Monday, June 02, 2008

Chancellor of UC Davis stepping down

Thought this might be of interest

Begin forwarded message:

From: Chancellor Vanderhoef <lnvanderhoef@ucdavis.edu>
Date: June 2, 2008 3:28:58 PM CDT
To: UC Davis Family:;
Subject: Leadership Transition

Dear Members of Our UC Davis Family,

I can't imagine greater good fortune than to have spent the past 24 years at UC Davis, first as provost, then, since 1994, as chancellor. Along the way, there have been challenges to be sure, but, together, we have helped this remarkable university to reach higher, to be bolder and to achieve great distinction. For those years and those opportunities, I will always be grateful.

So it is with conflicting emotions that I announce today that next year, our centennial year, will be my last as chancellor. I will step down on June 30, 2009. Following a sabbatical leave, I will return to the life of a faculty member, and will do whatever I can to support UC Davis as its chancellor emeritus.

To make our centennial year my last has been my plan for some time now -- a decision made finally realizing that there'd never be a stopping point if I waited for every initiative to be completed. Our 100th birthday seemed to me a particularly fitting time for a transition in leadership, as we look back with pride at our first century, and as we look forward to a second century that's sure to be as transformational as our first.

As well, announcing now provides our new UC president, Mark Yudof, with ample time to recruit a chancellor who will continue to elevate UC Davis among the nation's most distinguished universities. Ours will be his first opportunity to recommend a new UC chancellor to the regents.

So as we wrap up one academic year and anticipate the start of my last as chancellor, know that I approach this coming year as I did my first -- inspired by the opportunity, and keen to turn plans into action.

And, as was true then and even more so now, I am grateful for all that my wife, Rosalie, has done to support me and UC Davis -- particularly her tireless work to raise funds for the Mondavi Center for the Performing Arts and to introduce schoolchildren to the arts. To those many, many people with whom we've worked closely over the years, there's not enough room in this letter to express our appreciation. We'll try to catch you, one by one.

Sincerely,

Larry N. Vanderhoef
Chancellor, UC Davis


June 2, 2008

UC Davis Chancellor Larry N. Vanderhoef to Step Down in June 2009

Chancellor Larry N. Vanderhoef, who led UC Davis' climb up the ranks of the nation's finest universities while he helped open the campus's doors to the disadvantaged and advocated academic diplomacy to help resolve global conflict, announced today that he will step down in June 2009, at the end of the campus's centennial year.

Vanderhoef, appointed in 1994 as UC Davis' fifth chancellor, is one of the nation's longest-serving university leaders and is widely credited for nurturing future university presidents and provosts. He came to the campus in 1984, first serving as executive vice chancellor and then provost/executive vice chancellor. After what will be a full quarter century of service to UC Davis, he will take a yearlong sabbatical, and then return to the faculty as a professor of plant biology. He will also continue to support the campus as chancellor emeritus.

"I can't imagine greater good fortune than to have spent the past 24 years at UC Davis," Vanderhoef said in a letter today to the campus community. "Along the way, there have been challenges to be sure, but together we have helped this remarkable university to reach higher, to be bolder and to achieve great distinction. For those years and those opportunities, I will always be grateful."

The University of California System's top leaders -- UC's current president, Robert Dynes, and incoming President Mark Yudof -- led the chorus of many who praised Vanderhoef for his distinguished tenure.

Dynes pointed out that Vanderhoef "has been the senior chancellor of the UC system for several years, and all the other chancellors and I look to him for wisdom and experience." Yudof, outgoing president of the University of Texas, said that, from afar, he has "watched the campus go from relative obscurity to the front ranks among the nation's research universities."

Expanded access and opportunity

The first in his family to complete high school, and one of the very few in his Wisconsin foundry town to find his way to college, Vanderhoef has dedicated his time as chancellor to removing barriers to higher education. He elevated the campus's Division of Education to a new School of Education when other universities were downsizing theirs, expanded partnerships with community colleges, encouraged disadvantaged elementary school students to stay on track through the innovative "Reservation for College" program, and partnered with leaders of regional communities of color to raise awareness of UC Davis.

Enormous strides

On his watch, UC Davis has grown and prospered. The campus was invited in 1996 to join the prestigious Association of American Universities, representing the top 62 research universities in North America. Research funds, won competitively by UC Davis' faculty, increased from $169 million to more than $500 million annually. The campus has risen in national rankings, too. UC Davis is now ranked 8th among all U.S. universities in contributions to society (Washington Monthly) and 11th among U.S. public universities (U.S. News & World Report). Private gifts have jumped from $40 million to nearly $200 million a year, with more than $1 billion cumulatively raised in support of programs -- including $100 million from the Gordon and Betty Moore Foundation to launch a new School of Nursing, $35 million from Robert and Margrit Mondavi to name the Mondavi Center for the Performing Arts and the Robert Mondavi Institute for Wine and Food Science, and a $10 million gift from alumnus Maurice Gallagher to help fund a new building -- Maurice J. Gallagher Jr. Hall -- and endowment for the Graduate School of Management.

Under Vanderhoef's leadership and direction, UC Davis has also made great strides in recruiting a diverse and accomplished faculty and student body. Student enrollment has grown from 22,000 to 30,000, and the faculty has increased by 44 percent. More than 4 million square feet of classroom, lab, clinical, performance and office space have been added. And an ailing county hospital in Sacramento has been transformed into an academically distinguished and financially sound regional medical center.

Among Vanderhoef's most ambitious undertakings is a new south entry to the campus, anchored by the state-of-the-art Mondavi Center, the soon-to-open Robert Mondavi Institute and the under-construction Graduate School of Management, conference center and hotel buildings. On another campus flank will soon rise West Village, an innovative and environmentally sensitive neighborhood that will provide affordable housing for students, faculty and staff, as well as a Village Square and community college center -- a first within UC.

International academic diplomacy

But Vanderhoef's interests and influence have stretched far beyond northern California. In 2004, for example, in the face of considerable concern and disapproval, the chancellor led what he was told was the first high-level university delegation to visit Iran since that country's 1979 revolution. Vanderhoef wrote in a journal at the time, "We're not going to Iran to make a political statement, nor are we seeking publicity. We're simply one university wanting to talk to another university about ways in which we can work together. And, perhaps in the process, one small step can be taken toward a return to normalcy in the Middle East."

Vanderhoef has been asked to return to Iran this November, this time as a member of a small delegation of university presidents sponsored by the Association of American Universities.

Principled decisions in the face of criticism

Certainly, Vanderhoef's 2004 trip to Iran was not the first of the tough decisions he has made as a UC Davis leader. Indeed, it was a fiscal crisis in the early 1990s, when Vanderhoef was then provost and executive vice chancellor, that proved his mettle and ultimately positioned him to be chancellor. He oversaw painfully deep cuts and staff layoffs, yet in a collaborative way that restored a sense of stability and fairness to a campus in tumult. It was then that he initiated his series of brownbag chats that continue today, offering faculty, staff and students a regular opportunity to meet and talk with him.

When the UC regents in 1995 ended the use of race, ethnicity and gender in admissions, Vanderhoef vocally opposed the action, believing that without an immediate alternative to provide access for the disadvantaged a generation of students would be lost. Soon after, when it was UC Davis' turn to be featured at a regents meeting, he brought the diverse Gospel Choir to perform, and brought the regents to their feet.

In 2003, Vanderhoef made another controversial decision -- announcing that UC Davis would move from Division II to Division I athletics, knowing that the faculty as a whole would not be supportive. The chancellor said then that the campus really had no alternative. "We are seeking, in an evolving landscape, firm ground upon which to continue and to enhance a program that is centered around the student-athlete and the teacher-coach," he said at the time. The Big West Conference would offer Davis a better academic, philosophical and competitive "fit," he said, and align it with sister campuses UC Irvine, UC Riverside and UC Santa Barbara. In this, the first official Division I season at UC Davis, the Aggies sent 11 teams to NCAA postseason play.

In 1993, Vanderhoef disappointed students at the School of Law with his decision that broadcast media could not be barred from covering the commencement speech of U.S. Supreme Court Justice Harry Blackmun, a condition of the justice's speaking. Blackmun withdrew, and the unhappy graduates signaled their discontent by passing around a jar of sourballs at commencement. New York Newsday, however, wrote that "Maybe [Vanderhoef] is the one who ought to be on the Supreme Court."

Nurturing university leaders

To be sure, Vanderhoef has never been one to seek out controversy to raise his own profile. On the contrary, this unassuming and down-to-earth Midwesterner has always been more interested in bringing recognition to UC Davis than to himself, and in growing new academic leaders along the way.

In the past 15 years, more than a dozen UC Davis administrators have gone on to president and provost positions at major universities around the country. They credit Vanderhoef's collegial and collaborative approach to problem solving, and his belief in delegating both authority and responsibility, with providing junior administrators the experience to move on and up.

"That type of experience, particularly with an excellent, diverse team, provides strong leadership development," said Virginia Hinshaw, former UC Davis provost and executive vice chancellor and current president of the University of Hawaii-Manoa.

"Larry Vanderhoef sets a positive tone at the top for good behavior among administrators, and I believe this brings out the best in people," said Mark McNamee, former dean of biological sciences at UC Davis and now provost of Virginia Tech.

Still, Vanderhoef has garnered many personal accolades. Recognized for his "passion to make things happen," he was honored by the Sacramento (California) Business Journal as one of the 20 people who have contributed most substantially to California's capital region over the past 20 years. The Sacramento Metropolitan Chamber of Commerce named him Sacramentan of the Year in 2004, and the Arts and Business Council of Sacramento presented him with its Prelude to the Season Outstanding Contribution Award in 2003. And in 2006, the Northern California World Trade Center and the California Business, Transportation and Housing Agency presented him with the International Leadership Award, in recognition of his efforts to increase the campus's international engagement.

Early in his career, he was named an Eisenhower Fellow, a recognition given to emerging leaders from around the world to promote positive relationships and interactions between countries. He was awarded honorary doctoral degrees by Purdue University and Inje University in Korea, and an honorary professorship by China Agricultural University. He holds B.S. and M.S. degrees in biology from the University of Wisconsin, Milwaukee, and a Ph.D. in plant biochemistry from Purdue University.

Nationwide search

A nationwide search for a new Davis chancellor will be initiated, and a committee with regent, faculty, staff, student, alumni and foundation board representatives will be named to advise Yudof, the incoming UC president, in the selection of Vanderhoef's successor.

UC Davis, a land-grant institution, is a leader in interdisciplinary study, offering more than 100 academic majors and 86 graduate programs. It is the only campus in the UC system with schools of Education, Law, Management, Medicine, and Veterinary Medicine. The campus's breadth of academic and outside-the-classroom programs, commitment to providing an attentive and research-enriched education, determination to address society's needs and consideration of campus community members as family are truly distinctive.

What others are saying about Chancellor Larry Vanderhoef's distinguished tenure at UC Davis:

UC President Robert Dynes: "I heartily congratulate Larry for all he has accomplished. Larry has been the senior chancellor of the UC system for several years, and all the other chancellors and I look to him for wisdom and experience. During his tenure as chancellor, UC Davis has grown in size, stature and excellence, and everyone within UC is proud of it. Congratulations to a friend for a stellar accomplishment."

UC President-designate Mark Yudof: "Larry has done a remarkable job during his tenure at UC Davis. I have, from afar, watched the campus go from relative obscurity to the front ranks among the nation's research universities. I offer him my heartiest congratulations, and I am looking forward to working with him during his final year."

UC Provost Rory Hume: "Chancellor Vanderhoef has served both UC Davis and the UC system as a whole with great distinction. During his long period of leadership Davis has grown enormously in academic distinction, and in size. It has substantially broadened the scope of its academic programs, while retaining its highly valuable, distinctive nature. Much credit for those advances rests directly with Larry Vanderhoef. He has also been a superb citizen of the UC system, wise, measured, supportive and decisive. We could ask for no better colleague and friend."

Robert Berdahl, president of the Association of American Universities and former UC Berkeley chancellor: "Larry Vanderhoef has been an extraordinarily successful chancellor of UC Davis. Under his leadership, Davis emerged as one of the outstanding public universities in America. He has provided leadership within the University of California, where his voice and judgment are widely respected by the other chancellors, and he has been an effective leader on the national stage as well, including at AAU. His leadership has always been marked by intelligence, thoughtfulness, and generosity of spirit. I am proud to consider him a colleague and friend."

Vice Provost for Undergraduate Studies Patricia Turner: "It has been my privilege to serve on Larry Vanderhoef's leadership team. When he appointed me to my first senior position, I was relatively untested. He recognized managerial and leadership abilities I did not even see in myself. I believe his ability to identify and support strong leaders stands as one of his most significant gifts to the campus. As well, he has an uncanny ability to connect with undergraduate students and takes seriously their comments and suggestions. For the past 14 years, UC Davis students have been very fortunate to have a chancellor who prioritized their academic and extra-curricular well-being."

Robert and Margrit Mondavi, in nominating Chancellor Vanderhoef for a 2006 CEO Leadership Award: "Chancellor Vanderhoef's leadership has elevated the accomplishments and the reputation of UC Davis, and has inspired the support of people like us, who share his vision and see opportunities for creating a lasting legacy through investment in a remarkable university. We share with Larry Vanderhoef a commitment to innovation and excellence, and to the risk-taking that's inevitably required to be successful."

Then-Assemblyman Darrell Steinberg, in supporting Chancellor Vanderhoef's 2004 selection as "one of the 20 people who have contributed most substantially to California's capital region over the past 20 years": "When Larry arrived at UC Davis...he brought with him a commitment to not only guide UC Davis to the top tier of national universities but to ensure that the university was engaged with its broader community....UC Davis has clearly flourished under Larry's leadership and consequently has contributed substantially to the state's and the region's prosperity."

Fear and Loathing in Boston for the ASM Meeting


OK

Here is my confession.  I hate,  I mean hate, big meetings.  If a conference has more than 200 people I start to feel icky.  And now this AM I head off to Boston for the gigantic ASM "General Meeting".  I am in part dreading the whole thing.  Anytime one needs to use an online planner to schedule which talks one might want to go to, it is not really my kind of meeting.

But, I was invited to give the "Division R" lecture.  Division R is the "Systematics and Evolutionary Microbiology" section of ASM and this year they are having a session on "Linking evolution of protein families to genome annotation efforts."  This is right up my alley as it was for genome annotation that I first started working on phylogenomic methods (and for which I coined the phrase "phylogenomics") (e.g., see my 1998 paper in Genome Research for more detail on this and see my 1995 paper on SNF2 proteins in NAR where I first discussed using evolutionary trees to predict gene function).

And since the meeting is in Boston (where I was born), I agreed to go.  Add I am sure I will see some great things there.  But travel and I do not agree well right now and I am I guess dreading the whole thing.  If you want to learn more about phylogenomics go to the division R session (Kimmen Sjolander, Patricvia Babbitt, and Margrethe Serres are also talking). And I will try to blog from the meeting but we shall see ...

Saturday, May 31, 2008

Davis is indeed Friendly

I do not normally cross-post stories that I put on my blog about life in Davis, CA but I could not resist this one. Davis has been picked as one of the 5 friendliest cities in the US.

Here is the video from the Today Show. I suppose the people doing this did not take off too much for bloggers like me ...

Davis Really Is Friendly

Two years ago, when we moved to Davis, my wife and I kept talking about how absurdly friendly everyone was here. We still can't stop talking about it (yes, not everyone is friendly, but the average person is and I have never lived in a friendlier place).

Well, our feelings were confirmed by the recent Today show discussion of the five friendliest cities in the US and Davis was picked as one of them. Here is the video ...

Simpsons Evolution Video

Just a little post showing this Simpsons Evolution Video from YouTube

Friday, May 30, 2008

UC Davis Beats Stanford Game 1 of NCAA Baseball Playoffs

Not much else to say here ... Davis has beaten Stanford in the first game in the NCAA Baseball Playoffs. Good job Aggies.

Thursday, May 29, 2008

Colbert is now obsessed with Microbes

Yes that is right, Colbert is now obsessed with Microbes. He has started a new report ... "The Microbe Beat". On this first one, Colbert discusses Martian Microbes, Penicillin and other microbial things. This is perhaps the greatest coup for getting microbes the recognition they deserve since, well, since ever. Please make this the most watched Colbert video ever.

Thanks to my PhD student/employee Jenna Morgan for pointing this out.

Wednesday, May 28, 2008

Top 10 Things Francis Collins Might Do After NHGRI

As I have said, I think Francis Collins, upon leaving the NHGRI, is well set up to become an advisor to some presidential candidate (not that I would pick him as my advisor if I were running, but alas I am not running this time around).

But if he does not become Obama's science sidekick or McCain's genomics guru, well, there are lots of things he might do.  Here are some possibilities:
  • 1. The 1000 genome songs project.  He is already further along in this than the 1000 genomes project ...
  • 2. Get a job at Craig Venter's Synthetic Genomics.  Hey, Collins says he wants to try something new.  And Craig has a history of hiring people who used to work at funding agencies.
  • 3. Sequence Jesus' genome.  More on this later.
  • 4. Run the World Anti Brain Doping Agency (WABDA).  We need a crusader to run the organization.
  • 5. Start a blog.  Hey, there are worse things one could do with free time.  Not many.  But there are some.  
  • 6. Start a genomic information anti-discrimination lobbying firm.  Like others in government, he really should try to make money off of legislation he helped pass.
  • 7. Dancing with the stars.  He could even sing along too.
  • 8. Start giving talks about genetic inferiority of various races and genders.  Or did someone who once ran NHGRI already do that? 
  • 9. Try and apply for some of NHGRI's money.  Oh wait, he does not run a huge sequencing center, so he may not qualify.
  • 10. Make jewelry out of disk shaped beads.  Also known as sequinsing.  

Francis Collins SteepingStepping Down from NHGRI

Just got forwarded this email from Francis Collins to multiple people. Collins is stepping down. I wonder what specifically triggered this ... my guess is he is being recruited by one of the presidential candidates to be some sort of advisor. Nothing like having a prominent scientist who also is born again being on your team ....
From: FSCollins (NIH/NHGRI)
Date: Wed, May 28, 2008 at 11:58 AM
Subject: News

Dear friends and colleagues in the many wonderful team projects that I have had the privilege of being part of,

I am writing to let you know of my plans to step down August 1, 2008 as Director of the National Human Genome Research Institute, a position that has been both a joy and privilege to hold for the past 15 years.

The key to success is having wonderful scientific opportunities and stellar colleagues with whom to work. Many challenges lie ahead as genomics increasingly becomes a leading force in medicine, and I leave my position supremely confident that NHGRI and NIH will continue to achieve notable success in meeting them.

Looking back, I'm tremendously proud of our collective work in leading the Human Genome Project (HGP) to its successful conclusion in 2003, and of our wide range of large-scale projects that built upon the foundation laid by the HGP. Collectively, these projects and the priceless data they generated have transformed biomedical research and empowered researchers all around the world. I'm also proud of these projects' commitments to protecting the privacy of genetic information and addressing the ethical, legal and social implications of genome research.

My decision to step down as NHGRI Director came only after much personal deliberation and was driven by a desire for an interval of time dedicated to writing, reflection and exploration of other professional opportunities in the public or private sectors. Rest assured that NHGRI's leadership will be in good hands. Alan E. Guttmacher, M.D., the current deputy director of NHGRI, will become acting director of NHGRI on August 1, and Mark Guyer, Ph.D., the long-time director of the Division of Extramural Research will continue his able leadership. A formal search process for a permanent NHGRI director will get underway shortly.

Finally, I'd like to let each of you know that while I may be leaving the NHGRI Director's office in search of other challenges, I will be cheering for the success of your dedicated and creative scientific achievements over the coming weeks, months, and years.

Keep up the good work!

Francis

Genomics By Press Release Award #2: Lieden Leiden University and the First "Female" Genome

Ooh. Ahh. That is what we should all be saying as it has been announced that the first "female" genome has been sequenced. The press has eaten this up a bit, because of course, the other human genomes that have been sequenced have been from males.

Sure, in terms of public perception, it will be good to have a woman's genome sequenced. And in terms of science, there could be some major uses (e.g., if phenotypes such as health status are made available along with the genome one could try to use the genome to dissect female specific health issues). But as far as I can tell, this whole story is about perception with no reality involved.

The problem is that thethere is no there there yet. The data is not released. There is no paper (e.g., MSNBC reports ""No other scientists have yet verified the Dutch data, but some experts said they were eager to see the sequence.") This is just some group wanting to stake out some territory in an area that certainly others are working on at the same time. Their press release, by the way, has some icky stuff in it. Most annoying is that they make a point to emphasize that the woman whose genome was sequences is a clinical geneticist. And then they say
“If anyone could properly consider the ramifications of knowing his or her sequence, it is a clinical geneticist,” says professor Gert-Jan B van Ommen, leader of the LUMC team and director of the ‘Center for Medical Systems Biology’ (CMSB), a center of the Netherlands Genomics Initiative.
I do not even know what to say to this. What exactly makes a clinical geneticist better able to think about these issues than say, a genetic counselor, or a ethicist or a priest, or a bioinformatician?

Anyway, they also say
Following in-depth analysis, the sequence will be made public, except incidental privacy-sensitive findings
And for this, Lieden University is becoming the recipient of my second "Genomics By Press Release Award." (see my first one here, where interestingly, the discussion of sequencing a woman's genome came up when I announced I was going to sequence a genome on my new Excercycler machine).

Tuesday, May 27, 2008

What to do when a billionaire loves your brother ...


Well, many people confuse me with my brother, Michael. I guess, if they do not know us, it is understandable. He is at Berkeley. I am at Davis. He works on genomics related things. So do I. We both are passionate about PLoS and Open Access publishing. We both went to Harvard. We both spent time at Stanford. I could go on (we used to look a bit alike ... see the lovely family portrait). Sure, sometimes I get sick of people asking me questions about microarray clustering software and Drosophila.

But most of the time, it only is good for me. Like today. If people want to confuse me with my brother today, fine by me. That is because today, HHMI announced the selection of their new "Investigators". Becoming an HHMI Investigator is the scientific equivalent of getting a sugar daddy. They give you money to do whatever research you want to do. They call it "People, not Projects." or something like that.

So - I saw some of the press on this and mostly it was very general - just talking about how HHMI is really important when NIH budgets are flat and all. But then this afternoon, I was listening to NPRs "Marketplace" when they do a story on the HHMI announcement. And I am thinking - wouldn't it be cool if they mention my brother? And so my ears perked up. And they discussed some background a bit and then Tom Cech, the head of HHMI, was explaining why they want to give money to people with no restrictions and he said
TOM CECH: Often in the course of research, you stumble upon leads to your question that were different from what you originally proposed and by funding the person, not the project, we are freeing people up to follow those leads.

For example, he says, one investigator started out studying retroviruses, but he switched gears and started building miniature arrays to look at the expression of genes in an organism -- don't worry, I have no idea what that means either.

CECH: But before long, he was looking at typing various sorts of leukemias and lymphomas and breast cancers. So he moved into the cancer area with tremendous results.
Certainly sounds like he was talking about my brother, who worked on flu viruses for part of his PhD (ok, they are not retroviruses, but they are RNA viruses), and did a post doc working on arrays (with Pat Brown and David Botstein) and also then used arrays to do cancer classification studies. Sure, he could also be talking about Pat Brown but hey, I am going to pretend he was talking about my brother since it is pretty close.

So, sure, I am a bit peeved they did not select me (thankfully, it seems on first glance that they people they did pick all pretty much rock in terms of science so it is not like I lost out to a bunch of dolts). But I am not jealous. Proud would be more accurate.

Search for life on Mars



Well the Phoenix lander has, well, landed on Mars. And it is, well, on a mission. To search for evidence of life (OK, that is not the only part of the mission, but it is the coolest part).

And it is time to place bets. Who out there thinks they will find some sort of evidence for life and how strong will that evidence be?

I for one think there will be life on Mars somewhere. And the Polar regions are not such a bad place to look for evidence of past or present life on the planet. Not sure what others out there think overall but here is some stuff from the web to consider:

Oliver Morton, my favorite Martian Blogger (interpret that however you want) says at MainlyMartian:

Having witnessed two Mars lander failures, Mars Polar Lander before this blog was even born and Beagle-2 back when it was young and active (Landing and prelanding in the December 2003 archive, and the whole sad story in the Beagle-2 archive), and having been absent for all the other attempts that have proved successful, it seemed to me only prudent not to cover the landing of Phoenix this weekend

Oliver also points to a "In the field" blog from Eric Hand.

Neil Saunders says:

If there ever was (or is?) microbial life there, Phoenix has a pretty good shot at finding the signs.
Others out there I am sure have more to say. What do you think?
(1) Is there life on Mars now?
(2) Was there ever life on Mars?
(3) Will Phoenix find and positive evidence?

ASM Meeting Preview: Give your input to the National Science Foundation's Microbiology Programs ...

If you are interested in the funding of microbiology research from the National Science Foundation, there is a good opportunity coming up to find out what NSF's plans are and to give your input. James Collins, the Assistant Directory of the Biological Sciences Division at NSF will give a presentation at the ASM Meeting in Boston.

His presentation will be June 4, 2008
At the ASM Meeting at the Boston Convention and Exhibition Center
Room 052A
12-1:30 PM

If you are in town and interested in microbiology research funding, it would be worth going to give your input.

And if you are going to be in the area for the meeting or otherwise, you might consider going to the Division R Symposium that is from 8-10:30 in Room 156A. The talks in that session are:
  • Margrethe H. Serres -- Convener
  • Jonathan A. Eisen -- Division R Lecture: Phylogenomics and the Diversification of Microbes
  • Patricia Babbitt -- Functional Promiscuity and the Evolution of New Enzyme Functions: Implications for Annotation
  • Kimmen Sjölander --The PhyloFacts Microbial Phylogenomic Encyclopedia: Investigating Protein Superfamily Evolution across the Tree of Life
  • Margrethe H. Serres --Protein Families Provide Support for Functional Annotation and Reflect Metabolic Diversity of Organisms

Friday, May 23, 2008

Lederberg Workshop Rest of the Story

When I left off in my notes the first day of the workshop was basically ending. After the session ended, the speakers and the members of the Institute of Medicine Forum on Microbial Threats went out to dinner at a restaurant in Cleveland Park. A few of us walked over to the Metro together and talked along the way. Thankfully, I did not get lost, as (1) I grew up in the DC area (2) I worked around the corner from where the workshop was held for a summer 20 years ago and (3) Julian Parkhill from the Sanger Center was with us and I had sadly gotten very disoriented with him when I was at a NIH Human Microbiome meeting in Bethesda which is actually where I grew up.

The dinner was quite good and I had some good conversations with various folks about microbes and their lives as well as about science in general. Sometimes these types of events are a bit much for me but for whatever reason the whole dinner event was very pleasant. And this was despite the fact that I still had not even started working on my talk for the next day. Finally, as some people were getting coffee Stanley Cohen and a few others said they wanted to head back to the hotel so a gaggle of us left, and went back.

I then spent a few hours making an outline of my talk and finding some slides and worrying about what I was going to say. I was going to be the last talk of the meeting -- in essence wrapping things up. Normally I do not get stressed about such things but here I was at this workshop in honor of one of the greatest biologists of the 20th century. And many scientist's I really really respect were to be in the audience. To give those who know an idea of how big a deal I thought this workshop was - I wore a suit for both days of the meeting. Now, I have not worn a suit in probably two years. But it just seemed natural to do it here. Anyway, with all of these things together it was a big deal to me to give the closing talk of the workshop.

And so I slept very little piecing together a talk that I hoped would honor Lederberg and make people glad they stayed until the end. On a side note, I never met Lederberg. But I was trained in microbiology by one of his students - Ann Ganesan who worked as a Senior Scientist in Phil Hanawalt's lab where I did my PhD. Ann was amazing -- the grand guru of microbiology and I learned a great deal from her. And thus I felt a connection to Lederberg even if I did not know him.

And finally, after very little sleep, I headed out for day 2 of the workshop. And day 2 was as good or better than day 1. There was Stanley Cohen talking about Lederberg and plasmids, Julian Davies (one of my all time favorite speakers) discussing antibiotic resistance, Jo Handelsman talking about functional metagenomics and microbial commensals in insects, Steven S. Morse talking about emerging diseases, Peter Daszak from the Consortium for Conservation Medicine, Mark Woolhouse talking about the ecology of human pathogens, and then me. All of the talks before me were quite excellent. Thoughtful. Insightful. Entertaining. (I do not think I have ever been at a meeting like this - I normally cannot sit through more than a few talks in a day). Lederberg would have been proud.

And then me. I think I did a good job with the wrap up. A lot of the talks for the day had been about how we can use an understanding of the past to help predict the future. And I talked about the original of novelty and how understanding how new functions originate can certainly help us understand the present (e.g., analyzing genome sequences) and I tried to bring in examples from all the other talks at the meeting (ahh .. one of those times where having my laptop and modifying my slides during the day was a good thing).

And then there was a brief discussion session where some really good questions/suggestions came up and then it was over. But I did come back inspired. Lederberg was such an incredible scientist and person. His legacy hopefully lives on.

Tuesday, May 20, 2008

Lederberg Workshop LiveNotes

I am going to keep posting here notes from the various talks ...
  • A good short introduction by Peggy Hamburg of David Hamburg. Peggy is a scientist but had a funny story about how Lederberg gave her her first job - making cookies. She then introduced David Hamburg and said about him “he had many accomplishments including being my father”
  • Hamburg then gave a nice talk about Lederberg ... some highlights
    • When he was sick earlier this year, he still took time to come over to Hamburg's to discuss Hamburg's book that he was working on ... to give him input
    • Good story about Lederberg's building the department of genetics at Stanford
    • Told story about how Lederberg helped create the "human biology" major at Stanford
    • Emphasized that, despite the impression by many, Lederberg was not so aloof
    • Emphasized that Lederberg was deeply committed to educating the public about science and society and went to Hamburg one day saying he wanted Hamburg to introduce him to people at the Washington Post so he could write a column. And together they convinced the Post to do the column and Lederberg wrote it for many years. Many thought this was below someone with his scientific gifts but he was really committed to it. Note you can see his columns here See his papers here. I hope we would have liked blogging ...
  • Stephen Morse
    • Lederberg very interested in evolution
    • Coined phrase Exobiology
    • Good line of Lederberg's about how infectious disease is "our wits versus their genes and their have been evolving much longer"
    • Lederberg was an early adopter of email and bioinformatics and was a big fan of technology
    • In his office at Rockefeller, Lederberg had all sorts of awards posted in the outside office and then in his inner office he had two things on the wall. A picture of David Hamburg and his ham radio certificate.
  • Discussion
    • Peggy Hamburg said Lederberg used to take her tidepooling at Pescadero Beach
    • Lederberg seemed exceptionally fond of writing notes to people he knew to challenge them about some aspect of their work
    • Stanley Cohen mentioned how Lederberg was very helpful when he started out in the Genetics department at Stanford and when some people were questioning his desire to focus on plasmids
    • Julian Davies mentioned a story about giving his first "outside" talk - at Stanford - and being very nervous to go there with all the gurus of the field there. And Paul Berg warned him that Lederberg might appear to be sleeping during his talk but that he would ask some very challenging questions at the end. And Lederberg in fact did this - but that Julian had discussed the issue a bit during his talk. And with some trepidation, Julian said "Well, you may not have been listening ..." And though he was afraid of offending Lederberg, it did not.
  • Afternoon #1 - A really good session on beneficial microbes and microbial communities
    • Jill Banfield gave an exciting overview of her work on the Acid Mine Drainage ecosystem including examples of genome sequencing, proteomics, etc. But the most interesting part was a discussion of their work on microbe-virus interactions including looking at CRISPR elements. CRISPRs have been proposed (by Mojica et al, Makarova et al and some others) to be in essence a bacterial adaptive immune system to resist phage.
    • Jean-Michel Ane discussed plant-root symbioses including some very interesting stuff on how different symbionts interact with the same or overlapping host pathways.
    • Margaret McFall-Ngai discussed the Vibrio - Squid light organ symbiosis and among many things pointed out some detail about the signalling pathways and the develomental changes that occur in the squid
    • David Relman gave an overview of human microbiome studies and did a good job of pointing out not only what we know, but what we do not know.




Lederberg Workshop Intro

Well, I am sitting in the Lederberg workshop right now with David Relman talking about Lederberg and the workshop. He is emphasizing how "microbes as threats" (which is similar to the name of the panel that convened this workshop) is a bit of a biased view point and that beneficial microbes are important too and that Lederberg recognized this. Relman is also mentioning the importance of Esther Lederberg (Josh Lederberg's first wife).

Now - some update on last night. I got to the hotel around 3 went walking around DC and then came back to the hotel. All the speakers were supposed to be staying there so I lingered in the lobby hoping to bump into people I knew and find someone to go to dinner with. And I sat down and started reading a book I just got - Microcosm by Carl Zimmer. Zimmer's book is about E. coli and the history of studies of this magnificent organisms. And I started by lookng up in the index the stuff on Lederberg and read that. The book really seems to be quite excellent --- it covers a wide range of topics in biology at the same time as highlighting the importance of this organism. And then the gurus of microbiology started coming by. And I snookered my way into dinner with Julian Davies, Bruce Levin and Stanley Cohen.  And it ewas a great time --- talking about Lederberg, microbes, plasmids, selection, etc.   A good start to the meeting for me.  More later.

Monday, May 19, 2008

Joshua Lederberg Papers on the Web (well, most of them)

As a follow up to my previous post about a symposium in honor of Josh Lederberg that is coming up in Washington on Tuesday. There is a nice collection of his "papers" on the web - Profiles in Science: The Joshua Lederberg Papers

By papers they mean everything - letters, notes, drafts, communications, etc.  It is quite comprehensive and quite interesting including many discussions with other leading researchers key moments in the history of 20th century biological sciences research.  It is worth checking out.  I note - despite the availability of this great collection, one part of this life as a scientists is not completely freely available - his publications.  Not all are at this site and many are hidden behind the walls of various journals.  What a shame.  Just about every one of his papers is worth reading.

Saturday, May 17, 2008

Microbial Evolution and co-Adaptation: A Workshop in Honor of Joshua Lederberg - Institute of Medicine

Well, in a few days I am off to a cool workshop in honor of Josh Lederberg (for more detail see this link Microbial Evolution and co-Adaptation: A Workshop in Honor of Joshua Lederberg - Institute of Medicine). The goal of the workshop is to "to inform the Forum and the general public about the many scientific and policy contributions of Dr. Joshua Lederberg to the life sciences, medicine, and public policy."

The workshop is put on by the Institute of Medicine in Washington DC and it is open to the public. You have to register in advance and I am not sure how many more slots are available but it looks to be pretty good. The sessions topics are are: "The microbiome and co-evolution" "Microbial evolution and the emergence of virulence" "Mechanisms of resistance" "Anticipation of future emerging infectious diseases" and there are some heavy hitter speakers in there including David Relman, Jo Handelsman, Jill Banfield, Margaret Mcfall-Ngai, Stanley Falkow, Bruce Levin, Julian Parkhill, Stanley Cohen, Julian Davies, Steven Morse, Ian Lipkin, and well, me.

I will be blogging from there, but if you are in the DC area or can be, it could be a good workshop.

I am also going to be writing a bit more about Lederberg and his favorite bug (E. coli) in the next few days so stay tuned ...

Open Evolution - Open Taxonomy Mailing List

In my continuing series on Open Evolution I am posting an email I got regarding the creation of a new mailing list on "Open Taxonomy". For more on Open Taxonomy see "The Other 95%" which has some really good stuff on it.
Under the umbrella of the Open Biomedical Ontologies project (OBO; http://obofoundry.org/) we have created a new mailing list, called obo-taxonomy, for the discussion of ontological representation of taxonomies and phylogenies. The OBO Foundry supports the development of orthogonal, interoperable reference ontologies for biological science.

The Phenoscape project (http://phenoscape.org) develops methods and tools for using ontologies to integrate comparative morphological data with mutant phenotypes of genetic model organisms. As such we are very interested in participation from members of the evolutionary biology community to explore how best to integrate taxonomy into an ontological framework. Issues include proper semantics of the relationship between taxonomic groups, and between specimens and species.

Subscribe to the mailing list:
https://lists.sourceforge.net/lists/listinfo/obo-taxonomy

Additional info:
http://blog.phenoscape.org/2008/05/15/taxonomy-as-ontology-opening-the-debate/

Acknowledgments:
The Phenoscape project (http://phenoscape.org/) is funded by NSF-BDI and supported by the National Evolutionary Synthesis Center (NESCent; http://nescent.org).

Tuesday, May 13, 2008

Calling all microbiologists --- we need better PR to compete with the platypus and other cutesies

Well, much as I hate to admit it, I find myself agreeing with the notion that cuteness sells in genome sequencing. That is in essence the claim of Natalie Anger in an article in the New York Times about all the attention the platypus genome paper has been receiving over the last week (see
A Gene Map for the Cute Side of the Family - New York Times

Alas, microbiologists really do not have anything like this no? I mean, who feels that E. coli or yeast are, well, cute? (Well, even if you have one of those "giant microbes" stuffed animals, that just means you are a dork like me ... the public does not collect those). Sure, Carl Zimmer can get some attention for all the geeky tattoos out there and some of them did have something to do with microbes, but again, a platypus they are not.

So what are we forlorn microbiologists to do? We need better PR and imagery. We need cute microbes. We need more dark and evil microbes too (I mean, if anyone sequenced the T-rex genome - for real - it would get attention too).

So - I am calling all microbiologists and microbiology fans --- bring forth your imagery that will help microbes get the attention they deserve. And today I am suggesting just one simple thing we can all do to make a difference: get some new names.

That is, give your favorite microbe a good common name or nickname to bring out the cuddly or dark imagery we need. All microbes names should conjure up something to the public, like anthrax does (yes, I know, anthrax is the disease and not the microbe , but this adherence to rules is part of the problem we have).

Here are some proposed name changes for organisms I have worked on:

Wolbachia - "The Feminizer"
Tetrahymena - "The Hairy Beast"
Carboxydothermus hydrogenoformans - "Exploding Breath of Death"
Chlorobium tepidum - "Little Green Machine"

So - please - come up with nicknames for all your bugs and start to use them or at least post them here.

Friday, May 09, 2008

Wednesday, May 07, 2008

Icky Stuff at Long's




All I can say is I am glad I check my medicines before I take them.  I went to Long's in East Davis the other day to pick up some insulin and was given a box of my insulin pens.  When I got home I found that there was only one insulin pen in the box and that pen was used.  Not exactly confidence boosting in my pharmacy.  Only later did I figure out what happened which was even scarier.  This was insulin I had returned months before because of a defect that Long's was supposed to send back to the manufacturer (I had called the company who had handled this very well, and they told me a free box would be at Long's and that Long's would return the unused portion to them).  So I guess Long's put it in the fridge and did not return it and then saw my name on it and gave it back to me.  Yuck.  Even worse, they did it again, I think the next time I went in.  Double yuck.  

Note that I wrote this when it happened but decided not to post it (but saved it in my blogger account), since it seemed a bit too personal. But now (2009) I am having problems with Long's again and I figured I would make live some of my old postings about Long's.

Sunday, May 04, 2008

Help save Davis' Schools ...

Normally I do not put too many things about Davis here as I post them on my Davis Blog here. But I am cross posting today since I know many people from Davis read this blog.

There is a financial crisis of sorts going on in Davis. Please consider donating to the Davis Schools Foundation by May 15 in order to prevent cancellation of programs and/or termination of teachers.

See the video below which was made to showcase Davis' children and what we stand to lose if we don't all act fast!

See also Jamie Madison's blog.


Save Davis' Schools

There is a financial crisis of sorts going on in Davis. Please consider donating to the Davis Schools Foundation by May 15 in order to prevent cancellation of programs and/or termination of teachers.

See the video below which was made to showcase Davis' children and what we stand to lose if we don't all act fast!


SPARC and Science Commons release guide to creating institutional open acces policies

A nice new release from SPARC and Science Commons is out. They put together a guide to creating institutional open access policies (see Press Release)

In the guide they have an overview of the new Harvard Open Access policy, suggestions for what one can do on one's own campus and a plan of action for bringing about policy change. I know I am going try some of their suggestions here at Davis as I am hoping Davis and the UC in general adopts a policy like Harvard's (they mention the UC consideration of such a policy in their site)

Thursday, May 01, 2008

Science Commons » Blog Archive » Rockefeller U. Press Uses CC Licenses to Reduce Permission Barriers

Good Open Access news from Rockefeller Press. They have decided to change their publishing policies and are making them much more open. Emma Hill, who used to work at PLoS Biology and is now the Editor of J. Cell Biol. from Rockefeller has an editorial (with Mike Rossner) about the change including details of the new policy and some of the reasons for the change.

Among the changes they make and some of the reasons why
  • Giving copyright to the authors.
    • This is a good thing and about time for them to do it. They say: "Preying on authors' desire to publish, and thus their willingness to sign virtually any form placed in front of them, scientific publishers have traditionally required authors to sign over the copyright to their work before publication. "
  • Adopting a Creative Commons license.
    • They say "What does this Creative Commons License mean? It means that our published content will be open for reuse, distribution, data mining, etc., by anyone, as long as attribution is made to the original work. Share-alike means that any subsequent distribution must follow the rules set out in this license. Non-commercial means that published work can be reused without permission, as long as it is for noncommercial purposes."
    • This to me is the most important part of their policy. CC licenses change everything - they make it easy for everyone to use the material.
  • They retain an exclusive license for 6 months. After the 6 months, the material has the full CC license and can be distributed anywhere as long as it is attributed and not for commercial use.
Overall, I think this change is a good thing. It is still not the full Open Access I prefer, but it is a great step in the right direction. Also see a blog by Science Commons discussing the new policy - see Science Commons. They are overwhelmingly positive. See also Peter Suber here.

On extra nice thing about the policy is they are making it retroactive for all their publications in the past. So lots of Rockefeller press stuff from the past has now become much more open.

Wednesday, April 30, 2008

Metagenomics just keeps getting bigger ...

Yet another tip of the hat form the scientific community to the growing field of metagenomics. Today Ed Delong, one of the pioneers of using metagenomic methods to study microbes, was elected to the National Academy of Sciences. Congrats to Ed for this well deserved recognition (now I note, he has done many things in ocean microbiology that are not metagenomics ... but we will pretend here that this was all about his metagenomics work).

Other people elected of particular relevance to this blog -- David Hillis, a great evolutionary biologist, and Rosemary Grant, of Darwin's finches fame.

Francisco J. Ayala - Evolution - Scientists Who Believe in God - - New York Times

Good to see someone other than Francis Collins getting some press about bridging the gap between evolution and religion. Today it is Francisco Ayala, an evolutionary biologist at UC Irvine. There is an interesting story about him in the New York Times today (Francisco J. Ayala - Evolution - Scientists Who Believe in God ).

Now, I thought I knew a good deal about Ayala but I did learn a bit in the article about his life and background (e.g., he was a Dominican priest, which I did not know). I personally think the "religion" vs. "evolution" debate is pretty silly much of the time and succumbs to the modern obsession with controversy. Ayala's new book "Darwin's Gift to Science and Religion" apparently addresses this issue and I hope it does a better job than Collins' book, which I found to be wanting in many areas. Of course, I guess I am a bit biased since I have had a soft spot for Ayala for many years and since he just wrote a very positive review of my new Evolution textbook. Now, if Collins wrote a positive review, I do not think I would like his book any more, but who knows ...

Monday, April 28, 2008

Reminder About the NIH Public Access Policy

To all interested in Open Access publishing


Here is an email I just got from NIH

April 28, 2008

Dear Members of the NIH Research Community:

I am writing to remind you that the mandatory NIH Public Access Policy (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-033.html) applies to final peer-reviewed manuscripts accepted for publication on or after April 7, 2008. Making published research funded by NIH accessible to everyone, including health care providers, patients, educators and scientists, helps advance science and improve human health. We all have a role to play in achieving this goal, and I appreciate your efforts to make the NIH Public Access Policy successful.

The NIH Public Access Policy implements Division G, Title II, Section 218 of PL 110-161 (see http://publicaccess.nih.gov/policy.htm), which was signed into law late last year. Compliance with this Policy is a legal requirement and a term and condition for all active grants and contracts awarded as of April 7, 2008. Failure to comply may trigger one or more enforcement actions, depending on the severity and duration of the non-compliance.

Please see the Public Access Web site for the tools you need to comply with the Policy. The Web site houses Frequently Asked Questions (FAQs), training information, and other resources.

To ensure compliance with the Policy, please remember to:

Address Copyright - Make sure that any copyright transfer or other publication agreements allow your paper to be submitted to NIH in accordance with the Policy.

Submit Papers upon Acceptance for Publication

1. Some journals will submit the final published article on your behalf, without your involvement. See http://publicaccess.nih.gov/submit_process_journals.htm for a list of these journals.

2. For any journal other than those on this list, please:

a. When submitting a paper for publication, inform the journal that the final peer-reviewed manuscript is subject to the NIH Public Access Policy.

b. Make sure that any copyright transfer or other publication agreement allows the final peer-reviewed manuscript to be submitted to NIH in accordance with the Policy. For more information, see the FAQ Whose approval do I need to submit my article to PubMed Central? and consult with your Institution.

c. Submit the final peer-reviewed manuscript to NIH upon acceptance for publication at http://www.nihms.nih.gov/. See the Submission Process for more information.

Cite Papers

§ When citing your NIH-funded papers in NIH applications, proposals or progress reports, please include the PubMed Central reference number (PMCID) for each paper.

§ NIH will monitor compliance through citations. Effective May 25, 2008, when your NIH Program Officer reviews your progress report or application, he or she will be expecting a PMCID in the citation of every applicable paper that arose out of your NIH funding, or a manuscript submission system reference number (NIHMSID) if the PMCID has not been issued. See Section C of our FAQ for examples.

§ If you publish through a journal listed under http://publicaccess.nih.gov/submit_process_journals.htm, there might be a slight delay in assignment of a PMCID. That is okay. We have signed agreements with these journals that allow NIH to resolve submission with them without your involvement. To facilitate your Program Officer’s job, we ask that you indicate ‘PMC Journal- In Process’ until the PMCID is available.

The NIH Public Access Policy is a legal requirement and represents an important opportunity for science and medicine. We are very interested in your feedback on the Policy and are soliciting input through a request for information from March 31, 2008 to May 31, 2008. Please send any comments or suggestions to http://publicaccess.nih.gov/comments.htm.

Sincerely,

Norka Ruiz Bravo, PhD

NIH Deputy Director for Extramural Research

Tuesday, April 22, 2008

A good Earth Day for me

Well, Earth Day 2008 is almost over. And I guess I had a really good one. I was scheduled to give a talk at 1 PM at Lawrence Berkeley National Lab (LBNL) as part of their Genomics Division Seminar Series. Living in Davis, LBNL is about 1 hour away if there is no traffic and much longer if there is traffic. And so I said, why not try to honor the Earth and not drive and instead take the train. In part I was inspired by the Michael Pollan's article in this Sunday's New York Times about the little things we can do to help the Earth. In part I was inspired by Earth Day. In part I was inspired by going to the Department of "Energy". And in part I was just looking to get some exercise. But here is the story of my day ...

Part one of this adventure was pretty easy. It is about a fifteen minute ride on my mountain bike from my house to the Amtrak stop in Davis. So I headed out about 25 minutes before the train was supposed to leave. And I got my ticket and then hopped on the train with my bike.

And then we sat for 30 minutes or so at the Davis station waiting for a track inspection. Did I get frustrated? Nope. I had my iPhone and my laptop. And I worked on my talk while listening to Science Friday podcasts. And eventually we moved out of the station. And then we got stuck again near Martinez for 15 or so minutes. I was now getting a little worried about timing, but after a phone call with my brother in Berkeley, who I was going to meet, I calmed down (realizing that the people I was hoping to meet at Berkeley could wait for another day) and arranged to meet him at the train stop.

And we met a few blocks from the Berkeley Amtrak stop and began the ride up to LBNL. Past downtown Berkeley. Past UC Berkeley Campus. And up the hill past the Botanic Gardens. Now for real bikers and for me in my past, this would be nothing. But for a flatlander who only sees hills riding across the overpasses over roads, this was a big deal. And finally, we got there. And I changed into a PLoS shirt my brother brought and jeans I had brought and had lunch my brother made ( a PB & J sandwich using jam I had given him that I made from our apricots from my tree that I had frozen last summer). And I chatted with some people coming for my talk, including one of my co-conspirators for the my April 1 joke, Chris Patil, who writes the Ouroboros Blog. Also there were Eddy Rubin (my host and Director of JGI), Janet Jannson (an expert in the human microbiome, among many things), Paul Spellman, Todd Desantis (one of the top rRNA analysis folks around) Mina Bissel. And then I gave my talk (I think it went pretty well ... but I am not exactly objective).

Then after I talked to some people for 20 or so minutes. And then we rode down the hill. A lot quicker than up for sure. And I went to my brother's new lab on UCB's main campus for a party for one of his students who just passed his quals. After a little food and some discussions I headed out. And then I met my friend and co-author of my new Evolution textbook Nipam Patel for a 15 minute mini chat. And then I zipped down to the Amtrak station with 15 minutes to spare so I stopped at the Pasta Shop for a snack. And then I took the train back to Davis (it was on time) and looked out the window at the SF Bay and then the marshlands and then the farmlands. And finally, I rode back to my house by 5:30 PM to hang out with my family. What a nice day - no car. Some exercise. Some science. Some friends. Some fun. So - thanks for the inspiration, Earth, Michael Pollan and Michael Eisen.

Sunday, April 20, 2008

Trip to CALIT2 & CAMERA

Just got back from a one day trip to San Diego to visit the folks who run CAMERA, the metagenomics database being run out of CALIT2/JCVI. The main point of this meeting was to start to figure out how to take computational tools that we have developed in my lab or will develop in my new iSEEM project (with Katie Pollard and Jessica Green) and make them available in CAMERA.

But as usual, the most fun part of the trip was to see the CALIT2 toys. And boy do they have toys. Larry Smarr, the director of CALIT2 and the PI on the CAMERA project (funded by the Gordon and Betty Moore Foundation) gave us a quick tour around the building. My slide show is embedded below. Mostly we got to see the massive multimonitor "optiportal" display walls. We also got to see the big linux cluster that is the guts of CAMERA (and may favorite part, of course - the big PLoS Biology sign relating to the Global Ocean Survey papers in front of the computer).


CAMERA, which stands for Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (thus, why we say CAMERA), is a big and complex enterprise, hosting metagenomics sequence data, metadata associated with the sequence, and a variety of analysis tools for working with the data. You can find out more about it in a paper from PLoS Biology here.

Now, CAMERA is not the only metagenomics database out there. The other main one people seem to use is IMG/M from JGI. If you are interested in metagenomics analysis in any way, it is worth becoming familiar with both systems.


Saturday, April 19, 2008

Picnic Day Pictures

Tree of Life Runners

More little ditties here

Monday, April 14, 2008

Open Access Week

I guess, in my effort to catch up on work after spending time working on an April fools joke, I missed that last week was the first "Open Access Week" at least, as promoted by some key OA bloggers (see here, here, here, and here). This was done in honor of the new NIH policy on Open Access to Publications that commenced last week.

Se McBlawg for more detail at: 'Open Access Week': Some Posts from the Blogosphere

Saturday, April 12, 2008

Tree of Life Runners Web Notes

Well, I needed a name for little mini tidbits to post on and "Runners" has won the competition. So here is my first "Runners" entry of things from the web that caught my eye this week

Friday, April 11, 2008

Welcoming Pamela Ronald to the Blogosphere

Just a quick post here .... I recommend everyone check out the newbie Blogger on the Block, Pamela Ronald. In addition to having an office, at least temporarily, near mine, she is an author of a new book called Tomorrow's Table discussing multiple marriages of organic agriculture and genetic engineering, an international known plant biologist (see her lab web site)., and a great person to bounce all sorts of ideas off of. As I have been going around the world (in reality and virtually) recruiting active scientists to do more blogging I am very happy to see her start a blog. So I encourage everyone who reads my blog to check out her blog.

Wednesday, April 09, 2008

Confessions of an April Fool and the Dope on Brain Doping

Well, truth is imitating art in bizarre ways here. Nature today is running a news story by Brendan Maher (also see his forum here) and various related tidbits about a survey they conducted on brain doping. And the lead in to the news story? Well, it is the April 1 joke I coordinated where a group of co-conspirators (who I will name in a bit) and I posted stories about a new NIH crackdown on, yes, brain doping.
The US National Institutes of Health is to crack down on scientists 'brain doping' with performance-enhancing drugs such as Provigil and Ritalin, a press release declared last week. The release, brainchild of evolutionary biologist Jonathan Eisen of the University of California, Davis, turned out to be an April Fools' prank. And the World Anti-Brain Doping Authority website that it linked to was likewise fake. But with a number of co-conspirators spreading rumours about receiving anti-doping affidavits with their first R01 research grants, the ruse no doubt gave pause to a few of the respondents to Nature 's survey on readers' use of cognition-enhancing drugs.
So here I am going to tell the tale of the creation of this April 1 joke. In a way, it all started last April 1, when I created a fake New York Times story about how Craig Venter had been deceiving everyone with stories about sailing around the world studying microbes in the ocean, and in fact he has been studying the microbes living inside his body in order to scoop Francis Collins and others at the NIH on the "microbiome." I made the fake story by taking an article by Nick Wade on Venter sequencing his own genome, downloading the html for the whole web page on the archive of the story, with all the NY Times background material, and editing the text, simply changing the story but keeping the main outline. For example, the title of the real Wade article was "Scientist Reveals Secret of Genome: It's His" and I changed it to "Scientist Reveals Secret of the Ocean: It's Him."

I thought the html version of the story looked great. Here it is. And I tried to send it to people in email but they kept having problems viewing the thing. So in the end, I created a PDF file of the page and emailed that to a few key co-conspirators (who I knew knew a lot of people). And they sent it around. And around. And around. I did not originally post it on my blog, because, well I was worried that Venter would want to kill me. The funny part is, he liked it. And it was the real people who I had made up fake quotes from who wanted to kill me. ( I note, a friend of mine who works at Cold Spring Harbor Press and has the initials AG says he sent it to Nick Wade who also found it funny.)

Anyway, in the end, that April 1 joke worked OK but it has some limitations. First, since I did not post it on the web it did not really use the power of the blogging world to spread. Second, some people figured out it was fake when they went to YouTube or the New York Times web site to look for the things we claimed existed. So, I decided that for this year, if I could come up with a good April 1 joke, I would try and correct these issues.

So - somehow, I hit upon a funny story to do - a spoof in on the cycling and baseball controversies over performance enhancing drugs . But the target would be scientists. That was really the extent of my idea. And then I found the perfect venue to plan it. SciFoo camp (for more on it see here and here and here). Sponsored by Nature and the O'Reilly publishing group. At Google HQ. And with TONS of bloggers and other media types there. We ven considered having a session on humor in science. But that never happened. Fortunately, I cornered various people who seemed to think it would be fun to have a collaborative conspiracy to do an April 1 joke together. And they liked the performance enhancing drugs among scientists idea.

Alas, SciFoo camp was in August of 2007. April 1, 2008 was far away. And the plan slipped to the backburner. I created a private Blogspot blog for people to share information. And invited a few of the original co-conspirators. And we did not make much progress. And then I wrote to Bora (who, like Madonna, really does not need a last name). He was at SciFoo and I knew him through my new role in PLoS. And he knows EVERYONE. And I said:
Bora

Are you up for participating in a grand April 1 joke where I am
hoping to get lots of bloggers to write in different ways about the
same topic to make it really seem real?

J
And he agreed. And then he and I recruited some other bloggers. And then we saw a New York Times article on Brain Doping. We had not really completely formulated a plan to focus on brain doping per se yet (I still thought we could talk about EPO to have endurance at conferences, etc). And we got worried about being scooped by reality. But we soldiered on. At this point I thought maybe the best way to do the joke would be to have everyone separately write a story about some interaction with NIH that hinted at a crackdown on doping among scientists.

In the meantime, I came up with ANOTHER April 1 joke top do, but it seemed like this one had to be done before April 1 since for people to get it it needed to be done while the true news story was hot. So I posted a joke story spoofing the Eliot Spitzer resignation with my own fake resignation from my new position as Academic Editor in Chief of PLoS Biology over buying journal articles. I replaced his wife with my brother (and co-founder of PLoS) and placed a few friends in the story (Alex Gann at Cold Spring Harbor became my replacement, Emma Hill, who left PLoS Biology for a non fully OA journal became Kristen, and I made up a few quotes here and there). I had to post this before April 1 since I knew people would forget abouyt Spitzer quickly. And then I returned to the work on the brain doping joke.

And soon we saw that some people on the Nature Network were talking about trying to do a collaborative April 1 joke. And so I posted a message there and then recruited those who seemed interested. And we had a good core group of conspirators. And people were busy so not much happened. Although Chris Patil, who I used to work with at Stanford, made me freak out even more by posting a whole collection of stories about brain doping on our private blog.

And he and Anna Kushnir and others also said - we need a web site to link to and we need some story to jointly write about. So in a frenzy on March 31 I created a fake press release and a fake web site. To make the press release, I took a real NIH press release, and like with the New York Times story, I edited it a bit and then a bit more.

And fortunately, I had registered the domain name WABDA.ORG for the "World Anti-Brain Doping Authority) through Go Daddy and had paid a bit extra for their "WebSite Now" option, and using their not very easy to use system, I made a website and somehow got it live by about 12:10 AM on April 1.

And I sent the fake press release to the co conspirators, who did an amazing job or also writing fake blogs. And I send the story to lots of others too. And wrote my own fake blog post here. And then sat back and watched the story spread. Below are some of the formal or accidental co-conspirators blogs:
And then I got a call from Nature saying they were doing a REAL story on brain doping and wanted to interview me about the fake story we did. And I guess you can find out the rest at the Nature site.

Also see
UPDATE May 29, 2017 - going to try and rescue some of the links here by pointing to the internet archive.

Mutualisms Rule - So Says Olivia Judson at the Wild Side

Nice blog today on mutualisms by Olivia Judson who writes the Wild Side blog/column for the New York Times (I seem to be writing a lot about writers for the NY Times these days ... not sure what is going on with that). She even features one of my favorite organisms in the blog:
The clam Calyptogena magnifica, which lives on deep-sea vents, depends on a bacterium to supply it with nutrients; the bacterium is transmitted through the clam’s eggs
Last year we published a paper on the complete genome sequence of this symbiont (which I wrote about here when I was clearly in a whiny kind of mood). And Judson picks up on a part of the story on the clam that is rarely discussed - the symbionts are transmitted vertically from parent to offspring. Vertical transmission seems to be linked to multiple properties of the symbionts (see my discussion of this regarding the glassy winged sharpshooter symbionts here).

Judson's post is really worth checking out for the symbiosis fans out there. She does a good job of highlighting diversity and evolution of mutualisms in a relatively short post.


See my video of a dissection of a baby Calyptogena:

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