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.
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.
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.
"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)"
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.
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.
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 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.
Thank you for contacting the Davis Public Works Department.
contact Mr. McNerney, his direct line is (530) 757-5680.
Feb 15 - August 31 (summer)-- 7 days per week 7am to 1pm.
Sept 1 - Feb 14 (winter) -- Mondays only from 7am to 1pm.
from 3 to 5pm (winter).
at the Wetlands while firearms are being used in the adjacent fields.
first Saturday of the month from 3-5pm.
roads. We will be updating the signs to be clear about this issue.
feel free to contact me if you have more questions or suggestions.
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.
I'll be sure to update you if/when things change.
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.
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.
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.
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?
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).
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.
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.
Letter from Us Information Agency relating to giving a talk in China after Nobel Prize.
I will post more when I have a chance but if anyone else sees interesting ones out there please post them too.
Excellent article in the NY Times Magazine this weekend on hybrids of purebred dogs.
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.
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 www.calit2.net/metagenomics2007 .