Some tweets of mine with links about #PLoS papers by #Nobel winners

1. #Nobel winner Blackburn's 2004 #PLoS Biology essay: Reason as Our Guide -http://shar.es/140kQ3 minutes ago from ShareThis.com
2. #Nobel winner Greider's re #PLoS Genetics pub on telomeres in Primary and Tumor Cells -http://shar.es/140wf5 minutes ago from ShareThis.com
3. #Nobel winner Szostak has many #PLoSOne pubshttp://tinyurl.com/yeel5sthttp://tinyurl.com/ycb34c5http://tinyurl.com/yegusbc7 minutes ago from web
4. Yippe - another Nobel Prize for work in Tetrahymena - see my #PLoS Biology paper on the genome here -http://shar.es/140hE12 minutes ago from ShareThis.com
5. The Greider Lab | Johns Hopkins Medicine -http://shar.es/1406w #Nobel14 minutes ago from ShareThis.com
6. Blackburn Lab Research - http://shar.es/140G9#Nobel15 minutes ago from ShareThis.com
7. Szostak Lab: Home Page http://shar.es/140G3#Nobel15 minutes ago from ShareThis.com

Worst new omics word award: Omnigenomics by (surprisingly) @Genomicron

Well, been taking a break from this award, as I am in over my head with teaching right now. But could not resist this one. Based on a tip from Marcio Pie in Brazil I checked out T. Ryan Gregory's recent posting (Genomicron: Omnigenomics) on his normally excellent Genomicron Blog. And he has clearly been overcome with H1N1 fever or something like that, as he discusses in this new posting, his desire to coin a catchy new omics word to describe his work on comparisons of genome size across species.

And he has chosen, get ready

OMNIGENOMICS

Proposed neologism: "Omnigenomics"

Etymology: Latin "omnis" (all or everything) + genomics (study of genomes)

Sample usage: "What do you do?" / "Omnigenomics" / "What's that?" / "I study the total amount of DNA in different species of animals, which includes genes and all the other sequences, most of which are non-coding and..."

All I can say, as I did in the comments on his blog, is

Nooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooo.

And for this full slide down the slippery slope of omics words, T. Ryan Gregory is the recipient of my fourth "Worst New Omics Word Award." Check out previous winners:diseasome, ethomics, and Museomics. (I note if you look through Google results, domain names with omnigenomics in them have been registered previously and then allowed to expire. Those were good deaths. Hope the resurrection is short lived).

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: http://www.scied.science.doe.gov/SCGF.html

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.

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 - NYTimes.com).

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.




.

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.

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 ...

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.

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.

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 ....

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 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.

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.

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.

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

www.socialbehavior.biology.gatech.edu

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: www.socialbehavior.biology.gatech.edu

Application deadline: September 25, 2009

Questions, email to: socialbehavior2009@biology.gatech.edu

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:

• Ghost authors remain a chronic problem
• The Game of Ghost Writing
• Ghostwriting floods in medical journals
• Ghostwriters Lurk Behind Top Medical Journals
• Who you gonna call? Ghostwriting busters! - Schwitzer health news blog
• 
  

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 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

ucfacultywalkout.com

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? - NYTimes.com

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 ...

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 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.

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 - NYTimes.com

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.

#PLoS Currents is live, in case you missed it ...

PLoS Currents is live (as of last week). Check out the blog posting by Harold Varmus:A new website for the rapid sharing of influenza research | Public Library of Science

I am very excited by this --- it seems to be a new step on Open Science.

Ted Kennedy in Pubmed Central #openaccess

For those interested in open access and/or Ted Kennedy, you might be interested to know that Kennedy has a few articles available in PubMed Central - all available for free ...

Quality, Affordable Health Care for All Americans

Edward M. Kennedy

Am J Public Health. 2003 January; 93(1): 14.

PMCID: PMC1449947

| Full Text | PDF–123K |

Health care reform: workers beware.

E M Kennedy

Public Health Rep. 1996 Jan–Feb; 111(1): 11.

PMCID: PMC1381734

| Summary | Page Browse | PDF–188K |

The congress and national health policy. Fifth Annual Matthew B. Rosenhaus Lecture.

E M Kennedy

Am J Public Health. 1978 March; 68(3): 241–244.

PMCID: PMC1653906

| Summary | Page Browse | PDF–787K |

National leadership in confronting bioterrorism: 2.

E M Kennedy

Public Health Rep. 2001; 116(Suppl 2): 116–118.

PMCID: PMC1497282

| Summary | PDF–32K |

Discussions

Edward M. Kennedy

Bull N Y Acad Med. 1972 January; 48(1): 146–156.

PMCID: PMC1806655

| Summary | Page Browse | PDF–1017K |

1974 Yale Medical Student Council Lectureship: Partners or protagonists-Congress and the Academic Medical Centers.

E. M. Kennedy

Yale J Biol Med. 1975 March; 48(1): 1–7.

PMCID: PMC2595194

| Summary | Page Browse | PDF–904K |

UC asking for people to write letter to government

For those interested in supporting the University of California and encouraging the California government to increase the budget next year here is a link for you:

UC for California - a dynamic advocacy support network for the University of California

Good move or not? - UC decides faculty furlough's will not be

Just received this email (also attached letter)

Colleagues:

After speaking at length with all of you and a number of other people with an interest in the issue, we have decided that faculty furlough days will not occur on instructional days (days for which a faculty member is scheduled to give lectures, lead classes or workshops, have scheduled office hours, or have other scheduled face-to-face responsibilities for students).

The furloughs that have been necessitated by the severe University underfunding by the State are causing significant problems for faculty who have restrictions on research and service as well as increased teaching workloads; employees who have fewer days to do their work and sometimes fewer colleagues to help them; administrators who have reduced staff and budgets to accomplish their complex tasks; on top of lower salaries for everyone. Students too will suffer the effects of the underfunding--larger and fewer classes, and increased fees, as were imposed for this fall instruction period, among other burdens. In such difficult times, I believe that we must do everything we can to ensure that the students continue to receive all of their instruction. Asking the faculty to carry a full teaching load during furloughs is a large request, but in my mind is justified by the University’s paramount teaching mission. Research is permitted on furlough days, but for many faculty this extra research will not be remunerated unless they have grants in which there are funds that can be reallocated to pay for increased effort. And since furlough days are not “service days”, they can be used for outside professional activities that may be remunerated.

We understand that the furlough plan will cause hardships for the entire University family. As such, the President and the Regents are committed to do everything possible to ensure that the plan ends after 12 months.

We will continue to work closely with faculty, students, staff and administrators to find the most efficient and thoughtful way to address the problems that will arise this year. You have my pledge that we will make the University as effective and productive as we can under the current budget problems, after which we will help you all plan for better times ahead.

Best wishes,

Lawrence H. Pitts

Interim Provost and Executive Vice President

Academic Affairs

I am sure many of my colleagues will disagree with this decision by UC. The debate around campus here has basically been about whether there should be some teaching "consequences" to all the cuts being placed on faculty. I accept that it could be useful for there to be some pain and that teaching less would be a way to show that the cuts have real impact on education. But I think personally this would be a horrible political move right now. California's budget could still go down next year and there could be more cuts. UC needs as much good will as possible in Sacramento and around the state and having faculty cut teaching days does not seem to be the best maneuver.

What do other people think? I propose we slash committees, meetings, and other "service" activities like that. Many of them won't be missed by anyone.

YARFOS: Yet another reason for #OpenScience - getting useful input from reviewers

This is in the YARFOS (Yet another reason for open science) category.

A bit old here but was cleaning out my email inbox and just found a message about a cool Open Science story.

Seems Ivan Baxter and others had submitted a paper to PLoS Genetics (it is published now - see here). As described in his Ionomics Blog (yes, another omics, but we will let than slide here):

We just got the reviews back from Plos Genetics for our esb1 paper. There were many constructive suggestions and helpful suggestions, which is what we have come to expect from Plos Genetics (and why we submit many of our manuscripts there).

One of the reviewers actually came to Piims and retrieved some of the data that went into the paper to make the point that we should comment on the Mg effect of the mutation. Specifically, the reviewer pointed out that the mutation doesn't affect Mg, even though it affects Ca. They even included a figure of the data! I am posting the figure here, Blue is the mutant, and pink is the wild-type.

Go check out his post to see the figure. In the end, by putting their data out in the open, and by having a good intentioned reviewer, they got a really useful suggestion for their work ...

RIN/NESTA open science case studies project

Just got this email ....

RIN/NESTA open science case studies project

The Research Information Network (RIN) and the National Endowment for Science, Technology and the Arts (NESTA) are looking to fund a series of case studies which will look at what motivates researchers to work in an open way with their data, results and protocols, and whether there are advantages to working this way. The case studies will also examine the disincentives and barriers to such ‘open science’ methods. The RIN and NESTA are making available up to £15,000 for this project, which is intended to run from October 2009 until January 2010.

Expressions of interest are sought, in the form of an outline statement, on not more than a single sheet of A4, indicating the scope and rational of the proposal, the research methodology likely to be used and suggestions of case studies to be examined. The deadline is 9 September 2009. For more information visit http://www.rin.ac.uk/open-science

Thanks ASM for your offer of a Credit Card with APR of up to 17.99%

I had been growing somewhat fond of the American Society for Microbiology (ASM) recently.  I had a decent time at the annual meeting.  I am chair elect for Division R (Evolutionary and Genomic Microbiology) within ASM. And though their journals are not fully open access, they at least are making efforts to put material into Pubmed Central pretty rapidly.  But the amount of crap I get in the mail courtesy of ASM is really astounding.  And today could be the proverbial straw.  I got an offer for an ASM Credit Card via Bank of America with an APR that can be raised to more than 27% with one late payment.  Umm, thanks but no thanks.  And note to anyone out there thinking of signing up for ASM or their meetings - get ready for a massive waste of paper when your name and address get sold to marketers and annoying junk mail.  Fun fun fun.

Fun w/ web ads: Science words banned by @carlzimmer featured in his ads

Carl Zimmer has recently been writing about words that should be banned from scientific communication. Originally, I thought this notion was hokie but then I read his postings about it and am starting to warm to the idea. In essence he is railing against jargon. Words and phrases he thinks are to be avoided include

• Breakthrough
• Captive observation
• Demographic leveling
• Marine environment
• Material properties
• Morphology
• Phylogenetics

When I was browsing his posting something pretty funny started to happen. Ads popped up making use of the banned terms. The best is shown in the one below:

This features an ad from Phizer for its "Big Think/ Breakthroughs" campaign to "explore medical science at the cutting edge." I guess Zimmer has not yet set up an ad blocker system which will keep out ads that use the banned terms ...

Petition to Support the Redesign of Fifth Street in #Davis CA

Make Davis even more bicycle friendly. Sign the petition regarding 5th street redesign. See

Petition to Support the Redesign of Fifth Street Petition : [ powered by iPetitions.com ]

More phishing pretending to be from Elsevier ...

I got another bizarre phishing email with the lure being something to do with Elsevier journals. Note to any gullible people out there - if Elsevier were recruiting people to do something (e.g., write papers, be editors, etc) my guess is the request would come from an Elsevier.Com email address.

Anyway here is some of the latest:

BREAKING BOUNDRIES

The Editorial Policy and Practices Of The Elsevier Journals

1. The Editorial Board

Elsevier journals are headed by Editors and an Editorial Board Members. The Editors and Editorial Board is appointed by the Publication Committee of Elsevier Journals. Editors serve a 3-year term and Editorial Board members also serve a 3-year term. Board members are chosen based on the journal’s need for representation from a particular subject area in conjunction with the individual’s commitment to maintaining high journal standards as illustrated in objective and prompt reviews.

An Editorial Office Team is also appointed by the publication committee to directly assist the editors and editorial board members.

II. The Review Process

The Elsevier Journals editorial office policy requires each manuscript be reviewed by individuals who are highly competent and recognized in the particular field of the submitted manuscript. The editorial office contacts those reviewers that have been identified as qualified and/or recommended by the authors. Authors are also encouraged to submit in their cover letters names of individuals whom they feel are appropriate and qualified to review their manuscript. Once potential reviewers agree to read a manuscript they are given a one-week time-frame to complete the review

When the reviews are completed, a decision is made to either accept the paper or give the authors the opportunity to revise according to reviewers’ suggestions or to reject the paper based on the reviewers’ criticisms and the editors’ opinion of the paper. In some instances it is necessary to seek the opinion of other reviewers if further comment is necessary to make a final decision. When an editor has completed his decision on a manuscript, the decision letter and reviewers’ comments are sent to the author. Any questions or concerns regarding the editorial decision on any manuscript must be made directly to the Elsevier Journals editorial office. Revised manuscripts are evaluated to determine if the author(s) have adequately addressed and answered the critiques of the reviewers and editors. Depending upon this evaluation, manuscripts may be accepted, returned for further revision, or rejected. If a paper is accepted, the paper is immediately sent to the publication office and slotted for the next available issue. Elsevier journals tries to complete the review cycle in one week. This time, however, may vary depending on the amount of revision work that needs to be completed before the manuscript is acceptable.

111. Grounds for Declining a Manuscript

Elsevier Journals will decline a manuscript after it has completed the review process. Manuscripts that do not meet the standards of the journal are returned to authors with substantial comments describing the basis for the decision. Manuscripts may be rejected if it is felt that the findings are not sufficiently novel, do not provide sufficient new insights, do not contain enough new information, or are too preliminary to warrant publication.

V1. Guidelines

1. Obligations of an Editor

• The editor should give unbiased consideration to all manuscripts offered for publication, judging each on its merits without regard to race, gender, religious belief, ethnic origin, citizenship, or political philosophy of the author(s).
• The editor should process manuscripts promptly.
• The editor has complete responsibility and authority to accept a submitted paper for publication or to reject it. The editor may confer with reviewers for an evaluation to use in making this decision.
• The editor and the editorial staff should not disclose any information about a manuscript under consideration to anyone other than reviewers and potential reviewers.
• The editor should respect the intellectual independence of authors.
• Editorial responsibility and authority for any manuscript authored by the editor and submitted to the journal should be delegated to some other qualified person. The editor should avoid situations of real or perceived conflicts of interest. If the editor chooses to participate in an ongoing scientific debate within his journal, the editor should arrange for some other qualified person to take editorial responsibility.
• The editor should avoid situations of real or perceived conflicts of interest. Such conflicts include, but are not limited to, handling papers from present and former students, from colleagues with whom the editor has recently collaborated, and from those in the same institution.
• Unpublished information, arguments, or interpretations disclosed in a submitted manuscript should not be used in an editor's own research except with the consent of the author.
• If the editor is presented with convincing evidence that the main substance or conclusions of a paper published in the journal are erroneous, the editor should facilitate publication of an appropriate paper pointing out the error and, if possible, correcting it.

2. Obligations of Reviewers of Manuscripts

• Inasmuch as the reviewing of manuscripts is an essential step in the publication process, every scientist has an obligation to do a fair share of reviewing.
• A chosen reviewer who feels inadequately qualified or lacks the time to judge the research reported in a manuscript should return it promptly to the editor
• A reviewer of a manuscript should judge objectively the quality of the manuscript and respect the intellectual independence of the authors. In no case is personal criticism appropriate.
• A reviewer should be sensitive even to the appearance of a conflict of interest when the manuscript under review is closely related to the reviewer's work in progress or published. If in doubt, the reviewer should return the manuscript promptly without review, advising the editor of the conflict of interest or bias.
• A reviewer should not evaluate a manuscript authored or co-authored by a person with whom the reviewer has a personal or professional connection if the relationship would bias judgment of the manuscript.
• A reviewer should treat a manuscript sent for review as a confidential document. It should neither be shown to nor discussed with others except, in special cases, to persons from whom specific advice may be sought; in that event, the identities of those consulted should be disclosed to the editor.
• Reviewers should explain and support their judgments adequately so that editors and authors may understand the basis of their comments. Any statement that an observation, derivation, or argument had been previously reported should be accompanied by the relevant citation.
• A reviewer should be alert to failure of authors to cite relevant work by other scientists. A reviewer should call to the editor's attention any substantial similarity between the manuscript under consideration and any published paper or any manuscript submitted concurrently to another journal.
• Reviewers should not use or disclose unpublished information, arguments, or interpretations contained in a manuscript under consideration, except with the consent of the author
• Reviewers should respond promptly, usually within one week of receipt of a manuscript. If reviewers need more time, they contact the editor promptly so that authors can be kept informed and, if necessary, assign alternate reviewers

There is a letter attached to it and also the procedures on how to fill the form

We would appreciate if you contact us as soon as possible because we are updating our data sheet for reviewers and editors which we want to upload in our website soonest. Thank you for your co-operation. Please reply to board.elsevier@gmail.com

Please note that you are to pay $100, for more details please read the letter attached below.

Best regards

Chief editor

------------------------------------------------------------

Then the form asks for:

Please read the letter carefully before filling the form.
Before filling this form you have to accept the conditions stated regarding the payment and on our own part we are to pay you for each work sent to you.
Payment is done only when you are accepted to become a member.

Name of Editor
Date of Birth
Area of Specialization
Degree
No. of Articles Published

Name of Reviewer
Date of Birth
Area of Specialization
Degree
No. of Articles Published

And a separate PDF says

Dear colleague,
Elsevier publishes the largest journals online which is a close access
system. Each year we organize a routine test for all our reviewers
and editors to ascertain their level of research in the reviewing and
editing of articles before publication. We would like to know if you are
interested in serving as a member of our reviewing and editorial
board. You are required to pay $100 to enable us include your
name on our website. Successful candidate will be paid $30 per
page of manuscript given to review or edit. Please fill the form
attached.

Of Davis Interest: Video on New Urbanism

Nice Video on Science 2.0 w/ Stephen Friend, @jimmy_wales, John Wilbanks & @timoreilly (via @Boudicca) #openscience

Embedding the short and long videos here. Hat tip to Lisa Green for pointing these out.

Making the Web Work for Science - Short from Jordan Mendelson on Vimeo.

Making the Web Work for Science - Full from Jordan Mendelson on Vimeo.