Tag: open access

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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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:

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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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).
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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Open Access Rant: How Does Your Doctor Learn About the Newest Medical Findings??

Everybody would like to find a doctor who is knowledgable about the latest developments in medicine. Whether these developments relate to new treatments, or new methods of diagnosis, or treatments that are dangerous or do not work, we want our doctors to know this information. How do doctors find out about these things?

Well, there are many sources of this information, but one we hear a lot about these days is a little disconcerting. It turns out that a lot of doctors get the latest information from drug company reps who stop by the office and leave imformation pamphlets or who talk up their companies latest products. This could be OK, except for the fact that many of the drug company reps either purposefully provide misleading information, or in fact do not actually know what is good or bad information.

One reason this is such a big problem is that, like everyone else these days, doctors are really busy and overwhelmed. So they sometimes do not have any time to read the actual medical studies that might be relevant to what the drug company reps are saying. But that is a bit lame of an excuse, since it is their job to know these things. Thus I really think they should read more of the medical literature and not just drug company propaganda.

But herein is one of the biggest problems in modern medicine. Even if you have a really hard working doctor who is willing to read the latest papers, they may not be able to. This is because even though most of the medical studies were paid for by the government in some way, they are not freely available for the doctors to read, because they are published in journals that charge exceptionally high prices for subscriptions. Doctors in large institutions probably have good access to this information. But doctors in small groups may not. Imagine if congress passed laws but lawyers were not allowed to read them without paying a fee to someone. The system for medical literature is really absurd.

I got thinking about this when re-reading Lance Armstrong’s autobiography “It’s Not about the Bike.” In the book, Armstrong describes how when he had testicular cancer he had a friend who was a doctor bring him the latest studies on this type of cancer and he read all of them. Well, this only was possible because his friend must have had access to all the publications through a university or very large medical group. Wouldn’t it have been better if Armstrong could have just gotten the studies himself, given that most were paid for by the US Government in the first place? Well, if people doing medical research published their finding in Open Access journals, then anyone could read the articles, from doctors, to patients, to family members, to journalists. We would all benefit if this was done.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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