You'd Prefer An Argonaute


Posted in Lab Life, Science Journalism by YPAA on January 23, 2011

I don’t read many science blogs these days, but one I definitely recommend is Carl Zimmer’s The Loom. He recently dug up and posted this gem quote:

If I may throw out a word of counsel to beginners, it is: Treasure your exceptions! When there are none, the work gets so dull that no one cares to carry it further. Keep them always uncovered and in sight. Exceptions are like the rough brickwork of a growing building which tells that there is more to come and shows where the next construction is to be.

–William Bateson, in The Method and Scope of Genetics, 1908

Yes! Yes! Wise words for even the non-beginners, like me. In fact, my current project in the lab grew out of an exception, out of which I’ve built something. And when I think about other projects I’ve watched develop in the lab, exceptions have often propelled them. Behind many of them is a story worth telling, no?

Ain’t Nuthin’ But A “GWAS” Thang

Posted in Lab Life, Scientific Publishing by YPAA on November 11, 2010

If you could rename your favorite journals with musically referencing titles, what would they be? Some ideas:

Cell or Nature or Science = Magical Mystery Science Tour

Nature Genetics = Nuthin’ But A “GWAS” Thang

Genes and Development = Billie Genes

PLoS One = Come As You Are

PLoS Biology = Wish You Could Publish Here

Genome Research = C.B.R.E.A.M. (Computational Biology Rules Everything Around Me)

CSHL Protocols = Methods Man

RNA or Nucleic Acids Research = Base Sugar Phosphate Magik

Any others? Hey, first person to submit a comment below identifying all of my references and adding one good new one gets a free super-limited edition t-shirt. For reals!

Posted in Lab Life by YPAA on September 18, 2010

When lab is too much, I’m often like, “Whoa,” Keanu style.

RNA knowledge suppliers

Posted in Lab Life, Scientific Publishing by YPAA on August 12, 2010

Collectively we cook it up in the lab; they package it up nice and then sell it back to us for a profit. An honest exchange? No, of course not, but that’s the game. Even what product of our own we could save cannot compete with all that nectar they sling, so we’re addicts.

Here’s a list of prominent suppliers. We consume a lot of their product in RNA Journal Club, as you’ve probably noticed, especially from the triangle of cartels I call the “Big Three.” You’re warned that the quality can be highly variable:

The Big Three


The rest

Molecular Cell
Nature Structural and Molecular Biology (NSMB)
Nucleic Acids Research (NAR)
RNA Biology

Yeeawh, hit that #$%@.

Please direct questions to my projected computer screen…

Posted in Lab Life, Media, Talks by YPAA on May 4, 2010

What?! Now the US military is wasting as much time as we do on Powerpoint? Man, Joe. Q. Taxpayer could sure hit the Microsofties responsible for peddling this necessary evil in the nuts right now. Powerpoint has been used to cover up many a shitty talk!

Keep your presentations short and sweet. Limited free passes for unnecessary images can only be given for humor, that is IF you’ve got the funny credentials. Otherwise leave these to the experts. 🙂

Liquid and intellectual refreshment in S. Brenner

Posted in Lab Life, YPAA Journal Club by YPAA on April 4, 2010

Laboratory biological science hasn’t changed much in the last 40 years:

What, the reader may ask, did we do in the 6 years between starting C. elegans genetics and publishing the first article on it? Since the animal has a short life cycle of 3.5 days, it should not have taken all that much time just to complement and map the mutations. Many visitors who came to the MRC Lab in Cambridge thought that we spent far too much time eating, drinking, and talking. Observing us only during normal working hours, you could see their point. If one arrived at the lab at the reasonable hour of 10 am, there was just time to open one’s mail before adjourning to the canteen for morning coffee, usually prolonged by a very interesting discussion on some aspect of science. This did not leave much time before lunch, which naturally was also accompanied by discussion that was terminated only by rushing off to attend an afternoon seminar on the Bohr effect in hemoglobin or the like. That brought one to afternoon tea and after that there was hardly enough time to start anything in the lab before adjourning to the pub for liquid and intellectual refreshment. It was only after dinner that the real work started and the lab then filled up with the owls. Even these bouts of work had to be interrupted, of course, for midnight coffee and more discussions.

Sydney Brenner, from  In the Beginning Was the Worm . . .

Scooped Online

Posted in Lab Life by YPAA on February 6, 2010

As I put the finishing touches on a project, I incessantly peruse the literature online, less out of interest in new discoveries, but more out of desperation to not find that I’ve been scooped. Please don’t tell me I’m alone in this behavior/activity. Especially nowadays with all the online advanced releases, one cannot help but check them as they arise, rather than discipline themselves to only check weekly for the weekly journals, bi-weekly for the bi-weekly journals, etc. Embracing technology; chained by technology–inseparable sides of the coin. Less coinage please.

An “unsentimental education”

Posted in Lab Life, Media by YPAA on October 2, 2009

I’ve been thinking about graduate school and mental health recently. Depending on circumstances, working toward a Ph.D. can bring about pressures on the mind strong enough to disturb it. Situations that end in the most extreme outcomes, like suicide, of course can probably never be fully attributed to an experiment gone wrong, an adviser gone wrong, an institution, or impending dismal career prospects. These cases are highly personal; many other people in otherwise identical circumstances would not react the same way. So look out for your chums, and your non-chums/co-workers too.

I was considering writing a piece about mental health among grad students at MIT, although I have now dropped the idea–too close to home I think. But while I was still investing interest in this story, a teacher refered me to an article, by Stephan S. Hall, that appeared in The New York Times Magazine in November, 1998, titled “Lethal Chemistry at Harvard”. It is an excellently written, but nonetheless very sad story about a graduate student in the chemistry department at Harvard who took his life in 1998. In the story, Hall wrote a paragraph describing the archetypal journey of a graduate student in the sciences. I found it so realistic that I think it’s worth reprinting:

Graduate study in the sciences, however, is a very unsentimental education. It requires the intellectual evolution from undergrad who can ace tests of textbook knowledge to original thinker who can initiate and execute research about which the textbooks have yet to be written. What is less often acknowledged is that this intense education involves an equally arduous psychological transition, almost a second rebellious adolescence. The passage from callow, eager-to-please first-year student in awe of an often-famous faculty adviser to confident, independent-minded researcher willing to challenge, and sometimes defy, a mentor is a requisite part of the journey.

I haven’t gotten to the defy your mentor stage yet, but boy I can’t wait. I’ve seen others do it and it looks pretty cool.

Tagged with:

Me Blog You Long Time

Posted in Lab Life by YPAA on August 9, 2009

I went to a Catholic high school–a pretty liberal one in Oakland, CA. Every semester we had to take a religion class. (Incidentally, it was also here that my love of biology was precipitated by a wonderful biology teacher. A women at the time, she is now a man–how’s that for a lesson in biology!)

Some of the classes required reading the bible and religious textbooks and such, classes like “Hebrew Scriptures.” Other classes emphasized more general societal and moral themes, classes like “Marriage and Family.” And then there was one class called “Christian Sexuality” that was for all intensive purposes, a sex education class taught by a priest.

My teacher for this course was quite a character. In one class, he brought in the most recent copies of Playboy and Playgirl. The class was split up by sex, and us boys had to look at the Playgirl, and the girls the Playboy. This went on for ~10 excruciating minutes, and then we had a discussion.

The funniest part of this was the story the Father told us about how he bought these magazines. It goes something like this: He, a priest dressed in full regalia, walks into a liquor store, nonchalantly picks up the pair of magazines from the shelf, and walks over to the counter. He lays down the magazines to pay. The Playboy is face up, and the clerk does a double-take upon noticing his customer’s dress. They both somewhat bewilderedly nod in acknowledgment as the clerk scans the Playboy. Upon seeing the Playgirl beneath, the clerk expresses the facial equivalent of throwing one’s arms into the air exclaiming “I give up!”

Anyhow, later in the semester this Father did give us a gem of a piece of advice (especially for a room full of 14-year-olds): Never make an important decision when you are: (1) drunk, (2) horny, (3) depressed.

Here’s a laboratory never list. Based upon your predicted outcome of a new experiment, never: (1) order reagents you will only need if the outcome is met; (2) start round two of the experiment before all results from round one are in; (3) present your preferred outcome, in the form of fake data, in a lab meeting (a guaranteed jinx); (4) plan a vacation.

Confidently predicting experimental outcomes I think must be like novice bull riding. You’ll get bucked around a lot; you can’t predict when you’ll lose control; and don’t make any big plans for right after because after bucking you off, the bull might come back and step on you.