Tag: Misc.

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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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#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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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 …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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 —

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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 ….

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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

Announcing a workshop on social behaviors:
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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

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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