Preserved T. rex or bad science?

Science has published several articles in the past year or so, with much publicity, announcing that researchers had found preserved soft tissue from Tyrannosaurus rex that contained fragments of the original collagen proteins from T. rex. The researchers leading the research, J.M Asara and M.H. Schweitzer, claimed (Science 2007 Apr 13;316(5822):280-5) that the T. rex protein fragments were more closely related to birds than to reptiles. Very plausible, of course - and if correct, yet another bit of evidence linking modern birds to dinosaurs.

However, even though birds almost certainly are descended from dinosaurs, this series of articles is a textbook case of how even the best journals - Science, in this case - can publish bad science. The mass spectrometry in the Asara et al. articles was poorly done, and even they had to admit - in a letter published in Science last fall - that at least one of their protein fragments was falsely identified. Despite this admission - and they only had 7 fragments to begin with - Science published a second article this past winter by the same authors. What did that article (Organ et al., Science 2008 Apr 25;320(5875):499) contain? Nothing new about the T. rex material, but instead some additional analysis of crocodile and ostrich proteins and a repeat of the claim that T. rex is closer to birds. The title of the article, though, is "Molecular phylogenetics of mastodon and Tyrannosaurus rex" - astonishing, if you expect Science to publish only the best science. But maybe not so astonishing if seen in the light of the publicity that Science is always hungry for. Still, it's too bad.

But why am I so skeptical? Well, don't take it from me. In a comprehensive examination of the T. rex material and methods, Buckley et al. reported - in Science, no less (2008 Jan 4;319(5859):33) that the "ancient" DNA reported by Asara and colleagues failed all the standard tests for such material. In other words, it's a contaminent.

Now, the most recent news on this story, published in PLoS ONE (Kaye TG, Gaugler G, Sawlowicz Z 2008 Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms. PLoS ONE 3(7): e2808 doi:10.1371/journal.pone.0002808), shows that the most likely source for this DNA is a bacterial biofilm. Not really surprising, but it's great to see this correction of the record. Unfortunately, the Science articles got so much play in the press that they will likely be hard to "erase" from the public's memory. I suspect that far more scientists will have heard of the "T. rex tasted like chicken" stories (yes, that's how some of the press stories were headlined) than the new PLoS ONE article.

For a more detailed discussion of the biofilm story, see Tara Smith's recent blog post on this same topic.

So my conclusion about the original (2007) article in Science: those 7 protein fragments weren't from T. rex at all. They were bacterial contaminents. Asara, Schweitzer, and colleagues were simply wrong - perhaps wishful thinking clouded their vision. The article never should have passed peer review, and Science should make an effort to correct the record. Sometimes even the best journals screw up, and that's what happened here.

Victor McKusick, R.I.P.

The genetics world lost one of its pioneers this week - Victor McKusick died of cancer at age 86, at his home in Baltimore. McKusick was a professor of genetics at Johns Hopkins University for most of his career.

Dr. McKusick was known as the father of medical genetics, and became famous for his tireless efforts, beginning in the 1960's, at cataloging all human genes associated with disease. Eventually he compiled these into a book, Mendelian Inheritance in Man (the first edition appeared in 1966), which later became the widely-referenced database Online Mendelian Inheritance in Man, or just OMIM. OMIM is so central to research that it moved, many years ago now, to NIH's National Center for Biotechnology Information, which also houses GenBank. Over the years, this collection has grown from just a few genes to 18,850 entries today. (Many genes are linked to more than one disease.)

McKusick "retired" from Hopkins in 1985 but continued working, and was a big presence when I joined the faculty there in 1989. I only met him briefly, and I wish I'd had the chance to get to know him. He was a true visionary. I recommend the extensive Wikipedia entry to anyone who wants to know more about Victor McKusick.

Influenza vaccines and free sharing of flu data

I don't usually discuss my day job on this blog, but this week there's some overlap between the two. My comments in this blog back in November 2007 drew the attention of the editors of the journal Nature, and they invited me to write a Commentary for Nature on the flu vaccine and issues surrounding the open exchange of influenza data.

My Commentary appeared this week as part of a special Nature section on "Flu fighting" in the journal. See this link for the Editor's summary of the special section. The summary has links to my article and to other articles included in the special section. If you can't get the articles (a subscription may be required), then you can get a reprint of my article from my home page, under "Editorials and opinion pieces."

Coming soon to this blog: should doctors prescribe statins for overweight children?

And what else is acupuncture good for?

"Unclear whether acupuncture helps fertility"

I love this headline from Yahoo News/Reuters! It just appeared today on the Yahoo News site. So acupuncture doesn't boost pregnancy rates? What a surprise! I can't resist the obvious: acupuncture also doesn't help cure back pain, headaches, infections, depression, or cancer. In fact, the list of conditions that acupuncture doesn't help is endless!

But the Reuters reporter wasn't just making this up - there really was a presentation in London by a researcher, Sesh Sunkara, who conducted a review of 13 other studies (a meta-analysis) and found that "the current available evidence is not conclusive" on acupuncture's benefits on fertility. She apparently reported her results at the conference of the European Society of Human Reproduction and Embryology. The findings were also reported online by reporter Mark Henderson at the Times, under the headline

"Acupuncture has 'no effect' on pregnancy rates following IVF, say experts"

The Times reports that there was a reason for this study, which otherwise might raise eyebrows (why on earth do a study for which there's no plausible reason to find a positive effect?): in England, and maybe elsewhere, "acupuncture has become the most popular complementary therapy" for infertility. A number of hospitals in England have on-site acupuncture services for their patients, charging hundreds of pounds for the sessions.

Dr. Sunkara is quoted in the Times story as saying:

...every day we have patients who ask whether they should have acupuncture to improve their success rate. There have been all sorts of papers saying that sticking pins and needles increases the pregnancy rate, which have been widely reported in the media, and we are looking at women who are very vulnerable, who want to do everything possible to increase their pregnancy chances.

It's sad but true: practitioners of quack medicine - in which I include acupuncture - are quite happy to profit from the desperation of naive people who are looking for medical help. Kudos to Dr. Kundara.

And a big fat raspberry to Paul Robin, the chairman of the British Acupuncture Society, who is shocked, shocked to hear these results: "I've been treating people for 20 years and in my experience treatment does seem to improve their chances of becoming pregnant." Right, Mr. Robin - so will you be finding some other occupation now? Or maybe reducing your fees? Somehow I doubt it.

I invite readers of this forum to suggest other headines on treatments that don't work. How about "Homeopathy doesn't cure common cold"? The possibilities are endless.