Field of Science

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.
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.
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 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)

New and tasty header

Ever since moving to my new blog home, here at Field of Science, I have been looking for some appropriate and interesting image(s) for my header. Not being much a visual artist myself, I spent some time last week perusing various open source image galleries for inspiration and free graphics. Given the various keywords that you might imagine, I quickly gave up on that strategy hoping that the internet big brothers weren't watching too closely...

But as luck would have it, my colleague Maurine Neiman (who also works on the evolution of sex) suggested the image that now graces my header. Thanks, Maurine!

Cellular Mitosis (krispy kreme), (2005) is the work of the artist and photographer, Kevin Van Aelst. Kevin describes his work:

"My color photographs consist of common artifacts and scenes from everyday life, which have been rearranged, assembled, and constructed into various forms, patterns, and illustrations. The images aim to examine the distance between the ‘big picture’ and the ‘little things’ in life—the banalities of our daily lives, and the sublime notions of identity and existence. While the depictions of information--such as an EKG, fingerprint, map or anatomical model--are unconventional, the truth and accuracy to the illustrations are just as valid as more traditional depictions. This work is about creating order where we expect to find randomness, and also hints that the minutiae all around us is capable of communicating much larger ideas."
Some of you might recall Kevin's work above called Chromosomes (2005). I remembered seeing this clever piece which recently made its way around the scientific blogs. So after visiting Kevin's website and enjoying all of the interesting work, I decided to write him to seek permission for using the mitosis image for my header—which he granted right away (thanks, Kevin!). Although I suggested that he do a similar series for meiosis (which is much more interesting than mitosis!), he told me that he is currently not able to work on such a project. I assume that means that he is doing very well with many other projects; the evidence from his website is consistent with that interpretation.

Mary Roach orates on orgasms

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

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

In the meantime, enjoy...

Thanks to Pleiotropy for the lead.

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!

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).