On science blogs this week: Ooops!

DETHRONED MICROBE OF THE WEEK, BACTERIAL DIVISION. It was microbiologist Rosie Redfield, you'll recall, who blew the whistle on the assertion that researchers had discovered a bacterium that could substitute arsenic for phosphorous in its DNA. Her counter-paper was among those Science published last week, and she has followed up with several posts to her blog, RRResearch. One is a how-to for testing some of the more important claims, and another outlines how she is preparing to test them herself, although she says she has not yet decided to proceed.

Redfield then goes on to ask a pretty intriguing question: If this is a bad astrobiology paper, are there any good ones? (She can't think of any and lists a number of other bad ones.) And she asks her readers for examples of good ones — which are, by and large, not forthcoming. 26 comments at last count, many of them by Shawn Domagal-Goldman, who works in NASA's astrobiology program office and seems a tad defensive.

Goldman is also one of the writers of the newish PaleBlue.blog. Another of the writers, Ariel Anbar, who leads a NASA Astrobiology Institute team at Arizona State, was a co-author of the arsenic paper. Despite its gigantic subject, astrobiology appears to be a pretty small universe.

No doubt it will get bigger once we actually find some.

Anbar acknowledges the awkwardness of his position and asks readers for advice that applies to all blogging scientists. How, he wants to know, should authors of a paper talk about their work online — and the work of others? Of the arsenic paper, he also notes:

There’s much that I would like to say, but for me, personally, the trouble is that anything I write can be twisted out of context by those fishing for controversy about a highly public story (someone will probably twist that sentence out of context).

That someone is us, folks. So get busy, do the twist.

Some bloggers brought us handy cheat sheets summarizing all the science critiques, so we don't have to bother reading them ourselves.. See Derek Lowe at In the Pipeline and also John Timmer at Nobel Intent and also David Dobbs at Neuron Culture. And Jonathan Eisen has compiled helpful links to the paper, the critiques, news stories, and bloggery at The Tree of Life.

Finally, another new blog, A Tempting Science, this one by chemist Steven Benner, author of another of the arsenic bug critiques. His is a long post describing how the episode can serve as a teachable moment about how science is done and what counts as proof of an assertion in different fields.

DETHRONED MICROBE OF THE WEEK, VIRAL DIVISION.

Two new studies may not be the final nails in the coffin of the hypothesis that a mouse retrovirus called XMRV causes chronic fatigue syndrome. But the hammering is certainly getting louder.

So says clever Richard Knox at the NPR health blog Slots, from whom I will steal this lovely lede as soon as I decently can. If you're only going to read one thing on what Carl Zimmer calls the de-discovering of XMRV, this is a fine choice. But there are several others too.

In 2009, Science published a paper claiming that chronic fatigue syndrome is caused by XMRV, a mouse leukemia virus. The paper was embraced by the chronic fatigue community, which has for years has been struggling to persuade people that their symptoms of exhaustion and aching bodies are not all in their heads. But among scientists the idea that chronic fatigue was caused by this virus was always controversial.

With some reason, it turns out. Science has now published another in a string of studies that have been unable to find the virus in chronic fatigue patients — and another arguing that XMRV arose from mouse viruses by accident in a lab in the 1990s and any of it found in tissue samples is simply a contamination. At the Nature Newsblog, Ewen Callaway tells the tale. So does Carl Zimmer at The Loom, with engrossing details about how XMRV probably came into existence

But see ERV for even more juicy evolutionary particulars about the laboratory marriage of mouse viruses. ERV is the longtime scientist-blogger who studies the evolution of HIV and the epigenetics of endogenous retroviruses, and he has written a slew of skepticism (not to mention incredulity) about XMRV.

At Retraction Watch, Ivan Oransky reports that Science editors asked for the chronic fatigue paper to be retracted, but the authors declined. So Science issued an Expression of Concern about the paper, which is to say they disowned it. The public hanging was scheduled for publication June 2, but the Wall Street Journal preempted the news, so Science released it early.

At the Wall Street Journal's Health Blog, Amy Dockser Marcus writes about what the new findings may mean for a paper reporting finding retroviruses related to XMRV (but not XMRV intself) in the blood of chronic fatigue patients. That paper was published last year in another top journal, Proceedings of the National Academy of Sciences.

Tinker Ready's Boston blog quotes at length from a March Nature profile of the chronic fatigue paper's coauthor, Judy Mikovits. It's not flattering.

The commentary has been pretty much exclusively about XMRV and chronic fatigue synrdome. But in fact this virus first surfaced as a possible cause of prostate cancer. I have written about the epidemiological reasons to speculate that (at least some cases of) prostate cancer may be due to infection, perhaps with XMRV. There's a potential analogy here to cervical cancer, incuding possible sexual transmission.

XMRV was first discovered in prostate tumors in 2006, and there have been other positive studies (and negative ones) since then. One of the XMRV papers published this week. and also the press release from the National Institutes of Health, argue that these findings were probably due to contamination too. They have made quite a good case that the XMRV findings in prostate cancer should be disregarded. But that doesn't necessarily mean that prostate cancer isn't an infectious disease; its epidemiology remains suggestive.

Whether that applies as well to chronic fatigue syndrome I have no idea. I've never written about chronic fatigue and know next to nothing about it except that figuring it out has been, and is, a major mess. At The Scientist's Naturally Selected, Richard Grant considers where the XMRV findings leave folks with chronic fatigue. He asks:

Will the ban on blood donation be lifted? Will medics go back to not believing it’s a real condition? Is the suffering of those afflicted with ME [myalgic encephalomyelitis, aka chronic fatigue syndrome] now worse than it was before October 2009? It seems cruel to offer support for patients and advocacy groups trying to convince recalcitrant medics that this is a real disease, and then to snatch that support away, but what else can be done?