You'd Prefer An Argonaute


Posted in Blog Affairs, Gallimaufry by YPAA on December 6, 2009

The first snow of the season fell here in the Cambridge/Boston area last night, a fairly light one actually. To give a sense of what it is like, this blog should currently be snowing, right there on the screen, as you read these words, courtesy of WordPress. Is it cool? Lame? Annoying? I turned off the snow. Enough is enough.

Invoking elementary physics/chemistry, snow is associated with cold, low temps. Do you live in a place like Los Angeles, or say, Singapore? Then take your laptop over to a nearby cold room, lower it a few more degrees, go inside, fire up this here blog, and watch the beautiful snow fall. For added effect you can: 1) periodically stand in front of the fans blowing cold air, 2) fill an ice bucket with ice and then dump the ice all over the floor of the cold room and pace back and forth on top of the ice. Don’t fall, it hurts. I love New England winters. 🙂

Honey Bee Genetics

Posted in Blog Affairs, Gallimaufry, MIT by YPAA on November 19, 2009

The posts have been slow to rise lately, because I’ve been busy with things:

  • I’m writing a paper.
  • I’m still taking that Science Journalism course, and working on a final ~3,000 word piece, which I’ll put up–here or elsewhere–when I’m done. I can tell you it’s about some brilliant research coming from the lab of Dianne Newman, an MIT Professor.
  • As usual, I’m banging drums in an MIT jazz combo. This term we’re playing, among others, the James Brown song “Mother Popcorn,” and it’s sooo funky.
  • Other miscellaneous debris.

To tide readers over until a more steady stream of original content appears, I am posting something I wrote three years ago, when I was a wet behind the ears first year graduate student. The Department of Biology has a wonderful class, only for the first year grad students, called “Methods and Logic in Molecular Biology” (colloquially known as “seven-fifty” or “Methods”), an intense paper reading course led by several faculty. (Actually, eventually I should probably write some posts about these classes for potential students or others who are interested?)

Anyhow, our section for Methods became somewhat tight, and occasionally we exchanged emails about the current week’s assigned papers. Around 2am on the day of the last class of the semester, I sent the following email to my section. Clearly I was high on something–not a controlled substance; possibly a couple beers; likely joy at almost being done with the class/semester; as likely rebellion against being told what to read, instead choosing to read what I wanted to. Most of my classmates had already exhibited in spades dysfunctional behavior, it was my turn. I still think it’s a stimulating read:

On the eve of our last class, instead of re-reading the papers I did some Internet research into the fascinating area of honeybee genetics. Topic is more interesting than heat maps or MALDI experiments. Some things I found:

In a bee colony, there are three types of bees: few female queens, hundreds of male drones, and thousands of female workers. Females are diploid and males are haploid. Females develop from fertilized eggs. Haploid male drones develop from unfertilized eggs, and therefore they have no father! Sex determination is made at a single locus, the csd gene, of which at least 19 alleles are known. It seems that all alleles can be found in males and females. It was also shown that once activated, csd remains active throughout development. RNAi inactivation of csd causes diploid female eggs to develop male gonads, but does not affect haploid male egg sexual development. Therefore it has been hypothesized that 2 different alleles of csd somehow result in two protein products that can interact together to direct a specific step in the sex determination pathway towards female development. Hemizygous csd eggs cannot make this product, and thus the default state is male.

Female queen and worker bees develop from queen bee eggs fertilized by drone sperm. Females must be heterozygotes for csd alleles to survive. Diploid flies homozygous for a csd allele develop into sterile males, but soon after these larvae hatch from the comb, they are selectively removed and destroyed by worker bees (not sure how workers can recognize these larvae). (This also makes it difficult to develop inbreed stocks of honey bees, colonies die out quickly due to loss of csd homozygotes.) Since both queens and worker females come from fertilized eggs, what distinguishes them is that between larvae and pupa stages, queens receive a hormonal mixture called the “royal jelly”, whereas workers arise from larvae that have been denied this. Workers are sterile because they don’t develop ovarioles, and only live a few weeks. Queens usually mate once in their life and then live for years.

Queen bees must mate with many drones at one time early in there lifetime, and must do it 50-100 meters in the air and kilometers from their colony! (This makes it difficult for bee breeders to maintain isogenic stocks of bees, an intensely studied research problem in bee genetics.) The drones die after mating, and the queen returns to hive and doesn’t need to mate again. She will produce thousands of offspring from eggs fertilized from perhaps 5-15 drones. From an evolutionary perspective, the fact that she usually mates with multiple partners once early in life, and far from the hive prevents her mating with her own son, reducing the chances of producing half inviable progeny homozygous for csd allele, (which means fewer worker bees to support the colony). Pretty cool, huh.

Oh yeah, consider this my contribution to Thursday’s discussion.

Sorry, but I can’t remember my references.

Five thousand views? HECK YES.

Posted in Blog Affairs by YPAA on October 31, 2009

I know there are some blogs that get ~5,000 views per hour, while it took 7.5 months for You’d Prefer An Argonaute (YPAA), but hot damn, I don’t care. The mild success of YPAA proves RNA science is quite worthy of the blogosphere, worthy of interest and debate among scientists online, just as I originally intended.

Picture 2

Figure 1. Views per month since March 2009, when YPAA was born.

Most of the credit should go to my fabulous contributers for the RNA Journal Club posts: (in order of contribution) Anna, Joel, David W., Anonymous 1, Michael, Robin, Noah, Graeme, Anonymous 2, Anonymous 3, Vikram, David W. (2nd time), Jenny, and Anna (2nd time). These folks rock, they make YPAA what it is.

As the foundation for starting YPAA, the MIT RNA Journal Club–its organizer Margaret, and its many attendees–should also be acknowledged. (And the sponsors keep us coming by paying for lunch!)

Thanks also to my mom for hitting refresh 4,900 times. And of course YOU.

Thanks for visiting, please come again.

YPAA On Vacation

Posted in Blog Affairs by YPAA on August 11, 2009

Back in two weeks.


You’d Prefer An Argonaute Banned in China

Posted in Blog Affairs by YPAA on July 16, 2009


I have just received word from a close colleague of mine traveling in China that this blog is blocked there.


Actually, apparently all WordPress blogs are blocked in China. Thanks for the tip Yang. (See comments below.) Damn, and I could be getting like 5 million more views per day.

Modest Milestone

Posted in Blog Affairs by YPAA on June 23, 2009

Well it took a little over three months, but YPAA has just attained it’s first one thousand total views. Hooray.

Thanks for visiting.

In Progress: Keystone Nice

Posted in Blog Affairs, Conferences by YPAA on June 14, 2009

It has been very slow going, but I have been updating the Keystone Nice post. As of tonight, I’ve gotten through the Monday morning session (for the speakers that had my attention), so there are notes from talks by:

Andrew Fire
David Bartel
V. Narry Kim
Gunter Meister
Qinghua Liu
Bruce Paterson
Erik Sontheimer
Dinshaw Patel
Jin-Biao Ma
Scott Kennedy
Craig Mello
David C. Baulcombe
Peter Sarnow
Yukihide Tomari
Eric C. Lai

More talk notes to come later. I do realize there is some futility to this, since by the time I get all the information up, it will almost all be published! However, the post has been getting the most views on the blog, so I intend to finish what I started.


Posted in Blog Affairs by YPAA on March 15, 2009

Welcome to this RNA/science blog. I will post commentary from others and myself on papers that present new findings in the realm of RNA biology. I may also comment on what transpires in the science community that surrounds me.

My attendance to a small, weekly RNA journal club at MIT, and our discussions therein provide the basis for this forum. Each week I will cite the paper selected for journal club, and when possible, post commentary on the paper from either myself, a colleague, or from a group discussion (commentary will be clearly cited). Praise will be served, and criticisms asserted.

In the spirit of an unrestricted back and forth discourse on these topics, I want to extend an open invitation to all readers to submit responses to posts (‘Comments’), and your own commentaries on any RNA papers that interest you. Send me something interesting you’d like to post concerning a paper, or a more lengthy response to a previous post, and I will make every effort to post it, unedited.

(It is important to note that no papers whose authors have MIT affiliations can be chosen for the aforementioned journal club, and therefore a small, (but not insignificant!), portion of literature concerning RNA biology will be left out from postings highlighting these selected papers. Owing to this limitation, I strongly encourage submissions (to me) of commentary on papers in the field of RNA with MIT authors. Please consider me an unbiased referee, despite my academic affiliation.)

My hope is that this blog will encourage an exchange of ideas and opinions about new publications in RNA biology, transcending some traditional methods for such discourse: overly formal commentary submissions to scientific journals, and informal face to face conversations between scientists (requires both parties to be, yes, face to face). Scientific meetings and presentations remain excellent forums to discuss results, perhaps a blog like this one can extend scientists’ abilities to debate science, keyboard to keyboard.

I realize that there are some barriers to overcome for this to work. No scientist is unbiased, and some may find it difficult to post their opinion(s) about other people’s work for fear of embarrassment, contradicting other data that has not been considered, or a desire to maintain a ‘professional’ image. I don’t have an exquisite counter-argument to these issues, just, if you are a scientist or training to be one, you must debate to perfect your craft: be confident and logical; make every effort to be right, but don’t be afraid to be wrong.

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