Oakley Keeping his Eye on Evolution

I saw an interesting talk today and thought I would post on it. I was not expecting to be able to go to the talk as I was supposed to be at a workshop in San Francisco but had to bail on it because my kids have been sick. But I did go in to Davis for a brief spell to go to a seminar by Todd Oakley who gave a talk here today.

It was a generally insightful phylogenomic tour of the evolution of opsins and eyes in animals. He also mentioned a paper he had recently in PLoS One on Animal Opsin evolution. This is from the work of his graduate student David Plachetzki and it does a nice job of doing “phylogenomic” analysis in the way I think of phylogenomics — that is — a integration of evolutionary and genomic analyses. (NOTE – I think it is kind of lame that people use the term phylogenomics, which I coined by the way, to refer to “using genomes to infer evolutionary trees). It is a paper worth checking out if you are interested in the origin of novelty.

I am putting links here to some of their figures and embedding them in this blog because, well, I can since PLoS One uses a broad Creative Commons license. For example – see Figure 6 from their paper below (the citation is Plachetzki DC, Degnan BM, Oakley TH (2007) The Origins of Novel Protein Interactions during Animal Opsin Evolution. PLoS ONE 2(10): e1054. doi:10.1371/journal.pone.000105).

Figure 6. Ancestral state reconstruction of G protein-binding interactions for each metazoan opsin-mediated phototransduction cascade obtained by simulated mutational mapping [64] (see methods).For each class of opsin, the P value of the reconstructed ancestral G α interactions is represented in pie graphs. Ancestral G protein interactions in phototransduction cascades mediated by ciliary, rhabdomeric and Go opsins can be significantly resolved (P>0.95) but the ancestral states of the rhabdomeric+Go, and cnidops clades are equivocal. ML state reconstructions shown for each node as colored branches. Red, Gi/t; Blue, Gq; Green, Go; Black, no G protein interaction (as is the case for RGR/Retinochrome opsins); Grey, equivocal reconstruction from ML. Reconstructed ancestral amino acid motifs of the 4th cytoplasmic loop region of opsin are shown along branches in logos. Maximum vertical height scales to P = 1.0. We obtained clear reconstructed states for most of the residues in a conserved tripeptide motif (residues 310, 311 and 312, horizontal bar) for the ciliary, rhabdomeric and Go /RGR nodes. For the most part, the remainder of the residues in can be unequivocally reconstructed to the level of Dayhoff classes. B = HRK, X = LIVM, J = GATSP, Z = DENQ..

See also Figure 2

Figure 2. Unrooted metazoan-wide phylogeny of opsins, new cnidarian genes in bold, branches proportional to substitutions per site. Circles at nodes indicate Bayesian posterior probabilities (White = 1.0, Red>0.90, Blue>0.80, Green>0.70, Yellow>0.60, Black>0.50). cil = ciliary, rh = rhabdomeric.”

Open Access dinosaurs and way to go Paul Sereno

Well, I met Paul Sereno, the dinosaur hunter, for the first time at SciFoo camp (for more about that see here). I confess I was skeptical when he said he was committed to Open Access. But now he has really proven his OA chops. He has a new paper in PLoS One on some friggin cool dinosaur fossils.

The paper is Structural Extremes in a Cretaceous Dinosaur by Paul C. Sereno1*, Jeffrey A. Wilson2, Lawrence M. Witmer3, John A. Whitlock2, Abdoulaye Maga4, Oumarou Ide4, Timothy A. Rowe5

Check it out at PLoS One.

GME 2007 – Getting feedback on PLoS ONe

While at the GME meeting – I have now been approached by 3 people saying they really liked the discussion I initiated on PLoS One for a paper on metagenomics a few weeks ago. They were not saying they liked my comments but that there was an active discussion about some important topics. I think the function on PLoS One has great potential to engage the broad scientific community in discussions that might have previously been limited to journal clubs. So it is nice to see (1) that people are reading stuff on PLoS One and (2) that they seem to like the commenting function.

Rated my first paper in PLoS One


Well, PLoS One has announced its rating system is open. See Chris Surridge’s Blog for more detail here. This is basically the first good system for trying out ratings for scientific publications in much the way it is done at YouTube and other Web 2.0 type systems.

I personally am not sure if I think PLoS One is the perfect system for scientific publishing. But we desperately need to try out new systems and as an Open Access Web 2.0 scientific publishing system, the concept is worth trying. So – I decided to try it.

I rated my first paper. I picked a paper by Xiang Xia Min and Donal Hickey on DNA barcoding. Why did I pick this paper. Well a few reasons. First, when I searched PLoS One for “metagenomics” and “metagenomic” it was one of the papers that came up. As soon as I saw the Barcoding title line I knew I had to look at this paper. Why? Well a few years ago, I posted a “dissent” on Faculty of 1000 about a paper on Barcoding. I stand by my dissent in that article. Basically I said that Barcoding sounded a heck of a lot like what Pace and others have been doing with rRNA surveying of uncultured microbes for a long long time. And it seems to me that the barcoding researchers are rediscovering some of the same findings and challenges that Pace and others found. Of course, not all can see my Faculty of 1000 review. Why? Well it is not Open Access. Bummer. Especially since the response by Hebert was unconvincing too … he basically said that rRNA was not used to delineate species. Apparently he had never heard of phylotypes or any of the extensive work using rRNA to do EXACTLY what they are suggesting mitochondrial genes could be used for in plants and animals.

Anyway – enough about Faculty of 1000. In the new paper, the authors discuss some aspects of barcoding and in particular they address whether one gene can represent all the genes in a mitochondrial genome. Basically, they say yes. But that is beside the point here. You want to know more. Read there paper here. And my comment here. That is yet another benefit of Open Access.

I call on everyone out there to find a paper in which you are interested and rate it and comment on it at PLoS One.

Min, X., & Hickey, D. (2007). DNA Barcodes Provide a Quick Preview of Mitochondrial Genome Composition PLoS ONE, 2 (3) DOI: 10.1371/journal.pone.0000325

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.

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.

Harvard Crimson changes its mind – supports PLoS One

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

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

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

Perhaps most importantly, they end the editorial with

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

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

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.

PLoS One

Well, PLoS (The Public Library of Science) has announced a new publishing venture called PLoS One.

For those who do not know, PLoS was started a few years ago by a group of scientists (incuding my brother) with the goal of opening up access to scientific literature. For non scientists it may be surprising to find out that scientific and medical research is usually published in journals which are very expensive to purchase. Thus though the research is supposed to be for the benefit of humaninty, it turns out that one of the primary benefits goes to a few companies and societies that publish the journals. Amazingly, even though the journals frequently do little other than repackage papers written by scientists, they not only make enormous amounts of money off of this, they somehow get the copyright to the papers. In general, these journals are a massive roadblock to scientific and medical discovery.

PLoS started a few journals a few years ago to try and provide alternatives to the standard model. These journals are “Open Access” and thus much better for the world. What PLoS has done better than others attempting to make scientific literature open acces is to show that one can publish a very high quality journal that is still free to all (e.g., PLoS Biology).

Now PLoS has announced a completely new way to publish scientific literature. Called PLoS One this seems like a strong attemp to bring scientific publishing into the 21st century. Among the “features” they say will be there are much more rapid publication, publication of all science (with the only criteria being that it is validated by peer review – no restrictions will be made to force the publication to be radically novel) and development of an online community around the publications.

Stay tuned — we will have to see how it works out but the initial impression I have is that it sounds quite nice.