Category: Arsenic life

Dediscovery: My new essay for a new section of the New York Times

By Carl Zimmer | June 27, 2011 10:41 am

In the late 1800s, prominent astronomers declared that Mars was criss-crossed by canals–evidence, they declared, of an advanced civilization. But in the early 1900s, astronomers gazed through more powerful telescopes and discovered that the canals were mirages.

The astronomer Percival Lowell, who had become the leading champion of the canals, scoffed at the new findings He declared that the criticism came “solely from those who without experience find it hard to believe or from lack of suitable conditions find it impossible to see.”

Although the new evidence led many astronomers to abandon Lowell’s position, he never retracted his claim. It wasn’t until five decades after his death in 1916 that space probes finally went into orbit around Mars and sent back close-up pictures of a canal-free Red Planet.

I’ve always been fascinated by the way science casts aside bad ideas. For most of us, it’s easy to assume that science shakes them off quickly, but the truth is that it can take quite a while for the process to play out. Recently I was invited to contribute a piece to the new “Sunday Review” section of the New York Times, which just debuted this week. I wrote an essay on this phenomenon, which has been dubbed  “de-discovery.” I drew on three recent examples of high-profile research that many other scientists have declared to be wrong–arsenic life, clairvoyance, and a link from chronic fatigue syndrome to a virus called XMRV.

To keep my essay from exploding into a novella, I had to limit myself to just these three examples–but I could have picked many others. You just need to check out a blog like Retraction Watch to see how important this part of the scientific process is today. The first draft of my essay actually started out with a fourth example, which I decided to cut it in the end. It’s a peculiar case of a de-discovery of a de-discovery.

In 1981, the late Harvard paleontologist Stephen Jay Gould published an influential book about racism and science, called The Mismeasure of Man. Gould argued that social influences could lead scientists to misinterpret their data to suit their beliefs about European superiority. One of his key examples was the work of a nineteenth century anthropologist named Samuel George Morton.

Morton collected 1,000 human skulls from around the world and measured the size of their brain cavities with seeds or lead shot. Gould re-analyzed Morton’s data and published his results in 1978 in the journal Science. He declared that Morton fudged his measurements to ensure that Caucasians would end up with the biggest brains.

In 2000, a freshman at the University of Pennsylvania named Jason Lewis started to measure Morton’s skulls for a research project of his own. He was interested in the ways different human populations adapt to different climates—including changes in the shapes of their skulls. It was then that Lewis learned from his advisors about the controversies swirling around the skulls. (He was born a year after The Mismeasure of Man was published.)

As Lewis carried out his own measurements, he gradually realized that Gould had been wrong. He then set out to systematically investigate the matter—taking three years to measure Morton’s skulls, and then another five years to work through Gould’s claims.

Lewis, who just finished earning his Ph.D at Stanford University, wrote up the results with his colleagues and submitted a paper in 2008 to the journal Current Anthropology, which had published a less detailed critique of Gould’s paper in the 1980s. The journal rejected Lewis’s paper, eventually informing him that it was not important enough.

The researchers had better luck with PLOS Biology, which published their paper earlier this month. Lewis and his colleagues presented evidence that Morton did not bias his findings at all. Instead, the researchers conclude, it was Gould who used shoddy statistics. There are many sound scientific reasons to reject racist views of human biology, they argue, but an unfair trashing of Morton’s research isn’t one of them.

“Our analysis of Gould’s claims reveals that most of Gould’s criticisms are poorly supported or falsified,” they write.

When I was researching my essay, I asked Lewis about what he thought of science’s self-correcting process now that he’s finally done with his exploration of Gould and Morton. He has decidedly mixed feelings.

“We can come back thirty years later and get the story straight,” he told me. “But it takes thirty years.”

As I write in my essay in the Times, there are certainly ways to make dediscovery a smoother, faster process. But in an age of instant viral communication, I think we’re going to remain frustrated by inescapable lags.

[Image: Wikipedia. Thanks to folks on Twitter for pointing me to Martian canals as a textbook case of slow dediscovery]

Arsenic life creates a new blogger: Please welcome Steven Benner!

By Carl Zimmer | June 3, 2011 8:27 am

During the whole arsenic life kerfuffle, chemist Steven Benner expressed his skepticism early and often. He wrote one of the eight critiques that Science posted last week, six months after the initial paper.

Last night Benner sent me an email:

Carl:

I have now blogged on this, since the cycle of publication at Science is rather slow.

Steve

To which I can only say: Heh. And, Read it!

CATEGORIZED UNDER: Arsenic life

Arsenic life redux: how #arseniclife helped change science

By Carl Zimmer | May 27, 2011 5:06 pm

It’s been six months since #arseniclife became one of my favorite hashtags on Twitter. Over at Slate, I look at how the online conversation has changed the way scientists do their work. Check it out.

CATEGORIZED UNDER: Arsenic life, Writing Elsewhere

Arsenic life and all that: My new book review for the Wall Street Journal

By Carl Zimmer | April 22, 2011 6:06 pm

The Wall Street Journal recently asked me to review a new book called First Contact: Scientific Breakthroughs in the Hunt for Life Beyond Earth. Astrobiology is a tricky subject to write about these days. It’s intensely exciting, despite the fact that its main object of study–life on other planets–has yet to be discovered.

I’ve given some thought to how we journalists should cover such a paradoxical science. We shouldn’t dismiss it outright, because astrobiologists have discovered fascinating things about life here on Earth, even if they have yet to find aliens. Yet we shouldn’t feel obligated to pump up every claim about the possibility of life elsewhere. We should be content to paint a portrait of the scientific process–including the intense debates–in all its gorey detail.

By this measure, I don’t think First Contact works. The author, Marc Kaufman, declares at the outset of the book that “before the end of this century, and perhaps much sooner than that, scientists will determine that life exists elsewhere in the universe.” Not whether life exists, mind you, but that it exists.

I don’t think he backed up that bold claim. Instead, he pumps up intriguing, but inconclusive, evidence. He portrays the scientists who made claims for arsenic life, for example, as bold, out-of-the-box thinkers, and criticisms as little more than the rants of bloggers. He’s not alone–on Thursday, Time picked a member of the arsenic life team as one of their 100 most influential people of 2011. But these portrayals don’t match the reality of the arsenic life saga. I find the manufactured dichotomy between the supposed mavericks and the mean-spirited critics to be particularly off target. Remember, a lot of the critics of arsenic life are astrobiologists themselves.

For a better example of how to embrace scientific debate, check out Richard Panek’s The 4 Percent Universe: Dark Matter, Dark Energy, and the Race to Discover the Rest of Reality which I reviewed for the Washington Post in January. Panek doesn’t shy away from the intense competition and bad-mouthing that cosmologists engaged in as they rushed to establish the deep mystery of the universe. It’s a rich story that doesn’t shy away from the messiness and uncertainty that the big questions in science inevitably create.

Become an astrobiologist! (Or at least learn a lot about astrobiology)

By Carl Zimmer | December 9, 2010 3:15 pm

With so much attention given to one problematic study this week, astrobiology is getting an awful lot of attention–and probably not the sort that astrobiologists would like. If you want to broaden your view of this intriguing area of research, get thee to Itunes! Lynn Rothschild teaches a class on astrobiology at Stanford, and the winter 2010 edition of the course is available FOR FREE on Itunes. (I just started watching a couple classes and then decided to download the whole thing.) Also, check out the snazzy class web site for more on the study of life in the universe.

CATEGORIZED UNDER: Arsenic life, Link Love

Your daily dose of arsenic: On the Madeleine Brand Show on KPCC

By Carl Zimmer | December 9, 2010 2:48 pm

I just appeared this morning on the Madeleine Brand Show on KPCC in California to talk about arsenic life. Check it out.

Of arsenic and aliens: What the critics said

By Carl Zimmer | December 8, 2010 4:57 pm

A lot of people are interested in my Slate story yesterday on the arsenic aliens. It’s still the most-read story of the site at the moment, Slashdot and others have linked to it, and I’m doing some more radio and maybe other media (details to come).

I think that what has gotten so much attention to the story is just how many scientists had such critical things to say. The verdict was not unanimous, but the majority was large. I was only able to quote a tiny bit from just a few of the scientists I communicated with, so I thought, for those who’d like to delve more deeply into this, that I’d post a list of everyone I spoke to, and, when possible, post their reactions. A lot of scientists replied to me by email or even attached word files where they went on at length. I put together a similar dossier for another biological controversy–the search for soft tissue in dinosaur fossils–and I think (or at least hope) that this sort of exercise can help further discussion.

Of course, as I and others have reported, the authors of the new paper claim that all this is entirely inappropriate. They say this conversation should all be limited to peer-reviewed journals. I don’t agree. These were all on-the-record comments from experts who read the paper, which I solicited for a news article. So they’re legit in every sense of the word. Who knows–they might even help inform peer-reviewed science that comes out later on.

I’m going to post everything under the fold here, but it will take a little while. I’ll just re-save the post every time I add a new one, and I should be done before too long. So keep refreshing, or just drop by again later…

PS–Science has made the paper at the center of this controversy free. Get it here.

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Talking on the radio Wednesday at noon about arsenic life

By Carl Zimmer | December 7, 2010 4:49 pm

Quick note: I’ll be on the public radio show Word of Mouth show just after noon eastern time tomorrow (Wednesday 12/8) to talk about NASA’s cookie full of arsenic. You can listen live here. [Update: the podcast is posted now.]

CATEGORIZED UNDER: Arsenic life, Life Elsewhere, Talks

And the skeptics keep chiming in…George Cody on arsenic life

By Carl Zimmer | December 7, 2010 12:38 pm

One of the challenges of writing on deadline is that people are not waiting every moment of the day to answer your questions. My Slate piece on arsenic life was based on a dozen or so responses from an overwhelmingly skeptical group of experts. And now, an hour after my story went live, I got a reply from George Cody, a chemist at the Carnegie Institution who co-authored a major 2007 “weird life” report. Rather than let this thirteenth comment molder in my inbox, let me share it with you. It’s a bit technical but illuminating. I’ve condensed it for clarity (my clips marked by ellipses)–

I have been aware of the hypothesis of the possibility of substitution of arsenate for phosphate for some time…The issue that always comes up is the facility of hydrolysis of arseno ester bonds….The correct experiment to do would be mass spectrometry which would unambiguously determine whether an arsenate backbone was present or not in the DNA.  I cannot accept this claim until such an experiment (easily done) is performed. ..

I recall a summer intern in my laboratory accidently culturing up a bacterial biofilm from a solution of concentrated fumarate, urea, and ammonium hydroxide in ultra-pure water (not surprisingly ammonia oxidizing bacteria); we were surprised but evidently the microorganisms were able to obtain the necessary nutrients, e.g. phosphate, from somewhere to grow to a point be being readily observed.  Microorganisms can do quite a bit with a little.  I recall a report in Nature by Benjamin Van Mooy (WHOI) where it was shown that certain marine organisms could use sulfate in their lipids when the availability of phosphate is very low.  Actually, if arsenate had substituted for phosphate anywhere, I would have looked at the lipids first, again using mass-spectrometry.

Philosophically, if it turned out that an organism could use arsenate in place of phosphate, this would not in my opinion rewrite the rules of life as we know it; aside from the hydrolysis issue, arsenate is chemically very similar to phosphate.  A careful chemist could likely synthesize DNA oligomers with an arsenate backbone.  As I understand it this is precisely why arsenate is a poison.  Ultimately, the idea of a shadow biosphere is interesting, but it would have to be demonstrated to be truly distinct from extant biochemistry, e.g. truly novel metabolic pathways, different bases for coding, different amino-acids or better still enzymes that were not based on amino-acids at all.

As the old adage goes “Extraordinary claims require…”

Likely what I have said mirrors what you have heard from others.

Indeed, it has.

Arsenic life: My take on the backlash at Slate

By Carl Zimmer | December 7, 2010 11:33 am

LakeMonoSlate asked me to take a look at the scientific reactions emerging to last week’s big news about arsenic-based life. I got in touch with a dozen experts, and let’s just say, the results weren’t pretty. Check it out.

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

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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.
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