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.

People, Content & Technology @ ScienceOnline2010

I am a very frequent attendee and eager participant at scientific conferences: I have logged ~100 in my ~20 years in science. To me, meetings are easily one of the top five things that make being a scientist so much fun. Exchanging ideas (new & old), meeting people (new & old friends), showing off your work (usually new, but sometimes, old), having a good time (which never gets old!)....these reasons are all part of the experience. But sometimes meetings just get you fired up about something(s) and you leave with a fire lit under you. This was one of those for me. And although I knew that I would enjoy myself at Science Online 2010 (aka #scio10) and meet at least some of the criteria above, I was not prepared to leave with my rear side roasting with so many ideas and so much inspiration.

The jazz I got from #scio10 comes from three intertwined categories:

People. Meeting and interacting with people is my favorite conference activity. It's especially great when I first meet someone in person whose work I have followed. This is true for science meetings, but it worked on a wholly different scale for me at #scio10: of the 200+ attendees, I had previously met no more than 10 in person. However, I knew at least 50 more from their online work—mostly science bloggers. Come to think of it, that's probably alot like what happens at a graduate student's first scientific meeting, and I am reveling in that re-found sense of discovering a community that fits. And then there are the people that I met for the first time who I knew nothing about in advance. There are always new people to meet, especially when attending conferences for the first time. But I was stunned by the fraction of people I met who fell in the category of "why did I not know you before?". I can just hope that some of those folks had the same reaction to meeting me!

The intersection of people and content was probably the most amazing thing about this meeting. I have never seen such a meritocracy. Sure, science is based on merit, but there is a real ladder to climb and sometimes a glass ceiling to break. The participants at this meeting ranged from a 9th-grader who writes science computer games to internationally known science journalists (and a HUGE range in between). Many (probably most) of the presenters were self-made experts in newly emerging areas, some in the process of earning PhDs etc., and some that don't need to play in the academic world. Even in the currently-difficult times for both science and journalism (and many other things), there was a clear sense of "Yes we can!" that permeated #scio10 .

Content. The meeting couldn't have started out on a more content-relevant note for me: the first session I attended was "From Blog to Book: Using Blogs and Social Networks to Develop Your Professional Writing"As I am now digging into my sabbatical book project, this session jolted me to attention. The advice of Tom Levenson, Brian Switek and Rebecca Skloot was just what I needed. I must decide very soon whether to pursue the academic publisher route or to try the trade route taken by authors of most successful popular science books. Next on my schedule was "Rebooting Science Journalism in the Age of the Web" in which a panel discussed the sometimes uneasy ecosystem of blogs and more traditional media outlets. The somewhat controversial press-release site, Futurity, created some heat (and maybe some light), but the memorable lesson by Carl Zimmer about his reporting on the twisted biology of duck penises generated the most virulent meme of the whole meeting. In the third morning slot I joined the "Scientific Visualization" session in which Tara Richardson (@science_goddess) regaled us with the latest cool tools and facilitated some interesting discussion on this under-appreciated (and thus, under-developed) aspect of science communication.

On Saturday afternoon, I attended the helpful session "Scientists! What can your librarian do for you?"which reminded me that I can almost certainly make use of those smart people whose mission is to help me do my science (and writing) better. Next was "Open Access Publishing and Freeing the Scientific Literature (or Why Freedom is about more than just not paying for things)" moderated by friend and colleague Jonathan Eisen (aka @phylogenomics; pictured above). It's going to be a tough road to OA publishing, but I am starting to see that it is a fight worth waging. For the final session of the day, I joined the packed-to-the-gills session "Writing for more than glory: Proposals and Pitches that Pay" moderated by Rebecca Skloot with key insight from Ivan Oransky and Clifton Wiens. Although much of the session was aimed at pitching stories to magazines, there was a fair bit of discussion of book proposals and how to craft a project that publishers will buy—literally. Much to my chagrin, the first lesson was that the pitch "My book is on X" doesn't fly. Stories sell books and topics don't. OK, more homework for me...it might be a good thing that my book is "on Sex", but that isn't enough. So when the participants were invited to give their pitch to the experts, I knew that I wasn't up to snuff. However, shark researcher (and future author) David Shiffman (@whysharksmatter) bravely jumped right in—to our benefit. The most memorable line from the pitch-dissection was 'NPR is more important than PhD'; since David had been interviewed on NPR. Indeed, as I later found out to my surprise, David doesn't have his PhD (yet).

After a great banquet and party on Saturday night, I was ready to go again on Sunday morning, starting with "Broader Impact Done Right" hosted by a panel of postdocs, grad students and science communicators. The opening film, in which various portrayals of scientists in movies and television made us both laugh and cringe, presaged some great discussion about how we can appeal to various constituencies that we really need to reach. Since I wanted to hear more about science journalism, I next attended "Getting the Science Right: The importance of fact checking mainstream science publications — an under appreciated and essential art — and the role scientists can and should (but often don’t) play in it" I was surprised to learn about how unevenly the fact-checking is done, and when it is done, how arduous and expensive it can be! In the category of saving-the-best-for-last, the final session that I attended was "Blogging the Future – The Use of Online Media in the Next Generation of Scientists" in which a group of high school students from Stacy Baker's Biology Class individually presented their projects, ranging from an analysis of student use of blogging and the social web for education and fun to iPhone application development for science learning. These kids absolutely stole the show with their poise and content, giving many of us renewed confidence for science and its communication in the future.

Technology. As if the people and content weren't enough, in these three short days I also experienced some serious surges in my use of and appreciation for technology. For the first time ever, I didn't bring a pen or pad of paper to the meeting. I took all of my notes on my iPhone, which was the only device I used while onsite. In my office is a two-foot pile of legal pads and notebooks containing mostly illegible notes from 20 years of previous meetings. But in my difficult transition from paper to electrons (I am a very slow keyboard typist), I have gotten lazy about note-taking over the past years. So I was glad to find out for myself that I am a reasonably adept two-thumb note taker! And I can email myself my notes with one click!

I also jumped in with both feet to Twitter. As an occasional tweeter (@johnlogsdon), I use the medium for some things, but I had not yet figured out the ratio of function:fun. By using the hashtag #scio10 all of the meeting tweets were instantly readable by all of the twitter-ers (onsite & off) in REAL TIME. By the end of Day 1, I was hooked. As of writing, my total (13-month) tweet count is 235—of which ~70 were sent during the three days #scio10 (which currently total >6300)! Granted, some of those tweets were part of the fun game played at Saturday's banquet, in which the fastest tweet with the right answer won a prize. I apparently have mastered speed-tweeting, since I won one of the prizes: a signed copy of Rebecca Skloot's forthcoming book "The Immortal Life of Henrietta Lacks" (see image above).

There's so much more that I didn't say here, but I hope that my account will give you a sense of how pleased I am to have participated in #sci010. Thanks to Bora Zivkovic (pictured above), Anton Zuiker and everyone else (including the generous sponsors) who contributed to ScienceOnline 2010!

Mary Roach orates on orgasms

Mary Roach is the author of Stiff, Spook, and most recently—and very relevant to me—Bonk . She gave a very entertaining TED talk on "Ten things you didn't know about orgasm". It's both funny and informative.

I read Bonk last summer (?) and while I enjoyed much of it, I also had some mixed feelings. Perhaps I'll put together a review sometime.

In the meantime, enjoy...

Thanks to Pleiotropy for the lead.

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

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.

Green Porno

I can't believe that I missed this, but thanks to a colleague, I can now share....

In a series of short films that premiered at the Sundance Film Festival earlier this year, Isabella Rossellini plays the part of various invertebrates in various acts of sexual reproduction. You can now see them all online at the Sundance Channel website.

According to the press release:

"Green Porno is a series of very short films conceived, written, directed by and featuring Isabella Rossellini about the sex life of bugs, insects and various creatures. The films are a comical, but insightful study of the curious ways certain bugs “make love”.

Each film is executed in a very simple childlike manner. They are a playful mixture of real world and cartoon. Each episode begins with Isabella speaking to the camera “If I were a…(firefly, spider, dragonfly etc.). She then transforms into the male of the species explaining in a simple yet direct dialogue the actual act of species specific fornication. The costumes, colorful sets and backdrops as well as the female insects (all simple paper cut-outs and sculptures) contribute to the playfulness of the films. The contrast of this “naïf” expression and filthy sex practices adds to the comicality of Green Porno. This child-like manner allows us to describe things that could possibly come across as offensive to some."

My favorite is one of two non-arthropod shorts: the Snail (pictured above).

Here is a short piece I found on You Tube:



The vignettes remind me of the Dr. Tatiana televison series that was apparently too bold for US sentiments (but that I have been lucky to see!).

It looks like it's hitting the blogs now (Wired), so I had better get this posted. Enjoy!

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.

Evolution of Meiotic Genes: The Case of Spo11

In the vein of shameless self-promotion, it's my pleasure to announce that a recent paper from my lab has just been published as an Advance Access article in Molecular Biology & Evolution: Protist Homologs of the Meiotic Spo11 Gene and Topoisomerase VI Reveal an Evolutionary History of Gene Duplication and Lineage-Specific Loss (Shehre-Banoo Malik, Marilee A. Ramesh, Alissa M. Hulstrand & John M. Logsdon, Jr., Molecular Biology & Evolution, in press).

This paper is the first in a series of papers that is emerging from Banoo Malik's PhD thesis and is a result of a long-standing project with former postdoc Marilee Ramesh (now at Roanoke College). It's also the first of a number of meiotic "gene stories" that we have been untangling over the past few years. The image shown is a summary of the phylogenetic distribution of Spo11 homologs that we determined. The paper is not Open Access (sorry); however, if you are interested in reading it and do not have a subscription to MB&E, drop me an email.

Abstract
Spo11 is a meiotic protein of fundamental importance as it is a conserved meiosis-specific transesterase required for meiotic recombination initiation in fungi, animals and plants. Spo11 is homologous to the archaebacterial topoisomerase VIA (Top6A) gene, and its homologs are broadly distributed among eukaryotes, with some eukaryotes having more than one homolog. However, the evolutionary relationships among these genes are unclear, with some debate as to whether eukaryotic homologs originated by lateral gene transfer. We have identified and characterized protist Spo11 homologs by degenerate PCR and sequencing and by analyses of sequences from public databases. Our phylogenetic analyses show that Spo11 homologs evolved by two ancient eukaryotic gene duplication events prior to the last common ancestor of extant eukaryotes, resulting in three eukaryotic paralogs: Spo11-1, Spo11-2 and Spo11-3. Spo11-1 orthologs encode meiosis-specific proteins and are distributed broadly among eukaryotic lineages, though Spo11-1 is absent from some protists. This absence coincides with the presence of Spo11-2 orthologs, which are meiosis-specific in Arabidopsis and are found in plants, red algae and some protists, but absent in animals and fungi. Spo11-3 encodes a Top6A subunit that interacts with topoisomerase VIB (Top6B) subunits, which together play a role in vegetative growth in Arabidopsis. We identified Spo11-3 (Top6A) and Top6B homologs in plants, red algae, and a few protists, establishing a broader distribution of these genes among eukaryotes, indicating their likely vertical descent followed by lineage-specific loss.

Sexy Fungi

I just found out that ASM Press has recently published a new book entitled "Sex in Fungi: Molecular Determination and Evolutionary Implications", (Editors: J. Heitman, J.W. Kronstad, J.W. Taylor, & L. A. Casselton; ISBN: 978-1-55581-421-2). My Department colleague, David Soll, who wrote a chapter on mating type switching in Candida, let me borrow his copy for the weekend. It looks really great.

The release of this book is good timing for me, too. I have a recently-funded project in my lab to study the evolution of sex and meiosis in diverse fungi. A postdoctoral position is available in my lab immediately to work on this project. Send me an email if you are interested in hearing more.

Why Rosie doesn't work on Sex

My friend and colleague, Rosie Redfield, has written an interesting post about the origin of eukaryotic sex, entitled "Why I don't work on sex in eukaryotes ". She sums up what we do and don't know about deep eukaryotic relationships and how this impinges on the origin of sex and meiosis. One bottom line is that we still don't know what the earliest branch on the eukaryotic tree is. The other is that it might not matter for the origin of meiosis since work in my lab has shown that homologs of meiotic genes are present in all of the major protist lineages (e.g, this paper, but stay tuned for more details...). Rosie ends her provocative post by paying me a sincere compliment:

"I'm glad that John Logsdon has been working on this, rather than me."

Thanks, Rosie!

WARNING! (or, now I'm really proud?)

This rating was determined based on the presence of the following words:
* sex (20x) * penis (4x) * sexy (3x) * drugs (1x)

All of this "improvement" in just one day?!

SMBE 2007 in Halifax

First thing tomorrow morning, I'm heading off to the Society for Molecular Biology & Evolution (SMBE) annual meeting in Halifax, Nova Scotia. It is being held jointly with the Canadian Institute for Advanced Research (CIfAR, formerly known as CIAR), Program in Evolutionary Biology, which has been a major force in building Canada as a major powerhouse in molecular evolution and evolutionary genomics.

I usually go to each of these annual meetings separately, so having them together will make for quite a week! Both myself and Banoo Malik from my lab will be giving talks, so there will be some sexy gene evolution available for general consumption (in addition to the sex talk to be provided by Rosie Redfield). I'll also be spending time enjoying the wonderful city of Halifax (where I lived for 4+ years as a postdoc), catching up with many friends and colleagues and getting together with some bloggers, too.

Parental Advisory!

This rating was determined based on the presence of the following words:
sex (18x) penis (5x) sexy (1x)

Shehre-Banoo Malik, PhD!

Hearty congratulations are well in order for Banoo Malik, who successfully defended her PhD thesis last Thursday (June 14th). Banoo is the first student in my lab to both start and finish a PhD under my supervision. In her case, that entailed moving with my lab from Emory University to the University of Iowa. She has been a major player in my lab group and her work has made considerable, long-lasting impacts on the lab's research.

Banoo's dissertation, entitled "The early evolution of meiotic genes", is based on her in-depth analyses of the evolutionary histories of meiotic genes. She gave a really terrific talk on her work that led to a extensive series of questions from the audience. Banoo then successfully held court with her committee, who spent some of the time arguing amongst themselves on matters of scientific import (always a good thing in a defense!). The meeting was immediately followed by a celebration including bubbly liquid. On the following day, a party in her honor was held at my home. Good job, Banoo!

The Sexiest Animals on the Planet

Brian Larnder, over at Primordial Blog, which I had somehow missed until today, has a great running series of posts with nominations for the sexiest animal on the planet. Great stuff; just click on the Sexy Beast label for all of the nominees. I can't choose a favorite yet, but the latest candidate is the porcupine (per the classic query: how DO they do it?).

Thanks to Kate Hudson at Secret Sex Lives of Animals for the lead. Image from Gregory Ball.

Secret Sex Lives of Animals

A new blog appeared this month that is right up my alley: Secret Sex Lives of Animals by Kate Hudson, an "evolutionary biologist with an interest in the oddities of the natural world". Here is a description of the blog which looks GREAT so far:

"Birds do it. Bees do it. Humans do it. In fact every animal on this earth does it. But do they all do it the same way? Mating habits in the animal kingdom range from the sublime to ridiculous, but each animal, in their own unique way, accomplishes the same goal.

Welcome to the Secret Sex Lives of Animals, a weekly column written by an evolutionary biologist on the bizarre, wonderful, colourful and sometimes shocking world of animal mating habits. The Secret Sex Lives of Animals is published each Monday at and short updates appear throughout the week."

More weird and wonderful sex in the blogosphere. Gotta love it!

Thanks to Coturnix for the lead.