Wednesday, February 21, 2007

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.

Tuesday, February 20, 2007

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.

Saturday, February 17, 2007

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. ("


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.


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

Friday, February 16, 2007

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.

Wednesday, February 14, 2007

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

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.



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.


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

Monday, February 12, 2007

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

Saturday, February 10, 2007

Guardian on Open Access

An interesting and somewhat strange article in the Guardian. In it, Ben Goldacre, who writes the Badscience column discusses Open Access to scinetific papers. He says, correctly in my mind
There are some things which are so self-evidently right and good that it’s hard to imagine how anyone could disagree with you. The “open access” academic journal movement is one of those things. It’s a no-brainer. Academic literature should be freely available: developing countries need access; part time tinkering thinkers like you deserve full access; journalists and the public can benefit; and most importantly of all, you’ve already paid for much of this stuff with your taxes, they are important new ideas from humanity, and morally, you are entitled to them.

I completely agree with this sentiment and it sums up many of the reasons I support Open Access. He also points out that

These closed journals are hardly the kind of people whose pockets you would want to line. Reed-Elsevier ..... are the same company that runs the DSEI international arms fair in London, at which vile weapons are sold to murderous regimes for cash profit extracted from very real suffering and pain, in countries you will never visit on holiday.

Finally he discussed the Eric Denzenhall hiring issue:
These people do not deserve our charity, and I will be very pleased to see you outside DSEI later this year, 300th copper from the left: because when you are so wrong you need police, security, wire fences, and the pitbull of PR to defend you, then you know you're in trouble.
I like the tone here but one thing I did not get in his article is the claim that Open Access journals cannot
get journalists to directly link to their studies. I suspect newspapers like to fantasise that they are mediators between specialist tricky knowledge and the wider public, but I wouldn't be so flattering.
I have not seen this --- I have had multiple stories written about my Open Access work and many have directly linked to my papers .... anyone have any idea what he is talking about here?

Thursday, February 08, 2007

Trip to Sacramento Zoo got interesting with man's head getting stuck in photo booth

Well, went to the SacZoo with my daughter on Tuesday. Not the best zoo in the world, but it is a perfect size for her right now. She loves the Koi Pond in particular (but also the big cats and the flamingoes). The strangest part of this last visit was the guy who got his head stuck in the wooden animal cutout that you can have your picture taken in (you know, you stick your head through and take a picture from the other side).

Flock of Dodos - Evolution vs. Intelligent Design

Well, Randy Olson has done it again. Flock of Dodos is his new film. It is about the Intelligent Design vs. Evolution Debate and from what I can gather it skewers both sides of this issue quite a bit.

Randy was the head of Prairie Starfish Productions, which made some of the dorkier and funnier science moves I have ever seen including one about Loster Fisherman in New England. I first met Randy while on a Deep Sea cruise in the Gulf of Mexico where he was filming my then advisor Colleen Cavanaugh for a film about women scientists. He and I played some mischief on her associated with her first deep sea Alvin dive where we made a video of her stuffed panda being tortured.

But that is beside the point, Randy is really good about seeing through some of the facade of seriousness in science to get to the absurdities and dorkiness of some aspects of science.

So I suggest people try and check out his new film which is being screened around the country on Darwin's birthday next week.

Wednesday, February 07, 2007

Harold Varmus goes truly Open

Harold Varmus, one of the CoFounders of the Public Library of Science, has been featured on a NIH Profiles site. Through this site they are making a collection of his papers freely available. In addition, to co-founding PLOS, Varmus won one of those Nobel Prize thingies and was head of a little place called NIH.

Not that much is featured on the front pages. But if you go to the search page here you can search for all sorts of interesting stuff.

Some interesting ones I found:
I will post more when I have a chance but if anyone else sees interesting ones out there please post them too.

Tuesday, February 06, 2007

Evolution in action - Dog Breed Hybrids in NY Times

Excellent article in the NY Times Magazine this weekend on hybrids of purebred dogs.

It is basically a lesson in microevolution, inbreeding, and modern genetics. Some great lines are found throughout including

Havens moved on, like some strange Noah touring his ark — in which every tidy two-by-two had been split apart, jumbled and recombined into a single animal: “That’s a Chihuahua-bichon . . . here’s a half-American Eskimo and half-Lhasa apso” — his voice lifting each time as if to ask, What will they think of next? But he had dreamed up a lot of these things himself.

Dogs with separation anxiety are now commonly treated with psycho-pharmaceuticals. Maybe re-engineering the dog itself, hybridizing newer models, represents “the last piece of the puzzle,” Bob Vetere says. “Will they reach a level of convenience where you have a postage-stamp-size dog that makes you dinner when you come home and reads the paper to you before you go to bed? I’m not sure that’s going to happen. But certainly someone’s going to try it.” After all, the dog, which we’ve molded into one of the most physically diverse mammalian species on earth, has so far been uncommonly obliging to our needs. Why shouldn’t we be capable of driving the entire species toward its inevitable end, down a millennia-long trajectory from wolf to stuffed animal?

The blade runner future is nearly with us ... what is to stop more and more twisted projects from happening? Nothing really. I mean, dog breeds are already freakish. With a little extra push, they will just get more bizarre. The really bad part of this is that the breed dogs and then kill the puppies that don't cut it for whatever their goals were. That has been happening for ages but it still saddens me.

Despite some depressing aspects of the article, it is a good read.

3rd International Metagenomics Meeting

Just got this by email ---

Dear colleagues,

We are pleased to announce that the Annual International Metagenomics Conference (Metagenomics 2007 ) will be held July 11-13, 2007, at Atkinson Hall (Calit2) at the University of California, San Diego, California (U.S.) The meeting will kick off with a networking reception and keynote presentation the evening of the 11th (Wed), followed by a full-day meeting on the 12th (Thurs) and a half-day meeting in the morning and a half-day tutorial/demonstration in the afternoon on the 13th (Fri). This is the second meeting in San Diego and the third international metagenomics conference since Metagenomics 2003, which was organized by Dr. Christa Schleper in Germany. We will update information on the meeting via this mailing list. For more information, please visit the conference website at .

Best wishes,

Kayo Arima, PhD.
University of California, San Diego
California Institute for Telecommunication and Information Technology
9500 Gilman Dr. La Jolla, CA 92093-0440
Office: 858-822-4649
Fax: 858-822-5033

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