Nature's 15 Evolutionary Gems

This week's issue of Nature (1 Jan 2009) includes a 17-page article by Nature editors Gee, Howlett & Campbell entitled "15 Evolutionary Gems". It's a tidy summary of key articles published in Nature in the past decade that each provide clear evidence for evolution. The summary article (and apparently all of the primary articles) are "free to download and disseminate, and each is accompanied by a brief editorial introduction to its context and significance". The article is featured in Nature's special website Darwin 200.

The summary article starts...

"Most biologists take for granted the idea that all life evolved by natural selection over billions of years. They get on with researching and teaching in disciplines that rest squarely on that foundation, secure in the knowledge that natural selection is a fact, in the same way that the Earth orbits the Sun is a fact.

Given that the concepts and realities of Darwinian evolution are still challenged, albeit rarely by biologists, a succinct briefing on why evolution by natural selection is an empirically validated principle is useful for people to have to hand. We offer here 15 examples published by Nature over the past decade or so to illustrate the breadth, depth and power of evolutionary thinking. We are happy to offer this resource freely and encourage its free dissemination."

Obama: Science and Facts are Valued

I don't know much about Steven Chu yet, but I am pleased that Barack Obama has selected a real scientist for his cabinet.

I heard the following quote from Obama twice on my home from work yesterday and again this morning:

"His appointment should send a signal to all that my administration will value science, we will make decisions based on the facts..."

I cheered out loud! The full text of Obama's announcement can be found here. (Photo from Change.gov)

SMBE 2009 - Call for Symposia

Earlier this week, I posted a formal announcement on EvolDir that the organizers of SMBE 2009 are now accepting proposals for contributed scientific symposia. The proposals are due on January 12, 2009. See the meeting webpage (http://smbe2009.org) for more details.

I hope to get back to blogging soon!

I voted for Obama this morning

I like to vote on Election Day, and I sucessfully resisted the considerable urge for Early Voting this year. Since I was anticipating a wait at the polls, I got up a bit early this morning. I arrived with my 11-year old son, Evan, at the polling place for Coralville 6 (Wickham Elementary, his school) at ~7:40am. Evan went over to the Kid's Voting booth and voted while I initially got in the wrong line (no coffee yet)... After waiting in line for a few minutes, I realized that I needed to sign-in. So I did that and returned to the line to pick up my ballot. The line was ~20 people long and was moving briskly. There were ~15 voting carrels on one side of the gymnasium (the same gym that was jam-packed with Democrats on Caucus night).

The ballot was a two-sided legal-sized document with bubbles to fill in. As it turns out, I could have just bubbled-in the Democratic strait ticket. But it was a lot more fun to fill in the bubbles separately for Obama/Biden, Harkin, Loebsack and few others. I showed Evan my vote for Obama and he approved. We then together fed the ballot into the reader and each picked up "I VOTED" pins. All together it took about 15 minutes.

I am looking forward to a new start for this country!

Dodos: Free in Iowa City!

Tomorrow (Monday, Sept. 22) in Iowa City I will be co-hosting a free public screening of "A Flock of Dodos" in Biology Building East (BBE) 101 at 7:00pm. This event is part of Scienceblogs 10^6 comment festival, via our two Iowa City-based ScienceBlog-ers, Tara Smith (Aetiology) and Evil Monkey (Neurotopia). It is also associated with the Evolution undergraduate course (Biology, 002:131) that I teach with Bryant McAllister (can you say "extra credit"?)

According to Wikipedia:

"The film attempts to determine who the real "dodos" are in a constantly evolving world: the scientists who are failing to promote evolution as a scientifically accepted fact, the intelligent design advocates, or the American public who get fooled by the "salesmanship" of evolution critics. While Randy Olson ultimately sides with the scientists who accept evolution, he gives equal air time to both sides of the argument..."

Thanks to the filmaker Randy Olson for allowing us to screen this film for the public! I'm looking forward to it, since I have not seen it yet.

Publishing by Press Release: PNAS Lags Again

Here we go again...

I got an email message on Tuesday (August 26th) from the NSF announcing the publication of an apparently interesting and provocative new paper by Song et al. The message linked to a press-release from NSF (dated August 25th) entitled "DNA Barcodes: Are They Always Accurate?"

According to the NSF Press Release:

"DNA barcoding is a movement to catalog all life on earth by a simple standardized genetic tag, similar to stores labeling products with unique barcodes. The effort promises foolproof food inspection, improved border security and better defenses against disease-causing insects, among many other applications.

But the approach as currently practiced churns out some results as inaccurately as a supermarket checker scanning an apple and ringing it up as an orange, according to a new Brigham Young University (BYU) study.

The results are published online this week in the journal Proceedings of the National Academy of Sciences (PNAS)."

After repeatedly checking the PNAS Early Edition website all last week, I see that paper in question was finally released on Friday (August 29). It's even fully Open Access!

Hojun Song, Jennifer E. Buhay, Michael F. Whiting and Keith A. Crandall "Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified" PNAS published August 29, 2008, doi:10.1073/pnas.0803076105

This is really frustrating. All of that effort spent to publicize the paper and people can't even get their hands on it. If you are a journalist, do you wait until the paper appears before writing your story? Probably not, in many (most?) cases. That means writing your story without the paper at hand. By the time the paper comes out (in this case, four days later), it's probably no longer news.

Last fall, Larry Moran wrote a post on Sandwalk entitled "Mythical PNAS Papers" about this problem. I really wish that PNAS would listen to him...

By the way, I think that the paper deserves the PR!

Photo Credit: Biodiversity Institute of Ontario

Dawkins' Genius of Darwin

I just discovered that there is a new three-part series, The Genius of Charles Darwin, that was broadcast on UK Channel 4. I tried to buy the episodes on iTunes, but they are only available in the UK. Luckily they are all posted on YouTube.

Below is the first part (of five) of the first episode, available on YouTube.

You can read more about the episodes and find more links at RichardDawkins.net.

Sexy paper just out in PLoS ONE

My lab has taken its initial journey on the PLoS ONE train.

Yesterday, our paper entitled "An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis" was published in PLoS ONE. It's a updated and detailed report on the ongoing work in my lab to generate and curate an "inventory" of genes involved in meiosis that are present across major eukaryotic lineages. This paper focuses on the protist, Trichomonas vaginalis, an organism not known to have a sexual phase in its life cycle.

Here is the Abstract:

Meiosis is a defining feature of eukaryotes but its phylogenetic distribution has not been broadly determined, especially among eukaryotic microorganisms (i.e. protists)—which represent the majority of eukaryotic ‘supergroups’. We surveyed genomes of animals, fungi, plants and protists for meiotic genes, focusing on the evolutionarily divergent parasitic protist Trichomonas vaginalis. We identified homologs of 29 components of the meiotic recombination machinery, as well as the synaptonemal and meiotic sister chromatid cohesion complexes. T. vaginalis has orthologs of 27 of 29 meiotic genes, including eight of nine genes that encode meiosis-specific proteins in model organisms. Although meiosis has not been observed in T. vaginalis, our findings suggest it is either currently sexual or a recent asexual, consistent with observed, albeit unusual, sexual cycles in their distant parabasalid relatives, the hypermastigotes. T. vaginalis may use meiotic gene homologs to mediate homologous recombination and genetic exchange. Overall, this expanded inventory of meiotic genes forms a useful “meiosis detection toolkit”. Our analyses indicate that these meiotic genes arose, or were already present, early in eukaryotic evolution; thus, the eukaryotic cenancestor contained most or all components of this set and was likely capable of performing meiotic recombination using near-universal meiotic machinery.

Here are my impressions of publishing in PLoS ONE (so far)...

PROS:

• It was fast. Submission to acceptance was less than a month. It took us longer to revise the final copy than to gain initial acceptance.
• The PLoS editorial staff were very accommodating and helpful throughout the process. In particular, they quickly transferred our manuscript between other PLoS journals (where it was initially rejected).
• The review process was great. In this case, only one reviewer was contacted. S/he liked the paper, and gave some suggestions for improvement that were left up to us to incorporate. We heeded some, but not all of the advice given.
  
• It was (fairly) inexpensive. The "page charges" ($1125) were ~40% less than those levied for a similar non-OA journal that we have published in recently.

CONS:

• There was no opportunity given for making corrections to proofs. I have already identified an issue with one of the tables that would have been corrected in proof had there been an opportunity. There are always a few things that the author can notice that the copy editors (however talented they are) might miss. Why not add the author as a final checker?
• The Journal Management System (for e-submission and tracking) is a bit too complicated for my taste. It takes quite a while (1+ hour) to get all of the information pasted into the form. I may just need to get to used to this level of front-end effort. However, as noted above, the journal staff helped me by moving all of the manuscript info from one journal to another. If not, it would have been painful to repeat.
  
• As of this posting, our paper has not yet appeared in the listing of papers published yesterday. I assume (and hope) that this is a small and non-frequent oversight, but an annoying one when it's my paper!

I think that the PROS much outweigh the CONS in this case. Direct any comments on the paper itself to the PLoS ONE site.

Coitus Interruptus in Iowa

May 31 to June 3, 2009!

These are the dates for Evolution of Sex & Recombination: In Theory & In Practice.

Based on overwhelmingly positive responses from the previously scheduled speakers and registrants, we have decided to reschedule the meeting for next year. We are hopeful to have significantly drier weather in 2009.

The reborn Sex & Recombination meeting will immediately precede SMBE 2009, the annual meeting of the Society for Molecular Biology & Evolution that will also be held in Iowa City June 3-7, 2009. Both events are being hosted by the Roy J. Carver Center for Comparative Genomics with financial support coming from a number of sponsors.

I'll be posting here and on EvolDir as futher details become available.

Image shows the Iowa River as it runs through the University of Iowa on June 18th. Thanks to Monica.

Future Sex in Iowa??

Things have settled down a bit here in Iowa City. Although a significant portion of the campus has been hit hard by the flooding, my Department, lab and home have all been spared. We are "suspending non-essential activities" on campus this week, which means that my Department and lab are shut down for the rest of the week. Thanks to everyone for their concerns and kind wishes in this difficult time.

The organizing committee has not been able to meet to discuss the possibility of re-scheduling the Sex & Recombination meeting for a future date. I'll be querying the registrants in the coming weeks for their thoughts. I am also strongly considering attending the Evolution 2008 meeting in Minneapolis next week (as I had originally planned). If so, I'll be looking forward to hearing peoples' thoughts on this matter in person.

Again, thanks to everyone for their patience in this difficult time.