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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No, peer reviewers have not forced 22 percent of chemists to add errors to their research papers

The headline caught my eye, as it was intended to: “One in five chemists have deliberately added errors into their papers during peer review, study finds.” It’s introducing an article in Chemical and Engineering News reporting on a new article in the journal Accountability in Research by Frédérique Bordignon, who surveyed research chemists about their experience of the peer review process. The article’s abstract echoes the news headline, saying, “Some authors yield to reviewer pressure knowingly introducing changes that are clearly wrong.” That’s a fairly eye-popping result — peer reviewers are pressuring scientists to introduce changes that are clearly wrong into our descriptions of our research?

Well, here’s the funny thing: If I’d been a reviewer on that paper, I’d have said that statement in the abstract was an error. I’d probably also have said that it was a dangerous one.

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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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Yosemite to Acadia

A white-breasted nuthatch, doing the nuthatch pose at Glacier Point in Yosemite (Flickr)

We spent this June more on the road than otherwise. C drove down from Seattle over Memorial Day weekend, and after I spent a workweek packing for an extended stay on Puget Sound, we road-tripped north. We only had a three-day weekend, but we strung together some sightseeing stops along the way.

We had an overnight stay in Yosemite National Park, where I finally saw the Yosemite Valley — and not one but two new-to-my-camera lupine species, and a very cooperative nuthatch, the headline image for this post.

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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.

Boston!

Monday, I ran the 129th Boston Marathon. It’s something like 15 and a half years after my first marathon, and it’s taken me that entire time to get to Boston.

I ran my first marathon back in October 2009, in Portland. I’d tried a spring half marathon and survived it, and found a simple enough training plan to work my way up to a 26.2 mile (42km) distance, running through the rolling Palouse hills beyond the University of Idaho campus in Moscow, Idaho. Portland went well enough that I signed up for another the next year, and another the year after that.

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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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2024, in photos

Canada Jay taking flight on Rattlesnake Ledge, Seattle (jby)

Occurred to me this morning that I haven’t done a retrospective of the past year’s Flickr photostream as I did last year for plants, and birds, and mammals, and landmarks — and while I’m not going to manage that for 2024, at this point, I can and should still post my favorites. I’m getting a bit more comfortable with the camera, and the processing options in Adobe Lightroom, and I think I got some mighty nice results.

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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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