Caucus Conundrum: Considering Compelling Candidates

For those of you still tuned in, thanks. I hope to have some more science content to share in the coming year...

In the meantime, the Iowa Caucus is weighing heavily on me—at least for the next three days. I'm uncommitted so-far, and that is weird for me. I'm usually a man of strong opinion and steady conviction... But none of the candidates (Democrats, of course) are floating my boat this time around. Perhaps it's because I'd vote and probably even campaign for any of them in November. I just don't see huge differences among them.

Politically, Dennis Kucinich is closest to my convictions as was re-iterated by my third assessment by this poll. But I have a hard time supporting Dennis this time around, even though I caucused for him in 2004 (when he & Dean were the only anti-war candidates). That's not to mention that Kucinch has all but forgotten Iowa this year (too bad for us).

The other choices are really pretty good. Last week I was leaning toward Joe Biden, who I blogged about earlier this fall. The recent debacles in Pakistan have certainly made me think even harder about international diplomacy (per se, not just foreign policy in general) as a key issue. I have always liked Joe's frank style, even if it gets him in trouble sometimes.

A few weeks ago, I went with my family to see Barack Obama (and Oprah) and it was made clear to me why people are excited about him. I like Obama, but there seems to be something substantive that's missing. My wife and many of our friends are Obama supporters, but I'm not sure what it is that's keeping me from jumping on the train. I think that Barack will be the nominee.

Which brings me to yesterday. Although I had not paid much attention to Bill Richardson so far, I saw that he was in town giving a speech and attending a few house-parties. So I decided to go and see for myself. I was impressed. I asked him about education and he was right on the mark. He knows that we are in dire straights for science and math teachers. When I asked Bill to guess how many of this year's ~60 student class that I teach (mostly junior/senior biology majors) were planning to be teachers, he correctly stated "zero" (usually 2-4 in previous years). This is scary—where will the next generation of teachers come from?? Richardson's plan includes a national minimum salary for teachers ($40K), which is a great start. Bill has a national service plan that would pay college tuition in exchange for voluntary national service. He's not just talking military here, either. His credentials in the international diplomacy arena (where we have lots of catching up to do) are really amazing. When I asked him about Science Debate 2008, he was interested and asked me to forward some info to the campaign (which I did).

How about today? Only three more days to go! I spent an hour this morning reading the Des Moines Register special Caucus section after watching some of the Sunday political talk. Hillary Clinton is giving a speech on Tuesday in Iowa City that I will probably attend. John Edwards and Chris Dodd are also in town in the next day or two. I hope that I'll be able to decide by Wednesday.

Science Debate

"Given the many urgent scientific and technological challenges facing America and the rest of the world, the increasing need for accurate scientific information in political decision making, and the vital role scientific innovation plays in spurring economic growth and competitiveness, we, the undersigned, call for a public debate in which the U.S. presidential candidates share their views on the issues of The Environment, Medicine and Health, and Science and Technology Policy."

Chris Mooney and Sheril Kirshenbaum over at The Intersection have assembled a crack list of scientists and science bloggers to launch the the ScienceDebate2008 website. If you are so inclined, go over and pledge your support. They have also set up rapidly-growing groups over at facebook and myspace.

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.

I'm an Intellectual Blogger

The Evilutionary Biologist (aka John Dennehy) has tagged me with an Intellectual Blogger Award. Given my serious lack of posting lately, I'm not sure that I deserve it...but thanks!

The award traces to An Unquiet Mind where the stated rules are:

This award is intended for those bloggers who demonstrate an inclination to think on their own. This is what I think is needed in today’s blogosphere. The term ‘Intellectual’ has often been derided in recent times, and this is one way to resurrect the true meaning: “An intellectual is one who tries to use his or her intellect to work, study, reflect, speculate on, or ask and answer questions with regard to a variety of different ideas.” The rules are:

1. If, and only if, you get tagged, write a post with nominations for 5 blogs that you think are of “Intellectual Bloggers”.
2. Optional: Link to this page so that people can easily find the exact origin of the meme.
3. Optional: Proudly display the ‘Intellectual Blogger Award’ with a link to the post that you wrote.

I hereby nominate:

1. Tree of Life (Jonathan Eisen; even though he doesn't like these memes)
2. Aetiology (Tara Smith)
3. Twisted Bacteria (Cesar Sanchez)
4. Small Things Considered (Elio)
5. Evolgen (RPM)

and one that I was suprised to find has apparently not yet been included:

• Sandwalk (Larry Moran)

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.

Promoting Plants at the Expense of Fungi?

Ryan Gregory, over at Genomicron, found an interesting tidbit on the Discovery Channel website entitled Plants and Animals: Long-Lost Relatives?. He is surprised to read that

"organisms such as fungi should be given a demotion — placed further from animals on the tree — while green plants should get a leg up."

This is the case, apparently according to a recently-published paper from John Stiller at East Carolina University.

Gregory is (rightfully) annoyed at the suggestion of any group "getting "demoted" one way or another because this idea of rank (was) should have been abandoned 150 years ago." and that was the main point of his post. Ryan has been (again, rightfully) critical of science reporting and this doozey has all of the right parts, as detailed in his Anatomy of a bad science story.

However, there have been a series of comments about the veracity of the Stiller paper, so I thought I would make a few of my own here. First of all, it should be duly noted that the paper in question, Plastid endosymbiosis, genome evolution and the origin of green plants, is explicitly labelled as "Opinion"; this is on top of the fact that it is published in the review journal TRENDS in Plant Science—not a primary research venue. Neither of these facts are damning to the work, but they certainly suggest caution in reporting the findings.

Second, it is fair to say that this hypothesis (wrongly called "Stiller's theory" by the Discovery story) is way out of the mainstream of current thought. Again, this alone should neither preclude the publication nor, by itself, lend it to immediate scorn. It's great to see such examples of how science works in the marketplace of ideas. But we all know that just because something gets published, does not mean it's right.

In any case, there are two main components that Stiller argues in this paper:

1. that the "Plantae" [Viridiplantae (green algae & land plants), Rhodphyta (red algae) and Glaucocystophyta] are not a monophyletic group, and
2. that the Viridiplantae are more closely related to animals than are fungi.

The data on "Plantae" monophyly are certainly not so compelling as to rule out other possible answers. But recent work (here and here) is increasingly providing support for this relationship. Stiller has been a long-standing contributor to the literature on non-monophyly of green+red algae. I have worked on some of the same molecules that he has (i.e., RNA pol II) and he might have a point for there not being strong support in favor of "Plantae". However, I don't think that there is an alternative that garners anywhere near the consistent support that "Plantae" gets in multigene trees.

The data on the sisterhood of animals and fungi grouping to the exclusion of plants (e.g., Viridiplantae) is about as solid as deep relationships among eukaryotes can be. A nice summary of these results was recently presented in PLoS Genetics. Since the paper is Open Access, I won't repeat the findings here (full disclosure: although I am not an author of this paper, I do collaborate with them). Suffice it to say that there is not even a hint of evidence that Viridiplantae is closer to animals that are fungi as suggested by Stiller. Note also that these authors are not particularly bullish on "Plantae" either.

Stiller cites the presence of certain enzymes and protein domains in both plants and animals (apparently absent in the fungi) as evidence for a closer relationship of plants to animals. But the problem is that such things only have to be lost once in the fungal lineage (if they have been lost at all) to make these cases complete non-sequiturs. To explain why plants don't fit in with animals, Stiller would rather invoke some sort of bias in the data. Although such biases may exist, I am very cautious about invoking an entire reworking of the tree based on them.

Stiller ends with four "Future Perspectives" of which I find the following most telling:

"There should be no a priori assumption that the strongest tree-building signal in a given data set reflects evolutionary history rather than bias in the data."

I'll file that in the category of "Things that make you say Hmmm".

Favorite Science Blogs

As ususal, I am late to the party where everyone is discussing their favorite science blogs. This was a no-RSVP-required affair that The Scientist has been hosting under the banner of "Vote for your favorite life science blogs". Most of my favorites are listed in the "Other Interesting Blogs" on the left of my blog. I actually use this list as my major navigation tool for blog-visiting. Of these, here are my most frequently-visited (and therefore most favorite):

Daily (or throughout the day):
Sandwalk. Bravo, Larry!
Pharyngula. Does PZ sleep?
Tree of Life. Jonathan says things that I wish I would have said (& some I'm glad I didn't).
FemaleScienceProfessor. Wow. FSP is anonymous and it really works!

Slightly less than daily:
Aetiology
Evolgen
Fungal Genomes & Comparative Genomics
Genomicron
Scientia Natura
The Evilutionary Biologist
The Loom

More than weekly:
all the rest.

My New Device

Yes, it's as cool as it seems. My wife got me an iPhone for my birthday this year! How am I so lucky? Although I was excited about it from the start, I let it sit unopened for a couple of weeks while I figured out whether I was really prepared to pay for it. My cell phone was with Verizon, so to activate the iPhone required me to switch to ATT (@ $60/month) and start another 2-year contract. And that's on top of the device buy-in (which was purchased prior to the $200 price cut). Anyway, it's out of the box now and I am really enjoying it. I recieved and sent multiple emails today while stolling across campus. My iCal is seamlessly synched between my laptop (MacBook Pro) and my iPhone, which means that I don't have to lug my laptop around so much. Sorry if this post seems like advocacy, but sometimes you just have to let out the joy! Back to science shortly...

Joe Biden on Science Funding

Iowa is a great place to be if you are at all interested in national politics. Case in point: last Thursday I found myself in the same place as presidential hopeful Joe Biden. He was at the University Bookstore signing copies of his book, "Promises to Keep: On Life and Politics". The line wasn't very long, and I consider Joe to be one of my top three candidates this year. So I ponied up the $27 to buy a copy so that I could get him to sign it and throw a few questions at him.

I introduced myself as a Biology Professor and asked him about his thoughts on basic science funding. Without hesitation, he said that he would support a doubling of the NIH and NSF budgets. When I asked if I could post that comment on my blog, Biden agreed. He also was keenly aware that the although funding for both has increased in recent years under the current administration, it has not been effective at increasing basic science. I don't know how much of that was just telling me what I wanted to hear, but I was pleased.

He signed my book "Keep the faith. Keep on teaching" I don't know about the former....

On a related topic, check out the following link that matches your views to those of the current presidential candidates.

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.

Thomas "Vandy" Vanderford, PhD

Belated, but sincere, congratulations to Vandy on the successful defense of his PhD thesis on August 13th. His dissertation is entitled "Adaptation of a diverse SIVsm population to natural and non-natural hosts". Vandy was a student in the Population Biology, Ecology & Evolution (PBEE) program at Emory University and he was jointly supervised by myself and Silvija Straprans. Even though I moved from Emory to Iowa in 2003, Vandy continued to work with me on the evolutionary aspects of his research on SIV. To make things happen, he travelled mutiple times to Iowa City and I went to Atlanta a few times, too.

Vandy gave a clear talk which was followed by some questions by the audience and commitee members. His post-seminar defense was rather short--his committee didn't even grill him! What a lucky guy. Afterwards, Vandy was treated to a reception hosted by the Vaccine Center (where Silvija's lab was located--she is now at Merck). After the festivities, Vandy and I spent the remaining afternoon celebrating over a few beers (picture above taken at that time) while listening to The Raconteurs. Later, accompanied by Vandy's girlfriend, Mitzi (who drove) we had dinner and a few more beers at the Brick Store Pub. I'm proud to add Vandy to my list of PhD grads. Congratulations, Dr. Vanderford!

Dawkins Defends the OUT Campaign

Although I am a bit late to the party, I wanted to point OUT that Richard Dawkins has recently posted a nice essay about the OUT Campaign and why it is necessary. Here is a snippet:

"Our choir is large, but much of it remains in the closet. Our repertoire may include the best tunes, but too many of us are mouthing the words sotto voce with head bowed and eyes lowered. It follows that a major part of our consciousness-raising effort should be aimed, not at converting the religious but at encouraging the non-religious to admit it – to themselves, to their families, and to the world. This is the purpose of the OUT campaign."

PZ has already added his few cents to this and as I post, there are are already 319 comments.

Picture credit here. Thanks Matti A.

Biochemistry By Design

An excellent article appeared recently in TRENDS in Biochemical Sciences (subscription required) that is worthy of note here. The paper, entitled "Biochemistry by design" by BC Forrest & PR Gross, is a terrific primer and riposte to the so-called "Biochemical Challenge to Evolution" that Behe has been promoting in the past few years. The National Center for Science Education (NCSE) has already posted an article on their site about this paper. The authors are well-versed in the creationism/ID "wars" having previously written the book, "Creationism's Trojan Horse: The Wedge of Intelligent Design" which has just been published in paperback (with an updated chapter on the Dover trial). It's too bad that this great article is (apparently) not Open Access.

The Simpsons Movie

On Friday, I took my kids (ages 10 & 12) to see "The Simpsons Movie". There's always something fun (and risky) about seeing a movie on its opening day and this one actually delivered on the hype. We all enjoyed it, and I would generally recommend it. However, families should be aware that it's rated PG-13 for good reasons. There's quite a bit of off-color (adult?) humor and even a brief shot of Bart's penis (aka "doodle"). They clearly took advantage of the off-TV venue for some saved-up "mature" (?) content. But long-time Simpson's fans should expect some of this (like showing Otto smoking a bong).

The other reason to post here about The Simpsons is the fun piece in Nature this week entitled "Mmm...Pi" that discusses the science-based humor that has permeated The Simpsons for years. The "Top Ten Science Moments" are worth remembering.

The OUT Campaign

Sorry for the long haitus & thanks for staying tuned! Summer time has been keeping me busy this year.

So, what does this big red "A" above mean? Click it and find out for yourself. The folks over at RichardDawkins.net have launched an internet effort to let the world know that there are alot of us OUT there. I'm happy to be OUT. Here's a snippet from the site:

"As more and more people join the OUT Campaign, fewer and fewer people will feel intimidated by religion. We can help others understand that atheists come in all shapes, sizes, colours and personalities. We are labourers and professionals. We are mothers, fathers, sons, daughters, sisters, brothers and grandparents. We are human (we are primates) and we are good friends and good citizens. We are good people who have no need to cling to the supernatural."

When you see the A, you know!

Blogging for good

T. Ryan Gregory over at Genomicron asks: How much good can one blog post do? In a very moving post about the efforts of his father and stepmother to make a difference in Livingstone, Zambia, he asks us to help them in whatever way we can (suggestions are given).

The Livingstone Performing Arts Foundation (LiPAF) mission is to create and perform traditional and original works of music, song and dance which reflect the history, culture, languages and ethnic background of Zambia. Operating as a not for profit organization, LiPAF will enrich the community by providing opportunities for employment, sponsorship of a variety of needy programs and services, and educational programs on topics related to the human condition.

Tagged?!?

I have been tagged by Shalini over Scientia Natura, Here are the rules:
(although I don't think that she followed #5)

1. We have to post these rules before we give you the facts.
2. Players start with eight random facts/habits about themselves.
3. People who are tagged need to write their own blog about their eight things and post these rules.
4. At the end of your blog, you need to choose eight people to get tagged and list their names.
5. Don't forget to leave them a comment telling them they're tagged, and to read your blog.

1. I consider myself a native Iowan. Although I was born in Missouri (1965), I grew up in Iowa (1968-1983) and went to Iowa State University as an undergraduate (1983-1988). After various academic stints elsewhere, I returned in 2003 to join the faculty at the University of Iowa.

2. I shook hands with Dave Loebsack today at the Coralville 4th of July Parade. Dave is our freshman Democrat congressman who beat out long-standing incumbent Republican Jim Leach last fall. I asked Dave to "keep up the good work" and to pay particular attention to health care and science funding. He assured me that he will do so.

3. I have a motorcycle, but I don't ride it enough. It's a 1995 Honda Shadow VT600C that I got when I finished my PhD 12 years ago. I have been planning to upgrade to a bigger bike someday (a Harley Fat Boy would be nice).

4. I spent a year studying abroad at University College, Swansea (now Swansea University) in Wales as an undergraduate (1985-1986). I took philosophy and psychology courses there because I was unsure about biology at that time.

5. I like my coffee black and my art abstract. Peets Arabian Mocha-Java is my favorite coffee. Rothko and Pollack are among my favorite artists.

6. I played baritone sax when I was in high school. I was particularly interested in jazz and even once won a solo contest at the state level. I considered a music major in college, but quickly realized that I was not as prepared (and committed!) as I needed to be. Lately, I have been considering picking it back up (but I need to buy one first!).

7. My entire academic lineage is comprised of Members of the National Academy of Sciences. My undergraduate mentor, Steve Briggs, is now at UC San Diego. My PhD advisor, Jeff Palmer, is at Indiana University. My post-doc advisor, Ford Doolittle, is at Dalhousie University. I am proud of the accomplishments of my mentors, but they have placed the bar rather high!

8. I eat chocolate at least once a day. Almost anything will do. Snickers and Skor bars are standard fare, but I also enjoy high-end treats.

I hereby tag:

Tree of Life

T. taxus

RRResearch

Genomicron

Evolgen

Sandwalk

ScienceNotes

De Rerum Natura

Commenting to each of these blogs (aka Rule #5) will now commence!

Another Fun Blogger Gathering

I returned home late on Sunday (Canada Day!) from Halifax, Nova Scotia where I was attending the Society for Molecular Biology & Evolution (SMBE) annual meeting and the immediately following Canadian Institute for Advanced Research (CIfAR) Program in Evolutionary Biology meeting. There was lots of good science and one highlight was a dinner get-together of a few bloggers and blog-readers. Bloggers included in our group were RPM, Rosie Redfield, Jason Stajich, Reed Cartwright, and Jacob Tennessen. Both Reed and RPM have posted more about this gathering, including a complete list of attendees (pictured left). Thanks everyone for an enjoyable time! This is an activity that I hope to continue...

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!

Microbial-bloggers

As I mentioned a few weeks ago, a few science bloggers got together in Toronto while some of us were attending the American Society for Microbiology general meeting. ASM's MicrobeWorld (a.k.a Chris Condayan) captured us on video. My colleague Tara Smith reported on this earlier today, as did Ryan Gregory. Addendum: Jonathan Badger also reported on this.

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.

Tara is on top of things

Tara Smith, my U. Iowa colleague and friend who is over at Aetiology, has a couple recent posts of particular relevance here...

Tara reports on the selection of University of Iowa's new president, Dr. Sally Mason, who is currently (until July 31) the Provost at Purdue. I'm thrilled about Dr. Mason as our new leader, as are many of us here. She's a biologist, which makes me happy, but that's not all. I heard Sally speak last week at her interview and I left the room feeling truly inspired. I was surprised to have that reaction, but I came to find out that I was not the only one who did. When I heard Sally speak at her introduction on Thursday, she left me with the same feeling. I think we scored a great catch here at Iowa.

Tara also files a detailed report on her recent "Field trip to the Creation Museum". As she concludes

"...$27 million spent on a Creation "museum," not to mention all the hours of donated labor. Meanwhile, our kids are failing to learn even basic science knowledge in school. Disheartening to a scientist, to say the least."

Thanks Tara!

Parental Advisory!

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

Beach, Beer & Books

Sorry for the long delay in posting here. It's been an eventful few weeks. After my return from the ASM annual meeting in Toronto, I attended an excellent PhD thesis defense (Tetyana Nosenko from Debashish Bhattacharya's lab), and then left immediately for the 13th German-American Frontiers of Science Symposium. I'll write more about this meeting later..

From there, I went directly to the Outer Banks of North Carolina for a week of vacation with my family. The main agenda items for me are given in the title to this post. I spent 4 of 5 days on the beach, drinking beer, body-surfing and other water-frolicking, napping and reading books when possible (one day was spent recovering from a sun-burn).

Beach. We (12 of us, comprising both my immediate and extended family) stayed in a guest house in Hatteras which was situated ~5 min from the Atlantic Ocean. It was glorious. The kids (myself included) has a great time splashing in the waves and digging in the sand. Thanks to my sister, Beth, for making the arrangements.

Beer. Throughout the week, I emptied many bottles of Red Hook's Longhammer IPA. This was a perfect beach beer. It's both tasty and refreshing! Of course, there were a few bottles of Sierra Nevada Pale Ale (my standard libation) consumed, too.

Books. Although I brought more than I could possibly finish, here are the ones I actually cracked (and in a couple cases, finished): Blink (Malcom Gladwell); Sex, Drugs & Cocoa Puffs (Chuck Klosterman); Zen and the Art of Motorcycle Maintenance (Robert Pirsig); Killing Yourself to Live (also Chuck Klosterman).
So it's back to reality for me, but at least I enjoyed myself on the Outer Banks!

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!

Ken Ham's Creation "Museum"

It's probably not necessary to do so. But just in case it might get missed, I wanted to point everyone to the blog carnival that PZ Myers has assembled about the newly-opened Creation Museum. The "museum" is the product of Answers in Genesis and its CEO Ken Ham. As PZ put it:

"we can hardly believe that in 21st century America, this childish comic-book fantasy is being taken seriously by anyone."

The National Center for Science Education has posted an assembly of media reactions.

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.

Banning the word "prokaryote"

Here I am at the the American Society for Microbiology annual meeting which is being held in Toronto. As Larry Moran has already pointed out, there are a few of us bloggers that are getting together with him while we are here. This should be great.

My first day (actually, part day) was capped off with a really fun, but in many ways maddening, lecture from Norman Pace. Norm was on my PhD committee, and it was the first time I had seen him for 12 years. The talk was wonderfully vintage Norm—even some of the phrases were the same as I remembered. That's not to say that the talk was at all tired. Norm is so fun to see in the spotlight; in this case, he had a big and well-deserved stage on which to perform! As an historical aside, Norm's class on the biochemistry of nucleic acids at Indiana University was the only biochemistry course that I ever took that started by reference to a rRNA tree of life. Norm has been ahead of the curve for a long time...

A major—and provocative—theme of Norm's talk is that we microbiologists should strike the word "procaryote" (or prokaryote, as I prefer to spell it) from our vocabulary. This is not a trivial matter for the microbiologists in attendance, both from practical and intellectual points of view. This part of his talk followed directly from his recently published piece in Nature entitled "Time for a change." (2006) 441:289. I happen to strongly disagree with Norm on this point and am much more aligned with the views subsequently published by Martin & Koonin entitled "A positive definition of prokaryotes" in Nature (2006) 442: 868. Although I'm too short on energy to do so now, I'll try to decipher my notes and give a more clear account of what Norm said (and my reactions to it) in the coming days.

Parenting Beyond Belief

Since I have not posted for awhile, I'll follow through on a promise made in March. Here is my review of Parenting Beyond Belief that was published in the Iowa Secularists newsletter in April. I'll point out that the author/editor, Dale McGowan (pictured at left), has an interesting blog called The Meming of Life.

This I don’t believe: a parenting guide for us
A review of Parenting Beyond Belief. On Raising Ethical, Caring Kids Without Religion, by Dale McGowan (Editor) AMACOM/American Management Association (April 30, 2007)

A search of Amazon.com for books containing the word “parenting” in their title yields ~4000 hits. This sounds like a huge number, but for those of you with kids, it’s probably not terribly surprising. Parenting books are a major market. A quick browse through the titles reveals both general parenting guides and some very specific categories (Nighttime Parenting, Financial Parenting, Militant (?!) Parenting, You-Name-It Parenting…). Indeed, a considerable fraction of these books are focused on religious parenting of various flavors (for example, 87 titles contained “christian parenting”)—and this presumably excludes other parenting guides available only in religious bookstores.

If you have kids, you probably have at least a few—and possibly many—parenting books. In my home, we have no less than 24 such books; for us, that’s 12 per child! But none of these books are aimed at a significant part of our demographic: we are non-believers. With the impending publication in late April 2007 of Parenting Beyond Belief (herein, PBB) we—and many of you—will no longer be left behind. Depending on how you feel about parenting books, you may or may not consider this good news. But now you won’t have the excuse that none of them are aimed at secularist (atheist, freethinking, etc.) parents.

The PBB website (http://parentingbeyondbelief.com) touts that this book is “for loving and thoughtful parents who wish to raise their children without religion. There are scores of books available for religious parents. Now there's one for the rest of us.” Ok, so what if someone found an untapped niche in the parenting genre…is the book any good? The quick answer: it’s a really good, and in some places great, little book.

PBB is a collection of essays from a variety of authors on a wide range of parenting topics. Most pieces tackle issues specific to non-belief parenting but many also deal with more general topics. The editor, Dale McGowan, a writer, educator, husband and parent of three, has pulled off the difficult task of weaving together diverse parts into a very cohesive whole. It sure helps that most of these parts (the individual essays) are simply terrific! PBB is broken into nine topical chapters. For each chapter, McGowan provides a brief, but clear, introduction and synthesis; then he lets the contributors’ pieces stand on their own. Most of them do so with flair.

You can either read PBB from cover-to-cover, or pick-and-choose based on your topic of interest. If you do the latter, don’t skip the first chapter “Personal Reflections”. In my view, McGowan started with the strongest material—it simply blows away the standard parenting book drivel and sets a great tone for the rest of book. The essays by Julia Sweeney and Penn Jillette are truly wonderful. I really enjoy Penn’s no-holds-barred-style:

“Those of us who are out of the closet atheist parents have all the extra time on Sunday mornings to love our kids…Tell your kids that there’s no god and be done with it...your kids aren’t stupid.”

But this approach may not be for everyone and, to balance things out, some of the essays are more circumspect. I am also really pleased to see that a favorite essay from Richard Dawkins is included here. “Good And Bad Reasons For Believing” is an open letter that Dawkins wrote to his 10-year-old daughter on the nature of evidence and belief (reprinted from A Devil's Chaplain). I am moved every time I read it.

PBB is not only an interesting and enjoyable read, it is also stuffed full with good information and pointers to other sources. Each chapter ends with “Additional Resources” that includes websites, books and other helpful information. But it doesn’t even end there. On the website you’ll find a useful study guide available for free download. The reader is advised that “the study guide – like the book itself – is intended only as a starting point”. So don’t wait to get started.

© John M. Logsdon, Jr., Ph.D.

Encyclopedia of Life Launches!

The Washington Post reports that a major new project has been launched:

"A group of the world's leading scientists announced yesterday that they had joined forces to document the world's 1.8 million named species in a massive new "Encyclopedia of Life." The unprecedented $12.5 million effort -- a collaboration of Chicago's Field Museum, Harvard University, the Marine Biological Laboratory at Woods Hole, Mass., the Smithsonian Institution, the Biodiversity Heritage Library and the Missouri Botanical Garden -- aims to create separate Web pages on every known species within a decade."

The funding comes from the John D. and Catherine T. MacArthur Foundation ($10 mil) and the Alfred P. Sloan Foundation ($2.5 mil). Wow. This is big science for "organismal biology" and it will put a whole lot of good data in one open-access place. Congratulations to those who had the vision to get this launched and thanks to the funding organizations for making it happen!

Go have a look at www.eol.org. They already have some cool Demo Pages. For example, the image above comes from the Yeti Crab page. The home page says it all:

"Comprehensive, collaborative, ever-growing, and personalized, the Encyclopedia of Life is an ecosystem of websites that makes all key information about life on Earth accessible to anyone, anywhere in the world. Our goal is to create a constantly evolving encyclopedia that lives on the Internet, with contributions from scientists and amateurs alike. To transform the science of biology, and inspire a new generation of scientists, by aggregating all known data about every living species. And ultimately, to increase our collective understanding of life on Earth, and safeguard the richest possible spectrum of biodiversity."

Click here for the Press Release.

Genital Co-evolution in Ducks

In the category of sex & evolution I would be remiss to not post on this, even though I am a bit late to the game...

Just in case anyone missed it, I should at least point out a recent paper, "Coevolution of Male and Female Genital Morphology in Waterfowl" by PLR Brennan et al. in PLoS ONE. The study was the subject of an interesting article by Carl Zimmer in this week's New York Times, which has met with considerable discussion in the blogosphere including this nice summary by Coturnix.

Not only is the long and twisted penis an interesting feature itself, the correlated complex morphology in the female genital tract makes this a really provocative case of probable sexual conflict driving the evolution of genitalia.

The image (of an Argentine lake duck) comes from a 2001 paper published in Nature, "Sexual selection: Are ducks impressed by drakes' display?", by KG McCracken et al.

Luxuriant Flowing Hair Club for Scientists

By popular demand, I'm now a member of the LFHCfS!

However, my membership may be short-lived if we can raise enough money to support our Iowa City Darwin Day efforts! Click here to find out more. Once shorn, I'll be donating my hair to Locks of Love.

More on David Sloan Wilson

Blue, over at Blue Cat Blog, has posted extensively on David Sloan Wilson's new book Evolution For Everyone, which I have not found time to finish yet. Blue also found a recent lecture given by DSW entitled "Evolution and Religion: Two Sideshows and the Main Event", given March 8, 2007 at Hampshire College as part of their Science and Religion lecture series. I'm having some difficulty posting the video, so just click here.

Genomicron reaches ~1K hits

Genomicron: Hits. T. Ryan Gregory posted about his initial success in this medium. I seconded that emotion. He liked my blog title, too (Thanks!).

I need to figure out if my counter is looking at total hits or unique visitors (I assumed the latter; does anyone know?).

The image is from Gregory's recent book which, unfortunately, I have not yet read. It's been on my list for a while...