Coming soon: Crowd-funding a Joshua tree genome

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Joshua trees at Tikaboo Valley, Nevada (Flickr: jby)

Joshua trees at Tikaboo Valley, Nevada (Flickr: jby)

I’m very excited to announce a new project, with a new model for doing science: The Joshua Tree Genome Project, in which I’m working with a bunch of smart, accomplished folks to sequence the genome of my favourite spiky desert plant. A sequenced Joshua tree genome will provide the framework to understand how coevolution with highly specialized pollinators has shaped the history of Joshua trees, and to use the landscape genomics skills I’ve developed with the Medicago HapMap Project and AdapTree to understand how the trees cope with extreme desert climates — and how to ensure they have a future in a climate-changed world.

Perhaps most excitingly (terrifyingly?) we’re going to raise some of the funds to do the genome sequencing by crowdfunding, using the Experiment.com platform. So please keep an eye on the project site, follow our Twitter feed, and Like our Facebook page to make sure you don’t miss your chance to help understand Joshua trees’ evolutionary past and ensure their future.

Chronicle Vitae: On advice

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Truth in advertising. (Flickr: Alexander)

Truth in advertising. (Flickr: Alexander)

I’m back in Vitae this week, ruminating on the usefulness of personal advice — or rather, its frequent lack of usefulness.

The challenge with receiving and applying advice is to distinguish real, general principles from what may simply amount to another person’s recollection of a series of events that ended well. … Certainly in academia, as in any career, there are habits and choices that improve the odds of survival from graduate school to tenure. But simply making it to a particular stage doesn’t actually mean that you had all the right habits or made all the right choices — or even know which habits and choices will work for most other people.

In keeping with my established approach to these columns, I actually do circle back around to a way in which you can learn from other folks’ personal experiences, but you’ll need to read the whole thing to find out how.

How to do chili

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Not pretty, but it warms you right up. (jay)

Not pretty, but it’ll warm you right up. (jby)

We’re well into the time of year when, in Minneapolis, the air outdoors will freeze your nose hairs on the first breath, and snow has lost its charm. Here in Vancouver, the only substantial snow is on the mountains across the water, but there’s ice on the trails in Stanley Park, and the trees are lacy with frozen fog. In either city, it’s the time of year for soup: elaborately spiced pho, classic chicken-noodle, and chili.

I don’t so much have a recipe for chili as I have some rules of thumb. My preferred ratios of ingredients, and some of my spicing, are informed by the recipe in Mark Bittman’s magisterial How to Cook Everything, but really that one confirmed a lot of what I’d already arrived at through trial and error. This probably won’t win you a state-fair cook-off, but it’ll make a big pot of hot, hearty, fragrantly spiced chili of the sort that goes perfectly with some cornbread or over rice on a cold winter night.

Here’s what you do:

Continue reading →

In 2016, keeping an eye on the numbers

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(Flickr: An&)

(Flickr: An&)

Whether or not it makes any sense, the start of a new year is traditionally when we come up with lists of things we wish we did more, or less, or at all. At least it’s a chance to place a psychological flag in the sands of time and say, now is when I start keeping track of whether or not I do this thing. Reading other folks’ academic resolutions for 2016, I’ve seen some things I’d like to work on for my own sanity and scholarly productivity, and there’s a meta-resolution that ties them all together: counting.

I’ve long had a skeptical relationship to resolutions about achieving specific numbers of things — losing pounds, reading papers, writing pages. It seems like a lot of cognitive load for payback that is nebulous, at best. But as I look back on years past, I have to admit that what I count is what I get done.

I’ve run eight marathons in the last seven years, and most of my actual training has been simply aiming to run at least 30 miles a week. Over last year that added up to 1,882 miles — I’ve run upwards of 1,500 miles every year since 2010. I don’t fret about pacing or getting in just the right mood or the specific route I take — I just make sure I get to 30 every week. When I got my first activity-tracking wristband (I currently have a Fitbit) and started logging calories, I actually did find myself making small, sensible changes — walking more, eating more vegetables — to keep my daily numbers above 10,000 steps and below an activity-adjusted calorie count. Tracking my reading on GoodReads hasn’t gotten me to a goal of 20 books in a year yet, but it’s definitely gotten me doing more pleasure reading than I was before I kept count. And on the career front, I started out the 2015-2016 hiring season by building a spreadsheet to track my applications for faculty jobs—and I will, in fact, manage to get to 60 submissions. (Which have led to a non-zero number of interviews, about which I will say nothing further in any public venue lest I jinx something.)

In conclusion, counting a thing is a good way to help (me, at least) get more of that thing done. So, in 2016, I might as well count some other things that I would like to do more. Two things that have fallen by the wayside while I’ve moved across the continent and done all that job-applying are keeping up with the scientific literature (apart from what I read in the course of grant- and paper-writing) and writing rapidly and often. So I’m signing on for 365papers and 50posts. And here’s hoping for a non-stop new year.

https://www.youtube.com/watch?v=Slt18JWkdj4

Chronicle Vitae: Thanks to mentors

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In the field with my dissertation advisor, Olle Pellmyr (centre) and collaborator Will Godsoe. (Flickr: jby)

In the field during the first year of my Ph.D. research with my dissertation advisor, Olle Pellmyr (centre) and collaborator Will Godsoe (left). (Flickr: jby)

Over at Vitae, I’m contemplating an appropriate topic for the week of U.S. Thanksgiving: how much I owe to the many senior colleagues who’ve mentored me over the course of my scientific career.

In graduate school and as a postdoc, I’ve been exceptionally fortunate in my formal and informal relationships with senior colleagues. As I’m nearing (I hope) the day when I will begin teaching, training graduate students, and supervising postdocs myself, I’ve tried to keep track of specific ways that my mentors have aided me. It’s helped me define what I want to do as a mentor myself, but it’s also good, I think, to remember how much my career has depended on others’ support.

No, I don’t know why the piece is illustrated by men carrying turkeys, apart from the seasonal connection. Maybe the men are mentors and the turkeys are mentees? Maybe just go read the whole column and don’t over-think it.

Chronicle Vitae: Why the tenure track job hunt sucks — and why it maybe ought to?

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(Flickr: Alison Curtis)

(Flickr: Alison Curtis)

In a new post for the Chronicle of Higher Education’s Vitae blog today, I let off a little of the steam accumulated over four years (and counting) of writing applications for tenure-track faculty jobs.

Do you really need to receive letters of reference with my application? Yes, of course, you want perspectives on candidates from people who have worked with us in the past. Will you use their letters in the very first round of sorting through dozens (or hundreds) of applicants? Probably not. I have met a few faculty members who tell me that they do read letters for that first-stage decision — but those professors are the rare, possibly superhuman, exceptions. For candidates, making sure letters get delivered means making sure that three-to-five usually very busy senior collaborators know the general description of the job opening in question, the idiosyncratic method by which letters should be submitted, and the deadline for submission — then following up to ensure they meet that deadline.

I’d like to think this column is both a (reasonable) extended complaint, and a #SlatePitch-y rebuttal to said complaint — because I kinda think, actually, that as maddening as tenure-track applications can be, they might be pretty good at identifying people who will do well as faculty. To find out why, go read the whole thing.

Social Evolution Forum: Evolution in response to ecological conditions changes ecological conditions

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Daphnia magna adult and juvenile. (Flickr: NTNU Faculty of Natural Sciences and Technology)

Daphnia magna adult and juvenile. (Flickr: NTNU Faculty of Natural Sciences and Technology)

I am very happy to be among the members of the Evolution Institute’s new community blog, the Social Evolution Forum. The team includes a bunch of terrific geneticists and anthropologists and people with more social-science-y backgrounds … and me, with a publication record that’s easily 90% research on plants, which do not have societies in any meaningful sense, and interactions between plants and other things that are not really very social, either — moths, or bacteria. Still, nothing in biology makes sense except in the light of evolution, and evolution is very much what I study, and I have written about the biology of the most quintessentially social species, Homo sapiens quite a bit in the past.

All the same, for my inaugural post to SEF, I’m leaning into my role as the generalized evolutionary ecologist with a kind of post I haven’t written in some time, it feels like: a brief discussion of a cool new experiment in rapid evolutionary change and its ecological consequences.

Evolution in response to natural selection over a few weeks or months may not seem like it could matter much, but a recent experiment with one tiny evolutionary champion shows that it can, in fact, have measurable effects on a whole community of interacting species. The communities in question are the kinds found in ponds all over the world, in which swarms of small crustaceans compete to graze and prey on algae and other microorganisms, and evade death in the gaping maws of minnows and sticklebacks. One of these crustaceans is Daphnia magna, the common water flea, which has a life cycle that turns out to be quite convenient for scientists who want to watch evolutionary change in real time.

As you’ll find if you read the whole thing, Jelena H. Pantel and her coauthors raised clonally-reproducing Daphnia in artificial environments with communities of competing crustaceans for about three months — ten water-flea generations or so. They then used individuals sampled from those evolved populations to colonize new communities, and compared what happened to those communities to ones started with Daphnia that hadn’t had time to evolve. It’s a nice experiment in ecological consequences of evolutionary change — and how that change can actually feed back to alter the conditions that caused it in the first place.

And, when you’re done with that, check out great opening articles by Arun Sethuraman, Lee Alan Dugatkin, Jennifer Raff, and Anthony Biglan — that should give a pretty good sense of the variety of voices and expertise you can expect at SEF.

Chronicle Vitae: What is a postdoc?

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(Library of Congress: C.H. Kidurell)

Vitae totally found a picture of an old-time scientist with exactly my haircut. (Library of Congress: C.H. Kidurell)

Over at The Chronicle of Higher Education‘s Vitae site, I’m contemplating my own job description.

In the four years since I finished my doctorate, I’ve done at least another Ph.D.’s-worth of work on questions that, back in graduate school, I would never have thought I could tackle. I’ve been lucky — I landed a good postdoc on an interesting project with a mentor who gave me freedom to pursue just about anything I thought would be valuable. That is all exactly what I would want to do running my own lab as a principal investigator, with a faculty appointment. And isn’t that what I’m “training” to do, after all?

It ends up being, as you might expect, as much about the prospects for something to do after being a postdoc as the postdoc itself — but for that, you should go read the whole thing.

Actual sequences of authors on my bookshelves (a sampling)

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Adams, Anderson, Asimov.
Crichton, Christie, Clarke.
Dillard, Douglas, Duncan.
Hemingway, Herbert, Hiassen.
Irving, Irving, Isherwood, James, James.
Michener, Milne, Mitchell.
Pratchett, Pullman, Puzo.
Sagan, Scalzi, Shakespeare.
Stephenson, Thurber, Trollope.
Twain, Tolkien, Vinge.
Wallace, Warren, Westerfeld, Wouk, Willis.