Funny advert placement

I'm sorry to my more serious readers, but I just could not resist when I saw this. The ad placement next to a story about our work on sexual versus asexual reproduction is priceless. The full story appears here on the UPI site. The paper is here on the Molecular Biology and Evolution site.

Nasonia genomes published

I thought that I would devote my 2010 inaugural post to a report of three Nasonia genomes that appears in todays' Science. The genome paper is accompanied by a really interesting News Focus that appears in the same issue of Science.

A small group in my lab (Andrew Schurko, Danielle Mazur and me) contributed some analyses of the meiotic genes in the Nasonia vitripennis genome. Unfortunately, due to space considerations, our work fell on the cutting room floor for the Science paper. However, we do have a complete report of our findings that is in press at Insect Molecular Biology.

UPDATE: The Nasonia genome special issue of Insect Molecular Biology is now available online. Our paper, "Inventory and phylogenomic distribution of meiotic genes in Nasonia vitripennis and among diverse arthropods" is here.

(photo is copyright John H. Werren, 1980)

On sabbatical at NESCent!

After many months of blogging hiatus, I am planning to get back in the groove over the next few months. Starting this week, I am a sabbatical scholar at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. I'll be here through July, 2010. My major project will be to write a semi-popular book on the origin and evolution of sex. This will also be a great opportunity for me to recharge my batteries and to tie up some loose ends that have been accumulating.

I plan to use this blog venue to sketch some ideas that might end up in my book, so I hope that I'll be able to re-gain (or perhaps newly gain) your attention and comments! Stay tuned...

P.S. I'm twittering @johnlogsdon

GBE: Genome Biology and Evolution

Just a short note to promote the fact that the Society for Molecular Biology and Evolution (SMBE) has launched a new journal, Genome Biology and Evolution (GBE). The founding Editor is Takashi Gojobori and the Editor-in-chief is William (Bill) Martin, who was the previous Editor of the main SMBE journal, Molecular Biology and Evolution (MBE).

According to the GBE website:

"Genome Biology and Evolution publishes evolutionary advances at the forefront of genomics. Papers considered for publication report novel findings in the field of evolutionary biology that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution."

It is an on-line only, Open Access journal published for SMBE by Oxford Journals (who also publish MBE). See here for more information. Congratulations and good luck to Bill, Takashi and the Editorial Board! I had better read the instructions to authors and then get busy preparing my first submission (of what will likely be many).

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."

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!

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.

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.

No Sex in Iowa

Contrary to yesterday's post, the Sex & Recombination meeting has now been cancelled. The flooding is bad and is getting worse in Iowa City. This turn of events is very disappointing, but necessary. 

(Wet) Sex in Iowa

For those of you who might be wondering, the Evolution of Sex & Recombination meeting is continuing as scheduled (Monday 16 June to Thursday 19 June). Although parts of Iowa City are being hit rather hard with floods, the meeting venue and most of the accommodations are still in good shape. Updates will soon be available on the meeting website.

Photo by atoomsen.

Sex in Iowa

I'm sorry that I have been such an infrequent blogger for the past few months, but life has been busier than normal.

One of the things keeping me away is that I have been organizing a meeting, "Evolution of Sex & Recombination: In Theory & In Practice" to be held in Iowa City June 16-19.


We now have a final speaker schedule together and it looks to be a very exciting meeting! Registration is still open for poster-presenters and attendees.

Darwin Day is Today!

Just a short post to wish everyone a happy Darwin Day! Today is the 199th anniversary of Charles' birthday. We are busy here in Iowa City finalizing the arrangements for our celebration.

Update: we got some nice press from the local blog, CorridorBuzz.com

Iowa City Darwin Day

Reposted with light editing from the Iowa Citizens for Science site:

Darwin Day is fast approaching, and we’ll be celebrating with two and a half days’ worth of festivities here in Iowa in February, put together by Iowa City Darwin Day Inc. along with co-sponsors.

We’ll kick off Thursday night, February 14th at 7:00 pm, with Dr. Massimo Pigliucci reading from his latest book at Live from Prairie Lights, with drinks and snacks following at a location TBA.

Friday February 15th will consist of academic talks by Dr. Pigliucci and Dr. Martha McClintock.

On Saturday February 15th there will be a series of public talks followed by an informal reception in Iowa Hall.

• University of Iowa paleontologist Dr. Christopher Brochu will kick off the afternoon, whose topic will be “The Dead Speak: What we learned from the Tyrannosaurus.” Dr. Brochu was the lead researcher on the analysis of “Sue” the tyrannosaurus at Chicago’s Field Museum.
• Dr. McClintock will follow, discussing “Social Isolation and Breast Cancer: Psychosocial Regulation of Gene Expression”.
• Dr. Pigliucci will be the last of the afternoon’s talks, speaking on “What’s science got to do with it? When scientists misspeak about religion”–a topic sure to bring about some interesting discussion.
  

A panel discussion and Q&A session with all of the speakers will wrap up the afternoon, and the reception will follow.

Please join us! It promises to be an exciting and stimulating few days–and we’re also looking for ideas (and manpower!) for Darwin Day 2009.

Your Inner Fish

I just picked up a copy of Neil Shubin's new book and I'm really excited to read it. Shubin and his colleagues discovered the "transitional" fish fossil Tiktaalik. The LA Times reviewed the book earlier this week and Carl Zimmer reviews it in today's Nature (subscription).

There is a short excerpt available at the University of Chicago Magazine.

Stephen Colbert interviewed Shubin recently on the Colbert Report. Here it is for easy access:



Pharyngula already has an active discussion going on the topic...

Wired: Huckabee Denies Evolution

Wired Science has a good article on Mike Huckabee's denial of evolution. They feature the video that I have also placed here. This is a good opportunity to point folks to a great piece from Leonard Steinhorn and Charles Steinhorn where they consider "belief" in evolution: "Is the Theory of Evolution Really a Matter of Faith?".

Elvislution!

A little Mojo Nixon for your pleasure!

Judgment Day

It's been a busy term... So much that I missed the original airing of the NOVA program "Judgment Day: Intelligent Design on Trial" last week. Luckily for me, the entire episode is now available for viewing online, which I took advantage of tonight. If you haven't seen the show, you should. It's very well done from both scientific and journalistic points of view. It will soon be required viewing for my undergraduate Evolution course.