problems with all of them, too? Beyond that, Pharyngula, in his post about the NASA story, also has information on how arsenic in organic compounds is nothing new.

Third, I don't get why people have a blanket condemnation of Wikipedia. On current events/politics/living history, YES. But, in general, in the natural sciences, in more ancient history, and many other areas, Wikipedia is pretty reliable.

Fourth, ff NASA is using the same language as the Gizmodo post is, or left itself open to this, then, we're going past breathless science and getting close to bad science. That's what you get for hyping something you embargo, too, BTW.

Meanwhile, the PR should be labeled bullshit, not just breathless. More reality.

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.

That said, the NYT opens its story with its own "breathlessness":
Scientists said Thursday that they had trained a bacterium to eat and grow on a diet of arsenic, in place of phosphorus — one of six elements considered essential for life — opening up the possibility that organisms could exist elsewhere in the universe or even here on Earth using biochemical powers we have not yet dared to dream about.

It makes it sound like we're still largely clueless about chemical bonds and organic chemistry.

Again, though, this Wikipedia page says we aren't, listing other elements, like boron, in possible exotic life.

Finally, 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.

And, still more.

Not quite "breathless," but close, here, as Astrobio's coverage also appears not to have read the material referenced by Wiki and Pharyngula.
The recent discovery by Felisa Wolfe-Simon of an organism that can utilize arsenic in place of phosphorus, however, has demonstrated that life is still capable of surprising us in fundamental ways.

Again, not quite so true.

In short, this is about 1/10 of what NASA led people to expect.

And, Astrobio does redeem itself by citing a skeptic:
Steven Benner, a distinguished fellow at the Foundation for Applied Molecular Evolution in Gainesville, Fla., remains skeptical. If you “replace all the phosphates by arsenates,” in the backbone of DNA, he says, “every bond in that chain is going to hydrolyze [react with water and fall apart] with a half-life on the order of minutes, say 10 minutes.” So “if there is an arsenate equivalent of DNA in that bug, it has to be seriously stabilized” by some as-yet-unknown mechanism.

Benner suggests that perhaps the trace contaminants in the growth medium Wolf-Simon uses in her lab cultures are sufficient to supply the phosphorus needed for the cells’ DNA. He thinks it’s more likely that arsenic is being used elsewhere in the cells, in lipids for example. “Arsenate in lipids would be stable,” he says, and would “not fall apart in water.” What appears in Wolfe-Simon's gel-purified extraction to be arsenate DNA, he says, may actually be DNA containing a standard phosphate-based backbone, but with arsenate associated with it in some unidentified way.

Given budget cut talks, I honestly wonder if there's an ulterior motive to all this breathlessness. Create an adapted form of life under lab conditions, drop hints that get some tech sites to call it "alien," hint that it might be useful for expanding the search for exobiology ...

And, then, ramp up the push for new Mars mission money or something.


A 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."

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.)


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 above, the hydrolysis issue caught my 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.

Meanwhile, here's proof of NASA's fluffery on the arsenic compound/exobiology story that had nothing to do with alien life - the hed on NASA's announcement:
"Get Your Biology Textbook...and an Eraser!"


Anonymous said...

If you are going to oppose scientific research papers, can you cite from anything other then Wikipedia? Not really a realiable, trustworthy source.

Gadfly said...

The actual Wiki page in question is well-sourced. The only area where I have high skepticism towards Wiki is current affairs/history.

If you can find something wrong with that particular page, tell me.

Second, I'm not the only person, at least in my circle, who noted the "breathlessness" of this.

Gadfly said...

Ohh, and I didn't "oppose" the paper, either. I just said the advance PR was way overhyped. And, again, I'm not alone on that thought.

Anonymous said...

Oh come on, first anonymous. Gadfly addressed concerns about Wikipedia reliability briefly in his post. If you're going to oppose his use of Wikipedia, can you cite some sources about why it's so bad?

I don't get anti-Wikipedia sentiment myself. Wikipedia is the internet, only more so. Any yahoo can put up a web-page expounding total BS. Any yahoo can edit Wikipedia and add total BS. It's easier than putting up a web-page, sure, but it's also easier for the next guy to come along and take the BS out of Wikipedia.

If you don't trust Wikipedia (with appropriate caveats), then you shouldn't trust ANYTHING you see on the internet. Of course, you shouldn't trust EVERYTHING you see on Wikipedia, or the internet as a whole. Being a literate person in the information age means figuring out whether a source of information is trustworthy. Blanket condemnation of Wikipedia is ignorant. Look at the article, then judge. If it's on a scientific subject, does it cite primary literature? It usually does. I wouldn't cite Wikipedia in a research paper, but it's great for an introduction to the subject and it usually will point you to appropriate primary sources which you can cite.

Gadfly said...

Well put, anonymous No. 2. That said, I did somewhat expand my Wikipedia comments after anon. No. 1 first posted. It also "drove" me to do a separate blog post on Wikipedia and issues of reliability.

Anybody reading something like Greg Laden (I think that's where the person came from) should have enough critical thinking skills to do just as you say - evaluate pages individually.

Cognoni said...

It is sad but true that the current system of government funded science introduces huge distortions and necessitates incorporating politics into how one interprets findings. The global warming scam has cast a long shadow of doubt on all scientific pronouncements. Liberlism is now doing to science what it did to the arts.

Gadfly said...

Ahh, I've attracted a global warming denialist. If you'll read through by blog, in this week's post, Cognoni, you'll see one on how 2010 has tied 1998 and 2005 as warmest year on record.

That said, privately funded "science" has led to Big Oil's global warming denialism, Big Tobacco's secondhand smoke cancer denialism and more.

Beyond that, the NASA story and government funded science isn't about "liberalism," either. Is either peaceful nuclear power or nuclear weapons "liberal"? Space exploration?

Crawl back in your wingnut cave.