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

December 31, 2022

More Professors Should Start Companies #1: Autonomy

Filed under: Uncategorized — James @ 12:41 pm

One of the great things about academia is that is gives smart and motivated people without the social skills to do well in corporate world a way to be engaged and contribute to society.

I don’t do well with bosses. The one exception I ever ran into was my grad school mentor who was wildly known as somebody who gave grad students an enormous amount of freedom and autonomy. To the point that about half the students who joined his lab struggled with feeling directionless and to graduate in even seven years. The other half of students to join his lab seem to have loved and and gone on to be extremely successful professors and leaders in industry. Every other person I’ve worked for I’ve butted heads with consistently. Getting older I’ve gotten better at “managing up” but I still don’t enjoy it.

One of the great things about being a professor — especially a tenured professor — is that we can spend a lot of time feeling like we don’t have a boss. My poor department head (whose priorities I don’t agree with but who is a perfectly decent human being) has something like 70 direct reports most of whom she cannot hire or fire. Academia is a good place for people who don’t do well taking orders … but launching your own company is even better.

Do you know how long it took me to get a raise for my amazing lab manager in my academic lab? Four months. At least ten meetings with three different people. Biweekly follow up e-mails. Multiple appeal forms and reworking of position descriptions while crossing my fingers and doing my best to combat the bitterness I see setting in to an enthusiastic and motivated scientist who can’t understand why it’s taking me so long to follow through on the raise we’d discussed months ago. Responsibility without authority sucks. A lot.

Do you know how long it took me to get a raise for an outstanding plant breeder in one of my companies? Three minutes. Me to co-founder: “We should really raise $X’s pay, he’s taken on so much extra work this year.” co-founder to me: “I agree. How about $Y,000?” “Sounds good. I’ll e-mail our HR contractor.”

The same relative ratio of work applies to buying a piece of equipment. Or renting new space as your team grows. Or paying an invoice. Or hiring a new person. In academia I typically have to fight through layers of people whose job it is to make sure I don’t do the wrong thing and get the university in trouble. At the startup we just decide, it happens, and if we make a mistake we deal with the consequences.

Of course the power to give your team raises doesn’t matter if we don’t have money to pay that new higher salary. Securing the money to be able to do stuff is a big thing both professors and founders put a lot of their time and effort into. But that’s a discussion for part two.

December 19, 2022

The Paspalum Genome

Filed under: agriculture,biology,genomics,Plants — James @ 4:41 pm

A paper eight years in the making and sixteen months in review. A real credit to Guangchao. I don’t think it ever would have come out without his dedication above and beyond what anyone could expect from a postdoc – James.

A team of researchers, led by Dr. Guangchao Sun and Prof. James Schnable of the University of Nebraska just published the genome of paspalum (Paspalum vaginatum) alongside evidence that paspalum may employ some tricks that could help its relative, corn, grow better with less fertilizer. 

Illustration of a paspalum vaginatum inflorescence.
A flowering paspalum plant growing in the University of Nebraska’s Beadle
Center greenhouses.

The Nebraska team, in collaboration with researchers from the Department of Energy’s Joint Genome Institute, the University of Georgia, and the HudsonAlpha Institute for Biotechnology, wanted to use the new genome sequenced this resilient grass to understand what makes the grass so much more stress tolerant that closely related crops, including corn and sorghum.

Using comparative transcriptomic and metabolomic analyses of paspalum, corn, and sorghum under optimal and stress conditions they identified a specific metabolic pathway — trehalose — that was being produced in paspalum, but not in corn and sorghum, in response to stress. 

The team used a strategy called chemical genetics to convince corn plants to also start producing and accumulating trehalose and showed that these corn plants grew faster and larger in conditions without enough fertilizer than corn plants without extra trehalose. Finally, the team used a combination of experiments to show that the reason these corn plants were able to grow more with less fertilizer was because of a process called autophagy, essentially a recycling program within plant cells that breaks down old, damaged, and unneeded proteins into spare parts that can be used to make new proteins. 

Guangchao Sun working with Aime Valentin Nishimwe measure nitrogen stressed plants in the Schnable lab at the University of Nebraska-Lincoln
Dr. Guangchao Sun working with Aime Valentin Nishimwe to collect data from
plants grown without enough nitrogen fertilizer.

“I’m so excited to see this story come out,” said Prof. Schnable, who is currently taking leave from the University of Nebraska while working at Google. “Paspalum is vegetatively propagated which means we cannot just save seeds, we always have to keep living plants for our research. There was a period where no one remembered to water the paspalum plant for a couple of months. But the plant was completely fine. In fact it usually grows so fast it’ll try to invade the pots of neighboring plants and the greenhouse manager has to yell at me or folks in my lab to come down and trim it. With this genome sequence and all the great work Guangchao Sun and the team have done, we finally are starting to understand just what makes this plant so

Sun, G., Wase, N., Shu, S. et al. Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass. Nature Communications 13, 773 (2022) doi: 10.1038/s41467-022-35507-8

March 5, 2022

Zero Sum Games vs Real World Benefit: We’re Losing Scientists, Why Aren’t People More Worried?

Filed under: Life in Academia — James @ 8:53 am

Inspired by this tweet, which I started to answer and then realized my thoughts were longer and more complicated than could fit in a couple of tweets of my own.

My anecdotal observations have been the same as Seth’s. More and more high performing researchers in the public sector on leaving. Some for jobs in industry. Some for completely different positions. Some people are leaving tenured positions with no plan about what they want to do next. I could write about my ideas about why this is happening for a lot of paragraphs. But that’s not what I’m writing about today. Instead I want to think out loud about the question: Why aren’t decision makers worried about this trend? I think a big part of the explanation is that a lot of public sector researchers and administrators are motivated by zero sum incentives.


February 19, 2022

Things private sector jobs get right

Filed under: Life in Academia — James @ 1:18 pm

I’ve started companies. I’ve worked in academia. But my most recent experience working in the conventional private sector was a summer internship I did at Pioneer Hi-Bred all the way back in 2010. But I’ve been noticing a few interesting signs:

  1. Powerpoint. Meeting with a venture capital firm. The guy I’m talking to apologizes for having such a long slide deck. Based on my experience in academia I assumed this mean 60-70 slides.* Nope. The really long slide deck the VC guy was talking about was 12 slides.
  2. Meetings. Meeting with some folks at a company I am collaborating with. One guy shows up about ten minutes late to the meeting because of some stuff with his kids. We talk about the stuff that doesn’t need him at the start and talk about the stuff he needed to be there for once he showed up. Meanwhile in academia I frequently have days with 4-8 hours of zoom meetings scheduled back to back. Which is doable. At least it is until people at my next meeting start texting me on my cell phone to find out why I’m not in the meeting yet 2-3 minutes before the meeting is even scheduled to start.
  3. Vacations. One of the startups I helped found hired some new full time “business people” a few months ago. It is remarkable how much these folks are getting done so quickly. Part of that is the advantage of dedicated people vs one person trying to wear seven hats. Part of it is the new folks brought different skillsets (why we hired them). But what’s been remarkable to me is that, in between getting so much work done, it seems like these people are constantly taking vacations: going off to cabins, or hunting trips, or tropical vacations. Meanwhile I’m 36 years old, have been reasonably successful in my academic career by the standards of my field and my job still doesn’t provide me with paid time off (including no sick leave).

The thing is, as far as I can tell there’s no inherent reason that academia needs to do any of these three things differently (and more painfully) than the private sector. It doesn’t make us more productive. It’s largely not being imposed from the outside, it’s something we do to each other or ourselves.

*This isn’t consistent around the globe. The last time I gave an hour long talk in Germany, someone warned me to aim for only 25-30 minutes of presentation (~20 slides) so the rest of the time could be for questions and discussion. So I did that. And it was GREAT! I came around with good new research ideas, an understanding of what I was or wasn’t explaining well, and I think the people listening had a better time and took away more useful information than if I’d droned on through 45+ slides with 5 minutes for questions at the end.

February 9, 2022

The Growth of Plant Science Research In China (2009-2021)

The world changes fast. Once we form perceptions about the way the world is or works, we tend to be a bit too slow to update those perceptions in response to new data.

Last week I posted some analysis of where the scientists who publish in the most selective plant science journals work and live. The short version for those who don’t want to re-read that post:

40% of the papers published in The Plant Cell had a corresponding author based in China, 28% from the European Union plus the United Kingdom, 16% from the United States and 16% from the rest of the world (Japan and Korea are particularly well represented in this last category).

I also said that I was really surprised when I actually read through a year’s worth of issues and counted up the numbers. I would have guessed closer to one quarter of the papers came from scientists in the United States and another quarter from China. There are lots of potential reasons to explain why my gut was wrong, but a big one is that just in the length of my scientific career things have changed a lot and my perception is struggling to catch up with the current facts on the ground.

Tracking the changes in authorship of papers at The Plant Cell between 2009 and 2021. Data was only collected from odd numbered years and only from papers listed under the “Research Article” category.

I started graduate school in the fall of 2008. My first full year as a “professional” plant scientist* was 2009. At that time 7% of papers in The Plant Cell were published by authors working in China, 28% by authors working in the USA, 37% by authors working in the EU and 28% by authors working in the rest of the world. In the 12 years since that, China’s share grew to 40%, almost a 6x increase.

So what happened in that 12 year time frame? I don’t have good insight into Chinese policy and funding decisions. But at various points I’ve run into people who have told me that in China, human health research and agricultural research are treated as roughly equal priorities. And China invests a lot in funding plant science, including plenty of dedicated funding for institutes and professors. In the United States plant science is a very small slice of the research our country funds**, and much more of the funding we do have goes out as part of 3-5 year grants for specific projects. Here’s a great visualization of US federal government R&D spending from back when I was a grad student.

Anyway, I’m not sure what the key takeaways are here. I guess 1) It is possible for a country to take big steps forward in scientific discovery and innovation but only if we’re willing to pay for it 2) If you happen to live in the USA, like me, your subconscious may still be assuming that we play a much bigger role in the global plant science research community than we actually do.

The world changes. It is easy to fall behind.

*I was getting paid a bit more than $2,000/month to do plant science. It felt very adult at the time.

**Two big sources of funding for plant science when I started graduate school were the Arabidopsis 2010 project and the Plant Genome Research Program, both run through US National Science Foundation. As you might guess from the name, the Arabidopsis 2010 project ended a decade ago. Plant Genome Research is still around. However, it used to receive dedicated line item funding from congress to conduct research into agriculturally and economically relevant crop plants and the program is now funded at the discretion of the director of NSF.

February 5, 2022

Who Publishes in Competitive Plant Science Journals?

Filed under: Fun With Numbers,Life in Academia — Tags: — James @ 2:50 pm

Where in the world is important plant biological research happening today? It’s a hard question to answer. I could imagine looking at funding, or citation rates, or total papers published in the field. I can also imagine the downsides and potential for bias in all of those metrics. But I’m a strong believer that even imperfect data is better than none at all and I couldn’t find any useful data on this topic.

So let’s start with the easiest of these imperfect datasets to generate: where in the world are the home institutions of the authors of articles published in plant science journals?

I decided to start with The Plant Cell. The Plant Cell is published by the American Society of Plant Biologists, so we might expect it will have a bias towards more American authors and fewer authors from the rest of the world. One the other hand, among journals focused on plant science, and excluding journals that publish solely reviews*, The Plant Cell historically** has had the highest impact factor***, which has tended to attract a global audience of both readers and authors.

I have the breakdown below the fold, but before you look, take a moment to form your own guesses. What proportion of articles do you think came from the United States? From Europe? From China? From the rest of the world combined?


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.


January 2, 2022

Proso millet interview with 1010 KSIR Farm Radio

Filed under: agriculture,Dryland Genetics,Feeding the world — James @ 6:27 pm

If you want to become more self conscious about your own vocal fillers, sentence fragments and the general nonsense that comes out of your mouth, ask a really good transcriptionist to write out an interview you did.

Click “Read More” to view the full transcript

January 1, 2022

James and the Tiny Corn Part 3: Even Tinier

Filed under: biology,Genetics,Plants — Tags: , , — James @ 4:42 pm

Back in 2015 we were one of the first groups to get to try out Fast Flowering Mini-Maize (FFMM) [1]. The plants were about two feet tall, flowered in five weeks, and were ready to harvest only 61 days after we planted them. But what if I told you that the same genotype could be even smaller?

This past summer a technician in the lab rediscovered our carefully guarded stash of FFMM seeds and we decided it was time to increase them. While we did most of the increase in the greenhouse, the idea came up at the same time we were finalizing the plans for our summer nursery* so we decided to plant the line in the field as well.

And this was the result:

Fast Flowering Mini Maize in the field in Lincoln Nebraska in the summer of 2021.
Fast Flowering Mini Maize in the field in Lincoln Nebraska in the summer of 2021. Planted May 13th. Photo July 1st. Non-fast flowering non-mini maize in the background was planted approximately one week earlier.

December 31, 2021

The Dreaded Post Tenure Slump (2021 wrap up)

Filed under: Life in Academia — James @ 11:45 am

I wrote my first post on this blog at the start of 2008 when I was a 22 year old university student. Prime time for a quarter life crisis, which I think was a term people were already joking about back then. Almost exactly 14 years later on the last day of 2021, I am a 36 year old, have a faculty position at a university, and tenure.

It’s hard to put myself back in the mindset of that 22 year old, but I do remember spending a lot of time wondering what I was going to do with my life. I’d gone to college as an econ major. Switched to biology because I liked my hourly job working in a lab. Skipped a lot of class but mostly* managed to pull As and Bs by picking courses that focused on midterms and finals, not classwork/homework. As graduation approached, the econ majors were all interviewing for jobs at big NYC investment banks. I remember a guy I knew rushing back into class after taking a call: “They offered me a higher salary than my dad makes!” But what do you do with an undergrad degree in biology? I wasn’t sure. One thing I did know a person could do with an undergrad degree in biology was get a GRADUATE degree in biology. I was majoring in biology because I liked working in a lab, so grad school seemed like a reasonable next step. I applied. I got in. I went.

In retrospect it was very good I didn’t stay an econ major. The fall of 2008 was not a good time to be starting in investment banking. What with the world financial system melting down and all.

In any case: I got in my old car and drove 2,800 miles (almost all of it on I-80) from New York to California** and grad school. I was bad at some parts of it. Good at others. I joined a lab that let me play to my strengths. Published my first paper. Then another. And another. Got a lollipop (as is tradition) and a diploma. What do you do with a PhD in biology? In principle a number of things, but the main path you hear about is to get a postdoc. That’s what about 70% of people who get a PhD in biology do next. I got one of those. And after a postdoc? Well there is lots of competition, but some people are able to get tenure track faculty positions. About 15% of biology PhDs. Although that overstates how hard it is, since there are plenty of people who get a PhD but would run away screaming from the idea of being a professor (and hence don’t apply for those jobs). Anyway. I got one of those jobs. What do you do with a tenure track faculty position? You put your head down and you work hard and you try to get tenure. When it comes to getting tenure, working hard is necessary-but-not-sufficient. I worked hard, but I was also really fortunate to have great students and creative collaborators and good luck. In any case. I got tenure.

What do you do with a tenured faculty position?

I’m serious, what do you do? For the first time since switching my major from economics to biology in 2005 (when I was all of 19 years old), I don’t have an obvious default Next Step. At least beyond: Do more of the same stuff you did to get tenure.

In the field people call this either a “post-tenure slump” or “post-tenure depression.” Apparently lots of folks go through it although fewer people talk about it in person. In seems to share many characteristics with a midlife crisis (e.g. “what am I doing with my life?”).

I found out about the decision about tenure in 2019. Really if I was going to have a post-tenure slump or depression it should have happened in 2020. As it turned out, my attention, like almost all of ours, was focused on other things in 2020. And the first part of 2021. But this summer and fall it has really started to sink in.

In principle, I could spend the next twenty to forty years of my life doing the exact same stuff I did over the past five. And if I did that it would probably been enough to keep this job until I’m old enough to retire. And if my job ends up going away it is more likely to be a result of the overall health of the university I work for, a factor I have extremely limited capacity to influence.*** It’s a good situation to be in and it’s also terrifying.

For the first time in my adult life, I am not facing a major hurdle in the coming years where, if I don’t buckle down and work hard enough, I’ll be forced off my current trajectory and have to reevaluate my life (not getting into grad school, failing my qualifying exam and leaving with a masters, not getting a job offer, not getting tenure). If I’m going to reevaluate my life, I have to decide myself to do so. It won’t be forced upon me. My goal for 2022 is to do a little of that reevaluation.

Ideally I’d like come up with one or more answer to how to spend the next 20-40 years that feels a bit more appealing/fulfilling/meaningful than continuing to focus the vast majority of my energy, attention, and time on a job where I work on the same questions with the same methods.**** I’m not sure what answer does appeal, but I know that answer doesn’t.

Anyway, that’s my 2022 goal: To come up with some goals to have. In the meantime I have to go work on filling out my annual report.

Office (2021). Among various professional achievements over the past fourteen odd years, negotiating for an actual office with an actual desk still feels more real than “promotion and tenure.”

*General Chemistry and Organic Chemistry being notable exceptions. Frankly I’m lucky I graduated at all.

**In fairness there was a multi-month stop for the summer at my folks house in the middle of that, so it wasn’t 2,800 miles straight through.

***Declines in student enrollment, both domestic and international, are real. I don’t know what the international situation will look like in ten years but looking at the demographics domestic enrollment pretty much has to decline going forward because there are are fewer 14-year-olds than 15-year-olds in this country, fewer 13-year-olds than 14-year-olds, and so on.

****I’m also trying to make my peace with the fact that, no matter how hard I work or how much I accomplish in a given, so long as I have this particular job my department is still going to tell me every year that I still didn’t do enough stuff. It’s surprisingly hard for me to accept. I think I’m doing a good job. I think I am perceived outside the university as doing a good job. I think even inside the university when it boils down to it, there are people who believe I am doing a good job. Yet, even so, being told each year that I’m not doing enough work has worked its way under my skin to an extent that embarrasses me and to an extent that is neither healthy nor productive.

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