Jonathan Eisen

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:

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).
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.
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.

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.

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