Wednesday, September 30, 2009

New DOE Graduate Fellowships in Science, Math, Engineering

Secretary Chu Announces up to $12.5 Million in Recovery Act Funding for New Graduate Fellowships in Science, Mathematics and Engineering

New Funding Highlights the Administration’s Commitment to Empowering Students to Choose Careers in Science

Washington, DC – U.S. Energy Secretary Steven Chu announced today that up to $12.5 million in funding from the American Recovery and Reinvestment Act will be awarded in early 2010 to support at least 80 graduate fellowships to U.S. students pursuing advanced degrees in science, mathematics, and engineering through the newly created Department of Energy Office of Science Graduate Fellowship program. The goal of the fellowship program is to encourage outstanding students to pursue graduate degrees in physics, chemistry, biology, mathematics, engineering, and environmental and computer sciences – fields that will prepare students for careers that can make significant contributions in discovery driven science and science for national needs in energy and the environment.

“Training the next generation of U.S. scientists and engineers is critical to our future energy security and economic competitiveness,” said Secretary Chu. “This Fellowship is part of the Administration’s effort to encourage students to direct their talents towards careers in science and our nation’s next technology revolution.”

To be eligible for the Fellowship, applicants must be U.S. citizens and currently a first or second year graduate student enrolled at a U.S. academic institution, or an undergraduate senior who will be enrolled as a first year graduate student by the fall of 2010. Applicants must be pursuing graduate study and research in the physical, biological, engineering and computational sciences. Interested students can apply online at:

Each fellowship award will be $50,500 per year for three years to provide support for tuition, living expenses, research materials and travel to research conferences. Fellowships will be awarded on the basis of peer review. Applicants may begin submitting applications on September 30, 2009. Completed applications are due November 30, 2009.

Tuesday, September 29, 2009

NYTimes advice on probiotics: "go to Pubmed" but ignores #openaccess issues

There was an article on probiotics in the New York Times today. By Tara Parker-Pope it addresses some important issues rarely covered in the press about probiotics (see Well - Probiotics - Looking Underneath the Yogurt Label -

On the one hand, the article does a decent job of pointing out that there is great strain to strain variation among microbes labelled as probiotics. In this regard there is a great quote by Gregor Reid:
Lactobacillus is just the bacterium,” said Gregor Reid, director of the Canadian Research and Development Center for Probiotics. “To say a product contains Lactobacillus is like saying you’re bringing George Clooney to a party. It may be the actor, or it may be an 85-year-old guy from Atlanta who just happens to be named George Clooney. With probiotics, there are strain-to-strain differences.”
Personally I think the article did a poor job of discussing one of the real complexities of probiotics (and actually any drug) in that seems to suggest that particular strains are going to be useful for certain ailments or not. In reality, the human gut is a horribly complex place, and the effectiveness of particular strains is no doubt going to depend on health status, history, other microbes being present, gender, age, genetics, and much much more. Thus it would have been good to include some more discussion of just how complex the interaction between probiotics and "health" is likely to be.

Interestingly, the article suggests:
Consumers interested in probiotics should look for products that list the specific strain on the label and offer readers easy access to scientific studies supporting the claims. A good place to find studies on various probiotic strains is the Web site
On the one hand, I am very happy that the Times is suggesting consumers look up information in Pubmed, a great resource. On the other hand, much of the published work on probiotics is still hidden from consumers being the veil of corporate and society publishing practices. Perhaps the Times author had access to all these articles. But the consumer right now does not. Too bad the Times missed a chance to discuss this important component of getting consumers involved in making their own health decisions.


Saturday, September 26, 2009

East Quad Farmers Market

Another nice thing for the fall and spring on Campus at UC Davis - Wednesday from 10-2 or so there is a Farmer's Market in the quad. It is not huge, but if you want some fresh/local produce - this is a good place to get something. See here for more detail: East Quad Farmers Market

Follow #UCDavis Geology Prof. Dawn Sumner in Antarctica

UC Davis Geology Professor Dawn Sumner is heading to Antarctica for a research trip of ~ 2.5 months. And you can follow her journey/work on her blog "Dawn in Antarctica"

Dawn does some cool work at the interface of evolution, geology and microbiology so this could be something worth watching ...

Some #UCDavis students running 'Operation DeGeneres' trying to bring @TheEllenShow to town

Strange, funny, and true. Some UC Davis students are working to bring Ellen Degeneres to town.

From their site:

Operation DeGeneres was founded by UC Davis students and is an effort to have Ellen DeGeneres grace us with her presence at UC Davis--in either a speech to the campus or as keynote speaker at the 2010 graduation ceremony. She's funny, she's inspirational, and she probably has many words of wisdom.

For more information see:
Operation DeGeneres - Home

I note- my kids (4.5 and 2.5 yrs old) would like this - as Ellen is one of the voices in Finding Nemo ...

More on #UCDavis Prof. Emeritus Bernie Alder's National Medal of Science

More information on UC Davis professor emeritus Bernie Alder's National Medal of Science Award can be found here: UC Davis News & Information :: Prestigious National Medal of Science goes to physicist

Among his many achievements was pioneering work in the field of Molecular Dynamics. He also was one of the founders of the UC Davis Department of Applied Science. Oh, and my wife is good friends with his daughter Janet --- and Alder and his whole family are simply amazing.

#UCDavis expands programs to support alternative modes of commuting

UC Davis has started an enhanced program to encourage people to not drive to work. It is called "goClub" and includes programs for walkers, bikers, carpoolers, etc. For bikers, like me, see goBike
for more information.

Thursday, September 24, 2009

Against faculty walking out but sympathetic to student protests

I have already written extensively about why I think faculty should not walk out of classes today on this day of protests on UC campuses. Mainly this is because I think it is unfair to students for me to impose my will on their classes and that I think if faculty were to impose their will on students classes it would be a bad political move. (I note, I think the best response to this issue I have seen was an commentary in the LA Times by UC Riverside Professor Susan Straight, who is going to let her students decide what she should do with her classes today).

I am also not enthusiastic about the faculty walkout because I think that energy should be focused on changing public opinion and Sacramento opinion and not on the UC administration. That being said, I think the UC administration has not handled the budget crisis in an ideal manner. And I completely understand why many faculty, staff, students, and unions are not pleased with how things are going.

Thus, even though I do not support faculty walking out of class today, I am sympathetic to the protests and in particular to the student side of the protests. Students at UC and CSU are getting pummeled in many ways - from higher fees, to bigger classes to less access to education. They deserve our respect today and through all of these rough times ...

Wednesday, September 23, 2009

Why I do not endorse the UC Faculty Walkout ---

Today I have an Editorial in the Sacramento Bee, co-written with UC Davis Prof. of German Winder McConnell, regarding the proposed UC Faculty Walkout for Thursday 9/24/09 .

In the Editorial (My View: UC Davis strike: Teaching is more than just about being paid) we discuss why we do not support the idea of stopping teaching.

Some quotes:
And so it's painful to us that much of the basis for the proposed walkout is literally that many faculty wanted to "spread the pain" to students to make a political point about the effects of furloughs on education. This is an unacceptable use of students as pawns in this high-stakes game, especially those students and their families who are already shouldering a heavy financial burden that is soon likely to get much heavier.
We accept that the entire UC system could do a better job of communicating to Sacramento's policymakers about the "pain" and "consequences" of budget cuts, and that teaching less would be a way to show that the cuts have a real impact on education. But abandoning the classroom is the wrong way to go. It would be a horrible political move right now. California's budget could still go down next year and there could be more cuts. If UC works to build political capital in the coming year, then perhaps we will avoid some cuts next time around. But if we slash instructional time as a way to spread the pain, it will come back to bite us.

The Editorial does not capture all my feelings about the walkout but does capture some of them. I would like to add a few things here that relate to what led me to want to write more about this issue

One thing that really bugs me about some aspects of the proposed walkout is the suggestion that there is some sort of conspiracy by the UC Administration to do harm to UC -- For example, consider this from web site from the pro walkout group:
Under the cover of the summer months, UC administration has pushed through a program of tuition hikes, enrollment cuts, layoffs, furloughs, and increased class sizes that harms students and jeopardizes the livelihoods of the most vulnerable university employees. These decisions fundamentally compromise the mission of the University of California. They are complicit with the privatization of public education, and they have been made in a manner that flouts the principle of shared governance at the core of the UC faculty's capacity to guide the future of the University in accordance with its mission.
The lines like "Under the cover of the summer months" and "sent at the opening of a late summer weekend, with unimpeachably cowardly timing" (from other material) are both non-helpful and unsatisfactory. The throwing of such accusations is really too bad, since there are some valid complaints to be made. If you skip over the conspiracy accusations, which I have a hard time doing, I think the main complaints by faculty can be divided into two categories: 1) The budget and furlough decisions are not wise or fair and 2) The process of making the decisions was not inclusive enough.

Some aspects of these complaints are sensible. But do they rise to the level of calling for a walkout? I confess, though I sympathize with many of the faculty concerns, I just do not see the justification for a walkout at this point.

For example, in regard to the #1 complaint above (the budget/furlough decisions being unwise and unfair), it is hard for me to imagine ANY decisions that would make people happy. Somehow, either people have to get laid off or their salaries slashed. And somehow fees have to get raised. Or possibly, just possibly, money could be scrounged from various sources such as cutting new building, digging into reserves, etc. But that to me just says "lets pass on the pain to future times." From my perspective, the UC administration has been put in a horrible position. They get unpredictable, sudden, very large cuts in support the state government. And they are forced to balance the books somehow.

In regard to complaint #2 (that the process of making the decisions has not been inclusive enough) I can see why some faculty are not pleased with some of the decision making process. First UC solicited input about furloughs vs. pay cuts, then they announced that they would use furloughs as requested. Many faculty wanted this because they thought furloughs should happen on instructional days. But then UC did an end run around this by announcing that furloughs could not be taken on instructional days. This was no doubt a roundabout way to get to a policy and it was not handled very smoothly.

But in the end, as we discussed in the editorial, I think the decision to not allow furloughs to happen on instructional days was the right decision (See my previous blog about this here). One reason I support this decision is that I do not agree that we should spread the pain of furloughs to students as some have suggested. The logic here is that for Sacramento to understand the effects of the budget cuts they must see that education is truly affected and what better way to show this than to cut instruction? I agree this could work this way, but think much more likely this would backfire politically and the faculty would look spiteful.

I am not saying there are not things to complain about here. There are many. But I think the real complaints should be directed towards the State Government. The lack of support from the California government for UC and CSU and education in general is sad and mystifying given how important UC/CSU and public education is to the state. If the pro-walkout groups emphasized this in their language I might have supported the walkout. But with the way it is now, with suggestions of conspiracies in the UC administration and with nebulous complaints about budgets, it just does not make sense for faculty to walkout of classes. Mind you, I think the unions and students have some valid complaints of their own and I am not saying I object to their strikes/walkouts. I am just saying that the faculty walkout right now does not seem right.

Sunday, September 20, 2009

For all you brain dopers --- read this ---

Just a quick one here --- Article in the Guardian by Margaret Talbot who also wrote a recent New Yorker article. Some interesting stuff in here on "brain doping". See Can a daily pill really boost your brain power? | Science | The Observer

Lead in as follows:
In America, university students are taking illegally obtained prescription drugs to make them more intelligent. But would you pop a smart pill to improve your performance? Margaret Talbot investigates the brave new world of neuro enhancement
Would write more, but brain not doped right now ---

HHMI Focusing on Biodiversity ofr Holiday Lectures (in Dec2009)

Cool - UC Davis Alumni and brilliant microbiologist Bonnie Bassler will be giving one of the HHMI Holiday Lectures on Science as a WebCast. Anyone can watch Dec 3 and 4th. She will be talking with Baldomero Olivera and the topic(s) will be "Exploring Biodiversity: The Search for New Medicines". See HHMI's BioInteractive - Holiday Lectures on Science for more detail.

Wednesday, September 16, 2009

Better measure of scientific impact;: #PLoS Introduces article level metrics ---

This rocks - PLoS has introduced article level metrics for papers in PLoS journals (Article-level metrics at PLoS – addition of usage data | Public Library of Science). More detail can be found at this page which says
"The Public Library of Science (PLoS) is the first publisher to place transparent and comprehensive information about the usage and reach of published articles onto the articles themselves, so that the entire academic community can assess their value. We call these measures for evaluating articles ‘Article-Level Metrics‘, and they are distinct from the journal-level measures of research quality that have traditionally been made available until now."

And of course, like most others, I went straight to some of my own papers to see how they were doing. But never mind that, one of the more interesting things in the comparison of different topic areas (see Summary Tables here).

Types of information they are collecting and providing include article usage statistics, citations from the scholarly literature, social bookmarks, comments, notes, blog posts and rating ... and more is coming ... a good step in the direction of measuring the impact of articles not journals ....

Tuesday, September 15, 2009

Interesting new NCBI service: Rapid Research Notes

Just went to Pubmed and saw a link to a new service at NCBI called Rapid Research Notes (Rapid Research Notes)

Seems like right now all that is there is PLoS Currents (not that that is a bad thing --- I love PLoS Currents). Apparently more will be coming. From their website:

About Rapid Research Notes

The National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM) at NIH, is a national resource for molecular biology information and as such has a mandate to develop new products and services to meet the needs of the biomedical research community. Upon the recommendation of public advisors, NCBI developed an archival service to support research shared through new venues for rapid communication enabled by the internet. Introduced in August 2009, the archive, called Rapid Research Notes (RRN), allows users to access and cite research that is provided through participating publisher programs designed for immediate communication.

The RRN archive was prompted in part by the spring 2009 worldwide outbreak of H1N1 influenza and the call for a means to quickly share research information about this critical and emergent public health threat. To address the influenza information sharing need, the Public Library of Science developed PLoS Currents: Influenza, the first collection being archived in RRN. NCBI expects the RRN archive to expand over time to include additional collections in other biomedical fields and other critical topics.

Publishers interested in archiving online, rapid communications in RRN should contact NCBI at General guidelines for participation are described below; these guidelines are provisional and may change as NCBI gains experience with the new RRN archive.

The world of publishing is changing. With things like PLoS One, PLoS Currents, RRN, Nature Precedings, etc. and more coming. Time to buckle up and get ready for a good ride.

Monday, September 14, 2009

Congrats to #PLoS One for ALPSP Award

Congrats to #PLOS One and everyone behind it for winning the Association of Learning and Professional Society Publishing (ALPSP) Award for Publishing Innovation.

PLoS ONE Wins ALPSP Award for Publishing Innovation 2009 – “bold and successful and shaping the future of publishing” everyONE – the PLoS ONE community blog

I personally really really really like the PLoS One publishing model. PLoS One reviews papers based on technical merit (that is a paper has to be scientifically and technically sound). But it does not review papers based upon reviewers notions of "importance" or "interest" or "relevance". Instead, the goal is to let that evaluation happen after publishing.

This simple shift in publishing, which has been attempted a few times previously in various biomedical publications, is revolutionary. To go with this new approach to pbulsihing, PLoS One is working to encourage after publication commening and evaluation of papers. I simply love this model and think it is a great idea (I had nothing to do with the planning of PLoS One, so am not tooting my own horn here). I confess I did not completely get the concept behind PLoS One at first, but now I get it. And I embrace it. Consider my four most recent papers in Pubmed - three are in PLoS One (and one is in PLoS Genetics):

  1. The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).
  2. Assembling the marine metagenome, one cell at a time.
  3. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.
I really do like PLoS One.

Friday, September 11, 2009

Fwd: Social Behaviors workshop at Georgia Tech, Dec 2-4 2009

Announcing a workshop on social behaviors:

Microbes to Metazoans: Regulation, Dynamics, and Evolution of Social Behavior

Georgia Institute of Technology
Atlanta, Georgia, USA
December 2-4, 2009

Microbes to Metazoans is a 2 1/2 day-long workshop designed to facilitate discussion and collaboration on the study of social behavior. A select group of scientists will discuss and develop new experimental, theoretical, and computational tools to bridge multiple disciplines in the study of group tasks orchestrated by organisms from microbes to metazoans. Topical sessions motivated by a set of fundamental biological questions will be integrated with quantitative modeling and engineering talks. Applications for participation are now being accepted. There is no cost to attend, but space is limited. Information on workshop and application for participation can be found at:

Apply online at:

Application deadline: September 25, 2009

Questions, email to:

Confirmed speakers include:
Tim Cooper (Houston)
Iain Couzin (Princeton)
Alan Decho (South Carolina)
Kevin Foster (Harvard)
Kent Hill (UCLA)
Vanja Klepac-Ceraj (Harvard)
Elizabeth Ostrowski (Rice)
Philip Rather (Emory)
Kern Reeve (Cornell)
Vanessa Sperandio (Texas-SW)
Michael Strand (Georgia)
Gregory Velicer (Indiana)
Marvin Whiteley (Texas-Austin)
Frans de Waal (Emory)

Scientific organizers:
Brian Hammer

Ghostwriting in medical journals - more prevalent than we would like to believe?

Ghostwriting is much more prevalent in medical publications than many appreciate according to a new study discussed in the New York Times (Ghostwriting Widespread in Medical Journals, Study Says)

The exact details of this new study are unclear, since it is not published, but basically, a survey of authors reveals (among those responded) a remarkably high rate of "ghostwriting" where someone not on the author list made major contributions to the writing of papers.

As I have said before - openness is a way around this --- but of course only if everyone is honest. What people did as part of a paper should be reported in as much detail as allowed. Who did experiments? Who did analysis? Who did writing? Etc etc etc. It should all be stated somewhere. And many journals are moving in this direction. But alas, apparently people are not revealing all the details. Not sure what the solution to this problem is - but I can't help but think that we need to revamp the general discussion of authorship ethics within the scientific community ---

See also:

Tuesday, September 08, 2009

Proposed UC Faculty Walkout for 9/24

Dear Colleagues,

I just got this email. Not sure how I feel about this (I disagree with some of the statements here but sympathize with the feelings of many of the faculty)(UPDATE - I think this whole boycott/walkout concept is unclear and strange and will not participate in it --- ) but thought I would post it for people interested.
As you may have heard, there is a broad movement to defend the future of public education in California, to restore faculty's role in shared governance, and to protect the most vulnerable employees within the UC system. It has become increasingly clear that these goals require an immediate and firm rejection of the manner in which the administration has handled the budget crisis over the summer. Last week, a systemwide call went out for faculty to take action on September 24.

You can see and support this call, as of this morning, at

With limited circulation, this call has already been signed by hundreds of faculty in the UC system.

• It has been fully endorsed by the National AAUP.
• In coordination with this action, UPTE — an employee-run union with 12,000 members in the UC system — has called a strike and picket on 9/24
• The Solidarity Alliance at UCBerkeley has called for a "Walk-Out and Teach-In" on 9/24
• Option 4 at UCSB has declared "A Day of Learning, Solidarity, and Protest on 9/24"
• Saving UCLA has called for "A Day of Action" on 9/24
• The Graduate Student Union Organizing Committee at UCB is distributing an open letter calling for all UC GSIs to honor picket lines on 9/24, as they are contractually entitled to do.

These are some examples of the efforts already well under way to stand in solidarity with students and staff in defense of public education.

The call for the 9/24 actions, available at the website, calls for three demands on behalf of the future of public education in California. These demands are meant to insist upon:

1) Protection for the most vulnerable employees in the UC system
2) Respect for democratic process of decision-making
3) Information for public access concerning the handling of the budget cuts

If you support these basic goals as necessities for the University to pursue its educational mission, please sign on to the call at

If you would like further information on a simple, easy-to-organize action and education plan authored by UC faculty, we're able to provide this. Just ask.

With thanks and admiration for your commitment to the UC system and its future,

UC Faculty Walkout organizers

Flowers & #UCDavis in NYtimes article

Nice little article by Carl Zimmer in the New York Times today: Where Did All the Flowers Come From? -

The article discusses flower evolution and has some good points. One in particular comes from Jim Doyle from UC Davis, who points out that one needs the fossil record to understand the evolutionary emergence of fossils flowers. It is a good thing to remember for all the gene jockeys (like me) out there who sometimes seem to think everything can be figured out from DNA.

Stay tuned for more about this in my blog - I am teaching a 750 person class "Bis 002C - Biodiversity and the tree of life" with Doyle and Peter Wainwright this fall and will be posting some notes based on the class. Maybe Doyle will make some other key points there ...

Saturday, September 05, 2009

Bioforum for science teachers: @Calacademy. Genomics. Evolution. Oh, & Me.

The California Academy of Sciences is putting on a Bioforum for science teachers on:

Genomics: Insights and Impacts
Saturday, October, 3, 2009
9:00 am – 3:00 pm

Talks will be by me, Katie Pollard, Jeffrey Boore, and Nadav Ahituv

From their website one can get more detail on the Bioforum:
BioForum is a twice-annual seminar series for middle school and high school science teachers. Each symposium is held at the California Academy of Sciences and features presentations on current science and sustainability topics by renowned researchers. The presentations are followed by a panel discussion and question-and-answer session with the speakers and the moderator. BioForums are excellent professional development opportunities for science educators, providing up-to-date information on research that will enrich their teaching.
For more information see: Teachers: California Academy of Sciences

Gates Foundation Grand Challenges Round 4: Mostly About Infectious Diseases

Just got this announcement. The Gates Foundation has been funding some really cool stuff ... if you work on any of these topics it is probably worth thinking about putting in an Application

The Bill & Melinda Gates Foundation is now accepting grant proposals for Round 4 of Grand Challenges Explorations, a US$100 million initiative to encourage unconventional global health solutions. Anyone can apply, regardless of education or experience level.

Grant proposals are being accepted online at until November 2nd 2009, on the following topics:

New! Create New Technologies for Contraception
Create New Ways to Protect Against Infectious Disease
Create New Ways to Induce and Measure Mucosal Immunity
Create Low-Cost Diagnostics for Priority Global Health Conditions

Initial grants will be $100,000 each, and projects showing promise will have the opportunity to receive additional funding of $1 million or more. Full descriptions of the new topics and application instructions are available at

We are looking forward to receiving innovative ideas from scientists around the world and from all scientific disciplines. If you don't submit a proposal yourself, we hope you will forward this message to someone else who might be interested.

Thank you for your commitment to solving the world's greatest health challenges.

Wednesday, September 02, 2009

What should be the next genome sequenced?

What should be the next genome sequenced? Olivia Judson has turned this question into an analog of Fantasy Baseball. Submit your suggestions to her/the world at The Fantasy Genome Project - Olivia Judson Blog -

Or submit them here. For microbes it is so cheap that there is no point in doing this type of competition (e.g., for a bacterial isolate it would cost ~ 1-2000$$$ to do the shotgun sequencing for most species and then if you want to finish it would cost more, but still not very much)

My suggestion for a bigger genome to do that would be fun, interesting and important --- the blue whale. Biggest animal on the planet. Ever. Just must have its genome.

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