Category: Misc.

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

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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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Microbes, Minerals, and the Environmen – Abelson Lectures

I just had this site pointed out to me by Merry Youle.

This site is a collection of audio and video of lectures that were for the “Microbes, Minerals, and the Environment” symposium. The collection includes talks by David Stahl, Derek Lovely, Anna Louise Reysenbach, Faroq Azam, Jonathan Zehr, and Paul Falkowski, all relating to microbes in the enviornonment. I have not watched all of them but the ones I have seen are quite good.

The symposium was in honor of Philip Abelson, who died in 2004.

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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 and Education Win Another Round …

Well, the good news keeps pouring in for science education and the teaching of evolution. The Cobb County School Board, which had tried to insert religious points of view into the teaching of evolution, have backed down. They had placed stickers on biology textbooks that read

This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully and critically considered

Yet, of course they did not label any other area of science in this way. AP reports that

The Cobb County school board signed an agreement filed in U.S. District Court on Tuesday agreeing never to use a similar sticker or to undermine the teaching of evolution in science classes.

It is nice to see that they have had a change of heart, or at least have realized that they would lose this fight. Either way, science and education win this round. Unfortunately, the proponents of Intelligent Design, will try again and again. And they should be fought every step of the way to keep them from attacking the teaching of evolution in science classes.

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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 Darwin?

Well I have been surfing around looking for downloadable versions of some of Darwin’s books. Here are some links:

Anybody out there know of others please point them out.

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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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Announcement: Thinking Small: Microbial Diversity and Its Role in Conservation – The Center for Biodiversity and Conservation’s 12th Annual Symposium

Just thought I would post this here as it seems like it will be a really cool meeting (and I was on the steering commitee.

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Thinking Small: Microbial Diversity and Its Role in Conservation
The Center for Biodiversity and Conservation’s Twelfth Annual Symposium
American Museum of Natural History
April 26 and 27, 2007
http://cbc.amnh.org/symposia/microbes/

Symposium Theme
Microscopic organisms-including viruses, bacteria, archaea, and single-celled eukaryotic organisms-comprise the vast majority of life on the planet, yet startling little is known about their true diversity and the multitudinous roles that they play in the ecosphere. The knowledge that we do have tends to come from either those organisms that can be cultured in the laboratory (estimated to be <1% of all species) or those that make us or other organisms that are important to us sick. The revolution of using DNA sequences to discover and describe microbial diversity has drastically altered our view of the microbial world and its players, however. Less than two decades ago, using ribosomal RNA gene sequences, Carl Woese and colleagues proposed an entirely new classification of life, that of three domains of organisms-Bacteria, Archaea, and Eukarya-in opposition to the traditional five-kingdom schema. Now, new biochemical processes, including new forms of photosynthesis and even electricity-generating bacteria are being discovered as culture-independent and broader explorations into new habitats are performed. Yet, at the same time that we begin to uncover new hidden potential benefits of microorganisms, the news is also replete with stories of so-called emergent diseases that threaten humans as well as other organisms on the planet.

This symposium will bring together a diverse group of microbiologists and conservation biologists to explore this intersection of two fields that, until now, has not been considered in depth. We hope to address the broad questions of: How much microbial diversity is there on the planet? How does this diversity affect other organisms, both positively and negatively? How should conservation practices take microbial life into account?

Audience: This symposium will bring together scientists from the traditionally disparate fields of microbiology and conservation, including biogeochemists, marine microbiologists, disease ecologists, and microbial systematists. as well as conservation practitioners, wildlife managers, policy makers, educators, students, and interested members of the general public.

SPECIAL STUDENT PRICING WILL BE OFFERED!

CALL FOR POSTERS: The symposium will include a poster session. Details for content guidelines and abstract-submission requirements are available at http://cbc.amnh.org/symposia/microbes/.

TO RECEIVE SYMPOSIUM UPDATES AS THEY BECOME AVAILABLE, email biodiversity@amnh.org.

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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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Classic papers in genetics and evolution that are available in Pubmed Central – Paper 1 – Luria and Delbruck on the origin of mutations

I am starting a new series here —- finding and writing about classic papers in Evolution and Genetics and Molecular Biology that are available for free in Pubmed Central. And though plenty of classic papers are not avilable, a good collection of them are.

My first selection is Luria and Delbrück’s paper from 1943 on the origin of mutations. This papers is near and dear to my heart in many ways and I still remember looking it up for the first time when I was an undergraduate. I was taking a class from Jennifer Doudna on the origin of life, and we had to write a paper as part of the class. In the class we had discussed a new paper by John Cairns and colleagues that revisitid the origin of mutations question. Cairns et al. result suggested to them at least that bacteria could pick and choose the mutations they needed for increased fitness in a particular situation (suggestive of so-called Lamarckian evolution to them). I was fascinated by this work (so much so, that it became the topic of my grad. school application essays and the topic of my first two years of PhD research in Phil Hanawalt’s Lab). So I chose to write a paper on the origin of mutations.

Obviously, to write such a paper I had to go to Luria and Delbrück’s work since they were the first to experimentally test the question of how much mutations pre-existed selection and how much they arose after selection. I stillremember sifting through the old journals in the library at Harvard to find this and turning the pages in teh dust covered volume to read it.

Luria and Delbrück chose as their experimental system resistance to bacteriaphage and their model organism, Escherichia coli. In their paper first the describe the theoretical underpinning of their wor. In their theory they come up with a way to do an experiment to test whether mutations pre-exist selection or arise in response to it – something now generally known as a fluctuation test. Basically the idea is simple. Take a particular form of the bacteria. Innoculate multiple test tubes with a small amount and let each test tube grow up to a dense culture. Then expose bacteria from each tube to the selective pressure. If the mutations pre-exist selection then there should be big differences between the replicate test tubes in the number of mutants since in some the mutation would arise early in the growth of the culture and in some they would arise late (this is known as a jackpot distribution). If the mutations arise after selection then each tube should have somewhat similar numbers (with some variation around a mean).

And when they did the experiments the results followed very closely the jackpot model. They stated:

We consider the above results as proof that in our case the resistance to virus is due to a heritable change of the bacterial cell which occurs independently of the action of the virus. It remains to be seen whether or not this is the general rule. There is reason to suspect that the mechanism is more complex in cases where the resistant culture develops only several days after lysis of the sensitive bacteria.

And thus they showed that mutations unequivocally pre-exist selection. Now, it turns out that their experiment had a flaw – since they were using a lethal selection (phage) the system did not really allow for a long period of time for the mutations after selection to arise (when your dead it is hard to generate mutations). The Cairns experiment (and Ryan’s before him) showed that some unusual results occurred if you used a non lethal selection. So one cannot really use Luria and Delbrück’s experiment to disprove the possibility that mutations arise after selection. Nevertheless, their proof that mutations can exist before selection was a fundamental discovery. And their methods were used throughout bacterial genetics for years (to this day in fact). For more detail see Access Excellence page about Luria and Delbruck.

This is such a fundmentally important paper, and it is great that this paper is available, free to all, in Pubmed Central. See below:

Mutations of Bacteria from Virus Sensitivity to Virus Resistance.
Luria SE, Delbrück M.

Genetics. 1943 Nov; 28(6): 491-511.
PMCID: 1209226
| Abstract | PDF-1.3M |

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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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Petco as a surrogate for a museum

I took my daughter to Petco the other day again. We treat it as a zoo/aquarium which works perrty well. They have lots of fish, birds, mice, and other animals and she loves it. I know, it probably does not treat the animals exceptionally well, and I do not buy animals from there. But my daughter loves fish and this is a great way for her to see some without going too far.

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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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Passing of a Legend – Esther Lederberg

The New York Times ran an obituary today for Esther Lederberg, who passed away on November 11. Dr. Lederberg was one of the giants of microbiology and her research was the precursor for multiple Nobel Prizes and laid the groundwork for much of the molecular biology revolution. Among her many amazing pieces of work:

  • The isolation of lambda phage, a virus that infects the bacterium E. coli. This virus has been used as a model system for studying the molecular basis of life.
  • She and her husband invented replica plating, a method that revolutionized bacterial genetics.

Amazingly to me, and thanks to Pubmed Central and the American Society of Microbiology, her replica plating paper is available for free online here.

All microbiologists out there should read this paper and should say thanks for the work of a true giant in the field.

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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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