Category Archives: science

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.

The variety of queer scientists in The Queer Variable

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Shaun O’Boyle and Alfredo Carpineti have spent the last two years interviewing LGBTQ+ folks working in the sciences, and the result is now available today on the website of Pride in STEM: an e-book compilation of 40 edited interviews, The Queer Variable. I’m very glad to have been included, as just one voice in an impressively international (if necessarily Anglophone) chorus. The book is something of an oral history, not of a single event or project, but of the career trajectories of the interviewees and how their queer identities have intersected and shaped their work — a topic addressed in a more systematic (dry) manner in the second Queer in STEM paper [PDF]:

Three key processes emerged from our analysis of participant experiences and provide an explanatory framework for how queer STEM workplace identities are shaped by a combination of internal and external influences (see Figure 1). Defining explains how these individuals come to understand and name themselves as queer in terms of gender and/or sexuality; Forming refers to their construction of specific STEM identities; and Navigating describes how the interplay of professional and personal influences impacts expression of identity in places of work and study.

The Queer Variable effectively samples the wide range of ways LGBTQ folks have defined their queer identities, formed their place in a STEM field, and navigated the challenges of a career that incorporates both. Go download the free e-book and have a look.

On making the local news

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This is a bit of a rehash from the social media platform whose name I will not utter here, but earlier this month I made my first TV appearance as an “expert” on Joshua trees, talking about the Joshua Tree Genome Project common garden experiments as a first step towards assisted gene flow to help the trees cope with climate change. It was a weird experience! The reporter emailed to arrange things and I agreed to an interview on Zoom, but I didn’t fully realize I was being recorded for broadcast until we were wrapping up. Mercifully, he selected the most coherent bits of what I told him and I didn’t make too many weird faces.

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