Flu Evolution Revisited and Biology Direct's Foray into Open Peer Review

Anyone interested in scientific publishing and/or the flu should check out a new paper in the journal Biology Direct. The paper suggests a new way of thinking about flu evolution. Whether you agree with the authors or not (I am still not sure), what is most interesting about this to me is that the reviews are posted online as are the authors responses. See the paper here and some stories about it here and here.

Biology Direct is an Open Access journal that is experimenting with the peer review system. Their experiment is quite intriguing in its methods. For details see here and here.
Basically, the author is charged with selecting reviewers and then getting the reviews. Then the paper can be published along with the reviews, whether they were positive or negative. The author can make changes based on the reviews or can choose not to. Thus someone could publish complete crap, but since the reviewers will be named publically, hopefully the reviews will indicatethat it is crap. The key to this is that the author has to select people from the Editorial Board that then select the reviewers. So as long as the Editorial Board is reasonable, the review process should be OK (note - I am on the Editorial Board although I have not been asked to do anything yet).

Do I like this system? I am not 100% sure. But I admire Eugene Koonin and colleagues for trying something different and giving the world an example of a possible way to get around the flaws of the current review system. Of course, to me, the most important thing is that the journal is Open Access, which means that anyone out there can get a fascinating look at peer review for free.

For example, people should really check out the paper and the reviewers comments and the authors responses. Or even better check out some other papers in the journal. It makes for a good read.

Evolution and Politics

Scientists are acting up again. The New York Times reports that

75 science professors at Case Western Reserve University in Cleveland have signed a letter endorsing a candidate for the Ohio Board of Education.

This is great news if you ask me. Scientists seemed to be emboldened to play more of a role in politics. I think this is due to some of the recent pushes from anti-science coalitions, like the supporters of "intelligent design" as a scientific theory (which it is clearly not).

We desperately need more of this type of thing - with scientists speaking up. I do not want scientists to choose sides in truly political debates. And I hope scientists will avoid being too arrogant - such as when some suggest science can solve all the worlds woes. But when sound science is being ignored or belittled by politicians, scientists should speak up. The evolution debate is but one example. There are many more issues where sound science is being misused or ignored (e.g., global warming).

So - I recommend all scientists consider doing something to get involved. Lend your support to the folks in Ohio (e.g., Lawrence Krauss organized the group to write the letter). Or join an organization like SEFORA a new science based political action group. But just don't sit on the side and say "scientists should not get involved." If all scientists keep doing that, we are in deep trouble.

The latest genomics buzz

The latest buzz in genomics is about the honeybee genome. The people working on this genome have really done a good job of organizing themselves (a sort of model social genomics network in a way). They have a veritable slew of papers coming out this week on various things about the genome and about honeybees that were learned by making use of the genome.

There is an entire issue of Genome Research dedicated to studies of the honeybee (see the press release here) including papers on rates of evolution, circadian rhythms, chemical sensing, sex and death (of course), and even the royal jelly. If you don't know what royal jelly is, do a google search for that. There is also an overview article in Nature and a genome report in Science. In total 170 researchers were involved in these papers.

Mind you, I am disappointed that these were not published in Open Access journals. And this is particularly sad given that the funding came from the NHGRI, the same group of sanctimonious individuals who kept talking about how the "public" human genome project was "open" in every way for the betterment of humanity. Unfortunately, what they mean by "open" even for the human genome project is a bit of a misnomer. They meant that people could look at the data immediately. But they restricted how people could use the data, despite their attempts to pretend otherwise. Consistent with this, the groups funded by the NHGRI generally do not publish their papers in Open Access journals. Shame shame shame.

OK, enough sniping. The honeybee is so fascinating biologically in so many ways that this genome sequence deserves a bit of extra attention. First, honeybees are social creatures. They have in fact been one of the key models in studying both the evolution of social behavior but also communication among organisms.

Another aspect of their biology that is very interesting is their genetic structure. Like other hymenoptera they have what is know as a haplodiploid life cycle with males being haploid (the result of unertilized eggs) and the females being diploid. This unusual genetics is another reason that honeybees and other hymenoptera have been studied extensively by biologists for many years. In fact, a great little bit of history about this is in a book on the history of studies of altruism from Princeton University press. One of Darwin's biggest concerns in the origin of life related to the self sacrifical behavior, especially that in honeybee colonies. Apparently, honeybees were a topic of conversation among non scientists and the non reproductive worker castes were well known to the public. Darwin struggled quite a bit to come up with a good explanation that was consistent with natural selection for why some individuals would sacrifice their lives for others.

Dawrin actually cam up with a good logical explanation for this - that some individuals would sacrifice if they were related to others who would benefit. Bees and their relatives played a large part in studies that have revealed in much greater detail how altruism can evolve. They may not be as warm and fizzy as some other organisms being sequenced, but they certainly were a good pick for a genome sequencing project.

Science Lobbying - The role of science in politics and vice versa - Scientists and Engineers for America

I listened to a very interesting Science Friday Podcast today (I listen to them on my bike rides to/from work here in Davis, CA, the most bike friendly town in which I have ever lived). This particular podcast had as one of the guests Susan F. Wood. Some people may remember that she resigned from a top job at the FDA over what she felt was politics getting in the way of good science.

Well, rather than disappear as some higher ups in the executive branch do after quitting, she has jumped into a whole new realm. She has helped start a group called Scientists and Engineers for America. Their aim is to help elect to office people

who respect evidence and understand the importance of using scientific and engineering advice in making public policy

from the NY Times article about this.

They have even created a "bill of rights" for scientists. Among the rights they include:

Federal policy shall be made using the best available science and analysis both from within the government and from the rest of society.

The federal government shall never intentionally publish false or misleading scientific information nor post such material on federal websites.

Scientists conducting research or analysis with federal funding shall be free to discuss and publish the results of unclassified research after a reasonable period of review without fear of intimidation or adverse personnel action.

Federal employees reporting what they believe to be manipulation of federal research and analysis for political or ideological reasons should be free to bring this information to the attention of the public and shall be protected from intimidation, retribution or adverse personnel action by effective enforcement of Whistle Blower laws.

No scientists should fear reprisals or intimidation because of the results of their research.

Appointments to federal scientific advisory committees shall be based on the candidate’s scientific qualifications, not political affiliation or ideology.

The federal government shall not support any science education program that includes instruction in concepts that are derived from ideology and not science.

While scientists may elect to withhold methods or studies that might be misused there shall be no federal prohibition on publication of basic research results. Decisions made about blocking the release of information about specific applied research and technologies for reasons of national security shall be the result of a transparent process. Classification decisions shall be made by trained professionals using a clear set of published criteria and there shall be a clear process for challenging decisions and a process for remedying mistakes and abuses of the classification system.

I confess to being a little worried that they may become too partisan and to be effective I think they should try to be as non partisan as possible (although there is no doubt that the current administration has violated more of the items in their bill of rights than probably any previous administration). Neverthless, this sounds like a great idea and hopefully they can help increase the use of science in decision making.

To sign up go to http://www.sefora.org/

Genomics Education Bus

I just got back from the new version of the old GSAC meeting. It is now called GME or Genomes, Medicine and the Environment (or, as we like to call it - stuff Craig Venter is interested in these days). The meeting is organized by the Venter Institute and this year was one of the better versions of this meeting. There were some really interesting talks in a few topic areas (I will try and post some details about these later). But to me, the most interesting part was seeing the Venter genomics education bus (part of their Genomics Discovery program) on tour. They use this bus to go around to high schools and other places to do some genomics education.

Just before coming to the meeting, the bus apparently rolled into New Orleans (see Wired news story here). Lots of people like to complain about Venter and his style, but whatever you may think of him, I think this bus is a great idea. We desperately need more people who do science making an effort to interact with and educate people about scientific research. And since this bus is outfitten with lab equipment and various genome-related toys, it can go into a neighborhood without the best science labs and help introduce students to the fun and excitement of modern science.

Note - the photo was taken by me at the GME meeting in Hilton Head, SC. In the photo are Lisa McDonald, Jennifer Colvin, and (I think) Darryl Bronson.

Harvard Crimson changes its mind - supports PLoS One

Well, the folks at the Harvard Crimson have apparently changed their mind. In a new Editorial, two writers from the Crimson discuss PLoS One and open peer review. Unlike the previous Crimson editorial (see my blogs about it here and here), the two writers of this one now come out clearly in support of the PLoS One idea as well as some PLoS ideals.

For example, the liken the battle between Open Access and Closed Access publishing to the battle over democracy

Democracy has reached a new frontier, and we’re not talking about the Berlin Wall. It’s a new decade and a new millennium, and yet another wall is crumbling—this time, not between countries, but in the domain of scientific research.

Perhaps most importantly, they end the editorial with

Initiatives such as PLoS ONE will help promote free and unfettered scientific study, supplementing and revolutionizing an oligarchic academic process. It is both ignorant and regressive to reject this democratization.

Although they did not address the previous highly ignorant editorial in their own newspaper, Yifei Chen and Patrick Jean Baptiste deserve kudos for a well written, well thought out editorial on a key topic for the whole endeavor of science.

World's Smallest Genome of a Cellular Organism?

A one page paper in Science reports on what I think is one of the most exciting findings in microbial genomics in years. The reports describes the sequencing and analysis of the genome of a bacterial endosymbiont of an aphid. This bacteria, known as Carsonella, has a TINY genome - only 160 kbp in length. This is ~ 3 fold smaller than the previously known smallest genome - that of Nanoarchaeum equitans which has a genome of 490 kbp.

I think almost certainly this symbiont should be considered an organelle. It is missing many cellular functions found even in the most reduced symbionts. Thus in essence it may not be the smallest genome of a cellular organism. But who cares how we define it. If it is a new organelle - that is amazing. If it is a tiny cellular genome - that is amazing too.

One thing that strikes me as strange is the fact that the paper is only one page long. It contains so little detail on what was done and what was found in the genome that the story is woefully incomplete. This I would guess is somehow related to a rush to publish but also likely due to it being published in Science, which has severe page restrictions.

This paper has been getting ENORMOUS press coverage for valid reasons. But I agree with Craig Venter (see the New Scientist article) that this genome is not of much relevance to efforts to create a "minimal" genome. This is because the ideal minimal genome is one that can support independent life. Carsonella, is far from independent and thus represents a really wild evolutionary story, but nothing of much relevance to minimal genome studies.

Some related links:

• Commentary by Siv Andersson
• NPR Story
• Nancy Moran's Home Page (one of the corresponding authors of the paper)
• World Science article

Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H., Moran, N., & Hattori, M. (2006). The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella Science, 314 (5797), 267-267 DOI: 10.1126/science.1134196

Harvard Crimson Editorial Update

OK - so I am biased here but those interested in Open Access should check out my brother's letter to the Harvard Crimson that was published today. He wrote it in response to the lame editorial the Crimson wrote about PLoS One. Some of my favorite quotes from his letter

They did not, however, respond to your repellent effort to rally the forces of elitism to derail a project whose primary aim is to rapidly bring scientific knowledge to everyone.

....

Once they see PLoS One, we are confident that consumers of scientific papers will discover what employers have long ago: If you’re looking for the imprimatur of greatness, try Nature or Harvard—but if you want the real thing, try PLoS One or Berkeley.

Of course, I disagree with the use of Berkeley in this context. Yes it is a public school. But come one - to use Berkeley as the "anti"elitist school of the world is a big stretch. So if you want the real thing, try U. C. Davis, not Berkeley.

Open Access Biology highlights - The Intriguing Life of Endosymbionts

Two new articles published in the last issue of PLoS Biology bring forth some wildly interesting details about the lives of endosymbiotic bacteria.

One of the articles is about the role Wolbachia may play in speciation in Drosophila species. Wolbachia are a type of bacteira that are found to infect a wide diversity of invertebrate species. These bacteria are transmitted directly from mother to offspring much like mitochondria. Interestingly, many have evolved specialized means of negatively impacting male offspring. In the PLoS Biology study, the researchers were working on a type of Wolbachia known to cause cytoplasmic incompatability in which infected male offspring cannot produce offspring with uninfected females. Since these males can produce offspring with infected females, this helps contribute to the spread of the Wolbachia in the population. To make a long story short, the current paper proposes that not only can Wolbachia apparently lead to speciation through behavioral affects on the host, but that these affects can be stimulated even in species not infected by Wolbachia, if another similar species in the same area is infected. To learn more about the study read the synopsis here. I am personally interested in this story because we published the first Wolbachia genome a few years ago in PLoS Biology.

The second story to me is even more interesting. This relates to a bacterial symbiont that is found in the gut of a stinkbug species. The paper is important because the symbiont in this case does not live inside the cells of its host as do many other gut symbionts of insects. Instead, the symbiont lives in an extracellular capsule. Interestingly, the symbiont is transmitted to offspring not directly in eggs as in many other symbionts, but indirectly. The mother deposits a mass of the bacteria near the eggs and these are then consumed by the young just after hatching (the video of this is amazing).

The paper shows that these symbionts possess many of the genomic features found in other transmissable symbionts - including small genomes, high AT contents, and high rates of evolution (you can read more about this in my recent paper on symbionts of the glassy winged sharpshooter here or in my earlier blog). Many previously thought that these genomic features were related to the intracellular lifestyle of symbionts. But given that the same features are found in these extracellular symbionts, this suggests that the shared genome features are probably related to experiencing population bottlenecks in transmission from mother to offspring. See the synopsis of the paper here.

Harvard Crimson PLoS One "Commentary"

Well, the newspaper of Harvard has posted an editorial about what they call "Science in Print." The editorial is disappointingly a confusing mashup of ideas, facts, and flasehoods regarding PLoS One. The Crimson folks criticize online science journals under the idea that none of them are peer reviewed. They take issue in particular with PLoS One because they think it is to have no peer review at all. Fortunately, Chris Surridge, Pedro Betrao, and others have already posted messages to the comments section online about this correcting many of the mistakes in the editorial.

What is most disappointing to me about my undergraduate institution's newspaper's actions is that they seem to have written this editorial without even taking the time to read anything about the system they were criticizing. In doing some google searches I cannot even figure out where they got some of the misinformation they cite regarding PLoS One.

I completely understand people being uncomfortable with some aspects of the PLoS One system. Any change is scary to scientists and to supporters of science. But the experiment PLoS One is carrying out is not about replacing peer review entirely. It is about modifying the peer review system slightly (basically - papers will be reviewed for techincal quality only and not things like novelty) and also about adding a better evaluation system for scientific publications. I confess, I am not sure it is the perfect idea. But the world is a very very different place than it was when the current scientific publishing paradigm was established. We need to try some new ways of publishing if science is to take advantage of the internet driven, blogging, podcasting, mashup, [insert favorite technojargon here], world.

Metagenomics 2006

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

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

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

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

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

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

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

Genomics Education highlighted at 14th Annual International Meeting on Microbial Genomics

Just got back from the 14th Annual International Meeting on Microbial Genomics, where I gave talk on microbial symbiont genomics. This was one of the best meetings I have been to in a while. It had the right combination of everything including:

1. Many excellent talks and posters (OK, in the interest of not upsetting people for not saying their talk or poster was great, I will not make a big list of all the ones I thought were good, but I will give a few highlights below).
2. Excellent location (UCLAs Lake Arrowhead Conference Center, which is in the mountains east of Los Angeles). This is a place that is very conducive to getting to know colleagues and it almost forces interaction among people. There is one central building where there is a dining hall, a nice deck if you want to eat outside, the conference room, rooms for posters, and a large living room for hanging out. The rooms for sleeping are mostly great (e.g., mine was a split level condo like structure with a living room and a bedroom/bath on floor one and a bedroom/bath on floor 2). And being in the mountains is very pleasant. Plus there is a pool, jacuzzi, and sports facilities that are very nice. The only annoying thing is that the Lake itself, which is 100 yards away, but it really almost private, with most of the shoreline occupied by houses and private docks.
3. Good food. The food is not spectacular or anything but better than the food at 90% of the conferences I have been at.

In terms of talks, there were quite of few that were both interesting topics and very well presented. For example, Jessica Green from U. C. Merced gave a great talk about spatial distributions of microorganisms, Julian Parkhill from the Sanger Center put together a really nice story about mechanisms by which microbial pathogens generate phenotypic diversity, and Julie Huber from MBL impressed many with her talk about the "Deep Rare Biosphere."

But to me, the best two talks were ones on science education reform by two people from UCLA. Erin Sanders-Lorenz presented a summary of her course she has been teaching at UCLA that has students doing "phylogenomic" analysis which takes them from isolating and culturing organisms from environmental samples to building evolutionary trees of genes isolated from these cultured species.. This seemed like a very creative, hand on, novel way to teach students the excitement of science and some things about evolution. It sounded so well thought out that I asked for (and got) a copy of her lab manual.

Much as I liked this class, the one described by Cheryl Kerfeld knocked my socks off. She described a program they have developed at UCLA called the Undergraduate Genomics Research Initiative. This is an interdepartmental multi-course collaboration with the central theme involving the sequencing and analysis of the genome of a bacterium called Ammonifex degensii. The various courses are organized around a central course on genome sequencing. The linked courses include ones in many different departments at UCLA as well as various courses at other universities. They have clearly given enormous thought to how to do a truly project based course which likely will catch students attention and interest much more than standard lectures or standard labs.

There have been other successful hands on genome sequencing courses before - perhaps the first being one by Brad Goodner at Hiram College who had students participate in the sequencing and analysis of the genome of Agrobacterium tumefaciens (e.g., see a press release here). The Kerfeld UCLA UGRI program sounds like it has gone to the next level by integrating many courses across departments and by having creative ways to encourage participation of students in multiple aspects of the project. It really is worth giving a look at the UCLA UGRI program's web site.

Other tidbits about the meeting:

• Jeffrey H. Miller from UCLA organized it
• This is the same Jeffrey Miller who identified most of the mutator genes in E. coli with a really creative genetic screen
• There was another Jeffrey Miller from UCLA at the meeting (will leave this up to google for people to figure out who this other Miller is).

Top10 Novel ways to contribute to the Open Access movement

I am pleased to hear from more and more colleagues about how they support the Open Access movement in scientific publishing. Open Access journals are getting stronger and stronger and the tide is clearly turning towards Open Access. However, there are still many things that need to be achieved in order for Open Access to really become the rule. For example, of the colleagues who seem somewhat supportive of Open Access, but who still publish in non Open Access journals, the most common excuse is "I really need this for my resume" or something like that. What they mean is, the non Open Access journal they are trying to publish in is better known to their colleagues (and tenure review committees and job search committees) than a similar Open Access journal. In other words, they support Open Access in their heart, but are worried about the consequences for their careers.

I appreciate the concern of people worried about their jobs or promotions. Therefore, I think it is necessary for supporters of Open Access to turn up the heat even more and try and set up an environment where people to not have to make this choice. How can we do this? Well, I thought I had some good ideas about this but then saw Peter Suber's excellent web site about this here so I will avoid trying to be comprehensive.

Instead, I have made my personal top 10 list of ways to support Open Access that can make your life better and easier too. In italics are things you can do to show you REALLY support Open Access:

• 1. Review.
• Do not review for non Open Access journals. Ever. Not only will this save you time, it will ratchet up the cost of business for non Open journals.
• You can be really insidious about this and not even answer requests for review and gum up their works that way. This is best reserved for Elsevier journals.
• 2. First timers.
• Encourage colleagues who are Open Access virgins to submit some (or better yet, all) their papers to Open Access journals. Some will love it and never go back.
• 3. Promote.
• For papers you publish in Open Access journals, if you put out a press release, make the open nature a part of the release (e.g., see our release for the Tetrahymena genome paper).
• Send the press release to your program officer.
• 4. Legislate.
• Write to your legislators and librarians and university officials expressing support for Open Access.
• If you want to be extra supportive, write to local lobbying groups such as medical support groups and tax reduction advocates pointing out the follies of non Open Access.
• 5. Promote II.
• Find a good Open Access publication and promote it in some way - by writing about it in a blog or reviewing it for things like Faculty of 1000, submit reviews there only for Open Access articles.
• To be a true supporter, ONLY write reviews and commentaries about Open Access publications. Pretend like others do not exist.
• 6. Public.
• Promote Open Access publications (e.g., your own) to the public. Since the public cannot get access to most non Open Access publications, it is hard to use them to get the public interested in science. But it works well with Open Access publications.
• 7. Fair use.
• Take material from Open Access publications and (if allowed) use it to make "Open" educational materials, such as review papers or powerpoint presentations. People should be able to use it (e.g., for teaching) without worrying about copyright issues. Just make sure to cite them correctly.
• 8. Citations.
• For citations, when all else is equal, choose to cite Open Access publications. Not only will this increase their Impact Factor, readers will be grateful because they will be able to obtain the papers more easily.
• Note - I am not advocating not citing others, but just when you have to choose, to choose well.
• 9. Collaborate.
• Choose collaborators who support Open Access principles.
• If you want to really be good, only enter a collaboration is your collaborator is willing to publish the shared findings in Open Access journals.
• Do not collaborate with those not willing to make such an agreement.
• 10. Data
• Find a way to make all your data sets and supplementary material Openly available, regardless of where you publish.
  
• My favorite twist on this -a viral license to use your data. If someone wants to make use of unpublished data you have, only share it if they are willing to publish results in an Open Access journal. I am sure some people will say this is against the spirit of Open Access, but it is not. It is simply taking a longer term view of the movement.

Bike Friendly Davis could be Friendlier

Davis is championed as one of, if not the, best biking cities in the US. See for example:

• The city of Davis bike page here
• Paul Dorn's classic articel on biking in Davis here
• Davis, CA wikipedia entry
  

From my experience it certainly deserves this reputation. I live on one side of town and I work on the other side and bike to work whenever possible. I have tried to take as many different routes as I can to get to know the city. Over most of these routes, there are all sorts of bike-friendly features, like bike lanes, and traffic lights just for bikes, and even off road bike paths.

The off road bike paths are by far and away the best feature of Davis in terms of biking. These wind their way through many many communities and parks and generally make it incredibly pleasant, and safe to bike. I see so many kids on these routes going to and from school and it must be nice to know your kid can biek around possibly without ever crossing a road.

Yes despite this I am struck by the unevenness of the bike friendly features across town. For example, there is only one good off road route that head to UC Davis campus from the South side of town. This is the South Davis bikeway that it veyr nice and goes under I-80 and the railroad tracks. There is also a nice bike path on the West side of town (this one goes nearly all the way out to the next town in Winters). Ufortunately from the North and East sides of town, there is no direct route to campus that is off road. So in fact in these areas you see many many fewer people commuting within town on their bikes. I am sure the limitation is that it is hard to build bike paths into older communities. But if Davis wants to really become the best bike town in the country, it should try to find a way.

In addition, there are many very simple things that could be done to make biking around town and communiting to town much more pleasant. For example, there is what could be a really nice off road bike path connecting Davis and Sacramento. The problem with this is that it is incredibly exposed - both to the sun and to I-80 (it runs right next to 80 for much of its route). In some sections, judicious tree and shrub planing could greatly reduce both forms of exposure. It is unclear to me why this has not been done. But I am sure that this explains why this bike route seems to be so poorly used. Who would go out of there way to commute on their bike when they are so exposed to one of the most highly travelled freeways in the area.

I am very grateful to live in a place with such bike friendly features. But it seems that a few adjustments here and there could get even more people onto their bikes and off of the roads.

Vice Provost of U. C. Davis on the wrong side of Open Access

Well, my first incredibly disappointing moment at U. C. Davis. My brother sent me this link about a letter to Congress from some provosts and deans trying to go backwards on the issue of Open Access to scientific publications.

See the press release here.

And one of the signatories is the Vice Provost for academic affairs at Davis, Barbara Horwitz. Their letter contains many misleading statements in my opinion and seems to be overly biased towards the anti Open Access side of the debate. First, they say

In fact, some studies have already shown that research intensive universities would have to pay considerably more to gain access to the same amount of research under an author- pays model than a subscription model.

Where is the citation for this? This is counter to intuition and on its face seems ridiculous to me. It requires some backing up with evidence, especially in a letter to congress.

They also claim:

The free posting of unedited author manuscripts by government agencies threatens the integrity of the scientific record, potentially undermines the publisher peer review process, and is not a smart use of funds that could be better used for research.

How on earth does posting of unedited manuscripts threaten the integrity of the scientific record. That is like saying scientists should not give talks on anything until they have published it, and then they should only quote from their published papers. Or, maybe scientists should not even discuss their work at all in public and should just present it through papers published in journals. I am astonished that a Officer of my University would make such a statement.

Perhaps most amazingly, this collection of academic folks says:

As a member of the Senate Budget Committee, you are certainly sensitive to the various forces that shape and reshape the Federal budget from year to year. Recently, for example, we learned that the Biomolecular Interaction Network Database--the world's largest free repository for proteomic data--lost its funding and curtailed its curation efforts.

This too appears to be almost absurd and certainly misleading. BIND is in the true tradition of Open Access - a database of proteomic information for the world to share. And these provosts and deans are trying to use its loss of funding as an argument for LESS OPEN ACCESS. How completely nonsensical is that? But even more incomprehensible, BIND is a CANADIAN database effort, supported by Genome Canada funding. So how this relates to the funding by the US Congress is beyond me.

This collection of provosts and deans appear to be trying to do a slight of hand here with the details. I would be willing to wager that the driving force behind their letter is the desire to continue bringing in funds to their Societies or Universities that come from subscription based publishing. (Note it seems unlikely they are writing this letter as a statement of the official policies of their universities - certainly, I did not see any extensive discussion at Davis prior to Dr. Horwitz's signing this letter). A little survey of the backgrounds of the letter writers is informative here. What I have found with a little googling is that many of the signatories have active leadership roles in publishing non Open Access journals. Robert R. Rich is the Editor in Chief of J. Immunology, which does not support Open Access. Kenneth L. Barker is the President of SEBM, a publisher of non open access scientific publications. Barbara A. Horwitz, was the president of APS which sponsored this press release and publishes many non Open Access journals. I am sure many of the others have some type of similar roles. It would have been nice for them to mention that in this press release.

To keep in that spirit, as I have said before, I am on the editorial board of PLoS Biology and PLoS Computational Biology and I support Open Access publishing completely. I do not always disclose this in discussions of Open Access but then again, I have never written a letter to congress making use of my position in a university to promote a position with such obvious direct benefit to myself.

Some interesting links and tidbits related to this article:

• In their annual report from a few years ago, APS discusses how the DC Principles organization was founded specifically to counteract the Open Access movement.
• Peter Horwitz writes about the letter more here
• The APS we are discussing here is the American Physiological Society. Note it is NOT the same as the other APS commonly seen on science journals - the American Physical Society which is moving more to complete Open Access.

Note - thanks for T. Scott Plutchak at UAB for pointing out that it is possible to support Open Access without being a total jerk, and thus getting me to tone down some of the language from the original version of this post.

Good Open Access Biology Resources

Boring blog overall, but I wanted to put a collection of links here for information about Open Access, especially as it regards to biomedical literature. I will add more links to this over time, and welcome suggestions.

• Peter Suber's Open Access Overview
• Peter Suber's Open Access Blog
• Budapest Open Access Initiative
• PLoS Open Access Page
• BiomedCentral Open Access Charter
• Pubmed Central Open Access
• Directory of Open Access Journals in Biology
• Bioinformatics.Org
• Free Medical Journals Page

Tetrahymena Part of Recent Lasker Awards

The Lasker Award for Basic Medical Research was given a few days ago (see here). It went to Elizabeth Blackburn, Carol Greider, and Jack Szostak for work on telomerase, the enzyme that synthesizes the ends of linear chromosomes. The whole history of the discovery of telomeres and telomerase is fascinating and a good summary can be found at the Lasker site. The discoveries were made possible in a large part due to the unique and tractable biology of the single celled eukaryotes Tetrahymena thermophila, one of my favorite bugs. Perhpas most importantly, this species has a lot of telomeres and teomerase in each cell since it contains >200 linear chromosomes in the macronucleus and each are present in about 40-50 copies.

I of course have a vested interest in this since I have been in charge of the project to sequence the macronuclear genome of this species. We just published a summary of our findings in PLoS Biology (see the paper here). Research on this organism has led to some other fundamental discoveries in biology, including, for example, the discovery of catalytic RNA, which won the Nobel prize in chemistry in 1989.

Winning the Lasker award bodes well for Blackburn, Greider, and Szostak as many previous recipients have gone on to win a Nobel (the Lasker site has a good list of this connection here). However the Lasker listing includes people who won the Lasker AFTER they won a Nobel, which is a bit silly. I am sure they were happy to also get the Lasker Award, but that does not provide useful information for the Lasker as a predictor of the Nobel.

Anyway, a tip of my hat to team telomerase and Tetrahymena thermophila.

Royal Society just digs a deeper hole

The Royal Society has announced that they are making their full archive, including papers going back hundreds of years, available online for the first time. I read this line and thought - "Finally, the Royal Society is moving towards Open Access". After all, the US National Academy of Sciences provides full and free access to all articles 6 months after publication.

Then I read the next sentence, which says that the Royal Society wil provide this free access to their archive until December.:

And until December the archive is freely available to anyone on the internet to explore. ....

After December 2006 subscribers to our subscription packages (S, A and B) will enjoy privileged online access to the archives. Private researchers will also be able to access individual articles for a small fee per download.

The Royal Society appears to simly want to hold on to every little last shred of money they can get for things published originally hundreds of years ago. They could make a great contribution to the world by opening up their archive completely. But clearly, the Royal Society is not about making contributions to humanity. What they appear to be about is a scientific oligarchy that exists mostly to promote themselves and their freinds. I would like to point out again that of 1316 fellows, 62 are women.

So this group of scientists appears to be trying to continue the bad traditions started hundreds of years ago, like excluding women from science. I looked for but could not find information on minorities but can only assume that their record in this area is even worse, as they do not discuss it on their web site.

Perhaps some day the UK public will wisen up and stop giving money to this collection of Neanderthal wannabes.

Genomic Protectionism and Biopiracy

Well, it appears that the anti bio-piracy movement continues to spread into the genome sequencing realm. Today, an article was published in the Australian suggesting that Australia in essence stop working with the scientific community and to not let anyone else sequence the genomes of organisms from that country. The basic argument is as follows:

• Australia possesses some organisms with unique genetic resources
• Other countries have gotten more out of these resources than Australia has
• Australia is now letting other countries read the entire genetic code of some of these organisms and (gasp) putting this information into the public domain
• Australia loses out on some of the money and or intellectual property that could come from the sequence information
• Therefore, Australia should stop participating in collaborative genome sequencing projects, at least for native Australian species

My gut instinct is that this idea is absurd. But the more I think about it, the more I come to the conclusion that something needs to be done to encourage countries to share genomic information about their biological resources. I see two critical reasons this is needed. First, it will help encourage countries to protect their biodiversity in the hope that they will get something from it. Second, the more this information is shared and put in the public domain the more we will learn about life on this planet.

This is of course not the first time this issue has come up. Diversa, for example, which has sampled the world looking for novel enzymes, has been accused of biopiracy wherever it goes (e.g., see here). They have argued that what they are doing is bioprospecting, not biopiracy. However this argument did not always calm critics in various locations.

Diversa has been accused of biopiracy in part because they are a for profit company trying to benefit directly from other countries biological resources, much like those looking for new drugs in the tropics. Since Diversa did their work through molecular biology, they were viewed in many countries much like GMOs are. Many other companies doing "bioprospecting" have also been accused of biopiracy and I guess the truth of the accusations depend on the company involved.

However, what we have now is potentially much more damaging to scientific research. These people are in essence arguing against ANY release of genomic information regarding organisms native to other countries because once the information is out, the countries lose control over how it might be used. See for example

• Slashdot story about google being accused of biopiracy for discussing working with Venter on a map of genes across the globe (here)
• Interview with Venter where he responds to charges of biopiracy
• ETC discussions
• IPCB comments

The critics in essence consider this analogous to someone stealing seeds for some plant. I think we run the risk of genome sequencing becoming labelled as horribly evil in much the same way GMOs and biopiracy is. I guess I do not completely disagree with the critics, but I see so many potential benefits to the world from sharing genomic information that I am hoping there is a way to do this without committing egregious acts of biopiracy.

One possible solution that has been suggested would be for DNA sequence databases to contain some reference to the country which "owns" the biological resources behind the sequence data. But this does not really protect any potential intellectual property in the data. Patenting DNA sequence has been frowned upon by courts and governments alike, as well as many policy folks. Thus this is probably not an option. As a supporter of open data release and open access to publications, I cannot believe I am about to write this but ... maybe it would be worth considering the DNA patenting issue again if it allowed for release of sequence information and protection from biopiracy.

It seems that there may be a need for DNA sequence databases to record in some way that certain information was produced from a country's biological resources.

The hypocrisy of most projects with "Open" data release

There has been a growing trend in biological research, for scientists to release their data in some way or another prior to publication. This data release is meant to promote the advancement of science, and it frequently does. This is perhaps best seen with genome sequencing projects, such as the public version of the "Human Genome Project." In many if not most cases, centers that do the bulk of the sequencing work release the sequence data for searching by others, even before publishing papers on their own data. In most cases, restrictions are placed on how the data can be used, but the data is still released for others to look at.

This is of course in contrast to how much of science works, with researchers keeping their data to themselves until they are ready to publish something. The genome centers who have made their data available prior to publication deserve some credit for this openness. Especially since the data release in general by genome centers has been so far and beyond what biology researchers do. In fact, many of these centers go out of their way to promote getting such credit (they even got Clinton and Blair to play along) The best example of this was the public human genome project, which made multiple claims about how great they were for humanity for releasing the data "within 24 hours of gathering it." This data release policy was captured in something that became known as the Bermuda Principles, due to a meeting that took place in Bermuda (see a nice summary of this by John Sulston here).

What is appalling to me, however, is that these same centers that try to take credit for their openness, then turn around and usually publish their papers in non Open Access journals (for those who do not know, this means that then one has to pay money, frequently enormous sums of money, just to read the paper). I do not understand this. A paper about an analysis someone did on a data set may in fact be more valuable to the community than the data itself. If the genome centers like TIGR, JGI, Sanger, Whitehead, etc. really wanted to be on the side of openness, they should stop publishing their papers in non Open Access journals. Unfortunately these places publish very few of their papers in such journals.

For example, the Joint Genome Institute (JGI) which I am now affiliated with, is continually showing two faces on this issue. On the one hand, the issue press release after press release regarding their release of data on various genome projects (e.g., here). That is fine, although a little over the top sometimes. But then they almost never publish any of their work in Open Access journals (e.g., see their latest press release on a paper published about a genome in Science, a non Open Access journal). Any taxpayers out there should be disappointed with this as the genome centers get TONS of money to carry out this work for the public benefit. And then for the papers on the work to be hidden behind huge subscription fees is a waste of your money.

This is particuarly surprising coming from JGI since JGI is run directly by the Department of Energy (unlike most other centers which are either private or part of a university). Thus apparently DOE does not want to follow even the recommendations of congress and the senate regarding Open Access to publications. Nor does DOE apparently want to do the right thing by requiring their institutes for publish in Open Access journals. Too bad. Taxpayers hopefully will begin to get more and more upset about the waste of their money as these centers take enormous amounts of the federal science budget and convert it into documents that only a few can read.

Scientific claims you know are wrong

OK

I just read about this new claim, made at a meeting, regarding "phone telepathy" in which some people claim to know that someone is about to call them, just before the phone rings. Now, a researcher is claiming to have conducted a controlled experiment that supports this. For the key details seee the Reuters news story or the link at CNN. But here is the key part of the article:

Each person in the trials was asked to give researchers names and phone numbers of four relatives or friends. These were then called at random and told to ring the subject who had to identify the caller before answering the phone.

"The hit rate was 45 percent, well above the 25 percent you would have expected," he told the annual meeting of the British Association for the Advancement of Science.

"The odds against this being a chance effect are 1,000 billion to one."

Now, it is entirely possible that the Rupert Sheldrake who conducted this research is on the up and up. However, every time I have seen claims that make me giggle like this one did, they have turned out to be wrong. But rather than claim that after the fact, I will put it out there in the blog world. I state, with complete confidence, that the conclusions of Sheldrake (that people use telepathy to sense when someone is going to call) will be shown to be wrong. Now - I do not know how it will be shown to be wrong. For example, his method theoretically should have controlled for the fact that when the phone rings sometimes you can guess who is calling by the hour of the day or by world events (e.g., my brother will call just after any major REDSOX event). Nevertheless, it will turn out that something is amiss.

Anyway, people can get a good giggle out of doing a google search (giggle from google) with his name and checking out some of his other work (like that Dogs That Know When Their Owners Are Coming Home). Now I am not saying that we know everything about human perception. Nor am I saying that there is no way that we know everything about all the means of animal communication. But do people know, even when all behavioral variables are removed, who is about to call them simply from telepathy? I predict, the answer, despite how much fun it would be to be true, will be, alas, no.

Steve Irwin's death is a great loss for science education

As I assume many people know, Steve Irwin (aka the Crocodile Hunter) died today. He has been lauded as an environmentalist, which he clearly was. However, he should also be praised as one of the more effective science educators of the last 20 years.

In this day and age, most of the TV shows are either 24 hour news, or some bizarre new reality show, or some crime drama. But Irwin managed to be successful with what could be called a animal-encounters reality show. Except that unlike some other such shows (e.g., "When Animals Attack") his shows tended to be rich in moral lessons and education for the public about biology, life and animal behavior. We desperately need such little openings into the general public for education about science. Whether you liked his shows or not, whether you agreed with his methods for apporaching and protecting mean looking animals, I think everyone should say thanks today for Irwin's dedication to educating the public about life on this planet.

The Blogger World Favors Open Access Publications

Well, even though the traditional press did not pick up the story about the Tetrahymena genome paper, it seems that lots of blogs and online news sources picked it up.

Here are some:

• Slashdot discussion
• Ars Technica
• Structure and Strangeness Blog
• Open Source Pimp Blog
• mAd is an idiot blog
• Muton Blog
• Others: here
• The Design Matrix Here
• Cognitive Labs
• EZKept
• Genome Web News

Maybe the press release from TIGR did not excite the "real" press too much, I do not know. But nevertheless, it is good to see people discussing the article and even better to see that the article is currently the #1 viewed article for the week at PLoS Biology. I asumme that most of this comes from slashdot running an item about the article but I am not 100% sure.

I think the blogger world seems to run stories about Open Access publications much more than
about non Open Access publications since they can read them freely. It would seem that the blogger world is helping to promote Open Access papers and may explain why in the recent past I have gotten much more response to Open Access papers than even to papers in Nature or Science.

It is so important for scientific research to reach all people, not just scientists who can afford subscriptions to journals. Thus a partnership between bloggers and open access publications seems perfect for the new way of doing science.

Tackling the hairy beast - Tetrahymena genome

Just thought I would put out a little self-promotional posting here on a paper we have published today on the genome of a very interesting organism called Tetrahymena thermophila. This organism is a single-celled eukaryote that lives in fresh water ponds.

This species has served as a powerful model organism for studies of the workings of eukaryotic cells. Studies of this species have led to some fundamental discoveries about how life works. For example, telomerase, the enzyme that helps keep the ends of linear chromsomes from degrading, was discovered in this species. This may not seem too important, but many folks think that degradation of chromosome ends in humans is involved in aging. Perhaps even more importantly, (to me at least) studies of this species were fundamental to the discovery that RNA can be an enzyme. This discovery of catalytic RNA revolutionized our understanding of how cells work and how life evolved. Tom Cech and Sidney Altman were given the Nobel Prize in 1989 for this discovery.

Many (including myself) believe that having the genome sequence of this species will further spur research and its use as a model organism. In addition, we believe that some of the findings we report in our paper will further cement the importace of this species. For example, this species, though single celed, encodes nearly as many proteins as humans and possesses many processes and pathways shared with animals but missing from other model single celled species.

The project that led to this publication was undertaken while I was at TIGR (The Institute for Genomic Research) and involved a collaboration among people at dozens of research institutions around the world. It all started in 2001 when Ed Orias and his colleagues sought to see if anyone at TIGR would be interested in putting in a grant to sequence this species' genome. I responded to the email saying I was interested, especially since I had interacted with multiple people who used this species as a model system (e.g., Laura Landweber at Princeton and Laura Katz at Smith). So I went to a FASEB meeting where the Tetrahymena Genome Steering Committee was meeting and discussed with them how TIGR might help sequence the genome. And after talking to other genome centers, they selected TIGR to put in a grant proposal with them.

We ended up getting funding from two grant proposals - one from NIGMS and the other from the NSF Microbial Genome Sequencing Program. The sequencing was done in a rapid burst at the new Joint Technology Center which TIGR shares with the Venter Institute. And then we spent ~1.5 years analyzing the sequence data (and assemblies) that came out and in the end we fortunately were able to get our paper into PLoS Biology, in my opinion the best place available to publish biology research.

Importantly PLoS Biology is Open Access which allows anyone anywhere to read about our work. This goes well with the free and open release we made of the genome sequence data. In fact, many people published papers on the genome before we did (sometimes scooping us). In the end, I accepted the risks of releasing the genome data with no restrictions inexchange for advancing research on this organisms. I think this risk was well worth it as we still got our big paper published and the field has advanced more rapidly than if we had not released the data.

Other links that may be of interest to people:

• The Tetrahymena Genome Database
• Tetrahymena Web Links
• Ed Orias' Tetrahymena Site
• Tetrahymena site at TIGR

Eisen, J., Coyne, R., Wu, M., Wu, D., Thiagarajan, M., Wortman, J., Badger, J., Ren, Q., Amedeo, P., Jones, K., Tallon, L., Delcher, A., Salzberg, S., Silva, J., Haas, B., Majoros, W., Farzad, M., Carlton, J., Smith, R., Garg, J., Pearlman, R., Karrer, K., Sun, L., Manning, G., Elde, N., Turkewitz, A., Asai, D., Wilkes, D., Wang, Y., Cai, H., Collins, K., Stewart, B., Lee, S., Wilamowska, K., Weinberg, Z., Ruzzo, W., Wloga, D., Gaertig, J., Frankel, J., Tsao, C., Gorovsky, M., Keeling, P., Waller, R., Patron, N., Cherry, J., Stover, N., Krieger, C., del Toro, C., Ryder, H., Williamson, S., Barbeau, R., Hamilton, E., & Orias, E. (2006). Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote PLoS Biology, 4 (9) DOI: 10.1371/journal.pbio.0040286

The Disgrace of the Royal Society

I am astonished at the behavior of the Royal Society regardling publication. As dozens of funding agencies and societies and individuals move towards Open Access for publications, the Royal Society crawls back into the medeivel hole from which it originated.

In article after article, the Royal Society's publishing folks rant on and on about the evils of Open Access publishing. NOTE .... THANKS TO DBERGESSON FOR POINTING OUT THE MISTAKE IN THIS BLOG. I USED A QUOTE FROM THE WRONG ROYAL SOCIETY HERE. I AM LEAVING IT IN TO KEEP THE ORIGINAL POSTING. I STILL FIND THE REAL ROYAL SOCIETIES POSITION ON OPEN ACCESS TO BE ANNOYING. SEE COMMENTS FOR MORE DETAIL.

For example, in a recent article from RSC:

But the Royal Society of Chemistry’s director of publishing, Peter Gregory, disagrees. ‘We have absolutely no interest shown from our editorial board members, or our authors, for open access publishing,’ he said.

Gregory believes that the open access author-pays model is ‘ethically flawed’, because it raises the risk that substandard science could be widely circulated without being subjected to more rigorous peer review. This could be particularly problematic in chemistry, where rapid, open access publication could be used to establish priority ahead of more time-consuming patent applications from rival groups, he added.

What this basically means is that the Royal Society wants to continue to make money publishing the results of scientific research that is largely funded by the government and the public. And that they are willing to have people suffer (e.g., die unnecessarily because their doctors do not have a subscription to the Royal Societies journals) rather than use their supposedly brilliant minds to come up with a way to make money and simultaneously make the research freely available. The NIH, Wellcome Trust, and dozens of other groups are pushing for Open Access. Yet the Royal Society is sticking to their old boys club ways (to see how old boys clubbish they are go to here).
.

If we actually go to the details of the Gregory quote above, I have a hard time knowing where to begin with the flawed logic here. For example, the idea that substandard science does not get published in non Open Access journals is just absurd. Consider the latest example of the Korean Cloning scam. Those articles were published in top non open access journals. Same thing with just about every other case of bad science or scientific fraud in the last twenty years. The claim by Gregory is simply unfounded. First, Open Access journals do not say there should be no peer review and they tend to be peer reviewed even more carefully than non-open access journals. Just try publishing a paper in PLoS Biology, which I have found to be more stringent than Science. Why is this? Becuase scientists are more willing to commit time to reviewing for such journals because their work benefits humanity rather than some publisher like Gregory.

Another reason Gregory's claim is unfounded is evidenced by the physics community. They put preprints out for the world to see, which allows for global peer review, rather than peer review by a select list of people. The idea that peer review as it is in current non open access journals is perfect is completely ridiculous. Sometimes you get objective reviewers, but other times you get people that, even if they wished to be objective, would probably have a hard time doing so. This is unavoidable in any peer review system. The more open the publication system and the peer review system is, the more likely it is to avoid outrageous variation in quality.

The Royal Society should be ashamed. They are preventing the distribution of scientific findings and trying to maintain a publishing system that limits the speed of scientific advances and enriches the publishers at the expense of governments and the public.

So I suggest that anyone who knows someone harmed by a doctor who did not know what they were doing, or anyone who wishes for scientific advancement to proceed at a rapid pace, to consider writing to your favorite member of the Royal Society and asking how they feel about this.

To contact the Royal Society directly go here.

I have been unable to come up with email lists of society members but if anyone can find one I will post it.

Viruses as food additives

I find it sad that the world has come to this. The FDA announced that it has approved the use of viruses as a food additive. The particular viruses (known as phage in this case) target and kill common bacterial pathogens found in meat. It is entirely possible that this treatment will lead to reduction in deaths and illnesses. However, it is also possible that there will be unexpected consequences of this treatment and thus anything like this should be done with caution. What saddens me about this whole thing is that it is the wrong way to go about solving the problem. Most of the problem comes from the fact that our meat today in this country does not come to us in reasonable condition. The animals are usually kept in unsanitary conditions where diseases and nasty pathogens are prevalent.

The best way to think about this in my opinion is what I read in The Omnivore's Dilemma, the new book by Michael Pollan. In this book he talks about how animals now frequently live in what can be considered the equivalent of the slums of the industrial revolution. Cities of animals, frequently wallowing in excrement, is not the best way to prevent bad microbes from getting in our food.

So in recent years all sorts of practices have been developed to kill these microbes in food products. Irradiation, for example. And now, viruses, sprinkled on your meat, to keep the bacteria from growing too much. Give me meat from animals that have not been swimming in their own shit and piss and I will be happy to take my risks without dumping viruses on top.

Deceptive advertising by Amtrak

There is this nice train out here that runs from Sacramento to Oakland called the Capitol Corridor. I really like this train overall since I can take it from dontown Davis to Berkeley and i takes about the same amount of time as driving but is much more relaxing. There are issues with the on time performance of the train but mostly even when it is late it is better than driving if you are going somewhere near a train station.

However, I am pretty pissed off at Amtrak for one of the things they advertise relating to this train. On the Capitol Corridor web site, the highlighted item is frequently a promotion saying "Take the train to Oakland A's Games this season". It sounds great since there is now an Amtrak stop right at the Oakland Colliseum where the A's play. That is, until you look at the train schedule. For night games there is simply no way to take the train to games. This is because the trains stop leaving the stadium at about 8 PM, or just after night games start. Even for day games there is not much offered in the way of getting to and from games on a reasonable schedule. Even when there are technically late trains for Amtrak, most of the trains do not actually stop at the Colliseum. So I am having a hard time figuring out what they mean by "Take the train."

In other cities in which I have lived they reserve a train to leave just after the game ends. Not here thye don't (or at least they do not advertise this as an option). It seems lame to promote this idea and then to not have the trains to back it up.

Welcome

This is my blog about life in and around Davis, California (to go with my work blog "The Tree of Life").

SciFoo Camp Day 3

For Day 3 of FooCamp, I drove over to the Googleplex so missed out on the sociology of the bus. It is always interesting as a meeting progresses through the days to see people who did not know each other previously become more and more comfortable with each other. I supose that happened here too, but Jason and I wanted to be able to scoot on out of there once the festivities ended.

We had another high-quality google meal for breakfast, although it seemed that the nutritionist may have not been given full control since the majority of items at the meal were fried or soaked in sugar or oil (i.e., bacon, french toast, etc). But the food was still good and if one did not like it one could always grab some organic snack inside.

On a side note, I kept cracking up every time I had one of these "Organic FoodBars." This was funny for two reasons. First, the name of the bar reminds me of something from the movie Repo Man where in the background of scenes, various food items are labelled as "Beer" or "Food." But the other reason these bars were funny is that everyone kept talking about foobar, which is another one of the O'Reilly folks meetings they are planning and a play on words.

Anyway, this was the day I saw the presentation on HowToons.Com (see earlier posting). I did go to a few other good sessions, but I confess I also spent a decent amount of time in the camping area of the googleplex chatting with other people. I made so many good connections at the meeting it seemed like that was certainly as much in the spirit of the whole thing as going to all the sessions would have been. Eventually had a final scifoo wrap up session where the powers that be asked us for critiques and suggestions for improvement.

In my glee to report on the great aspects of this scifoo, I may have given the impression that all was perfect. This was not the case and there were areas in need of much improvement. I and others brought some such issues up in the discussion here. One thing that was really somewhat unusual and ironic that was less than ideal was how they presented the information from the registration to other scifooers. When we registered on Day 1 we filled out a slip of paper listing five key words or phrases to describe oneself. I figured, this would get converted to electronic format and posted on some web site somewhere or used in some type of RFID tags to meet like minded folks. I mean, we were at Google, for heaven's sake. But no, instead what they did was simply print out our pictures onto the forms (they were about 4 inches by 8 inches) and then post all the forms on a board. Generally, the whole thing was useless, as people wrote in tiny print and not always very legibly, since they had no idea they would be posted in this way. There were other things in need of work but most of them were minor and unnlike in many other contexts where people point out problems with something at scifoo the audience actually proposed solutions to the problems too. That was a nice touch from my point of view, as it is easy to complain and generally hard to find solutions.

Then, just like that, it was over.

SciFoo Camp Impressions Day2

You know a meeting is good when you simply have no time to check email let alone write in a blog. That was the case at scifoo and is why I am writing now a few days after the fact.

Day 2 was much more epic than the first since of course it was a full day of fooing. I managed to get up pretty early despite the late night (well, I cheated a little compared to others - I was up late but had only half a glass of very bad "single" malt). Many people looked a little rough around the edges in the morning in the hotel lobby... Nothing too surprising there as those who flew in, especially from overseas, met the wrath and illogic of modern airline security. The people from the UK in particular had some pretty good stories about being told they were not even allowed to buy books IN THE AIRPORT to bring on the plane. You might think then they would at least shut down the book sales, but of course no, that would cost them money.

So with TSA delays and jet lag and possibly some drinking I am not sure how they made it out early in the AM. We then all piled into a google provided bus and headed over to googleplex again. The conversations were lively along the way, although some of them had nothing to do with scifoo.

Then we got to googleplex for breakfast. As with food the night before, the food was mostly top notch although never pretentious or wasteful. Although I must say there were some unusual things mixed in (like some pretty heart attack inducing pieces of breakfast cake). I am sure the google nutritionist we met the night before was not overhwlemingly in favor of those items. Yes, google does in fact have some type of nutritionist. I never talked to her in detail to find out what that meant, but I did talk to a few scifoo folks about my theories that she was really a spy (she just seemed to pay way too much attention to all of the actual sessions to simply be the nutritionist; plus she always seemed to be talking on her two way radio). Maybe she had something to do with my theories about the addiction of the word google (see my previous post about this issue). Nutritionist - addiction --- seems like there must be a connection there.

Anyway, then the sessions began. Here's how it was set up. Outside, there was a coutryard with a paved patio section and a giant tent with tables for eating. Inside the main door was a giant room with camping stuff laid out all over the place (in homage to previous foo camps where people really camped). You had to walk through this open air camping section to get to the large grid showing the sessions being offered (people were still filling out session offerings throughout the day). Some sessions were downstairs near the camping room, and others were upstairs and a short 2 minute walk away. In addition, we were near a large cafeteria which including these giant bins with snack food (most of it on the healthy side of snack food which was fine with me) and a large fridge with a diversity of drinks.

I spent much of the day going to sessions relating to "open access" or "citizen science" but triedto force myself out of my box as much as possible. Among the most memorable sessions I went to were one on biology inspired robots (they had a robot gecko that could climb using millions of tiny hairlike projections like geckoes really use). See this Berkeley news release for some examples. Overall, the day was great. I got to catch up with some colleagues, and hang out with my brother who had been unable to come the night before. I also went to some great sessions on exploration (including of the earth's oceans and of Mars).

Not much was disappointing, although I was still somewhat dismayed to see how scientists support open source software, and open access to data, but then do not always support open access to publications. When asked why, they give the lamest explanations, like, "well, that is just the way it is done." Perhaps most tellingly, the technology and engineering and physical sciences folks seem to get the Open Access to publications movement more so than the biologists and other life science folks. Maybe that is due to the existence of the physics archives and things like that. Or maybe biologists do not like to speak up when there were multiple folks from Nature there, and they did not want to jeopardize their chances of getting a Nature paper. I think the real explanation is that many of them are, how should I put this politely, afraid of change (note I wanted to say chicken shit there but then decided to be polite).

Anyway, overall the day was great. I even did a presentation jointly with Tom Knight from MIT, where he discussed genome engineering and small genomes and I discussed how one studies mcirobes in their natural environments. I only wish I had thought of this more in advance and had done fewer slides and simply drawn on the board or just talked since we did not leave a ton of time for free discussion. Nevertheless, there were lots of people there and lots of really good questions were asked. Tom even inspired me to consider working on the group of organisms her works on (mycoplasmas, spiroplasmas and their relatives which are these really interested bacteria that do not have cell walls and tend to have really small genomes).

What I noticed happening was that as the day progressed, people spent less time sort of wandering around aimlessly between or during sessions and more time talking to other scifoo folks in the camping area of the main room. In addition, the google herders, in their black shirts, were frequently out in this area also having discussions (in addition to being positioned carefully at all intersections where we might wander off into nofoo land and possibly bump into some magical new google initiative we were not supposed to see). Message to google - you should be careful of the folks with the wandering insect like robots since they did not attract the attention of the intersection guards. In general, the google herders who were there were all very helpful and generally engaging but never obtrusive (they reminded me of stories Ihave heard about the staff on survivor who are always there but try to mostly stay out of the way).

And eventually, the main sessions came to an end and we wandered back outside for dinner in the open air or under the tent. By then everyone seemed to at least have someone they felt comfortable talking to and everything was much less awkward than the night before. Not to say that all was perfect - there were of course the awkward moments and some highly strange people. But unlike many conferences I have been to, since this was a pretty select crowd, even the highly strange people were generally quite interesting once you got past their veneer.

So eventually people piled in to the buses and went back to the hotel. Of course, the night could not end there. But this time, instead of going to the lame bars, we decided to have a party in the hotel lounge. A few of us went out and bought some stuff to drink at a nearby store and we then had a quite pleasant evening talking about Mars, evolution, Nature, and scifoo in the hotel lounge. The only drab moment was when the receptionist came in and said something to the effect of "guests are beginning to complain about the noise" that we shut the doors and talked a little more quietly. I even came up with a good term to use in a new paper I am working on thanks to some of the Mars exploration folks who were there. Eventually, I went to sleep. And thus Day 2 did end.