Category Archives: science

My comment on the proposed Regulation for Federal Financial Assistance: Scientific communication is essential to scientific discovery

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On May 29, the Office of Management and Budget posted OMB-2026-0034, a sweeping set of proposed changes to the ways that federal agencies administer funds granted to individuals and organizations, including the research grants made by the National Science Foundation and National Institutes of Health. The proposed changes are framed as preventing waste, fraud, and abuse, but in detail they create dramatic new restrictions on how federal funds are granted, how those funds may be spent, and what people working on federally funded projects may do. In brief: funding decisions would be made directly by political appointees, not by expert agency staff; use of funding for a variety of important activities like conference attendance, publication of results, or public outreach would be heavily restricted; and funded organizations would be restricted from speaking on a sweeping list of allegedly controversial topics, from climate change to human diversity.

Former NIH Program Officer Elizabeth Ginexi has detailed the many concerning rule changes, and helped lead a general call for people to provide comment on the proposals, from their perspectives as members of the American public, as federally funded scientists, and as representatives of scientific organizations. These comments are supposed to inform OMB’s decision to implement, revise, or scrap the proposed rule changes — and, more likely, provide an evidentiary basis for pushback by Congress and in lawsuits that seem very likely to be necessary.

I’ve signed on to statements by the scholarly societies in which I’m a member, and I’ve consulted a bit on some of the language in those; and the California State University system, my employer, also has a comment in process. Today I also submitted a comment from me, personally. Individual comments are limited to 5,000 characters, and specificity is key, so I focused in on a recurring theme I saw in the changes — restrictions on scientists’ ability to communicate. I’m posting the text of my comment here as an independent record, and in case any readers want some additional motivation or inspiration for their own comments. Comments on the proposal are still open until 11:59pm (Eastern time) on Monday, 13 July, and I’d encourage you to contribute if at all possible — you can do so here.

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Not the fittest, but the fitted

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A small butterfly with wings folded to show a white-and-gray checkered pattern with two big blue-black eyespots, perched on an inflorescence of tiny white flowers, all amidst clover leaves and blades of grass
A marine blue butterfly (Leptotes marina, native to the Americas) nectaring on the flowers of a white clover (Trifolium repens, native to Europe) in the lawn of a Los Angeles city park. (Photo by me)

A little knowledge of natural history is a dangerous thing. This is, first, because knowing a few things — the names of some common wildflowers, or the songs of some neighborhood birds — begets curiosity about more things, and soon enough you’ve gone from installing an identification app on your smartphone, to ordering a field guide, to pricing binoculars. But, second, it’s dangerous because once you know a little natural history, you start to notice living things are often not where you expect them.

Should the violet-blue flowers of a jacaranda really be shading the upper slopes of the Griffith Park ridgeline, overlooking the urban sprawl of Los Angeles? Can that really be an eastern gray squirrel chattering at you from the bushes in suburban Seattle? Why on Earth is a honeybee visiting the flowers of a Joshua tree, which offer no nectar and very little pollen?

The most immediate answer for all of these is, because humans put them there. Jacarandas and eastern gray squirrels and honeybees are just some of the species we’ve carried to new habitats for our own purposes. But in all three cases these organisms are not going about human-directed business — they’ve gotten away from the places they were introduced, to make a living on their own terms. And the questions they prompt apply much more broadly.

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

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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

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“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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Local boy makes op-ed

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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

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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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2023 in invertebrates

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Boisduval’s blue butterfly on a weedy geranium, on Santa Cruz Island. (jby)

As a final taxonomic catch-all for my 2023 nature photography, let’s go with … invertebrates? If I’m not taking a photo of a plant, a bird, or a mammal, it’s most likely an insect visiting a flower. I do love a good plant-pollinator interaction. And while larger animals are a challenge to manage well with my 150mm lens, I can frequently catch some nice close images of butterflies nectaring, like the blue above, or the Clodius parnassian below.

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The biology behind a superb superbloom, in the Los Angeles Times

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California poppies, fiddlenecks, lupines, and other wildflowers at the California Poppy Preserve back in early April. (jby)

Yesterday’s Los Angeles Times has an article that goes into some of the biology behind this spring’s “superbloom” in California — plants all over the state responding to an exceptionally cool, wet spring with profuse flowering. Corinne Purtill, the author, called up some rando to enthuse about all that spring greenery:

Those 31 atmospheric rivers delivered steady, nourishing rainfall from October to March. Regional temperatures remained moderate as well, without any sudden early-spring heat waves to kill off fragile baby plants.

The combination of those two factors has produced “an absolutely glorious spring,” one that has been more vibrantly colorful for longer than any in recent memory, said Jeremy Yoder, a Cal State Northridge biologist.

As the headline says, everything is blooming everywhere all at once, and it reflects how the life histories of plants in many California natural communities are adapted to periodic drought. Check out the whole piece for more from me and my fellow plant nerds on the science behind a spring bloom that has us all agog.

New paper: Conservation challenges and solutions for the Mojave Desert

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Burned Joshua trees at the site of the 2020 Cima Dome fire in Mojave National Preserve (Flickr, jby)

A big review article, written with Joshua Tree Genome Project co-PI Chris Smith and a bunch of other Joshua tree experts, went online today at Biological Conservation. In it, we attempt to comprehensively describe the challenges to biodiversity conservation in the Mojave Desert, and outline solutions — more detail over on the lab blog, or check out the paper itself via this sharing link, which provides free full-text access through January 20, 2023.

New publication: A genetic fingerprint of coevolutionary diversification

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A red milkweed beetle, Tetraopes tertophthalmus, on its host plant (jby)

A new paper from the lab — coauthored with all three of the Yoder Lab’s graduate student alumni — is now online ahead of print in the journal Evolution Letters. In it, we analyze population genetic data from 20 pairs of plants and herbivores, parasites, and mutualists that live intimately on those plants to test for evidence that the associate species’ population genetic structure aligns with that of their host plants. This is an expected result if adaptation to the host plant drives diversification of the associates — and we found that it is indeed a recurring pattern. This is a pretty neat result, and, I think, a nice contribution to a long-established literature on how intimate associations with plants has driven the diversification of groups like butterflies and beetles.