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.

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.

Dark Matter

A follow-up on a blog post from last year...

According to The First Post:

"The release of a new Meryl Streep movie about a campus killing spree, which was postponed last year after the shooting of 32 people at Virginia Tech, will not be delayed again – despite the recent spate of campus killings, including the gunning down of five students in a classroom at Northern Illinois University on St Valentine’s Day. Dark Matter is based on the true story of Gang Lu, a Chinese graduate student at the University of Iowa who shot and killed five people and paralysed another before killing himself in 1991. In real life, Lu's rage was fueled by his belief that he should have received honours for his doctoral dissertation that were instead awarded to a fellow student."

Here is a link to movie's website. (There is now a trailer that you can watch: Updated 7/29/08)

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?".

Tom Vilsack: Talking to Americans

In all fairness, Gov. Vilsack got hit too. These are so funny. We really enjoyed them when we were "Americans" living in Canada.

Mike Huckabee: Canadian National Igloo

Iowa Boy Goes to the Caucus

Last night I caucused for Joe Biden. Up until the last day, I was trying to choose between Joe and Bill Richardson. On the day before, I went to see both John Edwards and Joe Biden. Edwards was good (and a bit angry!) but Joe really sold me.

Biden's speech in Coralville was the best I had heard this year. He's really a smart, articulate guy. He's also a seriously-credentialed Democrat. And even though I don't agree with him on all the issues, I decided that he deserved a chance and my support. I truly thought he'd pull a decent fourth place that would launch him into the next contests. But that wasn't going to happen. At the end, only the big three (Obama, Edwards, Clinton) were left standing.

At 6:30 pm I arrived at Coralville #6 with my wife, Debbie, who was supporting Obama. The line was literally out of the door of our local elementary school. There was clearly something happening. After a few minutes in line, I got interviewed by the Press-Citizen (our local paper). I said that I'm supporting Biden since he is ready to be President tomorrow (admittedly, parroting his speech from the day before) AND that he can clearly beat the Republicans. Curiously, neither of these are reasons why I supported Kucinich in 2004, but I really don't want to see a repeat of the Kerry-2004 debacle...

In the end, 763 people showed up to caucus as Democrats in our fairly well-to-do upper middle class (and very white) precinct! This was almost twice the turnout of 2004. The results of our caucus were summarized by the Press-Citizen. But here's the inside view from my perspective.

First of all, the Clinton group was largely older people (50+), with a high fraction of women. Interestingly, they had a huge spread of food that was tempting me since I had not eaten... The massive Obama group was quite young, but included many middle-aged (35-50) people and some older. The Edwards group was largely middle-aged to older. The big three ruled Coralville #6.

Biden and Richardson were about equal in support and were largely comprised by middle-aged to slightly older people. At 42, I was among the younger of the Biden group. Dodd's group apparently shared a similar demographic to Biden's (no surprise).

The initial vote for viability indicated that the Big Three were all OK, but that neither Biden, Richardson, nor Dodd were viable. However, if these three could join up, we could generate a viable group (together, we had more than the required 15%). I was happy with this possibility since I was torn between Richardson and Biden until the end anyway. So I encouraged our Biden precinct captain to negotiate with the Richardson camp. The idea was to field an "uncommitted" delegate that would represent whichever of the three candidates were still standing by the time of the county convention. But the precinct captain for Richardson wanted to stick with him, so most of the Biden supporters left for the big three.

There was just not enough time (30 minutes) to convince most of the 129 (57+53+19) people that "uncommitted" was a viable option that would yield a delegate. Too bad. As it turned out, both Biden and Dodd dropped out last night, but we we couldn't know that... At one point, the Edwards captain was trying to get all of the Biden supporters to join in, including offering a possible county delegate slot in exchange. But there wasn't enough time...

Literally at the last minute in the second round of voting, I cast my lot with John Edwards. I still think that he is best Democrat of the Big Three. I had already decided that I he would be my #2. I'm glad that he got second place in Iowa. I hope that it will give him legs for the rest of the month. He's the real deal for populist Democrats. His message needs some more positives, but he's the only one telling it like it is for working people. I hope that this message will resonate.

I'm also really pleased for Barack Obama. Iowa showed its true colors last night even though we are not very racially diverse. I really think that most Iowans are color-blind and this result consistent with that assertion. I remain a bit uneasy about Obama as the nominee, especially against the Republican Nasties, but I'm optimistic for his chances.

The 2008 political banquet is now out of Iowa's hands. I hope that we set the table well..