boESCs
OKAY, OKAY. But where can we get some ObamaESCs? At least something to reprogram? We gotta clone that mofo.
Naked DNA
Sculptor Franco Castelluccio’s new work, “Double Helix XX-XY”, via Curated Magazine.
FalconCAST
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…
… 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
DEAR KANYE WEST,
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.
LET’S DO THIS,
David García
MIT and Whitehead Institute for Biomedical Research
Cambridge, MASSACHUSETTS, UNITED STATES OF AMERICA
“Big Bang Big Boom”
Visually stunning exposition of life, evolution, free will. Do watch it.
OH NOES
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.
SnowRNA
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
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
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.
Harry Noller got shafted by the 2009 Nobel Prize in Chemistry
“For studies of the structure and function of the ribosome,” the prize was awarded. Why not Harry Noller then, whose entire illustrious career has focused on the structure and function of the ribosome? That’s bullshit.
Unfortunately this egregious omission by the Nobel Assembly pollutes recognition of momentous work that has taught us so much about what RNA can do.
(Santa Cruz Sentinel article with Harry’s reaction here.)
Da Prize
You’ve probably heard the news by now: the 2009 Nobel Prize in Physiology or Medicine was awarded to Elizabeth Blackburn, Carol Greider and Jack Szostak for the discovery of “how chromosomes are protected by telomeres and the enzyme telomerase,” in the words of the Nobel Assembly. Awesome. Congrats to these superb researchers for their smashing work.
The Sounds of Science
While sifting through my iTunes library recently, I came across more than a handful of songs on the subject of science. Sometimes the lyrics directly address science, sometimes the reference is more tangential, and sometimes only the song title is relevant. I’ve included links to audio/video (of mixed quality).
Biology
Do it. Dooooooo it.
This land is mine, this land is free
I’ll do what I want but irresponsibly
It’s evolution, baby
General
The Sounds of Science – The Beastie Boys
I’ve got science for any occasion
Postulating theorems formulating equations
Cheech wizard in a snow blizzard
Eating chicken gizzards with a girl named Lizzy
Dropping science like Galileo dropped the orange
She said I made some new connections to astound them all
in ways we’ve never dreamed about
This is what we all dream about in lab. One of my favorite bands couldn’t have stated it better.
Yeah, damn this thing. Why must it insist on half-a-tick-mark accuracy on my P1000?!
Physics
Why Does The Sun Shine? (The Sun Is A Mass Of Incandescent Gas) – They Might Be Giants
Ok, this song definitely takes the cake for the scienceiest song from a legitimate rock band I’ve ever heard.
You must listen to it–it’s a real hoot.
The sun is a mass of incandescent gas
A gigantic nuclear furnace
Where hydrogen is built into helium
At a temperature of millions of degrees
What Is The Light? – The Flaming Lips
What is the light
That you have
Shining all around you?
Is it chemically derived?
Colors are a fascinating physical phenomenon. This song has a real nice melody, and sounds really sciencey too.
Chemistry
Polyethylene (Parts 1&2) – Radiohead
So sell your suit and tie and come and live with me
Leukemia schizophrenia polyethylene
There is no significant risk to your health
She used to be beautiful once as wellPlastic bag, middle class, polyethylene
Decaffeinate, unleaded, keep all surfaces clean
The Chemistry Of Common Life – Fucked Up
Here but for the spinning of a sphere,
Electric skies and vibrations rise the breach,
the birth, the seed inside,
The chemistry of common life
Chemical Elements
Cobain was speaking about atomic number 3; or maybe he was talking about mood stabilizing drugs.
Who cares the song rocks.
The great Detroit troubadour Jack White went simple for the lyrics to this song.
Oh yeah, and this track is off their album White Blood Cells.
AAaahhhhhhhhhhhhh!
AAaahhhhhhhhhhhhh!
AAaahhhhhhhhhhhhh!
BioMedicine
Better Living Through Chemistry – Queens Of The Stone Age
The blue pill opens your eyes
Is there a better way?
A new religion prescribed
To those without the faith
Sister Morphine – The Rolling Stones
Here I lie in my hospital bed
Tell me, Sister Morphine, when are you coming round again?
Oh, I don’t think I can wait that long
Oh, you see that I’m not that strong
Hey baby you better come here quick
This ol’ cocaine is making me sick
Cocaine all around my brain
Yeah, it’ll do that.
Space
If you believed they put a man on the moon, man on the moon
. . . Newton got beaned by the apple good. Yeah, yeah, yeah, yeah
. . . Mister Charles Darwin had the gall to ask. Yeah, yeah, yeah, yeah
The Apollo Programme Was A Hoax – Refused
No it wasn’t. It happened. Listen to the R.E.M. song.
Polemic and Beyond
Science fails to recognize the single most
potent element of human existence
letting the reigns go to the unfolding
is faith, faith, faith, faith
What Would Wolves Do? – Les Savy Fav
The world may seem cruel
The world may hate us
In time we will show the world why the world made us
God Makes No Mistakes – Loretta Lynn
You might be wondering why a song with this title is on this list. I find the lyrics really fascinating actually; while a scientist’s explanation for these “mistakes” may be far simpler, they are probably unlikely to resonate as profoundly as Lynn’s with most people.
Why I’ve heard people say
Why is my child blind
Why is that old drunk still livin’
When a daddy like mine is dyin’
our blessed father gives us life
has the power to take it away
There’s no reason for what he does
God makes no mistakes
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