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!

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)

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.

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

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.

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.

• #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!).

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)!

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:

• History. One of the mutants he was working on, corngrass1, was first discovered in a sweetcorn field before many in the audience had even been born, and he was able to tie the history of the mutant in with the history of the debate about corn’s relationship to teosinte the wild grass from which we now know corn was domesticated.
• Context. Starting out by discussing phase change in model organisms like C. elegans, as well as phase change in humans (more commonly known as puberty) before bringing it back to corn.
• Tiny unexpected things. The one datapoint he presented to suggest the system he’d found in corn might also be functioning in eudicts wasn’t the usual model system for eudicts (Arabidopsis thaliana, the first plant to have its genome sequenced). It was watermelon. “I’ve always wanted a reason to work with watermelons.” It was only the second time I’ve seen any biologic data on watermelons. (The first was the result of a fascinating discussion with my roommate about phloem loading in the cucurbits (a group of species that includes melons, squash, pumpkins and cucumbers).)
• I’m sure there were lots of other things I didn’t even notice. Like housekeeping, it’s what’s left undone or done badly is much easier to notice than what is taken care of perfectly. <– I don’t know how the analogy to housekeeping entered my vocabulary, sounds more like something a person who was alive for the 1950s would use.

Studying plant genetics (and probably a lot of other scientific fields as well) means seeing a lot of presentations that are difficult to follow, even though they’re presenting fascinating data, but it also means seeing the occasion speaker who has mastered both the concepts and methods of his or her field as well the techniques used hook an audience.

This isn’t true just of public speaking. I’ve heard people complain (though I haven’t formed an opinion of my own on the subject), that the papers that get published in Science and Nature, the two most prestigious scientific journals out there, don’t always represent the biggest scientific breakthroughs, but rather great science that’s been done by people who are the best at writing papers accessible and interesting to people not working in the exact same field as the authors. I’m still too unexperienced as a scientist to know if this is a real bias, or just represents bitterness by people whose papers don’t get accepted, but you can see how it would make sense if it were true, can’t you?

Science and Nature are both read by highly educated scientists across a wide range of disciplines. If you and I both make discoveries of equal scientific merit, but my paper is written up in such a way that NO one outside of plant science will be able to make heads or tails of it, and yours has a chance of being read and understood by people working in everything from the phylogenetics of archaea to human medicine, and maybe even get a few anthropologists interested enough to skim the figures, obviously your paper should have a higher priority for being published in journals that reach the widest audiences (like Science and Nature).

It really isn’t fair, but people who can do the research, and then turn around and effectively communicate their results clearly do have an advantage in science. That’s why I’m trying to make notes of what keeps me engaged during the best talks. My one attempt so far to present the results of my own research was an only slightly mitigated disaster.

As just for the record, unless you’ve already decided you want a 100% teaching position, great communication skills are NOT a substitute for actually producing interesting data. They’re complementary goods, not substitutes.

Pamela Ronald is actually going to be talking in Berkeley late next month, but, in addition to a sneak peak of the presentation (which was really good) listening the the question session following their talk was a great chance to resample the perspective of the other major group involved in the debate on genetic engineering (besides anti-gmo activists, corporate public relations people, and plant scientists like me), farmers and agronomists.

What Pamela and Raoul advocate, distilled down to a single phrase, is agriculture utilizing “the best technology and the best practices.” The best technology is pretty clearly going to incorporate at least some genetically engineered traits, but the best farming practices will definitely incorporate approaches from organic agriculture. Organic farmers have developed some really innovative and useful practices worthy of praise, but making to sure to show that those innovations are appreciated is also one way of softening the blow while telling the consumers of organic food that many of their fears about genetic engineering are either ungrounded, overblown, or don’t have much to do with the technology one way or the other.

The Q/A session after the talk (one questioner in particular) made clear spending too much time praising organic practices will start making the farmers and agronomists who are already embracing the technology (if not always the companies which are developing many of the traits currently on the market) feel like the contributions of their own practices* aren’t being fully appreciated. I’ve got a theory on why this may be happening, and if so there’s a simple solution.

Like the senators currently battling over health care reform in congress, compromising too much too quickly to win over people in the middle or on the right risks ending up with a compromise no longer acceptable to those on the left. In the senate those on the left are making sure everyone knows their support can’t be taken for granted (which in turn gives them more input into the process).

I’m hoping this talk convinced at least a few more people in the audience to become engaged and raise their voices so they will have a say in the way agriculture will change in the future to deal with an expanding global population, the stresses placed on farming by the global warming, and the desire to not only feed ourselves but make sure our children, grandchildren, and great-grandchildren will be able to do so as well.

We live in a democracy. In theory the views of the majority should be the most influential, but in practice an active and engaged minority is often much more influential even when their views aren’t shared by an apathetic majority. It’s a cliche, but it’s true that the squeaky wheel gets the grease.

If you read this blog you’re clearly interested in these issues as well (whether or not you share my own views). In the coming years we as a society and as a planet are going to be making decisions about farming and agriculture with long reaching consequences. We’re all going to have to live in the future those decisions create so get educated, get involved, and make some noise!

Pamela and Raoul’s talk itself was excellent. If you ever get the chance to hear them speak I’d definitely recommend jumping on it. My complements also to Anastasia of Genetic Maize and Biofortified who organized the whole thing including getting support and funding from this (ridiculously long) list of organizations:

Department of Agronomy; Bioethics Program; Wallace Chair for Sustainable Agriculture; Council on Sustainability; Department of Genetics, Development, and Cell Biology; Department of Plant Pathology; Center for Plant Responses to Environmental Stresses; Interdepartmental Genetics Program; Plant Sciences Institute; Molecular, Cellular, and Developmental Biology Program; Department of Ecology, Evolution, and Organismal Biology; and Committee on Lectures, which is funded by the Government of the Student Body; Student Organic Farm; Graduate Program in Sustainable Agriculture Student Association; Graduate Agronomy Club; Biochemistry, Biophysics and Molecular Biology Undergraduate Club; and Natural Resource Ecology and Management Graduate Student Organization.

Given how much work organizing this lecture (as well as a whole series of events both today and tomorrow) must have been, I’ve guessing it may be a little while she’ll have time to write up her own thoughts on the experience.

I filled several pages with notes** during the talk, and I’ll try to figure out what to do with them this weekend after returning to Berkeley.

*More controlled and targeted use of nitrogen fertilizer (often using GPS data to specifically fertilize only specific parts of each individual field that can most benefit from it) and the spreading adoption of no-till farming are two great examples of practices in conventional agriculture that are greatly reducing fertilizer run-off and soil erosion, and as a result are improving the water quality of states like Iowa.

**For me taking notes is a choice between using the iPhone (easier to decipher, but looks like I’m spending the whole talk texting) and using pen and paper (which, for me, is still a little faster, but often results in much puzzling over mysterious and undecipherable scrawls if I ever try to read the notes back). Given I was sitting in the second row, I chose cryptic scribbles over looking like obnoxious-text-messaging-guy.