Wednesday, September 30, 2009
Tuesday, September 29, 2009
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 www.PubMed.gov.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
Dawn does some cool work at the interface of evolution, geology and microbiology so this could be something worth watching ...
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 ...
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.
for more information.
Thursday, September 24, 2009
Wednesday, September 23, 2009
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.
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.
Sunday, September 20, 2009
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 enhancementWould write more, but brain not doped right now ---
Wednesday, September 16, 2009
"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
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 RRN@ncbi.nlm.nih.gov. General guidelines for participation are described below; these guidelines are provisional and may change as NCBI gains experience with the new RRN archive.
Monday, September 14, 2009
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):
Friday, September 11, 2009
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 ---
Tuesday, September 08, 2009
I just got this email.
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 ucfacultywalkout.com
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
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
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
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
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 http://www.grandchallenges.org/explorations 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 http://www.grandchallenges.org/explorations.
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
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.
Most recent post
New article out from the Eisen Lab: Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum
See Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum Paper based on PhD thesis work of Katie Dahlha...
Just got this press release by email. I am sick of receiving dozens of unsolicited press releases, especially those in topics not related ...
I have a new friend in Google Scholar Updates I have written about the Updates system before and if you want more information please see...
Word Cloud from the Acknowledgements So I always end up on Thanksgiving thinking about all the people I should thank for contributing ...