UCSD – Jonathan Eisen's Lab

Another Mostly Male Meeting from UCSD- should be called "Food and Fuel for the 19th Century"

Well, just when I thought meeting organizers from UCSD had learned their lesson regarding mostly male meetings – this comes along. Check out “Food and Fuel for the 21st Century” (I was pointed to this by a comment on a blog post of mine). The speakers are

That a ratio of 18:2 or 10% female.

Not that I know the cause of this but here are some other pieces of information to consider.

The Food and Fuel for the 21st Century Program lists 5 people on their Executive Committee. Any guesses on the # of these that are men? Well it is 5.

Fortunately they have an Advisory Committee too and that must have some women on it right? Nope.

Josh Graff-Zivin
George Tynan
Byron Washom
Bob Schmidt, Ph.D.
Tim Zenk

Reminds me a bit of the QBio meeting from 2013 organized by many from UCSD which I wrote about last year: Q-Bio conference in Hawaii, bring your surfboard & your Y chromosome because they don’t take a XX. I note – this years Q-Bio meeting is much better. But one can ask – does nobody at UCSD think about these issues when planning conferences and Advisory / Executive Committees. I personally don’t think one should choose women to just choose women. But as with the Q-Bio meeting from last year, I think there are an enormous number of highly qualified women working on topics directly related to “Food and Fuel for the 21st Century” and thus I am both surprised and disturbed by the gender ratio of this meeting and this organization.

UPDATE 3/4 7:21 AM

It took me a bit but I found details on the 2013 symposium from the same group. The web site for the 2013 meeting is not active as far as I can tell. However it is available in the Internet Archive. For example, here is a snapshot from June 1, 2013. From that snapshot here are the listed speakers

David Kramer, Michigan State University
Susan Golden, University of California, San Diego
Julian Schroeder, University of California, San Diego
Stephen Mayfield, University of California, San Diego
Steven Briggs, University of California, San Diego
Matteo Pellegrini, University of California, Los Angeles
Donald Weeks, University of Nebraska–Lincoln
Michael Burkart, University of California, San Diego
Chancellor Pradeep Khosla, University of California, San Diego
Farzad Haerizadeh, Life Technologies
Ben Hueso, California State Assembly
Bill Gerwick, Scripps Institution of Oceanography
Eric Mathur, SG Biofuels
James Van Etten, University of Nebraska–Lincoln
Fred Tennant, Heliae
David Dunigan, University of Nebraska–Lincoln
Xuemei Bai, Cellana
George Oyler, University of Nebraska–Lincoln
Gerry Mackie, University of California, San Diego
Mark Hildebrand, Scripps Institution of Oceanography
Lawrence Johnson, Salim Group
Craig Behnke, Sapphire Energy
Rebecca White, Sapphire Energy

For a ratio of 20:3.

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.

https://picasaweb.google.com/s/c/bin/slideshow.swf

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 http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=eisen-jcvi2-110301144306-phpapp02&stripped_title=phylogenomics-microbes-yada-yada-yada-talk-by-jeisen-at-jcvi-11811&userName=phylogenomics

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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Metagenomics 2006

Just got back from the “First International Conference on Metagenomics” which was held in San Diego. Despite that this is clearly NOT the first international conference on metagenomics it was not bad.

For those who do not know, metagenomics is the term used when people do DNA sequencing directly from environmental samples without isolating organisms in the first place. This term was coined by Jo Handelsman et al. in an article in 1998, where they referred to all the DNA and its coding potential in soil as the soil “metagenome.”

The meeting was hosted by UCSD/CalIT2 which are trying to move into the metagenomics field in a large part due to the large grant they have from the Moore foundation to build a metagenomics database with the Venter Institute. The database is called CAMERA and it is planning to have its first release shortly.

To be honest, even though I am involved in CAMERA, the UCSD/CAMERA folks would be better off not trying to make it seem like they are the only people organizing meetings in this area. Nevertheless, the meeting was pretty good.

There were talks by people focusing on different aspects of metagenomics, including data collection, databasing, and data analysis as well as some interesting biology. My favorites were one by Jeff Gordon, from Wash. University in St. Louis. He is doing some of the most spectacular stuff in studies of the human microbiome and he discussed a few of the studies from his group. Most importantly, he emphasized the use of germ free animals as a model system. Basically, they raise animals in completely sterile conditions and have produced mice and fish and other species that have no microbes associated with them. This allows them to do experimental manipulations to ask controlled questions about host microbe interactions. My other favorite talk was by Ford Doolittle, who even though I disagreed with some of the things he said, he always challenges the audience to rethink their assumptions. In this case, he talked about the species concept in microbes and why he thinks it does not have much us.

Overall, I got the feeling that people were being a little too worried about the difficulties in metagenomics. Yes, analyzing sequence data from environmental samples is complicated. Yes, all the bioinformatics is harder because you are dealing with a mixed sample of DNA fragments and you do not know which fragment comes from which organism in the sample. And yes, the databasing and data analysis can be very complicated because the amount of raw data and metadata can be huge. But in the end, metagenomics has the potential to be an incredibly powerful tool in studies of microorganisms in nature. And the fact that it is somewhat harder than standard genome sequencing does not mean that we are not already learning a lot from it. What we need to keep in mind is that it is simply a tool – and to try and turn it into a field (which is what it seemed like some of the players would like) is a mistake.

If you are interested in the meeting itself, the talks and discussion sessions are available here.