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
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.
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:
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
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 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
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
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 journalmovement 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?
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.
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.
AND
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.
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 .
Best wishes, Kayo
-- 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
The US Department of Energy and the British Library announced an agreement to develop a new international science portal aimed at sharing scientific information. It sounds like a great thing. Now if only DOE would require Open Access publishing of scientific research that they fund ... that would really show DOE's committment to Open Science. I recommend sending Dr Raymond Orbach, who is leading this initiative, an email message, the address for which you can find at this link at the top of the page.
Just heard another talk by Drew Endy about Synthetic Biology and his attempts to make the field work more like Engineering than Biology. Basically, what he is trying to do is to make biological parts (e.g., Biobricks) at the DNA level that would work like circuitry board parts do for making computer chips and related devices. As they get more biological parts, more people will be able to treat synthetic biology in an abstract way - that is they will not need to know per se how the biological parts work, just that they have particular properties.
My favorite part of the field of Synthetic Biology is IGEM, the The international Genetically Engineered Machine competition. Students compete to make cools things from their biological parts. Among the more interesting items that have been made is a bacterallawnthat work as a camera.
In general, I like synthetic biology and the potential it has to produce major benefits for the world, although I wish some of the practitioners were less flippant about the potential risks in the field. And, this minor blog would not be complete without the self interest. THe UC Davis Genome Center has just announced a new faculty position in this area (specifically in cmputational and experimental approaches to network and synthetic biology). So if you are in this field and want to join a great collection of faculty working in diverse areas of genomics, please apply.
Well, this kind of made my day. Nature is reporting that a group of non open access publishers have hired Eric Dezenhall to help them with public relations. Eric Dezenhall is a crisis management consultant (as well as a fiction author) who many may demonize but he certainly seems to be good at what he does. The article at Nature is worth checking out and points to the desperation of these publishers when they see the writing on the wall regarding Open Access. For example, Nature reports a person at AAP the Association of American Publishers says:
"We're like any firm under siege," says Barbara Meredith, a vice-president at the organization. "It's common to hire a PR firm when you're under siege."
Keep up the siege everyone. Their ship is sinking and they are grabbing at the last little pieces of wood they can find.
Just saw an interesting article in the Christian Science Monitor on the "end of the scholarly journal" which talks quite a bit about PLoS One. Definitely worth checking out -- many quotes from Chris Surridge of PLoS One and some discussion of Blogs and related sites.
Very interesting article in Wired magazine about an antibiotic resistant bacteria that is plaguing US soldiers in military hospitals in Iraq. It's got some stuff I would disagree with in there about gene transfer and evolution but overall this is a really good and interesting article about bacterial evolution and antibiotic resistance.
There is a funny/interesting letter to the editor in one of the local papers out here. It is basically about how an article on Neanderthals is interesting but how more should be written about current topics in evolution, which sounds great. Then the author proceeds to quote Fisher and Morgan regarding human evolution, not the most modern of research to quote. Anyway, the calculation they made I found to be quite interesting ...
Well, sorry for the limited number of postings here recently. I am working on increasing my own fitness --- we have a baby due next week and my blog has fallen a little behind. I will get back into blogging more in about 3 weeks. If I see anything interesting before then I will post but there may still be a short lull. Now back to getting 1,000,000 things done in one week.
Just saw an entertaining press release about the publication of the genome of the parasite Trichomonas vaginalis. I find this entertaining because it does a remarkable job of capturing the personality of Jane Carlton, the PI on the project, who I used to work with at TIGR.
I particularly like the end
Viewed under the microscope Trichomonas vaginalis moves quickly; it has four undulating flagella and a tail. "It is a gassy organism," says Dr. Carlton. It has special power-generating structures called hydrogenosomes. They produce hydrogen. "So it is releasing hydrogen into the liquid media, making it frothy," she says. "That is why the vaginal discharge is frothy."
The pathogen grows easily in the lab in test tubes containing some liquid media. And it has, as she says, "a real yuck factor to it." A good way to know the microbe is growing well is to smell the contents of the test tube. "It smells foul, it has a fishy odor; really nasty," says Dr. Carlton. "My technician used to get grossed out by that."
While it is true that Jane has no fear about saying things that make some people uncomfortable, it is entertaining to the it in the NYU press release.
The press release is worth reading for another reason - the history of this genome project is different from many other parasites. In this case, the genome was enormously bigger than had been predicted (usually they are smaller than predicted, in part becuase if you over predict the genome size, you will have some extra money in your grant to cover other issues). The press release gives a good impression of how much of a pain it is to run a genome project sometimes.
Anyway - back from a little layoff and just wanted to say - good job Jane.
Thanks to Jacques Ravel for pointing this out. U. C. Berkeley has begun posting many of its science classes as Podcasts which are avilable for download at a special Apple Itunes Site. Also posted are some lectures such as one by George Smoot who just won one of those Nobel Prize thingies. It seems Stanford is doing a similar thing although it does not seem as extensive.
Note sure what other Universities are doing this (I know some classes are podcasting but not clear how many Universities are doing it as extensively as Berkeley).
If anyone else knows of other such efforts please let me know (also see this list of free academic podcasts).
Well, 2006 is over and in terms of Open Access to Biomedical type publications, I think it was a pretty good year. The papers being published in Open Access journals continue to get better and better and there are more Open Access journals too. Perhaps to biggest new thing from last year was the start of PLoS One, which is not only an Open Access journal but one that is experimenting with a new type of peer review system.
But of course, more needs to be done. So I am posting here my personal list of Open Access New Years resolutions. These are things I hope to do and hope to convince others to do too (these are in no particular order).
1. Convince more collaborators to publish papers in Open Access journals.
2. Release more of my labs data in a more usable format to Open Data archives (see Bill Hooker's Open Reading Frame blog for more details about doing this).
3. Discuss Open Access to publications and data in all my scientific presentations/talks.
4. Write more blogs about Open Access and its benefits.
5. Convince some existing journals to switch to a more Open Access stance (e.g., I wish this would happen with Journal of Molecular Evolution --- I resigned my position as an Academic Editor when they would not shift but there is still hope).
6. Submit as many of my past papers that were not in Open Access journals to self-archiving repositories (see the comments on my previous blog about this - it seems that this is possible even for Nature papers).
7. Work with Pubmed Central to make self archiving possible there for more papers. Right now it is only possible to submit your own work to Pubmed Central if it was NIH or Wellcome Trust funded.
8. Discuss Open Access with more scientists. Some still have notheard about it and some do not realize what the issues are.
9. Discuss Open Access with more non scientists. To get Congress to pass more rules regarding Open Access, it will help to have more pressure from non scientists. When I have described the current publishing system to non scientists, they are usually astonished by the (1) wasted money and (2) closed nature of much scientific work.
10. Work to get researchers who publish in Open Access journals "extra credit" in promotions, tenure review and grant proposal review. These people are frequently taking risks for the betterment of the scientific community and to advance scientific knowledge. They deserve credit for taking these risks.
Well just got an email from Chris Surridge of PLoS One saying their Beta Site is open to the public. I am excited by this new journal and system and plan to submit many of our papers there. People should check it out for themselves and hopefully give comments to them to make the system better. Some detail from the email is given below.
The first paper there that struck my eye is a paper on polyploidy in halophilic Archaea. This paper, by Sebastian Breuert, Thorsten Allers, Gabi Spohn, and Jörg Soppa suggests that polyploidy is more common in archaea than was previously appreciated.
---------------------------- The email says:
Before your first visit, I want to let you know about the inherent challenges of this project and the philosophy that compels PLoS to confront them.
We want to speed up scientific progress and believe that scientific debate is as important as the investigation itself. PLoS ONE is a forum where research can be both shared and commented upon - we are launching it as a beta website so that the whole scientific community can help us develop the features.
What makes the site beta? Not the content, which features peer-reviewed research from hundreds of authors across a diverse range of scientific disciplines. It's the additional tools and functionality surrounding these papers that will be continually refined and developed in response to user feedback.
It is this union of continually evolving user tools provided by the Topaz publishing platform and extensive content that will make PLoS ONE a success.
....
The first beta release of PLoS ONE features tools that allow users to annotate articles and participate in discussion threads. Our goal is to spark lively discussion online and we'd like to invite you to participate. Future updates will include user ratings for both papers and the comments made about them, personalized content alerts and much more.
We will be watching with interest to see how our new platform and software responds to high volumes of traffic and encourage you to give your feedback on your first experience via the site itself.
Here is an Open Access must read. Bill Hooker blogs about pushing the Open Access envelope in the area of Open Data. That is, making sure the raw data from a scientific study is available. Although there are many efforts for this, he discussed something I have never really considered which is trying to make sure the journals do not somehow obtain rights to the raw data (e.g., by having it placed onto their site as Supplemental Information).
He has a suggested protocol for adding an addendum to the typical copyright agreement one might make with a journal, which is, in my mind, a great first step.
I just had this site pointed out to me by Merry Youle.
This site is a collection of audio and video of lectures that were for the "Microbes, Minerals, and the Environment" symposium. The collection includes talks by David Stahl, Derek Lovely, Anna Louise Reysenbach, Faroq Azam, Jonathan Zehr, and Paul Falkowski, all relating to microbes in the enviornonment. I have not watched all of them but the ones I have seen are quite good.
The symposium was in honor of Philip Abelson, who died in 2004.
Well, the good news keeps pouring in for science education and the teaching of evolution. The Cobb County School Board, which had tried to insert religious points of view into the teaching of evolution, have backed down. They had placed stickers on biology textbooks that read
This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully and critically considered
Yet, of course they did not label any other area of science in this way. AP reports that
It is nice to see that they have had a change of heart, or at least have realized that they would lose this fight. Either way, science and education win this round. Unfortunately, the proponents of Intelligent Design, will try again and again. And they should be fought every step of the way to keep them from attacking the teaching of evolution in science classes.
All these recent stories on the Neanderthal sequencing projects reminded me of a short story I wrote while in graduate school. I wrote this story for a class taught by Carl Djerassi, a professor at Stanford and an author of a variety of what he calls "Science in Fiction" novels. In these, he writes about the workings of science and thus the name of the genre.
For this class all the students were supposed to write short stories that were then shared among the students and with Djerassi and each week we would read and discuss two of the stories. The stories written by the other students were great overall - moving and interesting and fun to read and discuss. The class digressed at the end due to Djerassi's desire for the group to write a fiction "Renga." Renga is a form of poetry where one person writes a line and then another writes the next line and together a group is supposed to come up with a poem of interest.
So we wrote a story - with each student in the class writing a paragraph and then sending it on to the next author. In the end, the story was, in my opinion, much worse than all the individual's stories. But amazingly, Djerassi convinced Nature to publish the story and thus I am a co-author on what was the first (and probably last) short story published in Nature. The worst part of it was - Nature made us reduce the lenght of the story to fit some page restrictions. That would be fine I guess if we knew this in advance. But in the end, what this did was cause us to edit the story and remove any hints of the "Renga" nature of the story. I was embarassed by the story and wanted to use a pen name so people would not know it was me. I chose Joan Eisen but for some very particular reasons I had to change my author line back to Jonathan (long story).
OK -back to the main point. I wrote a story that is about sequencing Neanderthal DNA. And though I am not sure any more what I think of the story ... here it is.
David Cohn was unaware that, while he was camping in Death Valley, every five minutes his computer would contact U. C. Berkeley's mainframe system and download any email messages David had received since the last check. David did not find out that he had left his email program open until, fumbling for his keys outside his office, he heard his computer play two randomly selected segments of Mozart's clarinet concerto, announcing that two new messages had just arrived. David had been gone for three weeks and had come in early in the morning so he could check his email in peace before other people would arrive and start asking about his trip or reading his email over his shoulder.
Symposium Theme Microscopic organisms-including viruses, bacteria, archaea, and single-celled eukaryotic organisms-comprise the vast majority of life on the planet, yet startling little is known about their true diversity and the multitudinous roles that they play in the ecosphere. The knowledge that we do have tends to come from either those organisms that can be cultured in the laboratory (estimated to be <1% of all species) or those that make us or other organisms that are important to us sick. The revolution of using DNA sequences to discover and describe microbial diversity has drastically altered our view of the microbial world and its players, however. Less than two decades ago, using ribosomal RNA gene sequences, Carl Woese and colleagues proposed an entirely new classification of life, that of three domains of organisms-Bacteria, Archaea, and Eukarya-in opposition to the traditional five-kingdom schema. Now, new biochemical processes, including new forms of photosynthesis and even electricity-generating bacteria are being discovered as culture-independent and broader explorations into new habitats are performed. Yet, at the same time that we begin to uncover new hidden potential benefits of microorganisms, the news is also replete with stories of so-called emergent diseases that threaten humans as well as other organisms on the planet.
This symposium will bring together a diverse group of microbiologists and conservation biologists to explore this intersection of two fields that, until now, has not been considered in depth. We hope to address the broad questions of: How much microbial diversity is there on the planet? How does this diversity affect other organisms, both positively and negatively? How should conservation practices take microbial life into account?
Audience: This symposium will bring together scientists from the traditionally disparate fields of microbiology and conservation, including biogeochemists, marine microbiologists, disease ecologists, and microbial systematists. as well as conservation practitioners, wildlife managers, policy makers, educators, students, and interested members of the general public.
SPECIAL STUDENT PRICING WILL BE OFFERED!
CALL FOR POSTERS: The symposium will include a poster session. Details for content guidelines and abstract-submission requirements are available at http://cbc.amnh.org/symposia/microbes/.
TO RECEIVE SYMPOSIUM UPDATES AS THEY BECOME AVAILABLE, email biodiversity@amnh.org.
There can be no greater nightmare for a medical worker than to be accused of harming their patients. Even worse, if the allegations are untrue. Yet this is exactly what has happened to six health workers who have been sentenced to death for spreading HIV among Libyan children. Today we publish urgently an essay from Council on Foreign Relations Senior Fellow and Pulitzer Prize winning author Laurie Garrett, that warns of the terrible dangers not just to these workers but to health workers worldwide, and their patients in the poorest parts of the world if the executions go ahead. The essay is part of an increasing chorus of condemnation in scientific journals including Science and Nature . AAAS has a website which gives information on how anyone can add their voice to this campaign.
I am starting a new series here ---- finding and writing about classic papers in Evolution and Genetics and Molecular Biology that are available for free in Pubmed Central. And though plenty of classic papers are not avilable, a good collection of them are.
My first selection is Luria and Delbrück's paper from 1943 on the origin of mutations. This papers is near and dear to my heart in many ways and I still remember looking it up for the first time when I was an undergraduate. I was taking a class from Jennifer Doudna on the origin of life, and we had to write a paper as part of the class. In the class we had discussed a new paper by John Cairns and colleagues that revisitid the origin of mutations question. Cairns et al. result suggested to them at least that bacteria could pick and choose the mutations they needed for increased fitness in a particular situation (suggestive of so-called Lamarckian evolution to them). I was fascinated by this work (so much so, that it became the topic of my grad. school application essays and the topic of my first two years of PhD research in Phil Hanawalt's Lab). So I chose to write a paper on the origin of mutations.
Obviously, to write such a paper I had to go to Luria and Delbrück's work since they were the first to experimentally test the question of how much mutations pre-existed selection and how much they arose after selection. I stillremember sifting through the old journals in the library at Harvard to find this and turning the pages in teh dust covered volume to read it.
Luria and Delbrück chose as their experimental system resistance to bacteriaphage and their model organism, Escherichia coli. In their paper first the describe the theoretical underpinning of their wor. In their theory they come up with a way to do an experiment to test whether mutations pre-exist selection or arise in response to it - something now generally known as a fluctuation test. Basically the idea is simple. Take a particular form of the bacteria. Innoculate multiple test tubes with a small amount and let each test tube grow up to a dense culture. Then expose bacteria from each tube to the selective pressure. If the mutations pre-exist selection then there should be big differences between the replicate test tubes in the number of mutants since in some the mutation would arise early in the growth of the culture and in some they would arise late (this is known as a jackpot distribution). If the mutations arise after selection then each tube should have somewhat similar numbers (with some variation around a mean).
And when they did the experiments the results followed very closely the jackpot model. They stated:
We consider the above results as proof that in our case the resistance to virus is due to a heritable change of the bacterial cell which occurs independently of the action of the virus. It remains to be seen whether or not this is the general rule. There is reason to suspect that the mechanism is more complex in cases where the resistant culture develops only several days after lysis of the sensitive bacteria.
And thus they showed that mutations unequivocally pre-exist selection. Now, it turns out that their experiment had a flaw - since they were using a lethal selection (phage) the system did not really allow for a long period of time for the mutations after selection to arise (when your dead it is hard to generate mutations). The Cairns experiment (and Ryan's before him) showed that some unusual results occurred if you used a non lethal selection. So one cannot really use Luria and Delbrück's experiment to disprove the possibility that mutations arise after selection. Nevertheless, their proof that mutations can exist before selection was a fundamental discovery. And their methods were used throughout bacterial genetics for years (to this day in fact). For more detail see Access Excellence page about Luria and Delbruck.
This is such a fundmentally important paper, and it is great that this paper is available, free to all, in Pubmed Central. See below:
Mutations of Bacteria from Virus Sensitivity to Virus Resistance.
I took my daughter to Petco the other day again. We treat it as a zoo/aquarium which works perrty well. They have lots of fish, birds, mice, and other animals and she loves it. I know, it probably does not treat the animals exceptionally well, and I do not buy animals from there. But my daughter loves fish and this is a great way for her to see some without going too far.
If you are into cycling in any way, you should check out the route for Stage 2 of the Amgen Tour of California. The race, which will likely feature a collection of some of the top pro cyclists in the world, is coming through Davis on February 20, 2007. And they even give Davis a little plug:
Continuing east past Lake Berryessa, the peloton will head through Davis, recently named the best cycling town in the U.S. by Bicycle Magazine.
It should be a good day for the town, although I hope it is not raining too heavily. I am not sure what the plans are for closing roads and/or for town activities on that day, so if anyone out there knows anything please let me know.
From the map it looks like they will take Russell through town and then sneak on up to Covell to Road 102 and then on towards Woodland. It also looks like there will be a bonus sprint in town.
The New York Times ran an obituary today for Esther Lederberg, who passed away on November 11. Dr. Lederberg was one of the giants of microbiology and her research was the precursor for multiple Nobel Prizes and laid the groundwork for much of the molecular biology revolution. Among her many amazing pieces of work:
The isolation of lambda phage, a virus that infects the bacterium E. coli. This virus has been used as a model system for studying the molecular basis of life.
She and her husband invented replica plating, a method that revolutionized bacterial genetics.
Amazingly to me, and thanks to Pubmed Central and the American Society of Microbiology, her replica plating paper is available for free online here.
All microbiologists out there should read this paper and should say thanks for the work of a true giant in the field.
Here is another somewhat hidden gem in Davis. We have a 22 month old daughter. She gets rapidly bored with new toys. My wife discovered a great way around this. Every few weeks she goes to the Davis Resource LIbrary and Toy Closet provide by the city Child Care Services. For a $10 annual fee, you can check out up to five toys and five videos/books at a time. Although sometimes it is hard to take the toys back if our daughter becomes particularly fond of them, she always ends up enkoying the trips to select new toys. From their web site:
The Toy and Resource Library is located at 600 A Street, in Davis. Library hours are Monday through Friday from 8:00 a.m. to 4:30 p.m.
So if you have kids who get a little bored with their toys and you do not want to keep buying new ones, check out the library. Most of the toys are in great shape and the books there have also been popular in our house.
OK. I know I am not supposed to do this. But hey, are there really any rules for blogs?
I got my first major local press story since moving to Davis yesterday. The Sacramento News and Review ran a cover story on the U. C. Davis Genome Center, featuring me, Katie Pollard, and the director of the center Richard Michelmore. I of course do not recall saying any of the things that I am quoted saying but I certainly recall saying things close to what was quoted so in this case the reporter (Ralph Brave) seems to have done a fair job. I guess I would quibble a tiny bit with my portrayal in terms of the discussion of synthetic biology (I believe it is a powerful tool but that the practitioners downplay the risks).
The best part of the story - they featured my work on the glassy winged sharpshooter symbionts that we published in PLoS Biology earlier this year. That is (hopefully) good for me since the sharpshooter is a big deal out here in N. California since it is a vector for Pierce's Disease in grapes. Plus, they were able to use a figure from my paper since of course, the paper in fully Open Access. So my work gets some extra exposure that might have been more difficult for the paper to pull off if it was published in a non Open Access journal. In essence, Open Access publishing is the gift that keeps on giving. As long as I keep getting credit for it, it is great for me that people do not have to get permission or pay a fee to use figures from my papers.
Scientists from NASA have reported what appears evidence that not has Mars has water in the past, but that it has flowed on the Martian surface in the last seven years. When comparing photographs of the same site in 1999 and 2005 taken by the orbiting Mars Global Surveyor, the scientists found
appearance of a lightly-shaded patch that has all the hallmarks of being caused by water bubbling up from under the Martian surface and running down the 30 degree slope
While there may be other explanations, the pictures are stunning. If this is water, I think we have to start to come to grips with the high probability that life will be found on Mars. In other words, not only might life have existed there in the past, but I think it is reasonably likely that there is life there now. Now before you get all hoity toity on me - I am not talking about little green men here. But possibly little green microbes. Or little pale microbes that use chemical energy to fix carbon and grow. Such microbes are of course all over earth, in the deep sea, in hot springs, in tidal flats, in animal guts. The real questions (again, if this is really water) the become:
could life have evolved separately on Mars?
could microbial life from Earth have seeded Mars?
I think the answers to both questions, though unclear, could potentially be yes. For question 1, if we look at the origin of life on Earth, most studies now suggest it happened over a relatively short time scale (a few hundred million years) and possibly much faster. It may in fact have been somewhat inevitable - as long as the conditions for chemical evolution were present in the Early earth. This chemical evolution could have then set up the possibility for life to have evolved. Though the exact steps are unclear for the origin of life on Earth, it is not far fetched to imagine that they could have occured on Mars as well.
As for question 2 - I think life easily could have been transported between the two planets. All you really need is for a meteorite or comet collision with Earth to blast some moderately sized pieces of material off of Earth into space. Microbes in such material could have survived for some period of time on such pieces in space (remember, many microbes do not need oxygen, and can survive incredibyl harsh conditions on Earth). Imagine if a big piece of Earth was knocked off the planet - microbes in the center of such a piece would be protected from some of the radiation and other stresses of space. And you just need one of these pieces to end up on Mars for the cross-seeding event to occur. Of sure, there are a series of assumptions here and a multiplication of low probability events. But we can make up for low probability by multiplying by 3.5 or so billion years - the amount of time that life has existed on Earth.
So this raises one final issue for me. The person with the greatest job title in the world - John Rummel, better get moving. He is the "Planetary Protection Officer" for NASA - charged with protecting other planets from Earth and Earth from other planets. One of his main jobs is to think about how to make sure the Martian missions do not bring microbes with them to Mars so that if microbes are found there we can assume they are from Mars not earth. Unfortunately in my google searches about this it seems Dr. Rummel has been promoted within NASA and I cannot figure out who took over his old job. Does that alas mean we are temporarily without a planetary protection officer? I hope not.
Whether it turns out life exists or existed on Mars or not, the finding of apparently flowing water on the surface is wildly exciting and proof to me that Mars missions are critical to our understanding of the world around us.
There is a potentially controversial and very interesting article in the journal PLoS Pathogens on Flu Evolution. The study was led by Edward Holmes at Penn State, and co-authored by many researchers including colleagues of mine at my former institution TIGR. They performed a detailed evolutionary analysis of the cmplete genomes of 413 influenza A viruses of the H3N2 type (the H#N# system refers to the subtypes of Hemaglutanin and Neuraminidase genes).
The virus genomes were sequenced at TIGR using a high throughput flu viral genome sequencing protocol originally developed at described by Elodie Ghedin and colleagues here and here. The viruses they selected were from across New York State as part of a surveillance program.
Using a variety of evolutionary analyses including phylogenetic reconstructions and examination of substitution patterns, they come to a surprising conclusion - that
stochastic processes are more important in influenza virus evolution than previously thought, generating substantial genetic diversity in the short term
This may seem somewhat uninteresting to many out there but if true it is critically important in fighting flu and in understanding viral pathogen evolution. Right now there are substantial efforts to try and predict what future dominant flu strains will look like. These predictions tend to rely on assumptions that positive selection of viruses is critical in generating and maintaining diversity. If stochastic processes are as important as Holmes et al conclude, it would mean that more intensive monitoring of flu is needed in almost real time (since predicting random events tends to be, well, very hard).
I confess I have not tried to evaluate whether or not I think their conclusions are correct, but on first glance they seem sound. This just goes to show that general genomic surveys that try to be relatively unbiased in their sampling can reveal substantial novel patterns not seen before in highly target genome sequencing projects.
