Jonathan Eisen

Venter Global Ocean Voyage Press Conference

For those interested in metagenomics, microbial diversity and ocean microbiology, there will be a press conference tomorrow run by the Venter Institute relating to a series of papers (I am an author on some) coming out in PLoS Biology. The papers relate to Venter’s Global Ocean Voyage – sailing around the world collecting microbial samples. These were then used for environmental shotgun sequencing and the papers discuss various aspects of analzying the data.

Say what you want about metagenomics, and Craig and genomics, if you are a critic. But (1) read the papers, (2) give Venter some credit for publishing in an Open Access journals unlike many of the so called “public” genome effort folks who generally only pretend to support public/open access to anything.

Here is a link to view the live web cast of the PloS Biology GOS Expedition publication press conference. The press conference will be held tomorrow March 13 from 10-11 a.m. EST. After tomorrow an archive of the web cast will be hosted on the JCVI web site.

The papers are now live on the PLoS Biology Web Site.

The Global Ocean Sampling Collection can be found here.

My essay on Environmental Shotgun Sequencing can be found here.

Controversy over BP deal at Berkeley

Apparently, there is a building controversy within Berkeley over the recently announced $500 million dollar deal with BP on a biofuel program. A series of articles (e.g., here) in the SF Chronicle have been reporting on the deal and the more recent ones are starting to document some potential issues with the deal. Also see the Berkeley Daily Planet commentary.

From the Chron:

UC Berkeley‘s $500 million energy research deal with oil giant BP took a pounding at a faculty forum Thursday, with a host of speakers critical of the unprecedented partnership — some bitingly so.

I am quite interested in this because although I think it is great that Berkeley/LBL are going to now be moving big time into biofuels research, I have heard and read a variety of things regarding this deal that make one want to look at it more carefully. Some of the grumblings may be related to the standard anti-GMO opinions pervasive in Berkeley, but some of them may be more significant. For example when I gave a talk at Berkeley a few weeks ago, I asked as many people as I could why Berkeley picked U. Illinois to be their agricultural partner on the project and not Davis. And the answer was basically always the same – supposedly people at Berkeley were told by BP that Davis could not be involved because Davis had recently singed a collaborative agreement with Chevron over biofuels research.

Now folks at Berkeley are welcome to choose whomever they want to be involved in the project. But if they were told by BP that Davis could not be involved, that suggests academic freedom was tossed out the window. This thing is – I have been having a hard time getting any straight answers from people involved in the LBL/Berkeley side of things. So I had forgotten about the whole thing when someone sent me a link to the Chron story. What really caught my attention is the quote from Paul Rabinow in the article:

Anthropology Professor Paul Rabinow cited the 1998-2003 research deal between Swiss biotech firm Novartis and Cal’s Department of Plant and Microbial Biology. That deal, which provided for $5 million a year from 1998 to 2003, was intended to develop genetically engineered foods. It sparked campus protests and was criticized at the time by faculty members who felt it was implemented without collegial debate.

“The way the university handled it was completely, recklessly stupid,” Rabinow said.

The same mistakes are being repeated with the BP deal, he said.

“It should have been transparent, there should have been consultation,” he said. “This is silly. You should have given us more time to debate this.”

I met Paul at a workshop at Berkeley on the field of Synthetic Biology and he struck me as one of the most sensible people in the crowd even though he was not directly involved in Synthetic Biology research. He gave a talk at the meeting that was really spectacular (I think you see the talk here). Since newspaper articles do not always get the whole story correct, I am not certain how accurately they represent Paul’s real concerns regarding the BP deal.

But from the article it sounds like the Berkeley and LBL administration may not have consulted the faculty broadly on the nature of the deal. That would be a bad thing since such secrecy is, as Rabinow implied, not the right way to get community support. In addition, it sounds like some of the people involved in the project have let the large amount of money go to their heads (one faculty member was reported to have said that Berkeley “researchers can’t afford to fail on a project of such magnitude” as though it was the amount of money that determined whether one should do a good job on something, which is silly).

So I guess the question that is unresolved is – did Berkeley and LBL compromise their principles for a pot of gold? I do not know but I hope they get moving in front of this really rally fast and (1) make sure the deal is on the up and up and (2) become more open about the whole thing. This is particularly important because I think LBL and Berkeley could become world leaders in biofuels research. But they could also cause biofuels research to end up being treated like all genetic engineering work if they are not careful. And that would be a bad thing since if done right, biofuels have enormous potential. Here’s hoping Berkeley/LBL/BP change tactics, and get rid of the whole secrecy thing and move every detail of the project into the open.

A webcast of the meeting is here.

Gagging of scientists

From an article in the SF Chronicle

The federal agency responsible for protecting Arctic polar bears has
barred two Alaska scientists from speaking about polar bears, climate
change or sea ice at international meetings in the next few weeks, a move
that environmentalists say is censorship.

I try in this blog to not get involved in too many political issues – except of course those related to Open Access publishing. I do this because I think Open Access needs support from all sides of the political spectrum and because there are many things about Open Access that are consistent with political views throughout the spectrum. However, the treatment of scientists by the Federal Government just keeps getting worse and worse. Stem Cells. Evolution. Global Warming. Food science. And so on. The feds seem to think that scientific research is another form of spin. Scientists should read this chronicle article and really should start fighting back more.

So from now on I am adding intellectual freedom for scientists as another topic area of my blog.

OH, and thanks to Melinda Simmons at the Moore Foundation for suggesting this for my blog

Fun at Bodega Bay (U. C. Davis’ Marine Lab and site of the U. C. Davis workshop in Applied Phylogenetics)

Well, gave a talk today out at Bodega Bay as part of the U. C. Davis workshop in Applied Phylogenetics. I talked about my favorite topic, phylogenomics (always good to preach, even to the converted) and enjoyed meeting the students and talking to the other faculty. But the main resons for this blog — Davis’ marine lab on a nice day is simply spectacular. If I ever teach a workshop I am going to try and hold it there.

Why I am ashamed to have a paper in Science

So I just had a paper published in Science last week. In many ways, it has all the makings of one of those papers I should be really proud of. First, it represents a collaboration with my undergraduate advisor, Colleen Cavanaugh, the person who inspired me to go to graduate school and who got me interested in microorganisms, which I have worked on ever since (I published my first scientific paper on work I did in her lab). The paper is on one of the coolest biological systems on the planet – bacterial symbionts of deep sea animals that allow these animals to function much like plants (they use chemosynthesis in much the same way plants use photosynthesis). Studies of the deep sea and of chemosynthesis are important for understanding the origin and evolution of life, for understanding global carbon cycles, for understanding the rules by which symbioses evolve and much more. And on top of all of this, the paper reports the sequencing and analysis of the complete genome of one of these symbionts (that from the clam Calyptogena magnifica) – and one of my main areas of research is on the evolution of the genomes of symbionts. And, the genome was sequenced at the Joint Genome Institute, where I now have an Adjunct Position and am working with extensively. All sounds good right? And, I should be happy to get a paper in Science too, right?

Actually, in reality, I am not pleased with how this paper has turned out. This is really due to two things. First, my collaborators failed to keep me in the loop that the paper was accepted in Science. Thus I did not find out about the paper until I did a google search for some other reason and noticed this Deep-Sea News Blog which had a story, well, about the paper in Science. It would of course have been nice to know the paper was accepted and coming out. It would have been even better to have seen the page proofs, which might have given me the chance to catch some little and not so little mistakes (e.g., the paper claims that this species has the largest genome of any intracellular symbiont sequenced to date – which is unfortunately not true). Now, admittedly I was out sick for a while and maybe my collaborators just did not want to bother me with this information. More likely- people were just very busy – and this just slipped through the cracks.

But you know – it is a Science paper. I should be happy however it came into being right? Well, no. Completely and thoroughly wrong. You see, I do not support publishing things in Science. I object because Science is not an Open Access journal. I tried and tried to get Irene Newton the first author to submit this to another journal. But in the end, she did the brunt of the work, and thus she and her advisor, Colleen, got to pick the place. And in the time since Irene submitted the paper, I have become even more miltant against publishing in such non Open Access journals. Publishing in a non Open Access journal like Science make me feel icky in every way. In addition, by choosing to publish the paper there but not elsewhere, the field of deep sea symbionts may have been hurt rather than helped.

How could a Science paper hurt the field? Well, for one, Science with its page length obsession forced Irene to turn her enormous body of work on this genome into a single page paper with most of the detail cut out. I do not think a one page paper does justice to the interesting biology or to her work. A four page paper could have both educated people about the ecosystems in the deep sea, about intracellular symbionts in general, and about this symbiosis in particular. The deep sea is wildly interesting, and also at some risk from human activities. This paper could have been used to do more than just promote someone’s resume (which really is the only reason to publish a one page page in Science).

But of course, even more importantly, anyone without a subscription to Science, well, they can’t even read the paper. And AAAS gets to decide what happens to the text and figures in the future. So – count this as one of my papers I am not really proud of. I love that I helped my Undergrad. advisor and one of my favorite people in the world do this work. But by it not being in an Open Access journal, I have unfortunately contributed to a system that I think is bad for the world. And I just fell icky.

Some news stories and blogs are coming out on the paper:

Below I have embedded a video of a dissection of what I think was a deep sea Calyptogena, just for the fun of it.

This was taken during a deep sea cruise I managed to get on. For mroe detail on this cruise, see the NOAA Ocean Explorers site here.

Tour of California comes to town

Here are some pics and videos of the Amgen Tour of California as it left Davis, CA on Road 102.

Here are some videos too.

Badges – do scientists need any stinking badges?

Thanks to garry Myers at TIGR for pointing this one out.

I just got done browsing through the ScienceScouts Site. This comes from the Science Creative Quarteryly which I have never heard of before and seems to be some sort of blog. If anyone knows more about it let me know.

Anyway, the ScienceScouts site has “badges” like Boy Scout Badges, but for scientists.

Examples include:

“The “inordinately fond of invertebrate” badge.
In which the recipient professes an arguably unhealthy affinity for things of this category. (http://scq.ubc.ca/sciencescouts/index.html#30)”

and

The “I blog about science” badge.
In which the recipient maintains a blog where at least a quarter of the material is about science. Suffice to say, this does not include scientology.

(http://scq.ubc.ca/sciencescouts/index.html#6)

which of course, I am awarding to myself.

Garry suggests that I get them to add an “I support PLOS” badge, which I am going to do … People should check it out and award badges to unsuspecting individuals

Tony Hey visits U. C. Davis

Just got back from a dinner with Tony Hey, who was visiting UC. Davis to give a talk and meet with various people. Hey is currently VP for technical computing at some place called Microsoft. Hey has done some pretty interesting things in his career but what I know him from is his time as the head of the “E-science” initiative in the UK. Before I blather on about this … check out Timo Hannay’s blog about Hey’s visit to Nature which has a pseudo outline of his talk he gave there.

It is interesting to see Microsoft getting into collaborative science — I hope they stay serious about it because we need more “top down” types of efforts are big places like Microsoft. Whether Microsoft could make much money out of contributing to science I do not know, but if they put 1/1000 of the effort into this as they do into games and Office, science would almost certainly benefit. Many years ago when I was at TIGR, some Microsoft folks came to visit (when genome-stocks were going crazy) and expressed an interest in getting more involved in bioinformatics and genomics. Looks like that did not go anywhere. Maybe now is the time to try to get them doing this again?

I know Microsoft is viewed as Evil incarnate by many academics but hey (no pun intended), given the cool stuff being done by the Gates Foundation in various areas of science, maybe Microsoft will move a little more into science if only to support Gates Foundation efforts. Certainly, Tony Hey’s background suggests that they have the potential to do some interesting stuff.

Davis Wetlands – Beatiful Place, but Bizarrely Closed to Visitors most of the Winter

If you live near Davis you should check out the Davis Wetlands – a pseudopreserve over by the landfill. Its got amazing birds and some nice trails to walk around on. The only problem is, in the Winter, when it is wettest and the birding is best, the Wetlands is closed almost all the time. It is only open to the public for a few hours on Mondays. In addition, there are signs all over on most of the trails saying they are closed to vistors. What gives?

I found this to be completely lame and so I wrote to the Davis government about it

To whom it may concern

I am writing to ask some questions regarding usage policies for the Davis Wetlands. I think Davis Wetlands is one of the gems of this city. I have taken my now 20 month old daughter there many times to walk around and see the birds and animals and get a nice park-like experience. I am writing because I am concerned about the severe usage restrictions at the Davis Wetlands.

First, in the Winter months, the park is only open on Mondays which means those of us who work regular hours cannot use the park. I am wondering if there is some reason why the park is not open all days of the week in Winter and also how Monday was chosen as the day to be open. I would like to recommend that in Winter the park be open on at least one weekend day.

Second, I am wondering why such a large fraction of the park has signs that say “Park Employee’s Only” or something like that. These are all over the park on many of the levees and they mean that very little of the park can be seen by non employees. I am wondering why so much is off limits and whether there are any plans to expand public access. If not, I would recommend you do so.

The response I got was quick, although not what I expected …

Dear Mr. Eisen,
Thank you for contacting the Davis Public Works Department.
Your message has been forwarded to Mr. John McNerney, Wildlife
Resource Specialist, in-charge of the Davis Wetlands. If you wish to
contact Mr. McNerney, his direct line is (530) 757-5680.

If you have any questions, please call (530) 757-5686 or e-mail us
at: pwweb@cityofdavis.org

Thanks!
Maria Briilantes
Office Assistant

And then McNerny replied the next day

Dear Mr. Eisen,

Thanks you for inquiring about the access times for the Davis
Wastewater Treatment Wetlands. As you are aware, the current access
periods are:
Feb 15 – August 31 (summer)– 7 days per week 7am to 1pm.
Sept 1 – Feb 14 (winter) — Mondays only from 7am to 1pm.

In addition to the normal access times, a docent led tour is offered
the first Saturday of the month from 9 to 11am (during summer hours) and
from 3 to 5pm (winter).

The current access times were negotiated during the drafting of the
original purchase agreement with the neighboring landowners (Conaway
Ranch Conservancy). These periods and times were set to reduce Wetlands
visitor conflicts with adjacent land use activities (primarily hunting)
on the Conaway Ranch. The Sept 1 – Feb 15 period coincides with the
hunting season. There are obvious hazards associated with public access
at the Wetlands while firearms are being used in the adjacent fields.
Conaway Ranch agreed that no hunting would take place on Mondays or the
first Saturday of the month from 3-5pm.

We are currently planning on re-visiting our access agreement with
Conaway Ranch. We will be discussing the Monday only restriction and
hope to add at least one additional weekly access day during the winter,
ideally on a weekend.

To address your second question, it is important to note that many of
the roads within the Wetlands are narrow and winding. The auto tour
route has been improved for heavy traffic use including use by larger
vehicles such as buses. The “authorized personal only” signs are there
to help keep visitors vehicles off of these smaller roads. With that
said, we do encourage visitors to park in the designated parking areas
and walk around. Foot traffic is permitted on the “restricted” access
roads. We will be updating the signs to be clear about this issue.

A final note on the limited access to the southern portion of the
Wetlands. Being as the Wetlands serve hundreds of thousands of migrating
waterfowl and shorebirds, it is important to offer some quite and
undisturbed areas for these species to forage and rest. Promoting
increased human disturbance in these areas would be a less than ideal
management strategy.

Thanks for your interest in the Wetlands and its inhabitants. Please
feel free to contact me if you have more questions or suggestions.

Sincerely,

John

–>–>–>–>–>–><–<–<–<–<–<–
John T. McNerney
Wildlife Resource Specialist
City of Davis, Public Works
23 Russell Blvd.
Davis, CA 95616
530-757-5680 Fax- 758-0354

I guess this is understandable from the Conaway and the Davis point of view but it would seem to me given the size of Conaway Ranch that the hunters could stay away from the portions that border the Davis Wetlands without too much trouble. But maybe that is where the best hunting is — I do not know. Nevertheless, I am hoping that Davis changes its mind and tries to open up more access in the Winter. As of last week it seems no more access has been granted:

I am writing to find out if anything has been changed in terms of the winter access to the Wetlands.

I know the Winter is almost over, but I am still interested in expanding access during these months.

Jonathan

Hi Jonathan,

I have nothing new to report. We are still waiting on Conaway to commit
to a meeting time.

I’ll be sure to update you if/when things change.

Thanks for your continued interest,

John

–>–>–>–>–>–><–<–<–<–<–<–
John T. McNerney
Wildlife Resource Specialist
City of Davis, Public Works
23 Russell Blvd.
Davis, CA 95616
530-757-5680 Fax- 758-0354

Is it OK to have a young earth creationist get a PhD in Paleontology?

Very interesting article in the NY Times about a Young Earth creationist who just got his PhD in Paleontology at the University of Rhode Island. The main question of the article was – should biologists consider this a bad thing? That is, if someone plans to do the work of a PhD thesis and will do it well, should their motivation for doing the PhD be considered when (1) accepting them into the program and (2) giving them the PhD?

The person, Marcus Ross is now teaching at Liberty University and some are concerned is using his credentials as a PhD Paleontologist to promote Intelligent Design as a scientific theory.

I am pretty torn about this one. On the one hand, when there ar elimited resources for training and funding PhD students, why waste money on someone who will end up probably not contributing to the field in a useful manner? On the other hand, if he is able to separate his personal religious beliefs from his scientific work, all the power to him.

I guess I have no real objection per se to him being a Young Earth Creationsist and getitng the PhD – after all many many many scientists have conflicting beliefs about science and religion. But I would object to training him if I knew that he simply planned to use his credentials to make anti scientific statements. Similarly, if someone was in the Med School at Davis and I knew they were planning on using their MD to write prescriptions for themselves and their friends, I would not support their place in the Med School. In the end, intent is a part of education and training and simply doing the work required is not enough to have me spend time helping train someone.
You can read comments on the article at the Times Website here

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