Annus horribilis/ annus mirabilis

A chestnut-backed chickadee at That Spot in Stanley Park. (Flickr, jby)

This has been, for fairly obvious reasons, a hard year. Most of the institutions that define what I do for a living have been weakened to the point of desperation, if not outright dismantled — some inviting the vandals in, some forcibly invaded and hollowed out. It was a year in which I tried to explain to students that most of the research projects on our campus were under threat, threw together a local pro-science satellite rally, squinted at the text of the US Code to no discernible effect, wrote plaintive op-eds for the newspaper I read back in high school, tried to plan for what I’d do if immigration enforcement agents demanded entry to my classroom, and pressed on with projects whose long-term future is uncertain at best.

And yet, by any objective measure, it’s been a very fortunate year. I ran the Boston Marathon, and had a pretty good time of it, even if it wasn’t a personal-best time. I hosted a collaborator for a guest seminar on campus, and we took a day to drive out to the desert and see wildflowers, including blooming Joshua trees. I landed a sabbatical semester for the fall, with plans that let me spend most of my time with C in Seattle, from June onwards. We road-tripped north through Yosemite and Crater Lake National Parks, both first-time visits for me, and then took a long week in New England and New York City. I spent most of another week in Georgia for the Evolution Meetings, where I gave a high-pressure plenary that seems to have gone over pretty well.

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The walled garden at the end of the Internet

“Portal” (Flickr, Floriane Kratz)

I am not a fan of large-language model chatbots. I’m enough of a hater, in fact, that I don’t like calling ChatGPT and its LLM-powered kin “AI” — they are a particular class of products of a particular form of machine learning, which guess the correct response to a query as informed by associations between words and phrases in vast volumes of training text. One of the most painful lessons of the last couple of years, I think, is that what I’ve just described turns out not to be anywhere as close to “intelligence” as it appears.

I digress; the distinction is important, but it’s not exactly my point. My point is that it recently dawned on me that the LLM chatbots are the latest iteration of a now multi-decade process of big tech companies trying to fit the whole Internet into a box that they own and control.

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What can we learn from a Joshua tree?

Joshua trees on Ryan Mountain, overlooking the Joshua tree woodlands in the heart of Joshua Tree National Park (jby)

I have a new op-ed at LNC|LancasterOnline, making the case for the “curiosity-driven” science that the National Science Foundation has supported through much of my adult life — and which is under dire threat from cuts proposed by the Trump Administration and the budget bill under consideration in Congress right now. In it, I discuss some of the possible long-term applications of my lab’s research on Joshua trees, which seem at first like they might be too weird to tell us anything helpful in daily life:

Joshua trees’ pollination by a single species of moths serves as an informative contrast to plant and pollinator interactions that play out in more common, more complicated situations, such as pollination of fruit and nut trees by wild insects and domestic honeybees. By studying Joshua trees’ simplified system, my graduate mentor learned how cooperative relationships like pollination stay cooperative, with two different species trading resources and services, even when they have incentives to cheat.

My lab has also studied how weather influences Joshua trees’ very sporadic annual flowering. Most years, they either flower prolifically, or not at all — and until recently we didn’t know what made the difference between bloom or bust. For that project, we developed software to use machine learning models trained with easy-to-collect data, which may work well for many other species of plants. That could be helpful in agriculture, or in planning to protect rare plant species, or even in understanding how the environment limits where different species can live.

But — and this is the important part — work with Joshua trees and hundreds of other peculiar creatures in distant habitats is important even if it doesn’t pan out into applied discoveries.

Of course, none of these applications of Joshua tree research may pan out. For every Thermus aquaticus [the hot-spring bacterium whose chance discovery enabled modern genetic research] there are hundreds of scientific projects that end in nothing more than a peer-reviewed research article and some fond memories of fieldwork. But we need those hundreds of curiosity-driven studies to find that one lucky, world-changing discovery.

This column is a new iteration of the connection I made with my old hometown newspaper thanks to the Science Homecoming campaign, and anticipates the McClintock Letters initiative rolling out later this month. Go read the whole thing, and — please — call your congresspeople to ask that they preserve funding for NSF’s support of curiosity-driven science.

How to make the Smitten Kitchen Purple Plum Torte in March, 2025

The first step towards making the Smitten Kitchen Purple Plum Torte is to remember that you can make the Smitten Kitchen Purple Plum Torte. Say, midway through Sunday brunch, when you remember that you’ve accepted a dinner invitation for that evening and really should bring something, but nothing too complicated. You think of the recipe as the Smitten Kitchen Purple Plum Torte even though it was first published in The New York Times because you cancelled your Times subscription when they hired Bret Stephens.

For all the good that seems to have done.

Anyway the Smitten Kitchen Purple Plum Torte is perfect for a last-minute dessert because its ingredient list is so simple, you can run it down almost in your head and compare against what you know you have back in the kitchen at home. You’ll just have to make a detour on the way back from brunch to pick up some plums.

Oh, well, and eggs. Dammit.

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Local boy makes op-ed

Chicory, Cichorium intybus, which always makes me think of Mr. Longenecker’s biology class wildflower walks (Flickr, jby)

Cross-posted from The Molecular Ecologist.

Here’s a new one for my publications list: the Op-Ed pages of my hometown newspaper. I’ve spent the last weeks calling my congressional reps, and hassling other people to do the same, over the Trump administration’s vandalism of research funding (alongside its vandalism of just about every other function of the federal government), but it’s hardly felt like enough. One new option presented when I happened across Science Homecoming, a project to recruit scientists to speak out in support of federal research agencies in the newspapers of towns where they grew up. As Science Homecoming points out, local newspapers continue to have a huge audience across the country, and that’s an opportunity to reach people where they live, with stories that show how the current crisis impacts their local communities.

So I looked up the opinion section editor at LNP/LancasterOnline, the modern incarnation of the paper my parents have subscribed to since I was old enough to read it, which serves central Pennsylvania. I emailed her a pitch that I’d put together following Science Homecoming’s suggestions, and she wrote back to ask for a full column almost immediately. (The topic was already very much on the editorial staff’s radar.) A bit more than a week later, my column is online and in print, alongside a parallel piece from two geoscientists with local roots, on the front page of the Sunday Perspectives section.

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The morning after

When I planned out the schedule for my fall semester graduate statistics course back in August, I remember pausing, for a moment, over today’s date. Did I want to plan for a regular meeting the day after this election? In many of the best-case scenarios, the students and I would be thinking more about an ongoing vote count than whatever topic I slotted in for the day. But I had hope, and only so many days for the class, and I figured I could always make a call based on what actually happened.

It turns out my hope was misplaced, and we knew it before I finally went to bed last night.

So this morning, before I could bring myself to eat breakfast, I composed an email to the class. It’s turned out to be most of what I have to say this morning, so I’m posting it here for posterity, or maybe for other faculty who are still trying to figure out how to say some of this:

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Mastodon is also not rocket science

Weeks after Elon Musk took possession of Twitter and proceeded to tweet fast and break things, this Scientific American article by Joe Bak-Coleman offers a general theory of why it’s going so badly: social networks are complex systems rather than complicated ones.

On a social network, interactions between individuals create dizzying feedback loops and chaotic interactions that render simple mathematical models next-to-useless for predicting the future, let alone controlling it. Musk’s gamble is that applying his tinkering philosophy to Twitter will take him where no one has gone before: ownership of a large, healthy and profitable social network. The problem is that, unlike the moon or Mars, we have no idea how to get there—and that’s a challenge that engineering fixes cannot solve.

I saw this linked from Mastodon, where I (and now a pretty large fraction of my former Twitter network) have taken refuge. People there are generally passing it around in the spirit of schadenfreude that imbues most discussion of Twitter in the “Fediverse” distributed social network. However, I don’t see much awareness that what Bak-Coleman identifies as a problem for Musk running Twitter is also a problem for a network of mostly volunteer admins running Fediverse-connected Mastodon instances: we don’t actually know how design and moderation decisions will ultimately add up to create the decentralized social network we’re all using now.

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What was Twitter?

(Flickr: Buzz)

The science fiction novel Ender’s Game is best remembered for its primary plot, about a genius child who leads Earth’s forces to genocidal victory against aliens; but it also has a secondary plot line that seems, in retrospect, terrifyingly prescient. While the protagonist Ender is learning to become the greatest space-general in history, his near-equally-gifted pre-teen brother and sister, left behind on Earth, take up politics. Peter and Valentine set up pseudonyms on a global online message board and spar theatrically, building competing followings and eventually real-world political influence. By the novel’s end Peter has leveraged his online clout into the leadership of a worldwide government.

I read Ender’s Game in the mid-1990s, when it was truly science fictional to imagine the whole world connected in a single messaging system, much less using devices portable enough to carry in a backpack. By 2004, my final year of undergrad, I acquired a bulky Dell laptop which was, most excitingly, capable of using the wifi network that had just been installed in my campus apartment complex — and I’d already gone from a hand-coded HTML personal website to a series of blogs hosted on the most obvious choice, Blogger.com. Multiple of those blogs were social affairs, shared with friends, but their connection to people elsewhere on the Internet was entirely mediated by individual “<a href=” hyperlinks. Midway through graduate school, I accepted responsibility for building a website for a conference to be hosted by my home department, and decided to try embedding a new messaging platform I’d heard about: Twitter.

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STEM employers in North Carolina: Time to put your money where your mouths are

Morehead Planetarium on the campus of UNC Chapel Hill (Flickr: William Yeung)

Morehead Planetarium on the campus of UNC Chapel Hill (Flickr: William Yeung)

North Carolina’s got a shiny new law legalizing antigay discrimination and legislating where trans folk can pee. (More specifically, it forbids the state’s cities and municipalities from passing nondiscrimination laws that protect sexual orientation and gender identity, which some have done.) It’s probably in violation of current Federal regulations and the Constitution, but it could be years before that’s sorted out in court.

H2 was written, passed in a special legislative session, and signed into law in about 10 hours — so quickly that some Democrats walked out of the state Senate in protest of the procedural chicanery. There was effectively no time to mount any public campaign against the law before it became law. Which is a pity, because a similar law under consideration in Georgia is now literally up against Mary Poppins and Captain America: the Walt Disney Company and its subsidiary Marvel Entertainment are threatening to pull operations from the state if the bill passes.

I’m not aware that North Carolina has much of an economic stake in making superhero science fiction, but I do happen to know that the state is deeply invested in actual science. The Research Triangle is a development region created in a public-private partnership to foster science, engineering, technology, and mathematics (STEM) businesses with close ties to Duke University, the University of North Carolina, and North Carolina State University. It was named one of the “Top 10 Biopharma Clusters” last year. So this seems like it might be a problem for the academic side of all that partnership:

As interpreted by the Department of Education, Title IX of the Education Amendments of 1972 forbids discrimination against trans students in any school that receives federal funding. These schools are prohibited from excluding trans students from the bathroom consistent with their gender identity. The new North Carolina law, dubbed H2, rebukes this federal mandate by forbidding public schools from allowing trans students to use the correct bathroom. That jeopardizes the more than $4.5 billion in federal education funding that North Carolina expected to receive in 2016.

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In which I can kinda fake Sorkin dialogue?

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(Previously, on Twitter)

OPEN ON Toby Ziegler and Josh Lyman, walking down a hallway in the West Wing.

Toby: Nominee’s out. Merrick—
Josh: Merrick?
Toby: Garland.
Josh: Merrick Garland?
Toby: Merrick Garland.
Josh: What, did Hermione Granger turn us down?
Toby: Is she on the D.C. Circuit, or the 5th?
Josh: Aw, you know what I mean. He just sounds really—
Toby: White?
Josh: I was going to say WASPy, but sure.
Toby: You work for a Josiah Bartlett.
Josh: …
Toby: Anyway, he’s a good judge. Great experience. Prosecuted Tim McVeigh.
Josh: I just thought we were going to be more, uh, creative.
Toby: It’s a bad time for creative.
Josh: Is it ever a good one?
Toby: The Judiciary Committee isn’t going to end the freezeout for creative
Josh: You think the Judiciary Committee is going to end the freezeout for Merrick Garland?
Toby: Well, they’ll look dumb if they don’t
Josh: They look dumb anyway!
Toby: Gotta heighten the contradictions. Freezing out a boring, obviously qualified nominee
Josh: You think they’ll crack?
Toby: If they do, we get Justice Merrick Garland. If they don’t, we try again after the election.
Josh: AFTER THE ELECTION?
Toby: It’s nuts, I agree.
Josh: It’s NUTS.
Toby: The Republicans are nuts.
Josh: You’d think people who talked so much about the Constitution would—
Toby: Follow it?
Josh: Yeah.
Toby: Are you new here?
Josh: So if they freeze out Merrick Garland, AND we win the election, we can get creative?
Toby: More creative, yeah. Not much, though — because we still might not get the Senate back.
Josh: Jeez. Maybe nominating Hermione Granger would be more realistic.
Toby: [shrugs]

FIN