Connection between Video Games and Bioinformatics?

The Scientist Magazine has a nice piece on one of my favorite people in all of Science - Sean Eddy. In the article, they discuss how Sean is one of those bioinformatics folks who does not just hack together some code to do something but actually writes really good code for his programs. For those of you who do not know, Sean has made a whole collection of software tools for biologists (see his web site here). Perhaps the most widely used is HMMER, which is designed for making and using hidden markov models. But there are some other good ones he has put out. My favorite is Forester, which was made by Christian Zmasek in his lab and is supposed to be available here, although the site is not working right now (NOTE - Christian has posted a new link for it in the comments). I like this because, well, it is software for "phylogenomic" analysis.

Anyway - it is a nice article about Sean, especially the parts talking about how his background in video games contributed to his success in bioinformatics. Back to something I said above, Sean is without a doubt one of my favorite people in science. There are many reasons for this but here are a few.

• He is very open with ideas.
  
  Once, at a conference, I gave a talk on this bizarre new pattern we had found when we were comparing the genomes of E. coli and V. cholerae. We had found that when we did genome-level alignments of these species there was an X-like pattern (see our paper on this here). Anyway, in the talk I said something to the effect of "we have no friggin idea how these X-like alignments could be generated" And Sean, I think in the quesiton session, pointed out that in another paper of ours we had seen what appeared to be symmetric inversions occurring around the origin of replication and that could create the X-alignment. And lo and behold he was right. We got the paper, but in a large part it was his push that got us looking at the inversions sooner than we would have.
  
  
• He is very open with science.
  
  Most of Sean's work is on the open side of science. Open Source software. Open Access publications. Open everything. And I should point out that it was a talk by Sean that catalyzed my conversion into an Open Science supporter. I was attending a meeting in Ft. Lauderdale to discuss data release policies for genome projects. This meeting led to the "Ft Lauderdale Agreement" on data release, by the way. A the meeting there were many genomics players like Eric Lander and Francis Collins who were trying to push for not completely open data release policies where genome centers could release data but there would be constraints placed on the use of the data so that the genome centers would be the first to be able to publish genome scale analysis of an organisms genome sequence.
  
  At the time I was working at TIGR and I supported this notion of basically letting people search for a few genes of interest but preventing them from doing genome analyses. And then Sean got up and gave a talk and, well, blew my mind. I am sure I have notes somewhere from the meeting but basically what he said was - the genome projects whole point is to generate genome data for people to do genome-level analysis. So how on earth can we justify preventing exactly the type of analysis that the projects were designed to generate. He was not saying that we should not somehow protect the genome centers. What he was saying was that for the benefit of science, we need to find a way to allow people to do genome-level analyses immediately on the data. And he also said that the risks of releasing ones data with no restrictions are much less than everyone claims. I think he convinced many people that genome centers needed to open up their data release policies a bit more. And he convinced me.
  
  And so I went home from that meeting and decided to release the data from as many of my genome projects as I could, with NO restrictions (e.g., this is what we did with Tetrahymena). And also, this new found belief in openness helped pave the way for my conversion to being an Open Access publishing supporter.

Anyway, glad to see Sean getting positive press. It is well deserved. Now off to play some video games.

Future of Microbiology Funding at NSF?

Just got pointed to slides from Jim Collins' recent talk at the ASM Meeting in Boston (Collins is the Assistant Director of the NSF Directorate for Biological Sciences) . Unfortunately, I missed his talk but you can get a PDF file of his slides (with proprietary ones removed) and it makes for some interesting viewing.  

There are clearly some big changes planned at NSF for "microbial" research and there seems to be a plan to merge what used to be microbe focused projects into other programs such as NEON, Assembling the Tree of Life, and others. There do appear to be some "Microbe" specific programs that will still be around including a new one "Microbial Systems in the Biosphere" which seems to be replacing/merging with the Microbial Genomes and the Microbial Observatories program.  

Anyway ... it seems that some changes are afoot at NSF.  Since I missed the talk it is hard to tell what the general plan and big picture is here.  If anyone out there went to his talk or have seen other talks of his it would be useful if you could post some impressions here.

A million minds getting together can be confusing but might end up being really cool

Their is a possibly interesting paper in Genome Biology by Barend Mons et al: Calling on a million minds for community annotation in WikiProteins. I say possibly because the paper itself is quite confusing to me but the overall goal seems to be a cool concept. This group has created and is encouraging the use of "WikiProteins" a community annotation system for "community knowledge." Sounds a bit fuzzy? Well, reading the paper does not completely help. For example here is the abstract

WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data. Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated. We call on a 'million minds' to annotate a 'million concepts' and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org webcite.

I got really lost reading this I confess. But I moved on since the overall concept seemed quite intriguing, even if I did not get it completely. But it did not get much clearer further on. For example consider their description of a "knowlet"

The future outlook to integrate data mining (for instance gene co-expression data) with literature mining, as formulated in the review by Jensen et al. [2], is at the core of what we aim for at the text mining/data mining interface. To support the capturing of qualitative as well as quantitative data of different natures into a light, flexible, and dynamic ontology format, we have developed a software component called Knowlets™. The Knowlets combine multiple attributes and values for relationships between concepts.

Scientific publications contain many re-iterations of factual statements. The Knowlet records relationships between two concepts only once. The attributes and values of the relationships change based on multiple instances of factual statements (the F parameter), increasing co-occurrence (the C parameter) or associations (The A parameter). This approach results in a minimal growth of the 'concept space' as compared to the text space (Figure 1).

OK ... I got lost every time I tried to read this in detail. I do think they could benefit greatly by translating their paper from the language used by people who work on text mining to a broader presentation.

But reading between the lines here, this is a new, apparently open access system to try and get community annotation for "Concepts" and for relationships among concepts in biological sciences. Those concepts could include a wide range of things, including genes, genomes, proteins, as well as more standard concepts like functions. Whatever this system is, it seems worth checking out.

I leave you with their ending:

Once widely used and augmented, this resource could become an open, yet quality assured and comprehensive, environment for collaborative reference and knowledge discovery.

Now that I can say I understand and it sounds good to me. If anyone out there has any more insight into this, please give your input.

Deep microbes get all the love

Well, you know microbes must really be cool because Olivia Judson is blogging about them. You see, Olivia is also known as Dr. Tatiana. Judson's book "Dr. Tatiana's Sex Advice to All Creation" created and still creates a stir and helped make Olivia one of the go to people for discussions of the biology of sex and weird sex practices in the natural world. Now she has a blog (with what appear to be entries once a week) on the New York Times web site called "The Wild Side."

In the blogs of hers that I have read (note to New York Times --- your system of allowing access to the blog archive really sucks) I recall there being many references to microbes, even when the focus was not on microbes per se. And this week the whole darn blog is about them small little organisms. In this weeks blog, she writes about microbes living in the deep biosphere (some of my favorites) (see Meet the Intraterrestrials).

So - check out her blog. And encourage her to keep writing about microbes. We know they are cool but she can help convince all those others who are not yet microbe fans of this fact too.

Open Metagenomics: Selenium in the Oceans

Well, I have started previous an "Open Evolution" series here and now I am starting an "Open Metagenomics" series. I know, I have gotten grief from some out there (yes, you Rob Edwards - see comments here) about my support for somewhat non open things in metagenomics, so I am going to try and make up for that as much as possible.

In the first installment, I am pointing people to a new paper on PLoS Genetics "Trends in Selenium Utilization in Marine Microbial World Revealed through the Analysis of the Global Ocean Sampling (GOS) Project" by Yan Zhang, Vadim N. Gladyshev (hat tip to Katie Pollard for pointing out this paper).

In this paper the authors study selenium utilization using data from the first part of the Venter Global Ocean Survey (GOS) which was metagneomic sequencing from multiple samples - mostly surface ocean water.  The GOS data they use comes from the Rusch et al. paper in PLoS Biology (note for full disclosure ... I was an c0-author on this paper).  

There have been challenges with getting and using metagenomic data from other people's publications in the past and I note that the authors here obtained the data sets from CAMERA, a metagenomics database supported by the Moore Foundation.  I note - it is my support of this database that Rob Edwards gave me grief about since the database is not currently completely open (e.g., you need to register to use it and the software that runs it is not currently all open source). 

Anyway, they got the data from CAMERA, and then did a pretty comprehensive analysis to search for genes and features in the data that would be indicative of selenium utilization. Selenium is of great interest to many biologists for many reasons, including that it is required for the synthesis and function of Selenocysteine (Sec), which , if you do not know, goes occasionally by the nickname "The 21st amino acid"

Without going into all the details of the paper, the last paragraph sums up the major features

In this study, we report a comprehensive analysis of Sec utilization in marine microbial samples of the GOS expedition by characterizing the GOS selenoproteome. This is the first time that the microbial selenoprotein population is described in a global biogeographical context. Our analysis yielded the largest selenoprotein dataset to date, provided a variety of new insights into Sec utilization and revealed environmental factors that influence Sec utilization in the marine microbial world.

My favorite part of the paper is that they map some of the selenium related features onto the globe.  For example, in one figure they show the inferred selenoprotein "richness" in 

the different samples. (Selenoproteins are proteins that have selenocysteine in them).  Now I am sure there are many assumptions they made in leading to the inferences they have made about selenium utilization and I am also sure some of these will turn out to be a bad idea.  But to me, this paper is a good example of what researchers will be able to do with metagenomic data in the future.  Sitting at their computers anywhere in the world, researchers can now ask questions about the distribution patterns of functions in microbes in the world.  Pretty cool.  And the more open we are with the papers, the tools, and the data, the more likely this type of work is to spread.

The figures are from the paper and I am permitted to use them here because they were published under a Creative Commons license that allows anyone to use them as long as the source is cited. The source is Zhang Y, Gladyshev VN (2008) Trends in Selenium Utilization in Marine Microbial World Revealed through the Analysis of the Global Ocean Sampling (GOS) Project. PLoS Genet 4(6): e1000095. doi:10.1371/journal.pgen.1000095 

An Open Access pioneer - Trent Reznor

Normally, everything I write about here is at least indirectly connected to science in some way. However, today I am drifting into the world of music. The New York Times had an article a few days ago about Trent Reznor (Trent Reznor’s Frustration and Fury - Take It. It’s Free). Trent, the brains behind the band Nine Inch Nails (full disclosure - I am a fan of his music), has been railing against the constraints of the music industry for year.

And now he is going even further and in essence putting his music into the public domain as much as possible (see his web site NIN.com for more detail). For example

"Mr. Reznor even posts online all the raw digital tracks from Nine Inch Nails albums for anyone to remix. “I’m done with them,” he said. “Why not?”

And he is doing this even though the $$$ for producing his music does not come from the government. He does it in part because he wants his ideas and music to spread and he wants to contribute to musical development. There are obvious parallels between what he (and others) are doing in music and those who develop Open Source software and those who release their data and publications to be as free as possible. I know I am not the first to discuss this, but just thought I would put it out there.

Wanted - Summer Intern in Microbial Genomics/Diversity at the Gordon and Betty Moore Foundtion

The Marine-Microbiology Initiative at the Gordon and Betty Moore Foundation is looking a person to work there for the summer. This is

"a short-term opportunity for an advanced undergraduate or graduate student who would enjoy delving into the genes and genomes of the microbes sequenced as part of the Microbial Genome Sequencing Project (a.k.a the "Moore 155")."

For further details and links see the GBMF job ad. Note applications are due June 16, 2008. Here is more detail on what they are looking for:

Since 2004, the Microbial Genome Sequencing Project (MGSP) funded by the Marine Microbiology Initiative has produced the complete genome sequences of a diverse array of Bacteria and Archaea. To date, the genomes of over 130 microbes have been sequenced, annotated using automated computer algorithms, and deposited in public databases. The primary objective for the internship will be to research and synthesize information about the genome content, isolation habitats, and ecology for these microorganisms.

Specific goals include:

• -Synthesize important new discoveries from scientific publications resulting from the MGSP
• -Compare genomes to seek novel patterns of gene content as a function of organism’s habitat and physiology
• -Build 16S rRNA phylogenetic trees for major Bacterial and Archaeal clades for inclusion on the moore.org website
• -Research the primary scientific literature relating to viruses (phage) that infect MGSP microorganisms to investigate the influence of phage on microbial evolution and ecology

Preferred Qualifications/Skill Set:

• -Advanced biological sciences or computer sciences undergraduate or graduate student preferred
• -Strong research, writing, and oral communication skills
• -Strong interest and knowledge of microbial evolution and ecology
• -Experience working with microbial genomes or gene sequences preferred

Chris Smither on Darwin and Intelligent Design

Entertaining little song by Chris Smither on Evolution/Darwin/Intelligent Design. Scroll to the 2:00 time point if you cannot wait.
Thanks to Iddo Friedberg for the tip.

Good luck Chris Gunter ...

One of my favorite journal editors is moving on.  Chris Gunter, who has been one of the genetics and genomics editors at Nature is moving to be the "Director of Research Affairs at the HudsonAlpha Institute for Biotechnology." She has been a big promoter of "free access" to articles within Nature and was at least in part responsible for (if not the major person behind) the fact that many genomics papers at Nature were freely available to all (note they were not always fully OA publications but at least they were free, which was more than many other journals, even non profit ones were doing).

As for what Chris will do at HudsonAlpha, the press release says she "will work closely with Dr. Richard M. Myers, HudsonAlpha director, to raise awareness about HudsonAlpha and its research programs on a national level." RIck was the person who helped push me to formalize my ideas behind "phylogenomics" many years ago when we were both at Stanford and so now two of my favorite genomics folks will be in Alabama. I guess HudsonAlpha is a place to keep an eye on ...

Getting John Henry and his hammer into a scientific paper

Gotta love a scientific paper that quotes John Henry stories. In Andy Ellington's primer on ribozyme evolution (PLoS Biology - Man versus Machine versus Ribozyme) he leads off with

The steam drill was on the right hand side,

John Henry was on the left,

Says before I let this steam drill beat me down,

I'll hammer myself to death”—The Ballad of John Henry (American, traditional)

His point here is to talk about man versus machine and to then discuss the recent article in PLoS Biology on a "Darwinian Machine" which I wrote about previously. (I think he is also making a bit of a play on words with the hammerhead ribozyme, but I am not sure). Anyway, Ellignton's article is worth checking out. I especially like the ending

Machine-based continuous evolution should be the best of all worlds, combining man's mental ability to chart the future with automated control of selection stringency with the still unpredictable mode and tempo of evolution's relentless drive.

Figure from Ellington's PLoS Biology paper. I can put it here because it is a fully Open Access paper using a broad Creative Commons license. All I have to do is cite the source. And so I am. Andy Ellington. PLoS Biol 6(5): e132 doi:10.1371/journal.pbio.0060132

Figure reportedly by Angel Syrett (see comments).

Plant kin recognition? (Caution - Anthropocentrism ahead)

A fascinating story in the New York Times today on kin recognition in plants (see Plants Found to Show Preferences for Their Relatives ).

They report

The sea rocket, researchers report, can distinguish between plants that are related to it and those that are not. And not only does this plant recognize its kin, but it also gives them preferential treatment.

And

Dodder is unable to grow its own roots or make its own sugars using photosynthesis, the process used by nearly all other plants. As a result, scientists knew that after sprouting from seed, the plant would fairly quickly need to begin growing on and into another plant to extract the nutrients needed to survive.

But even the scientists studying the plant were surprised at the speed and precision with which a dodder seedling could sense and hunt its victim. In time-lapse movies, scientists saw dodder sprouts moving in a circular fashion, in what they discovered was a sampling of the airborne chemicals released by nearby plants, a bit like a dog sniffing the air around a dinner buffet.

The notion that plants sense and respond to their surroundings is apparently controversial. Or, maybe a better way to put it is, the attempts to compare plant to animal neural functions is controversial. So much so that many plant scientists got together to say enough is enough

Thirty-six authors from universities that included Yale and Oxford were exasperated enough to publish an article last year, “Plant Neurobiology: No Brain, No Gain?” in the journal Trends in Plant Science. The scientists chide the new society for discussing possibilities like plant neurons and synapses, urging that the researchers abandon such “superficial analogies and questionable extrapolations.”

I personally think there is an enormous amount of anthropocentrism here. Sure, plants may not have true brains. But even though many people like to think of animals in general and humans in particular as the be all end all of evolution, last time I checked, plants have been evolving for a long time. And there is no reason to think that they do not have all sorts of cool and wacky ways to sense and respond to the world around them.

The same anthropocentric point of view has led scientists to grossly underestimate the complexity of phenomena in microbes too. Microbes in fact can sense and respond to kin, they can count, they can tell time, they have immune systems. In other words, whether small or large, furry or not, simple or complex (in appearance) lots of cool things have evolved in lineages that do not lead up to humans.

Well, everyone. As we continue to delve into the biology of non animals more deeply, we are going to find all sorts of cool things out there. And yes, some of it will be even more complex and interesting and wacky than what we see in animals.

For other stuff on this story see

• Be nice to your plants—you never know what they are planning
• More Interesting Facts About Plants

Conflicts of interest, full disclosure, and ethical blogging

Well, I am sure many have heard stories about scientific research ethics gone awry.  The latest is an article in the New York Times about two Harvard Psychiatry Professors who failed to disclose all of their income from consulting to the University and to the government.  The story they report is pretty icky, with what appear to be clear conflicts of interest not being reported fully.  And this is of course nothing new.  Conflicts of interest and unethical behavior occur of course in every walk of life.  But scientists cringe at it because when it occurs it is really damaging to the whole enterprise.  

Well, what about bloggers?  Sure there are bloggers railing against conflict of interest and unethical behavior among scientists/MDs (e.g., see Steven Salzberg's discussion of the recent  "authorship without contribution" controversy).   But that is not what I mean.  What I am interested in here is - what about bloggers disclosing their conflicts of interest?  Is it done?  Is their an ethical code for bloggers?  Should there be?

So I did some web browsing and there is really a remarkable series of discussions about this on blogs and in other places.  For example:

• Science blogging ethics from Omphaloskepsis
  
• Help build the science blogging ethics wiki from Adventures in Ethics and Blogging
• The ethics of science blogging: help set the agenda.
  
• NC Science Blogging 2008: Ethics
  
• Hope for Pandora: Blogging Codes of Ethics
  
• The Scientist : NewsBlog : Science blogging conf.: Ethics, please ...
  
• Wired Science . Correlations | PBS
  
• Weblog Ethics Survey Results

These discussions cover every type of "Science Blogging Ethics" including things like how polite one should be, etc.  Personally, I am not sure I want to go so far as to say their should be a code of ethics.  I think the most important thing to think about is "Full Disclosure" of real and possible conflicts of interest.  Sort of like what "real" news entities do when they are reporting on a story they have some connection to (e.g., the New York Times always puts something like "The New York Times is owned by XXX and the company we are reporting on here is also owned by XXX"  

So from now on I vow to try and do this within my blog (I already do this much of the time when I write about PLoS or my brother but I will try to do it more thoroughly).

More Airport Dinosaurs - Denver This Time

Well, a few days ago I wrote with excitement about the dinosaur fossil in the Chicago Airport that I saw on the way to the ASM Meeting. Something about evolution in public is always a good thing. And then, amazingly, on the way home, while waiting for my connecting flight in Denver, I had a dinosaur moment there too. In Denver, there was some floor art that was some small embedded sculptures (mostly of dinosaurs) in the floor in the terminal. Maybe there is something I do not know here --- do all airports have to have something about dinosaurs?

A science blogger on Science writing about a science blog ...

Sorry - just had to make up that little title because I had a funny conversaiton with someone where I was trying to say, concisely, that Ryan Gregory, who has a nice blog called Genomicron, had blogged about how Science Magazine had written an article where they referenced my blog about "Genomics by Press Release."

But I was tired and it did not come out so well when I said "A science blogger wrote about science blogging and how Science wrote about my blog". And the person just stared at me.

Anyway, all I know now is that it is a lot easier to talk about when Nature writes about "science" blogging

You know the conference you are at is too big when ....

Now - I confess I was really impressed with how ASM handled this enormous meeting I was just at. If you are going to have a big meeting, ASM does a smashing job. And I can see how such big meetings can have their appeal - the diversity of work and activities relating to Microbiology are amazing. However, big meetings are still not my cup of tea.

So here is my top 10 list of "You know the conference you are is too big when ...". All are based on experiences from this meeting.

1. People communicate within the conference venue by email and cell phones
   
2. They give you a foldout map showing the locations of all the different venues/activities/
3. Colleagues contact you electronically after your talk rather than in person
4. The lines for food are longer than the lines for security at the airport
   
5. There are more:
   
• counters at the registration booth than at the airport ticket area
  
• meeting staff than scientists at the last conference you attended
• promotional booths than active players in Major League Baseball (OK, we are not quite there with this meeting but we are close)
  
6. The abstract book weighs more than your laptop computer
7. People use GPS to find their way in the conference center (I wish I had pictures but I saw this happening)
8. The bus/shuttle scheduling system is more complex than the travelling salesman problem
9. You need to plan your own schedule by searching a database
10. You do more walking inside the conference center than outside
    

ASM Phylogenomics Notes

Well, I just gave my talk on phylogenomic and functional predictions and am going to try and catch up with blogging.

In my talk I discussed how an understanding of function and prediction of function requires an understanding of how functions have evolved.  I am trying to get my talk slides posted here but, alas, I need to deal with some Copyright issues first (OK - here is a little slideshow of my talk ... no audio sorry)

Patricia Babbitt gave a talk after mine on another aspect of phylogenomics and functional predictions.  She has done some really interesting studies (see her lab site here) of functional diversifications and the molecular level by integrating genomic, structural, biochemical and phylogenetic analyses.  She showed some really nice tools for clustering and visualization protein families that, although not phylogenetic, seemed to be very useful for the onslaught of genome data.  Unfortunately, most of her publications are not in OA journals so I cannot use any of the figures here and am not going to bother linking to the papers.

Kimmen Sjolander is talking now about her phylogenomic studies.  She is discussion "Phylofacts" which are precomputer phylogenetic trees of gene families from across the tree of life.  One great thing about her work - most of it is published in OA journals and most of her software is available for free download.

More detail on Phylofacts is available in her Genome Biology paper here.  Kimmen has done some really great work on automating phylogenomic functional predictions and this is one example.  Also see her Flower Power and Sci-Phy and Satchmo and Intrepid and Phylo builder other tools (downlaods and other information are available at her website here.)

Gretta Serres will be speaking next.  I will post on here talk soon ...  And now I am posting on it ...

She is discussing "linking metabolic diversity to protein families" os something to that effect. She discussed something I never have thought of doing which is the following - take genomes, identify the size of protein families in each genome and then cluster genomes by their similarity of the protein family size.  I assume some others must have done this but it seems like a good way to identify similar duplication pressures on distantly related organisms.  

Yet another reason to avoid big meetings

Big meetings really do suck. I am on the bus from my hotel to the conference center where the ASM meeting is being held.  I knew I should have taken the subway.  But I took the charter bus.  And it seems to be more of a thing for tourists than scientists on the way to a conference.  On the bus they are playing tvs at a volume akin to the last rock concert I went to. No chance to talk to anyone.  No chance to think. No chance to relax.  Ick.  

Gotta love an airport with dinosaurs

On the way to ASM and justsaw a lovely dino in the Chicago airport

More airports need these

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 ...

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

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.

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.

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).

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

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.

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.

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.

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).

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.

Explorit Videos on Youtube

A variety of videos are available from the Explorit Science Center on YouTube. They are worth browsing.