James and the Giant Corn Genetics: Studying the Source Code of Nature

January 3, 2022

Predictors of salary among faculty in the same department

Filed under: Campus Life,Fun With Numbers,Life in Academia — James @ 6:59 pm

At most public universities everyone’s salary is a matter of public record. It’s always fascinated me that we don’t talk about this more often. It means it is straightforward to look at the total variance in people’s salaries in the same role and test different ideas for what might explain the differences in compensation between different people in the same role. So let’s take a look!

In my own department there are ~45 faculty with research appointments and entries in our school’s 21-22 salary database: Eight assistant professors, fifteen associate professors, and twenty-one full professors. Since assistant professors want to get promoted to associate professor and associate professors want to get promoted to full professors, the simplest model I can think of is to look at how well professor rank predicts salary.

Faculty salaries by academic rank within a single department.
Faculty salaries by academic rank.

Okay, so our extremely naive model is clearly on to something: average salary increases as people get promoted. But also salaries are much more widely distributed amongst full professors than among assistant professors. Lots of things that could be driven by. But what about the classic “let’s boil down research productivity to a single metric”: the h-index? Only 36 of the 45 professors in my department have google scholar profiles. But that’s not the big problem.


March 9, 2010


Filed under: biology,Campus Life,Genetics,genomics — Tags: , , — James @ 2:56 pm

Who could have predicted maize geneticists would be so interested in maize genes? The entry I posted last night on Purple plant1 and Colored aleurone1 easily received more traffic in its first day on the site (it’s still got a long way to go before it catches long term readership attractors like water chestnuts and the NIPGR tomatoes), than any entry since the heady days of the maize genome release back in November.

The relationships of the four grass species with sequenced genomes. The branches are NOT to scale with how long ago the species split apart. Green stars represent whole genome duplications. The most important one to notice in the one in the ancestry of maize/corn. That duplication means that every region in sorghum, rice, or brachypodium is equivalent to two different places in the maize genome, one descended from each of the two copies of the genome that existed after the duplication.

And this morning the dataset I drew that example from, 464 classical maize genes mapped onto the maize genome assembly plus syntenic orthologs in up to four grass species: sorghum, rice, brachypodium, and the other region of the maize genome created by the maize whole genome duplication (technically syntenic homeologs since we started in maize to begin with, by the principle is the same), went out to the maize genetics community (thank you MaizeGDB!).

A postdoc in our lab tells me more people have visited CoGe today than any day on record (and we hit that mark before noon!).

Anyway, thank you guys, it’s great to feel appreciated!

March 8, 2010

Scientific Posters

Filed under: Campus Life — Tags: , , — James @ 11:29 pm

I’m involved in the designing of two posters my lab will be taking to the maize meeting in a weeks time. What are scientific posters?

A cross between a very short paper and a very short, on demand, research seminar, a poster is a dozen square feet of scientific data. We grad students cobble together some figures describing the data we’ve painstakingly acquired though months of long days and nights in lab*, hang our poster a scientific conference and spend hours hovering nearby, ready to explain our research to anyone who seems even marginally interested.

Probably the most important role of posters is that designing them gets us thinking about the questions our research (what we actually do all day) is really trying to answer and how to communicate our results to people who don’t specialize in those exact same questions. A trap that I often catch myself falling into.

As for the value of posters as a real method of scientific communication… it’s best not to set your expectations too high:

The best general advice I can give a first-time poster constructor is to describe the circumstances in which a poster will eventually be viewed: a hot, congested room filled with people who are there primarily to socialize, not to look at posters. Because poster sessions are often concurrent with the “wine and beer” mixer, chaos is further increased by hundreds of uninhibited graduate students staggering around hitting on each other. It’s not a pretty sight.

And it gets worse: meeting organizers will invariably sandwich your poster between two posters that are infinitely more entertaining, such as “Teaching house cats to perform cold fusion” and “Mating preferences in extraordinarily adorable red pandas.”

Words that were comforting to read when I first started stressing out about never having put together a scientific poster before. (And just to be clear, I’m not saying posters can’t be very effective methods of communicating science, only that the worst case scenario for a poster is that it gets ignored. The worst case scenario for a paper is it comes back with a rejection notice and horrible reviews, and the absolute worst case scenario for a scientific talk is, I suppose, heckling followed by a mass walk out. My point is, by comparison, designing a poster should be a low stress activity.)

That said, I think we’ve got some interesting data to present, so if you’re going to be at the maize meeting next week and are willing to risk my inexperience with designing scientific posters, be sure to stop by poster #31 or #39.

The two posters discuss, respectively, the way extra copies of genes are lost from the genomes of plants following how genome duplications, and a project where we’ve identified equivalent genes between up to five grass genomes (which would be quite the trick since only four grass species have sequenced genomes, but since maize has its own whole genome duplication we count it twice) based on the conserved order of genes along chromosomes (synteny).

*At least that’s usually what ends up on posters. I can’t wait to find out what interesting stuff ends up on the Biofortified poster (#167)

February 26, 2010

The Sacrifices People Make For Science

Filed under: Campus Life — James @ 4:03 pm

Just to give you a sense what Macro Island looks like. photo: John Walker, flickr. (click photo to see in original context)

My heart bleeds for those poor scientists forced to spend the week at Marco Island for the Advances in Genome Biology and Technology conference. Not only do they have to put up with temperatures in the 60s (~20 C) and views like the one attached, but consider the grueling workload they labor under even after the sun goes down. (Excerpt from coverage by the Daily Scan):

The real marathon, though, came Thursday night with an increasingly competitive host of vendors vying to throw the best party. As far as Daily Scan can remember, you’d have to go back to the heady days of 2002 or so to see this conference with such participation from vendors, who have to be especially creative now that there’s no exhibit hall. Life Technologies and Caliper hosted parties showing off their new instruments, while Complete Genomics and Ion Torrent offered plenty of opportunity to schmooze with fellow attendees. Friday night we’re expecting fireworks (not the metaphorical kind) from Pacific Biosciences.

February 23, 2010

Science Confessions

Filed under: Campus Life — James @ 1:51 am

If you haven’t already, check out the hilarious/sad hash-tag on twitter #scienceconfessions.

A few that caught my eye:

SFriedScientist: I believe PCR works better if I wear a specific hat and pet the thermocycler#scienceconfessions

Mod_Scientist: Cried in the cold room… on more than one occasion. #scienceconfessions

ToasterSunshine: I’ve gotten stuck behind the -80C freezer.#scienceconfessions

Lost_Marbles: Almost got swept into the Caribbean Sea at 15 while collecting snails for science. Never wanted to do field work again #scienceconfessions

February 4, 2010

Thanks Brassica oleracea

Filed under: Campus Life — Tags: , , , — James @ 11:01 am

My claim to 15 seconds of fame?

If you see a guy holding this stalk of brussels sprouts reciting the definition of qPCR in a promotional video from Agilent, it just might be me. (How many biologists carrying telegenic vegetables are they likely to find on campus? 😉 )

Edit: For the record, qPCR is a technique used to estimate the relative proportions of different DNA sequences in a sample. Perhaps most commonly, this is used to measure how strongly different genes are expressed. (Isolate RNA from a tissue, reverse transcribe it into DNA and measure how abundant your the sequence of your favorite gene is in the same.) When a plant needs more of a protein (say one that helps defend against fungal infection), it will produce more RNA copies of that gene’s sequence, each of which can be used over and over as a blueprint for ribosomes to make more copies of that particular protein. The acronym itself stands for quantitative Polymerase Chain Reaction.Which isn’t the most coherent explanation of a molecular biological technique I’ve ever written, but it has been a long day.

A Reminder: National Lab Mustache Day

Filed under: Campus Life — Tags: — James @ 12:28 am

… is coming up a week from tomorrow (Friday, February 12th). It’s been two and a half years since I last sported a mustache, but I recently found out about this holiday and it’s too awesome not to bring back the ‘stache. (Temporarily of course)

For more on National Lab Mustache Day, check out … the NLMD blog.

All sorts of bad hair choices on display here. Not that some people can't pull off the mustache, I'm just not one of them. 😉

January 28, 2010

Grad School Admissions Essays

Filed under: Campus Life — James @ 4:19 pm

This is the second year I’ve had the privilege of reading the personal statements of the prospective new grad students being interviewed by our department. It’s interesting to see the strategies people take in trying to sell themselves. Broadly applicants can be grouped into three categories (at least successful ones, the department doesn’t let us see the essays of the people it rejects so I can’t comment on those):

  • #1 Ever since an early age I’ve been fascinated with plants…
  • #2 The research I already do on plants is so exciting let me tell you about it…
  • #3 There are a lot of problems with the world, in plants/agriculture/biology I see the potential for solutions, which is something I want to devote my life to because …

Of course, as with any gross over-generalization, this skips over a lot of complexity and individual variation* but these do seem to be the predominant, successful, strategies. I really wish I could take a peak at the reject pile though, to see if there are only so many ways to writing a personal statement for a plant biology program, or if it simply that these approaches appeal more to admissions boards than the alternatives.

Thinking back to my personal statement, I definitely fell into category #2 “I don’t have much interesting to say about me, but let me tell you about the awesome plant science I’ve worked on so far!”

*One repeated trait that showed up in some essays belonging groups 2 and 3 was “[I was going to be/my parents want me to be] a doctor, but…” I’m not sure whether I would recommend this to people writing their admissions essays or not. It seems to me that this can even come off as flattering (this person could have been making a six figure salary and do a job depicted on countless TV dramas, but they liked our field so much they chose it instead!) or annoying (so they didn’t make the cut/were afraid to apply to med school and though plant biology would be an easy fallback did they? I’ll show them!).

January 21, 2010

My First Day Teaching (prologue)

Filed under: Campus Life — Tags: — James @ 11:57 am

Random photo of the blooming zebra plant (of the Aphelandra sqarrosa variety) in my office. Because I've been writing too many picture-less posts lately,

I don’t actually start for another two and a half hours. But at 2 pm pacific time I’m going to assume the role of a graduate student instructor (Berkeley’s fancy name for a TA) in the first of the two discussion sections I’ll be teaching every week.

As first classes to TA go, this one feels like a good fit for me. It is an introductory course in plant biology aimed at non-science majors. A couple of the people in my year did this for the first time last semester with courses on plant biochemistry or computational biology and spent the whole time trying to keep one week ahead of their students in learning the material. In a course on introductory plant biology and agricultural/biotech issues we’re going to be discussing stuff I know and am excited about!

The professor who gives the lectures seems pretty awesome too. In a semester she’s planning to cover everything from basic biology cell cycle and DNA->RNA->protein to plant specific biology like floral development and plant pathogens, and at the same time get the students thinking and writing about their views on biotechnology, agriculture, and biofuels.

It should make for an exciting semester.

Also, lectures are in an auditorium with over 100 seats and at the first one, on Tuesday, every single one was taken and there were people sitting in the aisles. At Cornell the only plant biology class I ever took that even approached that kind of enrollment was the two weeks I took of Intro Botany. Great to see so many people excited about plants and their molecular biology (or at least willing to sit through a semester of lectures and discussion sections on the subject to fulfil some distribution requirement)!

January 20, 2010

How to Give an Interesting Research Talk?

Filed under: Campus Life,research stories — Tags: , , — James @ 2:07 pm

Corngrass1 a dominant mutant that keeps maize from making the transition to adult growth. The stalk of a normal maize plant is shown to the left for comparison. According to George Chuck, in some genetic backgrounds where they never flower, corngrass plants are potentially immortal, as cuttings of the stalk can be transplanted to new soil and simply continue to grow. (Normally corn plants are annuals, they stop growing once the end of their stalk turns into a tassel and eventually die off even if they're grown in temp. controlled greenhouses.) Photo courtesy of MaizeGDB.org

Just got back from a great talk given by George Chuck, who works on microRNAs that control the transitions between the juvinile and adult phases of plant development in maize at the USDA’s Plant Gene Expression Center. In trying to figure out why it was such a great talks (besides the obvious, that he had exciting data to present).

The obvious ones I could spot where: (more…)

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