Tag: open access

Why I am ashamed to have a paper in Science

So I just had a paper published in Science last week. In many ways, it has all the makings of one of those papers I should be really proud of. First, it represents a collaboration with my undergraduate advisor, Colleen Cavanaugh, the person who inspired me to go to graduate school and who got me interested in microorganisms, which I have worked on ever since (I published my first scientific paper on work I did in her lab). The paper is on one of the coolest biological systems on the planet – bacterial symbionts of deep sea animals that allow these animals to function much like plants (they use chemosynthesis in much the same way plants use photosynthesis). Studies of the deep sea and of chemosynthesis are important for understanding the origin and evolution of life, for understanding global carbon cycles, for understanding the rules by which symbioses evolve and much more. And on top of all of this, the paper reports the sequencing and analysis of the complete genome of one of these symbionts (that from the clam Calyptogena magnifica) – and one of my main areas of research is on the evolution of the genomes of symbionts. And, the genome was sequenced at the Joint Genome Institute, where I now have an Adjunct Position and am working with extensively. All sounds good right? And, I should be happy to get a paper in Science too, right?

Actually, in reality, I am not pleased with how this paper has turned out. This is really due to two things. First, my collaborators failed to keep me in the loop that the paper was accepted in Science. Thus I did not find out about the paper until I did a google search for some other reason and noticed this Deep-Sea News Blog which had a story, well, about the paper in Science. It would of course have been nice to know the paper was accepted and coming out. It would have been even better to have seen the page proofs, which might have given me the chance to catch some little and not so little mistakes (e.g., the paper claims that this species has the largest genome of any intracellular symbiont sequenced to date – which is unfortunately not true). Now, admittedly I was out sick for a while and maybe my collaborators just did not want to bother me with this information. More likely- people were just very busy – and this just slipped through the cracks.

But you know – it is a Science paper. I should be happy however it came into being right? Well, no. Completely and thoroughly wrong. You see, I do not support publishing things in Science. I object because Science is not an Open Access journal. I tried and tried to get Irene Newton the first author to submit this to another journal. But in the end, she did the brunt of the work, and thus she and her advisor, Colleen, got to pick the place. And in the time since Irene submitted the paper, I have become even more miltant against publishing in such non Open Access journals. Publishing in a non Open Access journal like Science make me feel icky in every way. In addition, by choosing to publish the paper there but not elsewhere, the field of deep sea symbionts may have been hurt rather than helped.

How could a Science paper hurt the field? Well, for one, Science with its page length obsession forced Irene to turn her enormous body of work on this genome into a single page paper with most of the detail cut out. I do not think a one page paper does justice to the interesting biology or to her work. A four page paper could have both educated people about the ecosystems in the deep sea, about intracellular symbionts in general, and about this symbiosis in particular. The deep sea is wildly interesting, and also at some risk from human activities. This paper could have been used to do more than just promote someone’s resume (which really is the only reason to publish a one page page in Science).

But of course, even more importantly, anyone without a subscription to Science, well, they can’t even read the paper. And AAAS gets to decide what happens to the text and figures in the future. So – count this as one of my papers I am not really proud of. I love that I helped my Undergrad. advisor and one of my favorite people in the world do this work. But by it not being in an Open Access journal, I have unfortunately contributed to a system that I think is bad for the world. And I just fell icky.

Some news stories and blogs are coming out on the paper:

Below I have embedded a video of a dissection of what I think was a deep sea Calyptogena, just for the fun of it.

This was taken during a deep sea cruise I managed to get on. For mroe detail on this cruise, see the NOAA Ocean Explorers site here.

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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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Badges – do scientists need any stinking badges?

Thanks to garry Myers at TIGR for pointing this one out.

I just got done browsing through the ScienceScouts Site. This comes from the Science Creative Quarteryly which I have never heard of before and seems to be some sort of blog. If anyone knows more about it let me know.

Anyway, the ScienceScouts site has “badges” like Boy Scout Badges, but for scientists.

Examples include:




“The “inordinately fond of invertebrate” badge.
In which the recipient professes an arguably unhealthy affinity for things of this category. (http://scq.ubc.ca/sciencescouts/index.html#30)”



and

The “I blog about science” badge.
In which the recipient maintains a blog where at least a quarter of the material is about science. Suffice to say, this does not include scientology.

(http://scq.ubc.ca/sciencescouts/index.html#6)

which of course, I am awarding to myself.

Garry suggests that I get them to add an “I support PLOS” badge, which I am going to do … People should check it out and award badges to unsuspecting individuals

——–
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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Harold Varmus goes truly Open

Harold Varmus, one of the CoFounders of the Public Library of Science, has been featured on a NIH Profiles site. Through this site they are making a collection of his papers freely available. In addition, to co-founding PLOS, Varmus won one of those Nobel Prize thingies and was head of a little place called NIH.

Not that much is featured on the front pages. But if you go to the search page here you can search for all sorts of interesting stuff.

Some interesting ones I found:

I will post more when I have a chance but if anyone else sees interesting ones out there please post them too.

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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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Science World Coming …

The US Department of Energy and the British Library announced an agreement to develop a new international science portal aimed at sharing scientific information. It sounds like a great thing. Now if only DOE would require Open Access publishing of scientific research that they fund … that would really show DOE’s committment to Open Science. I recommend sending Dr Raymond Orbach, who is leading this initiative, an email message, the address for which you can find at this link at the top of the page.

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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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Non Open Access publishers getting desperate

Well, this kind of made my day. Nature is reporting that a group of non open access publishers have hired Eric Dezenhall to help them with public relations. Eric Dezenhall is a crisis management consultant (as well as a fiction author) who many may demonize but he certainly seems to be good at what he does. The article at Nature is worth checking out and points to the desperation of these publishers when they see the writing on the wall regarding Open Access. For example, Nature reports a person at AAP the Association of American Publishers says:

“We’re like any firm under siege,” says Barbara Meredith, a vice-president at the organization. “It’s common to hire a PR firm when you’re under siege.”

Keep up the siege everyone. Their ship is sinking and they are grabbing at the last little pieces of wood they can find.

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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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Article in the Christian Science Monitor on PLoS One and related topics

Just saw an interesting article in the Christian Science Monitor on the “end of the scholarly journal” which talks quite a bit about PLoS One. Definitely worth checking out — many quotes from Chris Surridge of PLoS One and some discussion of Blogs and related sites.

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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 Education?

Thanks to Jacques Ravel for pointing this out. U. C. Berkeley has begun posting many of its science classes as Podcasts which are avilable for download at a special Apple Itunes Site. Also posted are some lectures such as one by George Smoot who just won one of those Nobel Prize thingies. It seems Stanford is doing a similar thing although it does not seem as extensive.

Note sure what other Universities are doing this (I know some classes are podcasting but not clear how many Universities are doing it as extensively as Berkeley).

If anyone else knows of other such efforts please let me know (also see this list of free academic podcasts).

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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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My Open Access New Years Resolutions

Well, 2006 is over and in terms of Open Access to Biomedical type publications, I think it was a pretty good year. The papers being published in Open Access journals continue to get better and better and there are more Open Access journals too. Perhaps to biggest new thing from last year was the start of PLoS One, which is not only an Open Access journal but one that is experimenting with a new type of peer review system.

But of course, more needs to be done. So I am posting here my personal list of Open Access New Years resolutions. These are things I hope to do and hope to convince others to do too (these are in no particular order).

1. Convince more collaborators to publish papers in Open Access journals.

2. Release more of my labs data in a more usable format to Open Data archives (see Bill Hooker’s Open Reading Frame blog for more details about doing this).

3. Discuss Open Access to publications and data in all my scientific presentations/talks.

4. Write more blogs about Open Access and its benefits.

5. Convince some existing journals to switch to a more Open Access stance (e.g., I wish this would happen with Journal of Molecular Evolution — I resigned my position as an Academic Editor when they would not shift but there is still hope).

6. Submit as many of my past papers that were not in Open Access journals to self-archiving repositories (see the comments on my previous blog about this – it seems that this is possible even for Nature papers).

7. Work with Pubmed Central to make self archiving possible there for more papers. Right now it is only possible to submit your own work to Pubmed Central if it was NIH or Wellcome Trust funded.

8. Discuss Open Access with more scientists. Some still have notheard about it and some do not realize what the issues are.

9. Discuss Open Access with more non scientists. To get Congress to pass more rules regarding Open Access, it will help to have more pressure from non scientists. When I have described the current publishing system to non scientists, they are usually astonished by the (1) wasted money and (2) closed nature of much scientific work.

10. Work to get researchers who publish in Open Access journals “extra credit” in promotions, tenure review and grant proposal review. These people are frequently taking risks for the betterment of the scientific community and to advance scientific knowledge. They deserve credit for taking these risks.

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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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PLoS One Beta is released – a new way to publish and discuss scientific papers

Well just got an email from Chris Surridge of PLoS One saying their Beta Site is open to the public. I am excited by this new journal and system and plan to submit many of our papers there. People should check it out for themselves and hopefully give comments to them to make the system better. Some detail from the email is given below.

The first paper there that struck my eye is a paper on polyploidy in halophilic Archaea. This paper, by Sebastian Breuert, Thorsten Allers, Gabi Spohn, and Jörg Soppa suggests that polyploidy is more common in archaea than was previously appreciated.

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The email says:

Before your first visit, I want to let you know about the inherent challenges of this project and the philosophy that compels PLoS to confront them.

We want to speed up scientific progress and believe that scientific debate is as important as the investigation itself. PLoS ONE is a forum where research can be both shared and commented upon – we are launching it as a beta website so that the whole scientific community can help us develop the features.

What makes the site beta? Not the content, which features peer-reviewed research from hundreds of authors across a diverse range of scientific disciplines. It’s the additional tools and functionality surrounding these papers that will be continually refined and developed in response to user feedback.

It is this union of continually evolving user tools provided by the Topaz publishing platform and extensive content that will make PLoS ONE a success.

….

The first beta release of PLoS ONE features tools that allow users to annotate articles and participate in discussion threads. Our goal is to spark lively discussion online and we’d like to invite you to participate. Future updates will include user ratings for both papers and the comments made about them, personalized content alerts and much more.

We will be watching with interest to see how our new platform and software responds to high volumes of traffic and encourage you to give your feedback on your first experience via the site itself.

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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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Check out Open Reading Frame Blog on Open Data

Here is an Open Access must read. Bill Hooker blogs about pushing the Open Access envelope in the area of Open Data. That is, making sure the raw data from a scientific study is available. Although there are many efforts for this, he discussed something I have never really considered which is trying to make sure the journals do not somehow obtain rights to the raw data (e.g., by having it placed onto their site as Supplemental Information).

He has a suggested protocol for adding an addendum to the typical copyright agreement one might make with a journal, which is, in my mind, a great first step.

So go read about it here

——–
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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