You'd Prefer An Argonaute

RIP Alex Rich

Posted in MIT by YPAA on May 17, 2015

Screen Shot 2015-05-17 at 3.27.53 PM

(Photo: Donna Coveney)

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iBioSeminars: RNA Splicing: What is a Gene?

Posted in Media, MIT, Talks by YPAA on November 28, 2014

iBioSeminars: microRNAs (part I)

Posted in Media, MIT, Talks by YPAA on May 26, 2014

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iBioSeminars: microRNAs (part II)

Posted in Media, MIT, Talks by YPAA on May 26, 2014

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iBioSeminars: microRNAs (part III)

Posted in Media, MIT, Talks by YPAA on May 26, 2014

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Extreme Tissue Regeneration

Posted in MIT, Science Journalism, Uncategorized by YPAA on May 26, 2014

Read my recent piece on the fantastical flatworm planaria here, in OZY magazine.

The neoblasts (pink) of a planarian.

The neoblasts (pink), a type of stem cell, of a planarian.

More evidence of non-boring scientists

Posted in Media, MIT by YPAA on December 17, 2011

Dennis is a cool dude; it’s self-reinforcing in his staff.

Remember, no grant could ever fund this kind of lab environment!

Kim Lab, Department of Biology, MIT

R.I.P., H. Gobind Khorana

Posted in Media, MIT by YPAA on November 14, 2011


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.

Evidence of non-boring scientists

Posted in Lab Life, MIT by YPAA on February 17, 2011

One of the most clever lab homepages I’ve seen:

Kim Lab, Department of Biology, MIT

Things like this instantly raise the coolness factor of a lab.

Bonus: they do schweet research.

Scott Valastyan teaches the AACR about microRNAs

Posted in Conferences, MIT by YPAA on April 23, 2010

UPDATE APRIL 2015: The work originally referred to in this post has been retracted. Please read more here.

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.

Venki Ramakrishnan: the Cadillac of ribosome structure investigators

Posted in MIT, Talks by YPAA on October 28, 2009


Give this man a Nobel Prize. Give it to him.

I know before I’ve made clear my affection for Harry Noller, and that affection still remains strong like a peptide bond, but lately I’m head over heels (head over sneakers) for Venki Ramakrishnan. Last week in his lecture for the MIT Biology Colloquium, Venki Ramakrishnan charmed me and several hundred other people with his humor, smarts, and beautiful structural work.

The scene of Venki’s lecture, titled “How the ribosome facilitates selection of the right tRNA during decoding of the message,” was quite a spectacle. There was an electricity in the air. Never had I seen room 32-123 so packed. Every seat was taken, of course, and there were at least one-hundred other people huddled in the back of the lecture hall, down the stair aisles, in front, everywhere. Some professors were seated on the concrete floor.

Venki’s faculty host had warned the audience before the lecture began that the aisles had to be clear (for fire safety reasons), and so they were cleared. But sure enough, ~10 minutes into Venki’s lecture, the honorable MIT campus police unkindly entered the room and, temporarily, ruined some beautiful science.

It was quite funny: Venki was captivating us from the lectern, as he faced a projection screen to his left. To his right, a plump MIT police officer sauntered in, unbeknownest to Venki, but knownest to everyone else in the room. The copper reached his arm out to the lectern to capture Venki’s attention, Venki stopped talking, and the officer motioned to follow him outside the lecture hall. Totally perplexed, Venki obliged and left the room, to a chorus of boo’s directed at the police. Moments later, Venki emerged calm as a clam, and succinctly directed movement of his audience into a fire-escape safe arrangement so that his lecture could continue.

Imagine what Venki’s story could sound like: “I won the Nobel Prize, went to MIT, and was accosted by the campus police at my own lecture!”

Venki gave a beautiful introduction, even making a jab at Jim Watson (Watson the man, not Watson the scientist). (He also later hilariously and appropriately mocked Tom Steitz.) He then proceeded to give the best structural biology talk I have ever seen.

He described how proper base pairing between the tRNA anticodon to the mRNA codon induces subtle structural movements between that end of the tRNA and small subunit RNA that are transmitted up through the tRNA toward its aminoacyl end, inducing residue movement in EF-Tu leading to GTP hydrolysis–a cascade of events leading to EF-Tu release and aa-tRNA incorporation. (For more, see Venki’s recent review.)

He ended by narrating an incredibly cool animated movie of all the ribosome structural movements he had just described in detail, and then reprised the movie with a version set to a soundtrack of snippets of classic pop tunes (e.g. by The Clash, David Bowie, etc.), arranged by his lab. The lyrics spoke to the molecular movements spotlighted in the movie. It was very entertaining.

I realize I could have proclaimed Venki the “Rolls-Royce” of ribosome investigators, since he’s at the MRC. But no. He’s American; he’s a Caddy.