Go PLOS Biology - getting lots of press coverage for recent pubs

Just got this email from PLoS Biology and thought I would share - it has links to press coverage of recent PLoS Bio papers  :


We are writing to update you on some papers recently published in PLoS Biology.This is a summary of our recent media coverage for PLoS Biology board members, friends, and for editors. Thank you again for your support of the journal.

On January 3, PLoS Biology published an article by Prof. Alex Rogers et al., which detailed a survey of Antarctic waters along the East Scotia Ridge in the Southern Ocean, revealing a new vent biogeographic province among previously uncharacterized deep-sea hydrothermal vent communities. This received significant coverage in the media, a selection of which is below:

BBC
The New York Times
The Guardian
Washington Post

PBS News Hour (video)
BBC World Service (audio)
Press Association
Discovery News
Reuters (video)
The Telegraph
Wired
Scientific American
National Geographic
Nature
ABC (Australia)
Sydney Morning Herald
MSNBC
CBC (Canada)
Fox News
New Scientist
The Mirror
The Daily Mail
Indian Express

In the same issue, PLoS Biology published an article by Dr David Ornitz and colleagues, which described how FGF20 signaling in mice is required specifically for the differentiation of cochlear outer hair cells - the cells most often damaged during age-related hearing loss. This also received attention in the media, including the following:

NHS Choices
Press Association
The Mirror
The Daily Mail
Scotsman
Irish Examiner

This is very cool: CrowdoMeter - consider signing in and participating

Just was catching up on PLoS Blogs which I do not read enough (some great stuff there).

And I discovered a really spectacular project described my Martin Fenner: CrowdoMeter – or trying to understand tweets about journal papers | Gobbledygook

Basically, this is an effort to crowdsource annotation of tweets about scientific papers. It is pretty simple - go to their website, sign in with a twitter ID, and start classifying. You can search for specific terms in the search bar, including "I'm feeling lucky" which will give you random tweets to classify. I first searched for evolution and four tweets came up. And then I played around with some other searches and I classified a few tweets. Not sure exactly where this is going but it is a cool idea and I will find out more at Science Online 2012 and will report back.

Very nice new #PLoSGenetics paper on "Functional Phylogenomics" of Seed Plants

Update2 - 12/22 - Data available here.  Thanks to the authors for clearing things up quickly.

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Update1 -  12/19 - Data for this paper seems to be unavailable - not sure why - but looking into this after a TWEET from Karen Cranston. The paper says data is available at: http://nypg.bio.nyu.edu/main/ but I could not find any there.  Note - this is one reason that all data sets should be made available at the journal or third party sites.

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Original post:

OK never mind that the terminology of "functional phylogenomics" is a tiny bit vexing to me (long story - some other time perhaps). The paper behind it - PLoS Genetics: A Functional Phylogenomic View of the Seed Plants is very cool.

Here's what the authors did (a very coarse summary)

1. Identified sets of orthologs between plant species using the OrthologID system (which has a phylogenetic underpinning) (the data input for this appeared to have mostly been Unigene EST clusters)

2. Constructed a "total evidence" phylogeny for these taxa (using a few approaches) 

3. Use this phylogeny to reinterpret some general features of the evolution of plants 

4. Searched for gene ontology categories (in annotated genes from these organisms) that agreed with the phylogeny. In essence, this seems to be a search for shared-derived traits (i.e., synapomorphies) in particular clades. 

5. Generated hypothesis about functional evolution in particular clades.

Overall, there is a lot that is really fascinating in here and this approach seems very powerful (though I note - I think something akin to this though not as comprehensive or as careful has been done for other groups but not sure).  Check out the paper for more detail ...

Lee EK, Cibrian-Jaramillo A, Kolokotronis S-O, Katari MS, Stamatakis A, et al. (2011) A Functional Phylogenomic View of the Seed Plants. PLoS Genet 7(12): e1002411. doi:10.1371/journal.pgen.1002411

PLoS picture of the day: Simon Chan from #UCDavis sports #PLoSOne shirt when presenting to @BillGates

Good to see here that Simon Chan, from UC Davis, knows what is the best outfit to wear to present his work to Bill Gates.  

Thanks to Simon for sending me the photo and to the Bill and Melinda Gates Foundation for approving it'sits use here.

Great paper showing the potential power of comparative and evolutionary genomics in #PLoS Genetics

There is a wonderful paper that has just appeared in PLoS Genetics I want to call people's attention to: PLoS Genetics: Emergence and Modular Evolution of a Novel Motility Machinery in Bacteria

In the paper, researchers from CNRS and Aix-Marseille in France used some nice comparative and evolutionary genomics analyses along with experimental work to characterize the function and evolution of gliding motility in bacteria.

Their summary of their work:

Motility over solid surfaces (gliding) is an important bacterial mechanism that allows complex social behaviours and pathogenesis. Conflicting models have been suggested to explain this locomotion in the deltaproteobacterium Myxococcus xanthus: propulsion by polymer secretion at the rear of the cells as opposed to energized nano-machines distributed along the cell body. However, in absence of characterized molecular machinery, the exact mechanism of gliding could not be resolved despite several decades of research. In this study, using a combination of experimental and computational approaches, we showed for the first time that the motility machinery is composed of large macromolecular assemblies periodically distributed along the cell envelope. Furthermore, the data suggest that the motility machinery derived from an ancient gene cluster also found in several non-gliding bacterial lineages. Intriguingly, we find that most of the components of the gliding machinery are closely related to a sporulation system, suggesting unsuspected links between these two apparently distinct biological processes. Our findings now pave the way for the first molecular studies of a long mysterious motility mechanism.

Basically, they started with some genetic and functional studies in Myxococcus xanthus.  They analyzed these in the context of the genome sequence (note - I was a co-author on the original genome paper).  And then they did some extensive comparative and evolutionary analysis of these genes, producing some wonderful figures along the way such as:

Figure 2. Taxonomic distribution of the closest homologues of the 14 genes composing the G1, G2, and M1 clusters, and genetic organization of the core complex. (A) For a given gene, the number of homologues in the corresponding genome is indicated by the numbers within arrows. The relationships between the species carrying the different homologues of the genes are indicated by the phylogeny on the left. Based on their taxonomic distribution, the 14 genes can be divided into Group A (grey background) and Group B (white background). (B) In all non Deltaproteobacteria and in Geobacter, the Group B genes clustered in a single genomic region.  doi:10.1371/journal.pgen.1002268.g002  

Based on their analysis they then came up with some hypotheses as to which genes were involved in key parts of gliding motility and what their biochemical functions were and they then went and confirmed this with experiments.  I am not going to go into detail on the functional work they did but you can read their paper for more details.

They wrapped up their paper by proposing an model for the evolutionary history of gliding motility.  I am not sure I buy all components of their model since our sampling of genomes right now is still very poor, but they have a pretty detailed theory captured in part in this figure:

Figure 8. Evolution and structure of the Myxococcus gliding motility machinery. A) Evolutionary scenario describing the emergence and evolution of the gliding motility machinery in M. xanthus. The relationships between organisms carrying close homologues of the 14 genes encoding putative components of the gliding machinery in M. xanthus are represented by the phylogeny. Green and red arrows respectively indicate gene acquisition and gene loss. The number of gene copies that were acquired or lost is indicated within arrows. The purple dotted arrows represent horizontal gene transfer events of one or several components. WGD marks the putative whole genome duplication event that occurred in the ancestor of Myxococcales. For each gene, locus_tag, former (agm/agl/agn) and new (glt and agl) names are provided. The number of complete genomes that contain homologues of glt and agl genes compared to the total number of complete genomes available at the beginning of this study are indicated in brackets. (B) The Myxococcus gliding machinery. The diagram compiles data from this work and published literature. Components were added based on bioinformatic predictions, mutagenesis, interaction and localization studies. Exhaustive information is not available for all proteins and thus the diagram largely is subject to modifications once more data will be available. Known interactions within the complex from experimental evidence are AglR-GltG, AglZ-MglA and interactions within the AglRQS molecular motor [13], [15]. For clarity, the proteins were colour-coded as in the rest of the manuscript 

Anyway - I don't have much time right now to provide more detail on the paper.  But it is definitely worth checking out.

More on the Bioweathermap project #NotAboutWeather #ItsAboutMicrobes #AndMoney #CitizenMicrobiology

Just a mini post here about Bioweathermap.  I had posted a mini post about this project in July: Desperate to know what microbes are on your money? This project is for you (with some cool side science benefits).  I got reminded about this by this PLoS Blog: DIY Science at #SciBarSpace 2 | The Official PLoS Blog.  The PLoS blog discusses a talk by Jason Bobe about Bioweathermap.

Bioweathermap is not the most accurately named project but it is pretty cool.  From their site:

The BioWeatherMap initiative is a global, grassroots, distributed environmental sensing effort aimed at answering some very basic questions about the geographic and temporal distribution patterns of microbial life. Utilizing the power of high-throughput, low cost DNA sequencing and harnessing the drive of an enlightened public we propose a new collaborative research approach aimed at generating a steady stream of environmental samples from many geographic locations to produce high quality data for ongoing discovery and surveillance. Our approach will provide a unique opportunity to engage the public in the scientific research process while we address fundamental questions such as “How diverse is the microbial life around us?” and “How do microbial communities in different habitats change over time?” and “How can advanced sequencing technologies best be utilized to address issues in biodiversity, public health, and biosurveillance?”

In other words, it is about microbes (suggestion to them - it might be good to have something about microbes in the title of the project - maybe "microbioweathermap" or something like that).  Anyway, to do the project they have been collecting dollar bills from various people:

From PLoS Blog.

And then characterizing the microbes on those bills.  I note - Jason collected the bill from me when we met at the book launch party for Thomas Goetz's "The Decision Tree".  Anyway - in essence this is a citizen microbiology project and it is worth checking out.  For more on it see:

• The Bioweathermap Sees The Germs Around Us - Forbes
• The Bioweathermap Facebook page
• Some of their videos on Vimeo

Seems to me there are more and more Citizen Microbiology projects out there.  For some other posts of mine about CM projects (got to give them an abbreviation) see:

• What microbes are lurking in your fish tank? 
• More on citizen microbiology project from @Penn_State & @NASA on thermophiles in water heaters via @scicheer @Sci4Cits
• Citizen Science
• Share the thermophiles lurking in your basement

Go microbes.  Go citizens.  Go citizen microbiology.

Some links on "ortholog conjecture" paper and critiques of it

Recently a paper by Matt Hahn was published in PLoS Computational Biology entitled "Testing the ortholog conjecture with comparative functional genomic data from mammals."  The paper created a bit of a stir as some aspects of it call into question some of the standard assumptions made in comparative genomic analysis.

I alas do not have time to go into all the details but fortunately others have tackled this and I am posting some links here:

• Comments at Faculty of 1000 (currently available for free but not sure for how long).
• Of mice and men and meta analyses (Richard Grant discussing Michael Galperin's F1000 dissent)
• The 'Ortholog Conjecture' | The Daily Scan | GenomeWeb
• Of Mice and Men or: Revisiting the Ortholog Conjecture (Iddo Friedberg)
• Friendfeed discussion: http://friendfeed.com/erickma... (see below)

Will try to post my own comments soon.  I note - I am skeptical of their conclusions but still going through the paper to understand everything before commenting in more detail.

New #openaccess journals welcome; competition good; not sure how they know it is "top tier" though

Great news from HHMI, The Wellcome Trust and the Max Planck: http://www.hhmi.org/news/20110627.html

Leading Research Organizations Announce Top-Tier, Open Access Journal for Biomedical and Life Sciences

The Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust announced today that they are to support a new, top-tier, open access journal for biomedical and life sciences research.

The three organizations aim to establish a new journal that will attract and define the very best research publications from across these fields. All research published in the journal will make highly significant contributions that will extend the boundaries of scientific knowledge.

A team of highly regarded, experienced and actively practicing scientists will ensure fair, swift and transparent editorial decisions followed by rapid online publication. The first issue of the journal, whose name has yet to be decided, is expected to be published in the summer of 2012.

The three research organizations developed their plans following a workshop in 2010 at HHMI's Janelia Farm Research Campus attended by a number of leading scientists. The participants concluded that there was a need for a model of academic publishing that better suits the needs of the research community.

Dr. Robert Tjian, President of the Howard Hughes Medical Institute, says: "The message from the research community was clear: we are fortunate to have many excellent journals, but there is need for a different, more appropriate and efficient publishing model."

Professor Herbert Jäckle, Vice President of the Max Planck Society, says: "A journal which aims to represent and publish the very best research outcomes needs an editorial team of experienced – and, crucially, actively practicing – scientists. It must also be editorially independent of those who provide the financial support."

Sir Mark Walport, Director of the Wellcome Trust, says: "We will attract the most outstanding science for publication by establishing a journal in which researchers have confidence in robust editorial decisions taken by their scientific peers. This will be a journal for scientists edited by scientists. The ethos of the journal will be to avoid asking authors to make extensive modifications or perform endless additional experiments before a paper can be published."

Recruitment is under way for an Editor-in-Chief who – together with the journal's editorial team – will be an experienced, active scientist. The editorial team will be editorially independent of the funders. They will rely on their scientific expertise and active research experience to identify the best papers, make scientifically-based judgments and exercise leadership in steering these papers through peer review.

The journal will employ an open and transparent peer review process in which papers will be accepted or rejected as rapidly as possible, generally with only one round of revisions, and with limited need for modifications or additional experiments. For transparency, reviewers' comments will be published anonymously.

As the journal will only exist online, it offers an opportunity to create a journal and article format that will exploit the potential of new technologies to allow for improved data presentation. The journal will be an open access journal, i.e. the entire content will be freely available for all to read, to reproduce and for unrestricted use. This open access system will also enhance opportunities to share content and to more directly engage the reader.

The three organizations have made a commitment to cover costs of launching the journal to ensure its success. The long-term business model will be developed by the incoming Editor-in-Chief and the team they build.

This is great news.  The more #openaccess journals we have the better.  Clearly some of the text here is a dig at existing journals, including PLoS Biology.  PLoS Biology definitely needs to work on some things - like transparency (e.g., if your article is rejected, the Academic Editor who advised the professional editors is not names).  PLoS Biology is also run by professional editors.  Thus it is not run by "active scientists" which is another one of the comments in this press release.  Personally I think it would be better if PLoS Biology was run by active scientists.  But that is not the system there.  I have a strange role at PLoS Biology - "Academic Editor in Chief" for a journal not run by academics.  In essence I am a senior advisor to the professionals who run the journal.  I personally would prefer it if academics ran the journal, probably for the same reasons that HHMI, Wellcome, and Max Planck make such a big deal out of it here.  But the professionals do run PLoS Biology.  And overall, they do a good job.  I think the journal could certainly be better - and thus this new competition should be good.  We will have to wait and see just how much competition it is.  It seems a bit weird for them to call this a "top tier" journal before it exists.  Maybe they should have said "aiming to be a top tier journal" or something like that.  But I think it probably will become one if HHMI and Wellcome and MaxPlanck scientists start publishing their good papers there.  I hope this helps catalyze some beneficial changes at PLoS Biology, but we will have to wait and see.

It is a good time for #OpenAccess when major organizations start to compete to create the best "top tier" open access journal.  In the end, this can only be good for science and scientists. 

A good day for the Public Library of Science and science in general: #PLoS opens up search API

Well, thanks to @yokofakun (Pierre Lindenbaum) and #gepasi (Pedro Mendes) on twitter I found out about the announcement from the Public Library of Science (PLoS) yesterday that they have opened up a search application programming interface (API) to allow outside users better access to PLoS searching (see the PLoS blog: PLoS API). This is a great step for PLoS and should accelerate the ways that people access and search for content at PLoS. For more information see:

• Announcing the PLoS Search API – build innovative applications that accelerate science
• Fields in the PLoS Search engine
• some examples using the PLoS API
• PLoS API developers group

To use it you need to register for an PLoS API Key (I just got one, not that I will use it, but was just checking ...). 

Looking forward to seeing what people do with this.

Strange things at #PLoS; a public call to get rid of the constraints of describing author contributions

Well, am working with some others to submit a paper from a DARPA project to PLoS Computational Biology. And yet again, we have to fill out this form regarding author contributions. And yet again, I am baffled by this. PLoS can be so wise in some areas of publishing. But yet remarkably non creative in others. They ask for you to say which authors "Conceived and designed the experiments" which "Performed the experiments" which "Contributed reagents/materials/analysis tools" and which "Analyzed the data" which "Wrote the paper." This has always seemed completely inane to me. First of all, this just does not work for some types of scientific research. Plus it seems so forced and arbitrary.

Why not actually let the authors say who did what in their own words? You can, I note, sort of get around this by badgering the copy editors a bit (e..g, see in my PLoS ONE: Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees where we added some additional categories of "Ideas and discussion" "Built microbial genome database" "Analyzed sequences linked to RecA and RpoB clusters" and "Analysis of distributions of sequences in GOS data."

Even Nature lets the authors use their own words. For example, in my Genomic Encyclopedia paper published with Nature's Creative Commons license for genome papers we wrote:

"D.W. (rRNA analysis, gene families, actin tree, manuscript preparation), P.H. (selection of strains, analysis, manuscript preparation, project coordination), L.G. and D.B. (project management), R.P., B.J.T., E.L., S.G., S.S. (strain curation and growth), K.M., N.N.I., I.J.A., S.D.H., A.P., A.Ly. (annotation, genome analysis), V.K. (CRISPRs, actin), M.W. (whole genome tree), P.D., C.K., A.Z. and M.S. (actin studies), M.N., S.L., J.-F.C., F.C. and E.D. (sequencing), C.H., A.La., M.N. and A.C. (finishing), P.C. (analysis), E.M.R. (manuscript preparation), N.C.K. (selection of strains, annotation, analysis), H.-P.K. (strain selection and growth, DNA preparation, manuscript preparation), J.A.E. (project lead and coordination, analysis, manuscript preparation)."

Which is more useful? I think without a doubt, the constraints by the PLoS system obfuscate what people did. And it is so unnecessary. Here's a public call for PLoS to get rid of this constraint. (I am sure some at PLoS will give me grief for a public call like this, but hey it is the Public Library of Science right?). It seems completely inconsistent with many other aspects of PLoS publishing. Let the author's describe what they did in their own words.

J. Craig Venter Institute, UCSD, Beyond the PDF, #UCDavis leadership, all in one trip

A wee bit late but thought I would give an update on a recent trip.  In January I went on a little trip to Southern California.  The trip started with a simple plan - Susan Golden invited me to give a talk at UCSD.  After my usual complications in planning, I finally agreed to a date (1/19) after finding out the Phil Bourne, Editor in Chief of PLoS Computational Biology was helping organize a meeting starting 1/19 entitled "Beyond the PDF" to discuss the future of scientific publishing.  So this seemed like a perfect mix.  Go down to UCSD for one thing and stay for another.  Short flight and easy to change.  Seemed ideal

Of course I had to make it more complex so I contacted some friends at the J. Craig Venter Institute to see if they would be around and unfortunately my friend Jeff Hoffman was not going to be around.  But he connected me to Craig Venter and his wife Heather Kowalski and though what I really wanted was to just see if they would be around for a visit or dinner - I ended up getting roped into giving a talk there on the 18th.





I note - for those not in the loop - I worked at The Institute for Genomic Research (TIGR) for eight years or so before moving to Davis.  TIGR was founded by Craig and Craig was the head when I interviewed for a job there in 1998.  But between when I interviewed and when I showed up, Craig had left to start Celera, and his then wife Claire Fraser took over.  The entire time I was there, until 2006, Claire was the president of TIGR.  However, I did work with Craig on and off on various projects over the years and also started to work with many of the people at the J. Craig Venter Institute.  When Craig left Celera there was a lot of tension between TIGR and JCVI and things got a bit nasty at times.  Someday I will write more about my thoughts on all that went on but for the purposes of this post, all that is needed is to say that I always got along well with many of the people at the JCVI, including Craig.

Day 1 (Jan 18) - Davis to San Diego to JCVI 
So after even more complexities in planning I had a plan.  I flew down on the morning on the 18th from Sacramento, and took a cab to my hotel (The Estancia).  Just staying at the Estancia was a bit of a complication.  You see, originally I has asked to get put up at the La Jolla Shores hotel because it is on the ocean and well, we don't get much ocean in Davis, CA.  Plus my kids were going to come and they wanted to stay near the water.  Then my wife and kids bailed and so I now had a little less reason to stay at the La Jolla Shores.

So I asked the assistant who was coordinating travel to switch me to the Estancia. Alas, she told me they were not having any visitors stay at the Estancia because there was no food available there.  This seemed weird and after asking around and then even calling the hotel I found out there were two restaurants there - one open for breakfast and lunch and another open for dinner.  So I told this to the assistant.  She then told me that was not true.  I had to basically beg to get moved to the Estancia.  I wanted to be there because it was walking distance to UCSD and was where many of the people for the Beyond the PDF meeting were staying.  Anyway - I finally got a reservation there.

So to continue - I headed to the Estancia from the airport.  I dropped my stuff and I tried to mooch a ride from some of my friends/contacts at J. Craig Venter Institute but they were not answering.  So I took a cab.  I got there, had a decent chat with Bob Friedman, and then went to set up to give my talk. Got set up, Craig came in with his new dog Darwin, and I talked.

Here are the slides (with audio but not yet synched as I write this)

Phylogenomics, Microbes, Yada Yada Yada - Talk by Jeisen at JCVI 1/18/11

View more webinars from Jonathan Eisen

After my talk I met with a few people around JCVI including Andy Allen and Roger Lasken.  Got a tour of some of their toys there.  And I saw a variety of old friend.  And then I went out to dinner at Zenbu Sushi with some of the crew there.  Ham Smith gave me a ride.  As usual, he was driving a very long American car.  He is quite tall.  But he also seems to like the classic American extra long cars.  We drove through traffic in La Jolla and talked about microbes and California.  Then we got to the restaurant, where eventually Clyde Hutchinson, Craig and Craig's wife Heather showed up and we had a very nice dinner.  I then mooched a ride back to my hotel with Ham.  I note Ham gave me some grief about my recent haircut as I noted on twitter later "Off to Salk/UCSD this AM - Tues spent PM at J. Craig Venter Inst.: gave talk, saw cool things/people & got dissed on haircut by Nobelist"

When I got back to the hotel I found that some of the people who were in town for the "Beyond the PDF" meeting were at the bar.  So, instead of working on my talk, I went to the bar and hung out with some of the publishing folks.  And finally I crashed.

Day 2 (Jan 19). UCSD.

I got up early in the AM and had breakfast at the hotel (yes, indeed, they had food there).  I thought I saw the UC Davis Chancellor Linda Katehi at breakfast but figured I must have been seeing things.  Then I walked from the hotel all the way across the street to the Salk Institute where my first meeting of the day was.  It was so close that I had 30 minutes or so to kill so I walked down towards the beach.  I believe I got close to it but it was so foggy I could only see about 30 feet in front of me and though I could hear lots of waves crashing I did not actually see the beach.

I then returned and found my way to Joe Ecker's office.  Had a great meeting with Joe (he does just phenomenally cool stuff on Arabidopsis and apparently on stem cells now too) and I have known him for many years since working together on sequencing and analyzing the Arabidopsis genome (I helped in analysis of the genome when I was at TIGR) (I note - the genome paper was supposed to be freely available forever at Nature's web site but as I write this it is not free).  Then my host, Susan Golden picked me up at Joe's office and we walked, in partial silence (she had laryngitis) from Salk to her lab.  Susan works on cyanobacteria and has done some fascinating work on circadian rhythms in these species.  I spent an hour or so with her lab in their lab meeting talking about science and then went off to lunch.  I had lunch at the UCSD Faculty Club with Larry Smarr who I have interacted with in a variety of ways for many years.  We spent most of lunch talking about personal data recording (e.g., medical tests, real time monitors, etc) (see one of his talks about his own personal data here).  We even went back to his office afterwards and I got to see some of his personal data and how he has ben trying to integrate genomic information with medical records and lab tests.  Afterwards I drifted back to Susan Golden's office, called her up and she met to take me to my next meetings with Joseph Pogliano and then Kit Pogliano.  Both are doing very very cool experimental microbial studies that overlap a bit with some of the things my lab has studied (e.g., Joe works on bacterial actin like proteins and Kit works on sporulation).  After meeting with them Susan and I then headed over to the seminar room where I had 30 minutes or so to get my thoughts in order and then gave my talk.  It was VERY similar to the talk I gave at the Venter Institute, but cleaned up a little bit with the Venter/TIGR jokes removed.

After my talk, Susan and her husband Jim drove me to dinner where I was very pleased to find out Susan had tracked down a friend of mine from grad. school, Kristin Baldwin, who was now on the faculty at the Scripps Research Institute.  It was great to see Kristin for the first time in 15 or so years.  After dinner I went back to the hotel and bumped into Pam Ronald (a friend and colleague of mine from Davis) checking into the hotel - she was in town for the Plant and Animal Genomics meeting.  I then went to the bar and discovered the entire Beyond the PDF meeting crew there.  I lingered a bit and then finally went to sleep.

Day 3 - UC Davis leaders and Beyond the PDF. 1/20

Running out of steam here.  So this section will be a bit shorter than the other days.

The highlight of the day was just after breakfast.  I walked out of the hotel to head over to campus and this time I was certain that I saw the new UC Davis Chancellor Linda Katehi there.  So I went up and said hello, reminding her who I was (we have met a few times now, but you never know).  She introduced me to her husband and to the new UC Davis Provost, Ralph Hexter.  I asked what they were doing at UCSD and they said there was a UC Regents meeting.  Not one to miss a chance to hang out with the UC Davis leaders, I walked with them to campus.  I spent the whole walk chatting with Hexter, who I note, was very very impressive.  I must say, I am a massive fan of Katehi.  Every interaction I have had with her has left me enormously impressed.  And I really like what she is trying to do at Davis.  And one other thing that impresses me is who she has been hiring into leadership positions at Davis.  Hexter seems perfect for a provost right now at Davis.  Humanities prof.  Ex university president (Hampshire College) and ex-Dean of UC Berkeley.  I talked with him for about 25 or so minutes on the walk and was left thinking UC Davis is in good hands.  Another recent hire at Davis is the Vice Chancellor for Research Harris Lewin who I am also very impressed with.

Anyway, after walking with them to the Regents meeting I then headed off to the Beyond the PDF meeting.  Since I am running out of steam here I call your attention to this sites with more information about that meeting: Beyond the PDF.  The meeting that day was OK.  Saw / met lots of interesting people.  The best part was hanging out with people like Kay Thaney who I never get to see enough.



And then went to dinner at the La Jolla Shores Hotel.  And went back to the Entancia and went to sleep.

Day 4 (1/21): Beyond the PDF and home

Well, completely out of steam now.  So all I am going to say is that I went to the Beyond the PDF meeting for the AM and then headed off to the airport to go home.  I think two talks/visits, plus one workshop was a bit much for my brain to handle.  Thus I am only now getting to writing up some notes.

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