The Lure of the Obscure? Guest Post by Frank Stahl

Image from Hochwagen Lab

This proposal was shouted out as “…one of the most important papers on the control of meiotic crossing over…” (Hawley 2006). Since then, “homeostasis” has been offered as the explanation for a variety of observations that demonstrate a degree of independence of crossover frequency (and sometimes crossover interference) from the frequency of double-strand breaks. As in the original yeast work, none of these papers questions whether “homeostasis” has anything to recommend it as an explanation because none has addressed the mundane possibility that crossover constancy reflects merely the normal operation of the system, rather than a reaction to a perceived aberration. 

Without trying to explore the universe of alternate explanations for “homeostasis” in this Blog, we offer just one simple one, based on the view that the crossover/noncrossover “decision” is made “early”, either before or at the onset of the period of double-strand-breaks (Storlazzi et al. 1996): In this none-too-original model, the first double-strand break to occur on a chromosome is immediately assigned to the pathway that leads to crossing over, accounting for both the “obligate crossover” (Jones and Franklin 2006) and the preservation of crossing over. Additional double-strand-breaks are directed to become crossovers when they meet the conditions imposed by crossover interference. [It appears notable that Drosophila, which clearly lacks an “obligate crossover”, has also shown no evidence of “homeostasis” (Stahl 2008).]

This blogger would like to be informed of any “homeostasis” data for which such a nonhomeostatic explanation fails.

  

LITERATURE  CITED

Chen, S. Y., T. Tsubouchi, B. Rockmill, J. S. Sandler, D. R. Richards et al., 2008  Global analysis of the meiotic crossover landscape. Dev. Cell 15: 401–415.

Hawley, R. S., 2006  "This is one of the most important papers on the control of meiotic crossing over..." Evaluation of: [Martini  et al., 2006  Crossover homeostasis in yeast meiosis. Cell 126: 285-295; doi: 10.1016/j.cell.2006.05.044]. Faculty of 1000, 14 Aug 2006. F1000.com/1033723#eval387934

Henderson, K. A., and S. Keeney, 2004  Tying synaptonemal complex initiation to the formation and programmed repair of DNA double-strand breaks. Proc. Natl. Acad. Sci. USA 101: 4519–4524.

Jones, G. H., and F. C. Franklin, 2006 Meiotic crossing-over: obligation and interference. Cell 126: 246–248.

Martini, E., R. L. Diaz, N. Hunter and S. Keeney, 2006  Crossover homeostasis in yeast meiosis. Cell 126: 285-295.

Martini, E., V. Borde, M. Legendre, S. Audic, B. Regnault et al., 2011  Genome-wide analysis of heteroduplex DNA in mismatch repair-deficient yeast cells reveals novel properties of meiotic recombination pathways. PLoS Genet. 7: e1002305.

Mehrotra, S. and K. S. McKim, 2006  Temporal analysis of meiotic DNA double-strand break formation and repair in Drosophila females. PLoS Genetics 2: 1883-1897.

Stahl, F. W., 2008  Countdown with Mehrotra and McKim. Online comment on Mehrotra and McKim (2006) 2(11): e200 doi:10.1371/journal.pgen.0020200.

Storlazzi, A., L. Xu, A. Schwacha and N. Kleckner, 1996 Synaptonemal complex (SC) component Zip1 plays a role in meiotic recombination independent of SC polymerization along the chromosomes. Proc. Natl. Acad. Sci. USA 93: 9043–9048.

Franklin W. Stahl
Molecular Biology
1229 Univ. of Oregon
Eugene, OR  97403-1229

My blog is back from the dead (sort of)

Greetings from New London, New Hampshire, where I am attending the Meiosis Gordon Research Conference this week. As such, it seems timely and appropriate to host a guest post on my (very dusty!) blog from Frank Stahl (pictured left). Frank contacted me recently to guest-post a short piece he wrote on crossover homeostasis. Enjoy!

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!

Nasonia genomes published

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

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

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

(photo is copyright John H. Werren, 1980)

SG&E has joined Field of Science (FoS)

Just when I thought that I would leisurely make my way back into blogging...

Over the weekend I got an invitation from Edward, the editor and proprietor of Field of Science, to join his stable of blogs. I was already a follower of Steven Salzberg's blog Genomics, Evolution and Pseudoscience which had recently moved to FoS. So I shot Steven an email to seek his advice, and on his hearty recommendation, I joined with little hesitation.

Now after little more than a day, I'm here with a brand spankin' new look and feel to my blog. I hope that you will enjoy it. Thanks, Edward!

Image from Public domain image

On sabbatical at NESCent!

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

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

P.S. I'm twittering @johnlogsdon

GBE: Genome Biology and Evolution

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

According to the GBE website:

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

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

Nature's 15 Evolutionary Gems

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

The summary article starts...

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

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

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!

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.

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?".

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.