UC Davis, home of "Explosive Evolution"

A semi quick one here.  I am writing this in part because it is really a lot of fun to be at UC Davis with all the excellent evolution and ecology stuff going on here.  Some links for those who might be interested in learning more about Evolutionary studies at UC Davis include:

There is more but that is a good start.  Anyway a recent press release from Davis caught my eye in part because I know the people involved and also in part because I was unaware of the details of what they have been working on.  The press release is titled “Explosive Evolution in Pupfish” and discusses some interesting research by a PhD student Chris Martin and his advisor, my colleague Peter Wainwright.  The work was published in Evolution and is entitled: “TROPHIC NOVELTY IS LINKED TO EXCEPTIONAL RATES OF MORPHOLOGICAL DIVERSIFICATION IN TWO ADAPTIVE RADIATIONS OF CYPRINODON PUPFISH” (DOI: 10.1111/j.1558-5646.2011.01294.x).  Alas it is not OpenAccess, but the paper is available on their lab web site here.

The work is a bit out of my arena, and I suppose I could critique the press release a bit, but I won’t right now. As a side note, I should mention I really love pupfish so that also caught my eye, and I have occasionally tried to convince Chris to look at the microbes in pupfish.  
Anyway, rather than bore people with my thoughts, I thought it might be nice to post some comments I got from Chris about the paper.  I got these is a series of emails and though they are a bit out of context, I am just going to post them here: 

Note that the press release is a bit confusing: there are other scale-eating fishes (has evolved at least 14 times independently), but this is the only scale-eating pupfish (and only scale-eater among all 1500 atherinomorphs). 

#2: Pupfish are indeed named after puppy dogs for their playful swimming behavior!

#3: I think the most exciting thing about this system is that it presents the opportunity to study the origins of ecological novelty in a very recent radiation (possibly as young as 8,000 years if we go by geographic dates of the lakes). This study leaves many outstanding questions that I hope to address in my future research.

For example, why does exceptional adaptive radiation occur on these two islands and nowhere else in the Caribbean? Is this due to lack of sampling, is there something unique about these two environments, or is there something unique about the founding populations in these two cases? Both lakes are large, isolated, productive environments with only 1 or 2 other competing fish species and this is surely part of the story. But, there are many other large lakes in the Caribbean, often with very similar fish communities. Further, note that the other competing fish species have not diversified at all: is this due to their time of arrival or is there something special about pupfishes? I’m currently planning to do broader sampling of pupfish populations and lake environments across the Caribbean to address these questions.

Second, what factors actually drive such dramatic rates of morphological diversification? I have just returned from a trip to San Salvador Island where I setup four field enclosures and added juvenile pupfish to estimate a fitness landscape for jaw morphology in this environment. Juveniles were F2 hybrids of the three species raised in the lab here at Davis in order to sample from the full spectrum of phenotypic variation. I will be returning in July to collect this experiment and I do hope my enclosures and some fish survive! This study should provide an estimate of the strength of selection on existing phenotypes as well as potentially unfit intermediate phenotypes.

Finally, why have different sets of resource specialists evolved in very similar environments? In particular, why has a specialized scale-eater failed to evolve in Mexico – there are obviously scales to feed on and the fish densities appear comparable. Scale-eating has evolved independently many times, but why don’t all fish communities contain scale-eating specialists?

Anyway, going to try to write more about Evolutionary studies at UC Davis in the future. I am always amazed at how much interesting work there is here.

Who owns UCDavis (& other University Names) in various Web Domains?

Well, this is awkward.  But apparently, some domain name registrars in China think I am the person to write to regarding UC Davis domain name issues.  Am I that high up in web searches somehow?  Perhaps I am if you do not use google, or maybe even if you do (I guess, perhaps most of the high hits to UC Davis are not people … just web sites).  Anyway this is the email I just got:(If you are not the person who is in charge of this, please forward to the right person/ department, as this is urgent, thank you.) 

Dear CEO,

We are the department of registration service in China. we have something which needs to confirm with you. We formally received an application on  August 26h  2010. One company called “Napa International, Inc.” is applying to register “ucdavis     ” as Brand name and domain names as below:









After our initial checking, we found the Brand name and domain names being applied are as same as your company! So we need confirmation with your company. If the aforementioned company is your business partner or your subsidiary, please DO NOT reply us, we will approve the application automatically. If you don’t have any relationship with this company, please contact us within 5 workdays. If over the deadline, we will approve the application  submitted by “Napa International, Inc ” unconditionally.

Best Regards

Rensis Ho

Not sure if this is a scam of some sort or not so I figured I would post.  Anyone seen anything like this before?  If it is not a scam, does this mean they really think I am the CEO of some UC Davis brand?  

Another question is – if this is not a scam – can places register a domain name using someone else’s trademark?  What is the protection for domain names outside the US?

Anyway – am forwarding this to people at UC Davis who I hope can answer the email … but am wondering how much I can sell the UC Davis brand name for in various places … could be a good fund raising opportunity

New Stem Cell ruling trickle down effects: changes in NIH grant review/submission

Just got this email from UC Davis administration that I thought might be of interest

Dear UCD Research Community:

Pursuant to a court order issued on August 23, 2010, NIH is not accepting submissions of information about human embryonic stem cell lines for NIH review.

If you are currently preparing a proposal to NIH that includes stem cell research and NIH has not pulled the RFP, please continue preparing your proposal and Sponsored Programs will submit to Grants.gov.

Per the Council on Governmental Relations (COGR):

In a press briefing today August 24, 2010,  Francis Collins, Director of NIH, described the impact of the preliminary injunction prohibiting NIH from funding embryonic stem cell research under the NIH Guidelines on current and pending grants.    A NIH Guide notice will be issued shortly containing greater detail. 


In short, NIH consulted with the Department of Justice to make the following determination:


·                    Current grantees – those who have received their award already – may continue with their research;


·                    NIH will freeze the funds for the current grants due for annual renewal (non-competing renewals) by September 30, 2010;


·                    Grants in the review process – initial peer review or recommended for consideration by the advisory council – will be pulled from further consideration at this time.


We expect to receive additional information shortly, which we will share when received.

When Universities Grow in the Wrong Places

A bit of a rambling post here but here goes anyway …

Well, normally I have avoided digging in to UC Davis too much here on my blog.  Mostly because it does not really fit with the themes of evolution, open access, microbiology, genomics, etc.  Plus, overall, I really really like Davis and UC Davis.  The town is very pleasant – simple – but very nice.  I lived on my bike in the Washington DC area, taking my life into my own hands, and now living in bike town USA is great.  In fact, I even have a blog about life in Davis.  And UC Davis is overall a great place to be for me, especially with its strengths in evolution and ecology, population biology, and various aspects of microbiology.

But alas, now all is perfect here in blissville. And one thing that drives me crazy is the mind numbing complexity of the bureaucracy.  I note, I moved to Davis from The Institute for Genomic Research (TIGR), a small non profit research institute that helped lead the genomics revolution.  And mostly I have suffered annoyances of the crazy giant complex system here in silence (except for with a few colleagues here and there).  However, I have been planning to start to discuss some of these issues in public more.  And just as I was thinking about this, it seems that others are also discussing some issues with the need to reform some UC Davis admin activities.

You see, last year we got a new Chancellor (the name they use here for the head of the University).  The new Chancellor is Linda Katehi.  I have met her a few times and overall I am very impressed.  Perhaps the thing that impresses me most is that in times of somewhat bad financial struggles she has decided to take on the bloat in the administrative side of things as one of her first activities.  And it seems this is not all talk.  For example our great local newspaper, the Davis Enterprise has been running a series of articles, most by Cory Golden, on some reports and announcements from UC Davis suggesting that Katehi really will be trying to change things around here.  Alas, the Davis Enterprise is not available for free on the web for all to read.  If you want to get some really insightful stories about UC and UC Davis, you should subscribe.  It is not much and if you have any connection to Davis it is worth the money.

Fortunately for me, and perhaps for you, the Davis Enterprise has agreed to let me post extensive quotes from their articles especially as they relate to UC Davis.  I will delay a bit in posting to try and respect their need for subscribers (unlike with scientific publications, which should all be open and freely available, I do not feel that way about private enterprises like newspapers).  Anyway – I am posting below two stories by Cory Golden of relevance to the UC Davis attempts to change the way things are done here.  One is about reorganization of some administrative functions.  And one is about an outside evaluating group that just wrote a report on some of the challenges for research at UC Davis.  A third is about a campus “vision” statement put out by Katehi.

The main gist is, that UC Davis has enormous potential that is being impeded by some bureaucratic complexities and inefficiencies.  Some good quotes include:

Those included “overstaffing, ineffective personnel and playing ‘lawyer games’ to be sure that no risks threaten the organization.”

“Over many decades Davis has developed a culture that permeates its institutions and people, one that can best be described as risk-averse, modest and insular.”

And Katehi seems like she is going to try and fix many of them.  No – the plans are not exactly what I would do.  But more on that later.  The direction things are moving is very appealing to me.  I was not inspired by the previous leadership of UC Davis.  I am much more hopeful now and am awaiting these changes very impatiently.

Anyway – thanks to the Davis Enterprise for allowing me to post here.  And please consider subscribing to the paper.  That way you will get stories as they come out …


Reorganization ramps up at UCD

By Cory Golden

August 18th, 2010

Enterprise staff writer

UC Davis leaders have OK’d in spirit a plan to cut up to $16 million in staff positions while rolling campus information technology, human resources and finance offices into a single shared services center.

An all-staff forum about the reorganization is set for Thursday at 10:30 a.m. in the UCD Conference Center Ballroom.

Chancellor Linda Katehi said last week that her goals for the effort, dubbed the “Organizational Excellence Initiative,” are to redirect money to academics, student services and other priorities while improving the service given to the campus.

For now, staff members are left with questions and union leaders have growing concerns.

Among them: how many jobs will be eliminated, how positions in the proposed new center willbe filled, how fast UCD will make the changes and how much money the campus will invest in technology intended to increase efficiency.

Some answers may come from a meeting of the chancellor’s cabinet Aug. 31.

At its last two-hour meeting, last week, the cabinet decided to move forward on the outlines of recommendations made by the Atlanta-based consulting firm ScottMadden, based on more than three months of on-site assessment.

About 6,500 finance, HR and IT employees would be affected by the first phase of the project, as drawn up by the consultant.

“On the amount of savings projected, what percentage of that is from staff positions?” asked a woman in the audience during a presentation Monday to employees of administrative units that would be part of the proposed center.

Answered Karen Hull, associate vice chancellor for human resources, “Those savings reflect staff positions.”

Just how many would be cut, she said she didn’t know.

“We don’t know that for a couple of reasons,” Hull said. “One is that we don’t know for sure whether the cabinet will support the recommendation that ScottMadden has made, so that’s one big variable.

“(It) would be very misleading to connect the (estimated savings) to actual positions,” she added. “There’s a lot of dynamic changes that occur. We have natural attrition every year. We have natural turnover. We have retirements. We will not be wanting to fill any of those positions while we are forming the shared service center.

“I know that it sounds alarming — and it is alarming. These are your jobs, but I think that when we get the picture painted in a more detailed manner it will be more clear as to what will be the potential job loss.”

The consultant found that, at a core cost of $54 million a year, the campus’ human resources, information technology and finance staffing exceeded those of similarly sized organizations.

Among its recommendations: creating a shared structure with one director, improving the use of technology for timekeeping, purchasing, accounting and other tasks, and simplifying policies and processes.

The report pegged one-time or recurring costs, much of it from computer software systems, at about $19.5 million. If UCD follows its suggested timeline, the report says the university should begin saving money in less than three years.

Under the proposed model, about 80 percent of faculty, staff and student questions would be handled through self-service, either through a web portal or interactive phone system.

In what’s likely to be a controversial recommendation, the consultant suggests that the campus create job descriptions for the shared services center, then have employees apply for those positions.

“They recommend kind of an open slate. Everyone has an opportunity, and you compete for those jobs,” Hull explained, adding that the administration may yet choose another way to staff the center.

Among existing problems the consultant’s report pinpointed: large amounts of the same or similar work being done by multiple departments, excessive reviews, delayed service and multiple IT help desks. It also found “manual data collection, transcription of data, high error rates and significant rework.”

One employee at UCD might process about 1,065 invoices per year, working on paper with a long approval process. At Johns Hopkins University, which uses a shared service center model and automated system, one employee can process 45,000, the report says.

Union leaders interviewed Tuesday wondered aloud if the reorganization was an attempt to weed out their members.

Dorie Decosta, president of UCD’s chapter of the Coalition of University Employees Local No. 7, said there was a “general feeling of unrest and discomfort” among staff.

The prospect of automation replacing personalized customer service “sounds like hogwash,” she said.

“You need that element of continuity and what UCD says it stands for: caring about students, caring about staff, caring about faculty.”

Wrote Susan McCormick, president of the University Professional and Technical Employees Local No. 6, in an e-mail message, “I am getting the feeling that UC is finding ways to eliminate the highest-paid employees. They are eliminating at the top of the pay scales, those at UC the longest and those with the most knowledge.”

ScottMadden’s contract calls for a fee of $350,000, plus up to $70,000 in expenses.

The proposed reorganization comes as UCD continues to grapple with an unprecedented $150 million in state budget cuts since 2008-09. It has cut 1,062 positions: 459 layoffs or employees who had hours cut, the rest through attrition or voluntary separation.

The campus has cut 30 percent of its administration’s core budget, compared to a 15.4 percent cut for academic units.

UCD faces another $38 million to $78 million shortfall depending on the outcome of state budget talks this year.

— Reach Cory Golden at cgolden@davisenterprise.net. Track him at http://twitter.com/cory_golden.

Reports rap UCD research
By Cory Golden
August 15th, 2010

Enterprise staff writer
If UC Davis is to continue its climb in national status, it has its work cut out for it, according to a blunt assessment by an outside consultant.
While the campus has its share of advantages, including its broad research portfolio and location, it has been stymied by a risk-averse culture and a bottleneck in its research support structure, according to the Washington Advisory Group.
The advisory group, led by Eric Bloch, a former director of the National Science Foundation, interviewed more than 100 people on campus, from senior administrators to graduate students, over three days.
Many of the themes its 74-page assessment sounded were echoed in recently completed reports by two in-house “blue-ribbon” committees, one each on research and technology transfer. In an interview last week, Chancellor Linda Katehi said the campus would begin making changes in response to the three reports this academic year.
UCD ranked 36th among U.S. universities in the 2009 Academic Ranking of World Universities.
Despite state general fund cuts that could total more than $228 million since 2008, depending on the outcome of state budget talks, UCD “knows what it has to do,” the consultants write, to improve to a rank of between 20th and 30th. That group includes Northwestern University, UC Santa Barbara and the University of North Carolina, Chapel Hill.
Katehi has set a new goal of $1 billion in outside research support. UCD more than doubled such funding from $295 million in 2001 to a preliminary estimate of $679 million for 2009-10.
Claire Pomeroy, the chair of the blue-ribbon committee on research and dean of the School of Medicine, called it “a new era” for research.
“There’s a pent-up desire among the faculty and the staff and the students to really optimize how our research enterprise is functioning and a recognition that we have some work to do in that area,” she said.
“The statement that we made in the blue-ribbon report on research that UC Davis is ‘less than the sum of its parts’ reflects the idea that we have incredible excellence here, and if we can just bring it together and support the people and give them the administrative support and infrastructure support, then we can really propel this university up to the next level.”
Campus culture
To reach such heights, UCD will need to undergo a personality change, the advisory group writes:
“Over many decades Davis has developed a culture that permeates its institutions and people, one that can best be described as risk-averse, modest and insular.”
While collegiality can result in the interdisciplinary research that UCD touts, it “can also have negative consequences when events and behaviors are tolerated that in other similar institutions would cause friction and result in remedies. The prime example we heard about is tolerating decision-making delays that at times may have dire consequences.”
The university has been slower than its peers to embrace partnerships with industry, described by the consultant’s report as “frowned upon by former administrations as counter to what a university is all about.”
A lack of aggressiveness has sometime been costly in other ways, the advisory group writes. For instance, UCD “seems to have missed the opportunity to expand programs in human genetics, genomics and other ‘omics at a time of explosive growth in funding in these fields. This problem must be rectified swiftly.
“UCD and its accomplishments are not as well-known as they deserve to be, in large part because of some of the cultural traits discussed,” the report says.
Andrew Hargadon, chairman of the blue-ribbon committee on tech transfer and professor of technology management at the Graduate School of Management, said he did not think the campus suffered from “collegiality to the point of complacency.” However, he acknowledged “a long history of cultural conditioning” on the campus: feeling forever overshadowed by UC Berkeley and UCLA.
“We had such a huge growth of faculty in the last decade, and the increase of research dollars as a result,” Hargadon said. “When you look at the faculty we’ve got — they weren’t there in the ’50s and ’60s; they weren’t there when that identity was being shaped.
“They would very much like to have an impact, even if it comes at the cost of driving their agenda forward.”
Research support
The main target of the complaints that the advisory group heard: the Office of Research.
Those included “overstaffing, ineffective personnel and playing ‘lawyer games’ to be sure that no risks threaten the organization.”
The office is made up of three sections: sponsored programs, which submits thousand of grant applications; institutional review boards, which govern protocols for clinical trials; and technology transfer and business development, which handles applications for patents and royalties and acts as a broker between researchers and the corporate world.
Those interviewed by the advisory group said the sponsored research group is often “overbearing,” “dictatorial” and “prone to almost missing filing dates for proposals, thus jeopardizing the opportunity to participate in important competitions,” the report reads.
The blue-ribbon committee on research, in its own 20-page reported submitted Thursday, writes that its members are “greatly concerned that UC Davis, including its research administration, has become overly bureaucratic and risk-averse, and is too narrowly focused on compliance with rules and constraints. This risks frustrating creative researchers and reducing the level of scholarly creativity and productivity.”
Said Pomeroy, “We need to find the right balance between, of course, emphasizing safety and research quality and research compliance with being at the cutting edge of discovery. I think there has been a desire to minimize risk, sometimes at the expense of efficiently processing some of the research applications.”
Additions like expanded use of technology can help speed the process, she said.
The 12-page report by the tech transfer committee recommends creating a new office that would concentrate decision-making authority for technology licensing and industry research agreements. It also urges the establishment of standards for transparency, timeliness and accountability of patenting, licensing and processing industry research agreements.
The advisory group also found that area sorely lacking: “We did not get the impression that UCD has taken this general subject of intellectual property rights and technology transfer very seriously.”
UCD doesn’t have a long tradition of spinning off businesses, Hargadon said. That means that while there are faculty who have started a business, they aren’t great in number. So those who aspire to do so must lean on the tech transfer office for help.
“There’s no hard and fast rules on tech transfer. There’s no clear value with any intellectual property,” he said. “There’s a lot of clear-cut ways to go wrong, in terms of the legality of contracts and conflicts of interest, but there’s not clear-cut ways to go right.
“It would have taken a lot of strong leadership and vision to get the process to one where the university could make bold bets and make a claim that a particular patent would have more impact if it got out than if it got out with some sort of onerous revenue obligation associated with it. As a result, the office, without that sort of leadership vision, ended up weighing compliance and weighing risk mitigation higher than was really good for the system.
“Basically, we spent more time trying to stay out of trouble than trying to launch companies.”
Increased workload
The doubling of research funding has meant a greater workload for staff. That money has increasingly come from the federal government, which has steadily imposed more stringent regulations and reporting guidelines.
At the same time, the office’s staff has been trimmed from about 90 to about 75, said outgoing Vice Chancellor for Research Barry Klein.
He said of his staff, “These are very good people working very hard for the university, but very good people working hard doesn’t mean there aren’t ways to make our organization better; there are.
“If you look across the country at organizations that have these sort of hot-button service roles as we have, they are always subject to criticism. It’s impossible to be perfect,” Klein added.
“The faculty are like thoroughbreds. They want to win the race. It’s a mad dash to the finish line, but that causes a lot of tension and getting things in at the last minute and quickly, so there’s always this dynamic tension with the research office.”
Klein said being less “risk-averse” will increase the risk of violations and fines, but his staff would oblige.
“The people in my office don’t make the rules, they implement the campus culture,” he said. “And if it’s a culture that’s emerging now where you’re putting more things back to individual responsibility — having less oversight of details and assuming the departments and colleges and individuals will follow the rules — staff will move in that direction as well.”
One of the longest-serving vice chancellors for research in the UC system, Klein was due to step down in June 2009 but he said he stayed on to smooth the transition for the new chancellor, who arrived last August. His return to the physics department, announced last December, was a joint decision with Katehi.
“I was ready for a change and it was good for her to bring in some fresh blood,” Klein said.
Other findings
Among the other findings in the advisory group’s report, UCD:
** Lacks a five-year strategic financial plan;
** Needs a new strategy for technology transfer and business development;
** Suffers high student-faculty ratios in some areas;
** Should invest in technology on par with peer institutions;
** Needs a well-organized campaign to make itself and its faculty more visible if it’s to become a household name; and
n Faces a space crunch, including a lack of Biosafety Level 3 and 4 containment facilities, and should build them elsewhere if the community is opposed.
The advisory group also found that school- and college-level strategic plans were “meaningful and well-documented” but that “an institution as complex and broad as Davis requires a five- or 10-year strategy, plan and budget. No such interlinking documents exist today.”
Katehi recently unveiled a vision statement for the campus. Next, units will set out plans to meet those newly stated goals and, sometime next year, UCD will begin funding those priorities, the chancellor said.
The advisory group found it worrying that it received different financial information about research depending on who provided it.
“One wonders: What are the numbers that are at the chancellor’s disposal?” the report asks.
The advisory group also received complaints of “bloated” administration generally, despite recent cuts. UCD is rolling out a new effort this month to further reduce and reorganize its administration.
UCD paid the Washington Advisory Group $226,000, plus up to $30,000 in expenses.

— Reach Cory Golden at cgolden@davisenterprise.net. Track him at http://twitter.com/cory_golden

Katehi details campus vision
By Cory Golden
July 30th, 2010

Enterprise staff writer
UC Davis Chancellor Linda Katehi and other campus leaders have crafted a “Vision of Excellence,” 10 months in the making, to guide the campus for the next 10 years.
The 17-page document combines many of the themes Katehi has sounded since her arrival last year, about the campus’ readiness for greater national and international prominence, with long-standing notions of UCD’s land-grant identity.
Released last week, the vision statement received a warm response from faculty, staff and student leaders reached for comment for its positive tenor, even against a backdrop of ongoing financial turmoil.
“To transform our university, we must chart a new course of action, an equally transformative vision to guide our actions and define our future,” Katehi writes in the document. It lays out goals like “foster a vibrant community of learning and scholarship” and “champion health, education, access and opportunity.” The document also describes how progress toward each goal will be assessed.
Bob Powell, chair of the Academic Senate, said the vision statement spells out change in ways both big and small.
“Before, it was about collaboration and now it’s about leadership,” he said. “It’s one thing to say you’re going to develop joint or international programs to enhance UC Davis, but this, to me, is a step above anything we were talking about before.”
Powell read one line aloud: “UC Davis will provide an efficient, professional administrative organization that is committed to serving and advancing the university’s academic mission.”
“From the outside, people would say, ‘Isn’t that obvious?’ Well, I’ve been here 26 years and it’s never been obvious,” he said. “To have that as an explicit statement is really important.”
Powell said he believed the document would go a long way toward building “grassroots support” when it falls to the colleges, schools and divisions to flesh out corresponding goals and plans to realize them.
An example of the document’s approach is its emphasis on increasing UCD’s international reach.
UCD will seek to increase the number of faculty, scholars and students from abroad and the number of students and faculty who pursue academic experiences overseas, the document says.
To accomplish those goals it will evaluate its needs in attracting, retaining and supporting international students; develop joint, collaborative international graduate programs; launch academic and clinical health research projects that tackle global challenges; strengthen and expand international alumni and global business ties; and provide the technological tools, cultural programs and student services to expand international dialogue.
Linda Bisson, professor of viticulture and enology and past chair of the Academic Senate, said the “solid” document is important for what it includes — and what it does not.
“It is different than what we’re used to because it has metrics,” Bisson said. “Typically, these kinds of vision statements are kind of just platitudes stuck together.
“This is going to sound weird,” she added, “but the change of focus that I see is that we’re not apologizing for who and what we are. Previously, things like this have read like we’re apologizing for not being (UC) Berkeley, the jewel of the UC crown.
“But this says, this is our value internationally: We’re problem-solvers — we’re a different kind of animal than Berkeley. It says we are very strong and proud of what we do — and that we’re not going to chase esoteric things when there are real things to be addressed.”
Though talk of breakthrough discoveries and spinning off research into new businesses can sometimes leave those in the humanities left wondering where they fit in, Margaret Ferguson, a professor of English and former chair of her department, said in an e-mail message that she felt that was not the case here.
“Im thrilled to say that this vision statement does speak to many of the questions that preoccupy those of us in the humanities, arts and humanistic social sciences,” she said. “These areas are mentioned early on as among the comprehensive research universitys ‘core disciplines,’ and the vision statement includes among its goals some that will particularly excite those students and faculty whose work focuses on deepening and expanding our understanding of past cultures as well as on creating new ideas for the future.”
She said she also was happy to see the goal of increasing need- and merit-based financial aid for both undergraduate and graduate students — which is “especially important for humanities graduate students, who are rarely supported by federal grants.”
Dan Wilson, chair of the Academic Federation, praised the vision statement’s emphasis on collaboration across disciplines, its promise of incentivizing success and its commitment to UCD’s land-grant role in improving the fates of the state and region.
Money, of course, remains the $228 million question mark. That may yet be the size of state cuts, dating back to July 1, 2008, depending on the outcome of the stalled state budget.
Bruno Nachtergaele, chair of the mathematics department, said in an e-mail message that he and many of his colleagues felt the document took into account their goals while also showing “the personal vision and commitment of the chancellor.”
“The recession we all suffer through is a hurdle, but not one that will stop her from promoting this vision and the long-term project of making UC Davis into the best university it can be,” Nachtergaele said.
Chair Peter Blando said in an e-mail message that the Staff Assembly was “extremely pleased to see a positive campus vision that takes us beyond the near daily concern over our job security and the university budget.
“While both are important,” he added, “staff morale is helped by providing any positive vision of the campus.”
Jack Zwald, president of the Associated Students of UC Davis, said he liked what he read, too, but was left wondering how Katehi would manage to increase the size of the university’s endowment while expanding programs. Likewise, he had questions about how UCD will be able to expand need- and merit-based aid to students.
“I think they’re going to give it a shot, but do I think it’s going to get done? I’m not overly optimistic it’s going to happen,” he said.
Wilson said the chancellor was right not to set the university’s sights lower because of the financial crisis.
“We don’t want to crawl into a shell — we want to move forward as a university,” he said.
To read the full document, see http://vision.ucdavis.edu.
— Reach Cory Golden at cgolden@davisenterprise.net. Track him at http://twitter.com/cory_golden

Has your scientific research been wasted?

I had a good Thanksgiving weekend this year – spending time with family and friends. But as I go back to work this week I have now gotten somewhat depressed over something I did Sunday night. I decided to remove myself from the UC Davis internet proxy to see how many of my past papers that I have published I can obtain without the UC subscriptions. So I went to pubmed, and typed in my name (Eisen JA) and got most of my papers, which are listed at the bottom of this blog (some do not come up due to publication off the pubmed grid or due to co-authors screwing up my initials). (NOTE  – LISTING DELETED 4/09 BECAUSE THE FORMATTING IS ALL MESSED UP)

And then I went to see how many of my papers were freely available and how many were not. What I was most interested in was – what is the deal with papers I wrote before becoming an Open Access convert? For many it is easy to figure out if they are freely available – Pubmed has a link saying “Free in PMC” which refers to Pubmed Central. For others, it was a little trickier.

The results were both good and bad and a summary is below. A few things struck me. First, a lot of my life’s work is not readily available without paying other for it. In the day and age of the internet, this means that these papers will simply be read less and less as time goes by. And that makes me very sad. If I had chosen to publish those papers in other journals, anyone in the world could get them at any time. Thankfully I did publish many papers in journals like PNAS, and ASM journals, and NAR – journals that have now decided to release them to Pubmed Central. And also thankfully (but less so) I published some papers in journals that have at least made them freely available on their web sites.

Most surprisingly to me is that a reasonable number of my papers in Nature are freely available on the Nature web site as part of their Genomics Gateway program. Nature deserves serious kudos for doing this and they stand out compared to Elsevier journals (which do not seem to ever do this) and even Science. This is disappointing as Science is published by a scientific society but apparently does not seem to care much about access to publications. Nature, a commercial publisher, is in my opinion doing more for scientific openness than Science. Now, Nature has a long way to go, but I am SO glad I listened to their editors like Chris Gunter and Tanguy Chouard who made a big deal about the Genome papers being free. I did not think it was that big a deal, but in retrospect they were ahead of me in thinking about availability. Plus Nature clearly makes more of an effort to provide free online material than they have to – and certainly make more available than Science.

So in the end – I am sad about my partially wasted past. But I am pleasantly surprised that at least some papers I thought would be more restricted are actually free (although only on the Publishers site for now – Hopefully these journals will submit them to PMC at some point). I guess – you win some and you lose some and some are somewhere in between.

Summary of openness — other scientists should do this exercise

In Pubmed Central and Open Access

Available free on publisher’s sites (notideal but better than nothing)

Must buy paper

Not available anywhere

UC Davis Research Blog

Well, U. C. Davis (where I work) shows that it is both hip and dedicated to Science research with a new “Research Blog” put out by its University Communications office. It is called Egghead and its goal is:

Egghead is a blog about research by, with or related to UC Davis. Comments on posts are welcome, as are tips and suggestions for posts. General feedback may be sent to Andy Fell. This blog is created and maintained by UC Davis University Communications, and mostly edited by Andy Fell.

I am not sure how many other Universities have an officially sanctioned blog from the press office, but I could not find any.

My favorite post at Egghead so far is the one about a website called Adopt a Microbe. There is
absolutely no Davis connection to this site yet the wrote a tiny blurb about it anyway. I hope they continue to do things like this – it can get tedious if the blog is all about promoting Davis research only. It will certainly get read more if there is a diversity of stuff there.

It is good to see that Biology is the top subject there … not that there is anything wrong with other fields but one of the reasons I wanted to move to U. C. Davis was because of the amazing diversity of biology-related research going on on campus.

Now if they could only get a weekly podcast going …

If anyone out there knows of other Universities with interesting Blogs from the press office, let me know.

Harvard Crimson Editorial Update

OK – so I am biased here but those interested in Open Access should check out my brother’s letter to the Harvard Crimson that was published today. He wrote it in response to the lame editorial the Crimson wrote about PLoS One. Some of my favorite quotes from his letter

They did not, however, respond to your repellent effort to rally the forces of elitism to derail a project whose primary aim is to rapidly bring scientific knowledge to everyone.


Once they see PLoS One, we are confident that consumers of scientific papers will discover what employers have long ago: If you’re looking for the imprimatur of greatness, try Nature or Harvard—but if you want the real thing, try PLoS One or Berkeley.

Of course, I disagree with the use of Berkeley in this context. Yes it is a public school. But come one – to use Berkeley as the “anti”elitist school of the world is a big stretch. So if you want the real thing, try U. C. Davis, not Berkeley.

Vice Provost of U. C. Davis on the wrong side of Open Access

Well, my first incredibly disappointing moment at U. C. Davis. My brother sent me this link about a letter to Congress from some provosts and deans trying to go backwards on the issue of Open Access to scientific publications.

See the press release here.

And one of the signatories is the Vice Provost for academic affairs at Davis, Barbara Horwitz. Their letter contains many misleading statements in my opinion and seems to be overly biased towards the anti Open Access side of the debate. First, they say

In fact, some studies have already shown that research intensive universities would have to pay considerably more to gain access to the same amount of research under an author- pays model than a subscription model.

Where is the citation for this? This is counter to intuition and on its face seems ridiculous to me. It requires some backing up with evidence, especially in a letter to congress.

They also claim:

The free posting of unedited author manuscripts by government agencies threatens the integrity of the scientific record, potentially undermines the publisher peer review process, and is not a smart use of funds that could be better used for research.

How on earth does posting of unedited manuscripts threaten the integrity of the scientific record. That is like saying scientists should not give talks on anything until they have published it, and then they should only quote from their published papers. Or, maybe scientists should not even discuss their work at all in public and should just present it through papers published in journals. I am astonished that a Officer of my University would make such a statement.

Perhaps most amazingly, this collection of academic folks says:

As a member of the Senate Budget Committee, you are certainly sensitive to the various forces that shape and reshape the Federal budget from year to year. Recently, for example, we learned that the Biomolecular Interaction Network Database–the world’s largest free repository for proteomic data–lost its funding and curtailed its curation efforts.

This too appears to be almost absurd and certainly misleading. BIND is in the true tradition of Open Access – a database of proteomic information for the world to share. And these provosts and deans are trying to use its loss of funding as an argument for LESS OPEN ACCESS. How completely nonsensical is that? But even more incomprehensible, BIND is a CANADIAN database effort, supported by Genome Canada funding. So how this relates to the funding by the US Congress is beyond me.

This collection of provosts and deans appear to be trying to do a slight of hand here with the details. I would be willing to wager that the driving force behind their letter is the desire to continue bringing in funds to their Societies or Universities that come from subscription based publishing. (Note it seems unlikely they are writing this letter as a statement of the official policies of their universities – certainly, I did not see any extensive discussion at Davis prior to Dr. Horwitz’s signing this letter). A little survey of the backgrounds of the letter writers is informative here. What I have found with a little googling is that many of the signatories have active leadership roles in publishing non Open Access journals. Robert R. Rich is the Editor in Chief of J. Immunology, which does not support Open Access. Kenneth L. Barker is the President of SEBM, a publisher of non open access scientific publications. Barbara A. Horwitz, was the president of APS which sponsored this press release and publishes many non Open Access journals. I am sure many of the others have some type of similar roles. It would have been nice for them to mention that in this press release.

To keep in that spirit, as I have said before, I am on the editorial board of PLoS Biology and PLoS Computational Biology and I support Open Access publishing completely. I do not always disclose this in discussions of Open Access but then again, I have never written a letter to congress making use of my position in a university to promote a position with such obvious direct benefit to myself.

Some interesting links and tidbits related to this article:

  • In their annual report from a few years ago, APS discusses how the DC Principles organization was founded specifically to counteract the Open Access movement.
  • Peter Horwitz writes about the letter more here
  • The APS we are discussing here is the American Physiological Society. Note it is NOT the same as the other APS commonly seen on science journals – the American Physical Society which is moving more to complete Open Access.

Note – thanks for T. Scott Plutchak at UAB for pointing out that it is possible to support Open Access without being a total jerk, and thus getting me to tone down some of the language from the original version of this post.