Why medicine needs scirate.com

Defenders of the traditional publishing model for medicine say that health-related claims need to be vetted by a referee process. But there are heavy costs. In quantum information, one might know the proof of a theorem (e.g. the Quantum Reverse Shannon Theorem) for years without publishing it. But one would rarely publish using data that is itself secret. Unfortunately, this is the norm in public health. It’s ironic that the solution to the 100-year-old Poincaré conjecture was posted on arxiv.org and rapidly verified, while research on fast-moving epidemics like H5N1 (bird flu) is
delayed so that scientists who control grants can establish priority.
All this is old news. But what I hadn’t realized is that the rest of science needs not only arxiv.org, but also scirate.com. Here is a recent and amazing, but disturbingly common, example of scientific fraud. A series of papers were published with seemingly impressive results, huge and expensive clinical trials were planned based on these papers, while other researchers were privately having trouble replicating the results, or even making sense of the plots. But when they raised their concerns, here’s what happened (emphasis added):

In light of all this, the NCI expressed its concern about what was going on to Duke University’s administrators. In October 2009, officials from the university arranged for an external review of the work of Dr Potti and Dr Nevins, and temporarily halted the three trials. The review committee, however, had access only to material supplied by the researchers themselves, and was not presented with either the NCI’s exact concerns or the problems discovered by the team at the Anderson centre. The committee found no problems, and the three trials began enrolling patients again in February 2010.

As with the Schön affair, there were almost comically many lies, including a fake “Rhodes scholarship in Australia” (which you haven’t heard of because it doesn’t exist) on one of the researcher’s CVs. But what if they lied only slightly more cautiously?
By contrast, with scirate.com, refutations of mistaken papers can be quickly crowdsourced. If you know non-quantum scientists, go forth and spread the open-science gospel!

Entangled in the Membrane, Entangled in the Brain?

Bad New Scientist has an article up today entitled Brain ‘entanglement’ could explain memories, which certainly must have sent Roger Penrose’s brain into a state of multiple correlated back-flips (twistor flips?) However, from the article:

Subatomic particles do it. Now the observation that groups of brain cells seem to have their own version of quantum entanglement, or “spooky action at a distance”, could help explain how our minds combine experiences from many different senses into one memory.

First of all, damnit New Scientist, entanglement is not just between “subatomic particles.” Second of all, the effect described is as similar to spooky action at a distance as the fact that when you look at my feet you’ll most likely see that I have the same color sock on both of my feet. To suggest that the effect described in this PLOS biology paper where they observed correlated local field potential mesurements in a monkey’s brain has got anything to do with quantum entanglement is…well…just plain wrong.
(Which is not to say that quantum effects might not arise in the brain: we simply don’t have any evidence of such effects and speculations about such effects arising are, so far, physically implausible. I.e. that’s how a scientist says: probably not, but I’m always ready to change my opinion with some good hard evidence.)

TTAGGG Nobel Prize

The Nobel Prize in Physiology or Medicine for 2009 has been announced and has been awarded to Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak for “how chromosomes are protected by telomeres and the enzyme telomerase.” I’m sure the medicalbioblogs here on Scienceblogs will have some fine coverage of this. But one thing jumps out at me: Carol Greider was, I think, a graduate student when she worked did this work! So, dear graduate student procrastinating by reading this blog, please get back to work and win that there Nobel Prize!
Oh, and of course, in the Nobel counting game, I am happy to report “Go Bears!” Cal is where Greider got her Ph.D. (and where the work on telemorase was done.)
Also, first Nobel prize to a Tasmanian (Blackburn)?
Oh, and yes, I just checked GERN stocks spiked this morning 🙂

Watching BioBarCamp From Afar

Over at Science in the open, the the ScienceOpener (Cameron Neylon) is attending BioBarCamp. Now, IANAB (that stands for “I am not a stamp collector” 🙂 ) but there are a ton of cool talks at BioBarCamp: many on open science / social media / science 2.0 etc (for which biologists are kicking everyone’s rear at.) Here is the schedule on google docs. Because I’m supposed to be working on a talk for an upcoming review, I need something to listen to and watch out of the corner of my eye, as I work on the review. And ScienceOpener provides: A lifefeed of the event.
Which is cool, because now I can hear awesome interesting ideas, while trying to work on my presentation (with less awesome ideas, BTW.) And I even get to see familiar faces (well…familiar people lounging while listening):
How cool is that. Science, it is a changing, my little pea sized mind thinks 🙂

Amateur Bioengineering?

Bill Gates thinks that robots are at the equivalent stage that computers were when he and Paul Allen and a ton of hobbyists helped fuel the PC revolution. But is he right? Here is a radical proposal: might not bioengineering be the next field where amateurs have a huge impact? Such is the hypothesis of DIYbio which had its first meeting in Cambridge, MA on May 1st:

In the packed back-room of Asgard’s Irish Pub in Cambridge, a diverse crowd of 25+ enthusiasts gathered to discuss the next big thing in biology: amateurs. Mackenzie (Mac) Cowell led-off the night with an overview of recent history in biological engineering, and asked the question: Can molecular biology or biotechnology be a hobby? Will advancements in synthetic biology be the tipping point that enables DIYers and garagistas to make meaningful contributions to the biological sciences, outside of traditional institutions? Can DIYbio.org be the Homebrew Computer Club of biology?

Inspiring Talks: Drew Endy

Good talks are rare gems. Good talks about interesting topics even rarer. Good talks that make you want to change fields and design E. Coli which smell like bananas are the best. I saw a good one earlier this week, and its now online: Learning to Program DNA by Drew Endy. If you get a chance, check out the picture of Drew going off a waterfall in a kayake on the Lower McCloud river. That’s very close to where I grew up (and don’t you city folk come up there and ruin that beautiful neck of the woods. Stay way slicker!)

The Shrimp! They See Me Polarizations!

A new entry in the best title ever competition: arXiv:0804.2162, “The secret world of shrimps: polarisation vision at its best”, by Sonja Kleinlogel and Andrew G. White. Secret lives of shrimp? That sounds more like an expose on the secret drug habits of the Roloffs on the T.V. show Little People Big World, than the title for a scientific article. (Yes it is politically incorrect to call little people “shrimps.” Having spent the first many years of my life being stared at for have a little person as a sister, however, I think you can cut me some slack, and just laugh 🙂 ) Let’s see if makes it by the title police.
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