Paul Offit on the Poling Case

Paul Offit has a typically brilliant op-ed piece in today's New York Times. He takes a logical look at the Vaccine Injury Compensation Program and the potentially destructive fallout of the recent and highly publicized Poling case. An especially compelling (and often missed) point is the harm that cases such as this may do to autism research and, indirectly, to affected children. Every dollar spent trying to prop up the discredited vaccine-autism link is a dollar diverted from research that might lead to a better understanding of a complex disorder.

Note: There is also the obligatory asinine response from David Kirby at Huffington Post.

Moon Jellyfish

Scripps Aquarium, 3/26/2008.

On Rejection

Ferric Fang has a commentary in Infection and Immunity called "On Rejection." It is certainly worth reading if you've ever received (or written!) a rejection letter. The calls for civility on the part of editors, reviewers, and authors have certainly been made before, but it is a theme that bears repeating.



Fang, F.C. (2008). GUEST COMMENTARY: On Rejection. Infection and Immunity DOI: 10.1128/IAI.00315-08

Google Sky

Google Sky. Outrageous.

Design and the Elastic Mind

I recently went to the Design and the Elastic Mind exhibit at the Museum of Modern Art. Here is the website text describing the rationale behind the exhibit:

Over the past twenty-five years, people have weathered dramatic changes in their experience of time, space, matter, and identity. Individuals cope daily with a multitude of changes in scale and pace—working across several time zones, traveling with relative ease between satellite maps and nanoscale images, and being inundated with information. Adaptability is an ancestral distinction of intelligence, but today’s instant variations in rhythm call for something stronger: elasticity, the product of adaptability plus acceleration. Design and the Elastic Mind explores the reciprocal relationship between science and design in the contemporary world by bringing together design objects and concepts that marry the most advanced scientific research with attentive consideration of human limitations, habits, and aspirations. The exhibition highlights designers’ ability to grasp momentous changes in technology, science, and history—changes that demand or reflect major adjustments in human behavior—and translate them into objects that people can actually understand and use. This Web site presents over three hundred of these works, including fifty projects that are not featured in the gallery exhibition.

The group that I visited with included a mathematician, a music journalist, an obstetrician, three seven year-olds, and me. I was absolutely stunned at the ability of nearly all of the projects to appeal to everyone in that group. The web site is worth a look, with everything from computer animation of the Dicer enzyme to curved origami to "accessories for lonely men." Link.

E. coli and your receptors

Ok. This is cool. I took a break from grant-writing to read this paper, and I’m glad that I did. Starting with an in silico screen, Cirl et al. showed that some pathogenic bacteria (they focused on uropathogenic E. coli) secrete proteins that are homologues of a domain of the mammalian toll-like receptors (TLR). TLR are the sentinel molecules of the innate immune system, detecting conserved pieces of pathogens (peptidoglycan, lipopolysaccharide, or good-old bacterial DNA) and initiating immune responses. They are present on all kinds of cells, including the epithelial cells that line the urinary tract. The E. coli proteins that this group found bind to the TIR domain, the part of TLR that are responsible for transducing signals, and interrupt the signaling cascade, effectively silencing the alarm. This blunts the immune response and, presumably, protects the bacteria from attack. The paper is a great piece of work, telling a coherent story and taking the idea from the initial screen to a mechanistic investigation that has real clinical implications. Well done!

Link to article. (Sadly, not open access.)


Cirl, C., Wieser, A., Yadav, M., Duerr, S., Schubert, S., Fischer, H., Stappert, D., Wantia, N., Rodriguez, N., Wagner, H., Svanborg, C., Miethke, T. (2008). Subversion of Toll-like receptor signaling by a unique family of bacterial Toll/interleukin-1 receptor domain–containing proteins. Nature Medicine DOI: 10.1038/nm1734

NIH Public Access Policy -- Public Comments Needed

The following is an email that went out to the PLoS ONE Editorial Board today. Please do consider contacting NIH in support of the Public Access Policy and against the attempts to further delay its implementation. Thanks.


_____________
Dear Editorial and Advisory Board Members,

Apologies for sending this email round to everyone as this policy mostly applies to people in the USA, especially people funded by the NIH. However, anyone is free to comment.

As I am sure many of you know, the US congress recently passed a bill to require public access to NIH funded research. A summary of developments is here http://www.plos.org/cms/node/308.

The deadline for the implementation of the NIH Public Access Policy (4/7/08) is fast approaching and some traditional publishers are trying to delay this important step.

The NIH seeks your input immediately.
To fully understand the scientific and taxpayer community perspective of this important initiative, the NIH urges you to add comments at this website http://publicaccess.nih.gov/comments/comments.htm
by Monday 3/17 5pm EDT.

Please comment in your own words – however, you may find the following ideas useful in framing a response.
The proposed NIH policy:

Positively contributes to the advancement of science
Serves the public health—by enabling discovery, speeding treatment, and cures
Provides a direct return for public investment in the NIH
Keeps the USA in step with other countries who have recently enacted similar polices
Democratizes teaching and learning—by providing new resources for scientists to use in new and innovative ways.

If you have questions about the policy and how it affects you, you should ask these questions on the website, but we’d encourage you to preface them with a statement of support (it would be a shame if such questions were misinterpreted as a lack of support for the policy).

These comments will be considered alongside verbal presentations at the Open Meeting on Public Access on 3/20 (you may also register here http://publicaccess.nih.gov/comments/registration.htm to attend this meeting by Monday 3/17 5pm EDT).
Thank you, in advance, for letting the NIH know that you and your community supports this policy.

Please do feel free to forward this message along to U.S. colleagues, friends, and family members, as this policy affects researchers, patients, and the taxpaying public.

Best wishes,
Mark

Mark Patterson
Director of Publishing

Public Library of Science
European Office:
7 Portugal Place
Cambridge
CB5 8AF, UK

t: +44 (0)1223 463331
e: mpatterson@plos.org
w: www.plos.org
---------------------------------

Screening for new antibiotic resistance genes

A recent article in PLoS ONE takes a broad look at antibiotic resistance in Pseudomonas aeruginosa, an environmental organism and a cause of opportunistic infections. Pseudomonas infections are particularly difficult to treat, as it is frequently resistant to numerous classes of antibiotics. Children who are predisposed to chronic colonization or infection with Pseudomonas, such as those with cystic fibrosis, may eventually harbor bacteria that are resistant to all available antibiotics. Fajardo et al. (citation below) screened two transposon libraries of P. aeruginosa looking for genes that either increased or decreased susceptibility to a panel of antibiotics. Their results are of interest, as many of their hits (genes associated with a change in susceptibility) were in classes of genes not previously linked to resistance. A weakness of the study is that they do not go on to make defined mutations in these genes or to complement the phenotype by expressing the mutated gene on a plasmid, but it is an interesting screen that has the potential to provide targets for future antimicrobial development.

Here is the PubMed link so that you can reach the PubMed Central version of the article if the PLoS ONE site continues to be slow.

Fajardo, A., Martínez-Martín, N., Mercadillo, M., Galán, J.C., Ghysels, B., Matthijs, S., Cornelis, P., Wiehlmann, L., Tümmler, B., Baquero, F., Martínez, J.L., Falagas, M. (2008). The Neglected Intrinsic Resistome of Bacterial Pathogens. PLoS ONE, 3(2), e1619. DOI: 10.1371/journal.pone.0001619

Shameless promotion for my friend's new book...

My good friend Sam Wang and his coauthor Sandra Aamodt have just published their book, Welcome to Your Brain. The subtitle is "Why You Lose Your Car Keys but Never Forget How To Drive and Other Puzzles of Everyday Life." It is simultaneously useful, thought-provoking, and funny, and it has already gotten wonderful reviews (summarized at welcometoyourbrain.com). Give it a try! Amazon link.

A high-profile retraction

There are an announcement and a news article in the current issue of Nature retracting a paper from Linda Buck's lab about mapping olfactory connections in the mouse. The paper was retracted following the inability of their group and others to reproduce the data. There is often a great deal of controversy following a retraction like this, but it seems that this is one good example that the system of peer-review, publication, and independent replication works well as a road to scientific truth. Falsification (or legitimate, unintentional error) may persist for a while in the literature, but eventually, we hope, the truth comes out.

This is, of course, yet another argument in favor of making published research reports and even primary data as widely available as possible.


Zou, Z., Horowitz, L.F., Montmayeur, J., Snapper, S., Buck, L.B. (2001). Genetic tracing reveals a stereotyped sensory map in the olfactory cortex. Nature, 414(6860), 173-179. DOI: 10.1038/35102506
.

CDC vaccine safety site

The CDC has a new vaccine safety site. This is a much better place to get scientifically valid information than, for example, a Republican presidential candidate.

Avery and the pneumococcus

I gave a lecture on Streptococcus pneumoniae (pneumococcus) in our global antimicrobial resistance course today. Despite more than a hundred years of work, the pneumococcus remains a major cause of morbidity and mortality worldwide. We have vaccines, we have effective antibiotics (fewer and fewer…), yet pneumococcal infection still kills about a million kids every year.

Here’s something that I do when I want to feel small: I look back at the papers that Oswald Avery published on the topic of the pneumococcus between 1915 and 1946 in the Journal of Experimental Medicine. (Thanks, JEM, for opening up your archive back to the very first issue!). Not only is the paper defining DNA as the transforming substance in there, but nearly everything that we understand about the pneumococcus was done or predicted by Avery. The carrier state, capsular polysaccharide (and the fact that one can diagnose pneumococcal infection by detecting it in the urine), autolysis, hydrogen peroxide production, discovery of C-reactive protein, and how to make a conjugate vaccine: it’s all there. Our best diagnostics and vaccines are still offshoots of his work.

As with any great scientist, he did not work alone, and many others have contributed to advancing the field, but I remain in awe of Avery.




Dochez, A.R., Avery, O.T. (1915). THE OCCURRENCE OF CARRIERS OF DISEASE-PRODUCING TYPES OF PNEUMOCOCCUS . Journal of Experimental Medicine, 22(1), 105-113.