You'd Prefer An Argonaute

Theo Jansen’s Amazing Evolutionary “Live” Forms

Posted in Evolution, Gallimaufry, Media by YPAA on November 30, 2014
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Science of the flying V formation in birds

Posted in Evolution, Gallimaufry, Media by YPAA on January 15, 2014

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Richard Pryor examines predator–prey relationships

Posted in Evolution, Gallimaufry, Media by YPAA on January 4, 2014


Posted in Gallimaufry, Lab Life by YPAA on February 29, 2012

OKAY, OKAY.  But where can we get some ObamaESCs?  At least something to reprogram?  We gotta clone that mofo.


Naked DNA

Posted in Gallimaufry, Media by YPAA on May 30, 2011


Sculptor Franco Castelluccio’s new work, “Double Helix XX-XY”, via Curated Magazine.


Posted in Gallimaufry, Lab Life, Media, MIT by YPAA on May 18, 2011

More than a year ago a pair of Peregrine Falcons made their new home on the roof of our institute. They endeared us with their swooping through the air, their calling and playing, and their leaving various rodent body parts on outside windowsills. So cute!

This spring some furry chicks emerged, and now one can watch the whole family on a live webcam, FalconCAST. It’s a way to kill that time during your 4 degree spin. See the chicks roost, feed, and projectile poop.

Update 6/15/11

Man, they grew up fast. The following message was posted on our internal site this morning:

The falcons that hatched on Whitehead’s 7th floor have fledged and left their nest. Two of the falcons flew off earlier last week, and the last one departed on Saturday, June 11th. The parents will continue to feed the fledglings as the young learn the finer points of flying and mid-air hunting. Because the nest is no longer occupied, the FalconCast has been turned off.

Update 2012

The falcons and FalconCast are back online with hi-res camera.

You have a nice figure…

Posted in Gallimaufry by YPAA on December 16, 2010

Michel et al., the paper on Science Express today that mined Google Books to draw trends of word use in the English language over the last 200 years, from published books.

There’s no data post-2000, but cell and micro-biology are clearly declining in the genome era, where lazy computational biologists eat pizza and ice cream all day.

But why didn’t they plot “RNA”? It’s got to register at least as good as sushi did.

The Kanye West Genome Project

Posted in Gallimaufry by YPAA on July 29, 2010


I have been following your new Twitter account. IT’S AMAZING. So amazing. I am a scientist at MIT and I have a proposal for you: WE WANT TO SEQUENCE YOUR GENOME–YOUR KINGISH DNA ………… I’M DEAD SERIOUS. I work in the dopest laboratories IN THE WORLD. Come visit, after the V.I.P. tour you will see how SCIENCE WILL MAKE YOU BEYOND FAMOUS.


David García
MIT and Whitehead Institute for Biomedical Research

“Big Bang Big Boom”

Posted in Gallimaufry by YPAA on July 28, 2010

Visually stunning exposition of life, evolution, free will. Do watch it.


Posted in Gallimaufry by YPAA on April 10, 2010

Re-posted from Hydrocalypse Industries (from, like, a year ago):

Reminds me of a friend in college who spent his adolescence in Scottsdale, Arizona and said that in the summers there it got so hot he could feel his proteins unfolding.


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.

Strange Cambridge Fauna

Posted in Gallimaufry by YPAA on October 25, 2009

From my archives–spotted near Central Square in autumn. Untill this, neither in the wild nor in the laboratory was I aware of success in mating a large, furry, horned animal to a mountain bicycle. U-locked to a signpost, I was unable to mount and ride the forsaken beast. No sightings since.