mateotambien's posterous

mateotambien's posterous

Matt Larson  //  Postdoctoral Fellow at UCSF, contributor to the NPR program Snap Judgment, and an assistant producer with the Stanford Storytelling Project.

You can find more of my audio essays here: http://www.prx.org/users/105198-mateotambien

Apr 15 / 10:04pm

Running the numbers (or, how to thank a scientist)

080818185209
Below is the first part of my dissertation acknowledgements section (and the only part of the thesis worth reading). I didn't thank God, but only because I assumed He was upset that I unlocked one of His deepest, darkest secrets: how RNA polymerase terminates at the end of a gene!

Enjoy.

I have always been terrible with the estimation of large numbers: I have no idea how many people live in San Francisco, and I couldn’t even begin to guess the size of the NIH annual operating budget. This, I believe, is due to a lack of concrete experience with such large quantities. I have never greeted all 815,358 of my neighbors in San Francisco, and unless inflation proceeds at an unprecedented rate, I would never hope to hold 31.2 billion dollars of hard cash in my hands.

Among other things, my 6.5 years at Stanford were an exercise in matters of scale. This extended period in my life, which accounts for the greater part of my 20’s, was marked by great intellectual variety, but also by a steady and excruciatingly regular routine. Each morning for 1,690 days (assuming a 260 day work-year, give or take a few excused and likely unexcused absences from lab), I rolled up my right pant leg, hopped on 1 of 2 bikes I have owned since moving to California, and rode an average of 2.3 miles to work. Upon arriving at Herrin Labs, I walked down 22 stairs and entered my 6-digit code into the key pad for the first of at least 20 times that day (over 200,000 keystrokes in total).

On 2-3 days out of the week I would begin preparing for experiments on the optical trap. On an average day I would consume ~15 tubes and at least half a box of pipette tips (at 96 tips per box, that’s ~40,000 over the entire length of my PhD) in order to prepare a sample of 1.5 x 109 RNAP molecules. Out of those billions of molecules, a select few would receive the daily spotlight. I would watch each of these chosen molecules (individually!) move at a rate of 10-20 bp/s (3-6 nm/s) over a 1 μm piece of DNA. They were the special few that beat the odds (a billion to one) and got the chance to reveal Nature’s secrets to the world.[1] I explored parameter space to the tune of at least 150 different conditions. Based on an average of 20 records for each condition (not including an equal number of traces thrown out because of excessive noise or short observation time), that’s 3,000 molecules that I sat and watched for an average period of 3 minutes. Based on a 2 kHz sampling rate, that’s 360,000 data points per trace, or 1 billion data points over the course of 6.5 years, all towards the publication of 2 (hopefully 3) manuscripts.

On two mornings I would attend group meeting. I would drink at least two cups of coffee (6-8 oz each) while I listened to each lab mate (sometimes not individually!) describe their research, the research of others, or just the goings-on of their own personal lives. These were the moments of grad school I cherished most. The number of people I have met at Stanford is not beyond count, but their value in my life is certainly beyond measure. I would like to thank them all here. There are too many to mention individually, and in some sense I have limited it to those that I think might actually some day read this thesis. To the rest of you, please accept my sincere (if implicit) gratitude.



[1]Oddly enough, the proportion of molecules that actually saw the light of day on the optical trap is probably equal to the number of people (compared to the total world population of 6.9 billion) that will read this thesis in its entirety.

 

 

Sep 17 / 2:52pm

Lab Rat on NPR's Snap Judgment

Snap_judgment
(download)

This is an edited version (think sweetened condensed goodness) of the piece "How to Catch a Lab Rat" below. 

Apr 8 / 1:45pm

Dump start

Guest producer Rebecca Pffifner and I explore the San Francisco Dump and discover what working artists, a falconer, and school children already know: trash can be just the beginning.

Bench_curl

Bench Curl, by Scott Oliver (http://www.sunsetscavenger.com/AIR/oliver.htm)
Scavenged lumber, hardware, and house paint
2007

(download)

Apr 8 / 11:59am

Once upon a unicycle

A group of 4th and 5th graders prove themselves on the basketball court. On unicycles.

Hula_hoops

(download)

 

Welch Riders Halftime Show:

 

Apr 7 / 11:22am

How to catch a lab rat

A real-life story of scientific fraud

Lab-rat

 

(download)

Apr 7 / 11:04am

Mundane superpowers

Everyone has one. It's just a question of digging deep and finding your inner superhero. The piece below might give you some ideas.

 
Mundane_superpower

Photo credit: Chris Leah (http://www.chrisleah.com/portfolio_1.html)

 

(download)

Apr 7 / 10:21am

Two women, a Frenchman, and Seth Rogen all walk into a bank

A radio piece about the genetics of sperm donation
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Photo credit: Rachel Weill

(download)