Sames/Sezen investigative reports released

18Jul11

A little late to the party on this one, but: FOIA requests have resulted in the release of investigative reports on the infamous case of Columbia chemist Dalibor Sames and onetime star student Bengu Sezen, now confirmed to have committed large-scale misconduct during her time in the lab.

The C&EN article links the complete reports. What’s really mind-boggling about this case isn’t the fraud, but the carelessness. If Sezen’s notebooks were garbage, how did she come off in day-to-day interactions as an active and productive researcher, much less one deserving of distinction? Even before suspecting fraud, why did no one speculate about possible error or contamination when multiple people reported difficulty reproducing the reactions? I can see being reluctant to speculate that someone is being dishonest, but questioning their competence is par for the course in grad school, isn’t it?

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Soy and PCA

18May11

http://www.ncbi.nlm.nih.gov/pubmed/19127598

So the current candidates are vitamin D/calcitriol/herring, artichoke(yasukawa10), and soy(http://www.ncbi.nlm.nih.gov/pubmed/15087261, 19127598). We’ll try caloric restriction (i.e. vegetable puree and red pepper) too.

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N-Acylethanolamine deficiency increases longevity?

12May11

* Mark Lucanic,1
* Jason M. Held,1
* Maithili C. Vantipalli,1
* Ida M. Klang,1, 2
* Jill B. Graham,1
* Bradford W. Gibson,1
* Gordon J. Lithgow1
* & Matthew S. Gill1, 3

* Affiliations
* Contributions
* Corresponding author

Journal name:
Nature
Volume:
473,
Pages:
226–229
Date published:
(12 May 2011)
DOI:
doi:10.1038/nature10007

Received
24 March 2010
Accepted
17 March 2011
Published online
11 May 2011

Dietary restriction is a robust means of extending adult lifespan and postponing age-related disease in many species, including yeast, nematode worms, flies and rodents1, 2. Studies of the genetic requirements for lifespan extension by dietary restriction in the nematode Caenorhabditis elegans have implicated a number of key molecules in this process3, 4, 5, including the nutrient-sensing target of rapamycin (TOR) pathway6 and the Foxa transcription factor PHA-4 (ref. 7). However, little is known about the metabolic signals that coordinate the organismal response to dietary restriction and maintain homeostasis when nutrients are limited. The endocannabinoid system is an excellent candidate for such a role given its involvement in regulating nutrient intake and energy balance8. Despite this, a direct role for endocannabinoid signalling in dietary restriction or lifespan determination has yet to be demonstrated, in part due to the apparent absence of endocannabinoid signalling pathways in model organisms that are amenable to lifespan analysis9. N-acylethanolamines (NAEs) are lipid-derived signalling molecules, which include the mammalian endocannabinoid arachidonoyl ethanolamide. Here we identify NAEs in C. elegans, show that NAE abundance is reduced under dietary restriction and that NAE deficiency is sufficient to extend lifespan through a dietary restriction mechanism requiring PHA-4. Conversely, dietary supplementation with the nematode NAE eicosapentaenoyl ethanolamide not only inhibits dietary-restriction-induced lifespan extension in wild-type worms, but also suppresses lifespan extension in a TOR pathway mutant. This demonstrates a role for NAE signalling in ageing and indicates that NAEs represent a signal that coordinates nutrient status with metabolic changes that ultimately determine lifespan.

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Earth Day and Columbia Medical Center

23Apr11

According to Dean Goldman, Facilities and our CUMC energy coordinator, our campus generated 58,000 metric tons of carbon dioxide equivalent in 2010. Current plans for improvement include automated building management systems, labeling and education, and air handling and lighting improvements with new construction and renovation, which will apparently go toward a 30% CO2 reduction by 2025.

Not the most ambitious set of goals. I understand that the fundamental mission of the campus- temperature control, is a fundamental energy sink, but one could certainly see more direct attacks than education and even “building management”: our old infrastructure means that even with the most efficient environmental controls, most of our air goes to poorly insulated environmental rooms and directly out of non-weatherized plain glass windows. In 15 years, with appropriate planning, insulation, green roofs, and heat storage/heat exchange, the entire campus could be net carbon neutral. In principle, there is no reason why any configuration of physical infrastructure should be designed to emit more carbon than it takes in. Though managing costs over the long term isn’t the easiest project.

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Behavioral Economics and Science Financing

23Apr11

Mankiw recently points to a Brookings institution in-depth summary (a.k.a. “textbook”) of recent research in economic decision-making and psychology.

NIH funding dodged this year’s bullet, unusually. I still think it’s worth considering how public funding of science exhibits market failures and externalities. Hopefully someone will eventually run the numbers and use them as ammunition for public and private efforts to increase the positive influences of science in society.

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Interesting thoughts on open-access publishing

06Apr11

Somewhat to my chagrin, I never actually read in detail the much-discussed study supposedly finding that open-access scholarly publication increases citation rates. Turns out that’s not quite right; online access, open or not, increases citation rates (Dept of Duh calling…). It’s hard to generalize to other fields, but at least in science, the reality is that institutions at which a lot of science is done all subscribe to the publications of interest – and blustery threats about library subscription rates aside, that isn’t going to change in the near future, diluting the impact of open-access publication on distribution.

So now we have a report from the Scholarly Kitchen of a new OA study finding that OA articles are more widely distributed, but with no difference in citation counts, suggesting that:

The real beneficiaries of open access may not be the research community, which traditionally has excellent access to the scientific literature, but communities of practice that consume, but rarely contribute to, the corpus of literature. These communities may include students, educators, physicians, patients, government, and industry researchers.

Now the next question: is the current low level of contribution from these communities a feature of their indirect engagement with research, or their traditional lack of access to the existing literature? Will we start seeing more genuine contributions from hobbyists and ‘citizen scientists’ without the direct involvement of a professional scientist?

On the other hand, as enthusiastic as I am about the consumption access side of OA, the production access side remains problematic, as SK notes:

…I find suggestions that authors can purchase their way to increased citations by paying author fees deeply disturbing. If there is indeed a citation advantage to open access publishing, is it acceptable for publishers to try to rake in more fees by inducing authors to game the system this way? Does this potential pathway toward buying status favor the well-funded laboratory, allowing the rich to become richer?

If an alleged citation advantage is behind an author’s motivation to pay fees, then what happens if all journals become full OA publications and the playing field is leveled? Without the conferred advantage, will authors continue to accept the new economic conditions?

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Worth noting

10Mar11

Google has named 21 Science Communication Fellows (http://blog.google.org/2011/02/making-sense-of-science-introducing.html), and Nature points out the existence of a network of global science festivals (http://www.sciencefestivals.org)…

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Jolecule

03Mar11

Full HTML5 protein viewer with collaborative annotations. http://jolecule.appspot.com

Hey, check out my active site: RNase H.

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The disheartening attrition of

15Feb11

would-be scientists may be the worst part of the career choice: while other professional programs essentially supply graduates to viable careers (even law!), science Ph.D.s are taught early on that they are likely to shift into completely unrelated fields following graduation. This is largely a result of shortsighted federal funding policy, of course- but the endless drumbeat of consulting and finance career fair emails (that are equally accessible to non-Ph.D.s) highlights the fact that there is insufficient economic structure to support distantly useful curiosity. My solution? A global pool for scientific risk.

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Knowledge bias

13Feb11

From Krugman:

It’s particularly troubling to apply some test of equal representation when you’re looking at academics who do research on the very subjects that define the political divide. Biologists, physicists, and chemists are all predominantly liberal; does this reflect discrimination, or the tendency of people who actually know science to reject a political tendency that denies climate change and is broadly hostile to the theory of evolution?

I’d take this one step farther: those familiar with interpreting data are generally more familiar with the large divide between human expectations and observation. The implication for supporting policies that fit with social realities are clear.

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