#arseniclife Links

I am participating in a seminar involving undergraduate journalism students and graduate students from my department (Ecology & Evolutionary Biology) and the Department of Natural Resources and the Environment. Its purpose is to give journalism students a chance to practice their interviewing skills and to give science students practice at communicating their work to reporters. For our last meeting this year, we decided to talk about the #arseniclife episode. What I've collected below are links and resources we'll use in our discussion.

Participants: All of the resources linked to below are relatively short and easy to read (except for Rosie Redfield's posts -- just try to get a sense of her objections, don't worry about the details). Scientists will especially want to ponder the question of how peer review works in very public science, and journalists will want to think about Carl Zimmer's take on Tom Clynes' Popular Science piece about the controversy and Clynes' response. The Deepak Singh video gives a non-biologist, non-journalist take on the role of Twitter in the controversy (hence the hashtag in the title of this post).

Media advisory from NASA announcing an astrobiology discovery (29 November 2010)

WASHINGTON -- NASA will hold a news conference at 2 p.m. EST on Thursday, Dec. 2, to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life. Astrobiology is the study of the origin, evolution, distribution and future of life in the universe.

NASA press release accompnaying news conference (2 December 2010)

Researchers conducting tests in the harsh environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components.

"The definition of life has just expanded," said Ed Weiler, NASA's associate administrator for the Science Mission Directorate at the agency's Headquarters in Washington. "As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it."

Rosie Redfield's blog post criticizing the paper¹ (4 December 2010)

Here's a detailed review of the new paper from NASA claiming to have isolated a bacterium that substitutes arsenic for phosphorus on its macromolecules and metabolites. (Wolfe-Simon et al. 2010, A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus.) NASA's shameful analysis of the alleged bacteria in the Mars meteorite made me very suspicious of their microbiology, an attitude that's only strengthened by my reading of this paper. Basically, it doesn't present ANY convincing evidence that arsenic has been incorporated into DNA (or any other biological molecule).

Carl Zimmer's² article in Slate (7 December 2010)

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.

The controversy over the Martian meteorite still sputters on today because they contain only a few alleged fossils, rather than living bacteria. There are only a limited number of tests that scientists can run on the rocks, and their results remain murky. Fortunately, that's not the case for GFAJ-1. Critics say that a few straightforward tests on the bacteria would show whether they really do have arsenic-based DNA once and for all. And the NASA scientists say they're ready to hand out GFAJ-1 to researchers who want to study it. This controversy may be burning brightly at the moment, but it probably won't burn for long.

Tom Clynes' article in Popular Science (26 September 2011)

Last December, Felisa Wolfe-Simon announced the discovery of a microbe that could change the way we understand life in the universe. Soon she found herself plunged into a maelstrom of bitter backlash and intemperate criticism. A dispatch from the frontiers of the new peer review.

Carl Zimmer's blog post commenting on Clynes' article (20 October 2011)

It's a good article. I won't be forgetting the opening scene anytime soon, when Wolfe-Simon is ambivalently posing for a television crew, and she sinks into the mud of Mono Lake, where she first encountered GFAJ-1.

But I do share some of the reservations that science writer David Dobbs expresses over at his blog Neuron Culture. As a genre, the profile is one of the most addictive and enjoyable of all. It doesn't matter if the profile is of a hero or a scoundrel; the story is good as long as it's full of human nature in all its extremes. But profiles of scientists are tricky, because science transcends any single individual scientist. To do the science justice, you may need to pull the spotlight away and get into the less human stuff, like chemical reactions and pH levels.

Clynes' response to Zimmer (21 October 2011)

To that end, I'd like to add a bit of context to a paragraph that you quote, regarding the storm of criticism and the paper's authors going "underground." You follow the excerpt with your comment that "Clynes has us believe that this barrage of extraordinary, brutal criticism (or perhaps questions from journalists) forced Wolf-Simon and her colleagues to go into witness protection."

Actually, I don't believe that, nor would I have my readers believe it. I think it would have been useful to your readers for you to have included my next paragraph, which makes it clear that I am in fact spotlighting both sides of a polarized dialogue regarding this particular point:

Microbiologist Jonathan Eisen of the University of California at Davis called the lack of response "absurd" and told Carl Zimmer from Slate, "They carried out science by press release and press conference. They are now hypocritical if they say that the only response should be in the scientific literature."

Though I didn't state my opinion in the story (better for readers to decide for themselves), I will here: I think that Eisen is on the money here.

The latest from Rosie Redfield (25 November 2011)

I'm not going to do any more work on this - not going to do experiments to find out why arsenate stimulates growth, unless the mass spec shows that there really is arsenic in the DNA of arsenate-grown cells. The growth stimulation I'm seeing isn't a replication of Wolfe-Simon et al's report that their cultures grew with arsenate but not without it, but it might reflect the same biological process.

Deepak Singh³ provides a video overview. Read the posts above before you watch the video. The video won't make much sense without that background.



If you really can't get enough of #arseniclife, here are some more links:

The version of the Wolfe-Simon paper as it originally appeared on ScienceExpress: (2 December 2010)
The version of the Wolfe-Simon paper as it finally appeared in Science: (3 June 2011)
Table of Contents for Science (scroll to the bottom for the technical comments): (3 June 2011)
Links from The Guardian through the end of December 2010: (Story Tracker)
Various blog posts I made in which I mentioned arsenic-based life (Uncommon Ground)
Bora Zivkovic' comprehensive collection of #arseniclife links (A Blog Around the Clock)
A one-year anniversary update (Cosmic Log)