are there substantive critiques of agentic coding that envision the future of software development without it?
michael catchen
@mdcatchen.bsky.social
data scientist/research software engineer, Schmidt Center for Data Science and Environment @ UC Berkeley. building open software for bioacoustic monitoring. phd in ML for biogeography of species interaction networks. gottacatchenall.github.io he/him
Mathematician Levent Alpöge found a counterexample to the Jacobi conjecture using Claude Fable! This conjecture claims that if F: ℂⁿ→ℂⁿ is a polynomial map whose Jacobian is invertible at each point, F has a polynomial inverse. Open since 1939. But no more! (1/n)
Jacobian conjecture - Wikipedia
en.wikipedia.org
Spent the last two years developing a new Intro to Physics course for undergrad biology majors. It features tons of examples from biology (especially Ecology & Evolution!) and requires only middle school-level math. Lecture note here shorturl.at/0PiVp Any comments or feedback are highly welcome!
physics_for_biologists.pdf
drive.google.com
🚨 New preprint! What happens to bumblebee pollination networks as species ranges shift due to climate change? 🐝🪻🕸️ In the Rocky Mountains, we predict these networks are becoming "vertically disassembled" as the ranges of interacting species shift upward in elevation at different rates.
new diamond open-access Journal of Statistical Ecology launched 🎉🎉🎉 jse.centre-mersenne.org @fredbarraquand.bsky.social @oaggimenez.bsky.social @marieaugermethe.bsky.social @vianeylb.bsky.social (apologies to any Bsky editors I missed)
Journal of Statistical Ecology Journal of Statistical Ecology
jse.centre-mersenne.org
Are interacting species showing more similar responses to environmental predictors than expected by chance? Is this similarity protecting species pairs from interaction disruption under climate change? If you want to find out, join us for a fully funded Ph.D. with @epic-biodiversity.org 🌎🧪
Join us! We are looking for a Ph.D. student to work on the response of ecological network structure to environmental drivers; this line of research can be adapted to questions on climate change, phylogenetic conservatism, and more! 🧪🌎 epic-biodiversity.org/opportunities/
Information about species interactions is very scarce! In a new preprint, @gabdans.bsky.social shows that the methodology that enables biodiversity monitoring and reporting also supports the detection of species interactions, leading to multi-use monitoring. epic-biodiversity.org/blog/2026/05...
Where should we look to monitor species interactions? | ÉPICBiodiversity
epic-biodiversity.org
🚨🐭🦠 New preprint! Monitoring wildlife disease is expensive, so we need to be smart about where we sample to get as much useful info as possible. We show how SDMs can guide adaptive sampling for zoonotic disease surveillance, using case studies in rodents.
This is, not a joke, one of my favourite papers in a long time. Absolutely stellar co-authors, but also a straight line from "nitpicky little nerds obsessing over sampling" to "translational research with clear implications for management". Go read all about it here: ecoevorxiv.org/repository/v...
A protocol for biodiversity-informed wildlife disease surveillance
ecoevorxiv.org
🧪 New @mdcatchen.bsky.social preprint! Here's how we can decide where to look for wildlife disease, based on combinations of biodiversity, uncertainty, and prevalence data. This is a really cool paper, that is pushing the boundaries of what we can do with sampling and monitoring techniques.
🧪 New @mdcatchen.bsky.social preprint! Here's how we can decide where to look for wildlife disease, based on combinations of biodiversity, uncertainty, and prevalence data. This is a really cool paper, that is pushing the boundaries of what we can do with sampling and monitoring techniques.
Effective sampling of wildlife disease from biodiversity data | ÉPICBiodiversity
epic-biodiversity.org
I'm just worried. Even pre-AI, it was really pulling teeth to get some (not all) PhD students to take the time to look up the formula the R package used, make sure its what they actually want to calculate, and validate what R spits out (note: I don't take students like this anymore)
Noteworthy because it was my first time adding a polygon provider using the interface @mdcatchen.bsky.social built for one of our component packages 🎉
We have added support for ESRI administrative areas to our species distribution #JuliaLang package — a lot more stable than GADM (although limited to level 1 divisions). 📗 Read more: poisotlab.github.io/SpeciesDistr...
One week left to apply to the UVA Biology PhD program! If you or someone you know are interested in contagion from a complex systems perspective, please reach out! I'm looking for a grad student! bio.as.virginia.edu/how-apply-gr...
How to Apply to the Graduate Program
bio.as.virginia.edu
And like a brown bird nesting in a Texaco sign I got a point of view
Hi all! I am seeking an ecology or applied math PhD student interested in quantitative ecology, specifically ecological theory, food web modeling, or population dynamics. If you are interested, have a look at our lab website below and reach out to me. resiliencelab.github.io/join/
Join Us
resiliencelab.github.io
My friends, don’t you know that I never want this minute to end? And then it ends.
Our software paper on SpeciesDistributionToolkit.jl is now published in @peercomjournal.bsky.social - peercommunityjournal.org/articles/10....
A Julia toolkit for species distribution data
peercommunityjournal.org
What kind of animal Needs to smoke a cigarette? Grass in the pasture Is sharper than a bayonette Sometimes a pony Sometimes a pony Sometimes a pony gets depressed
When I go downtown, I always wear a corduroy suit, ’cause it’s made of a hundred gutters, that the rain can run right through.
A beautiful visualization of the state space of puzzles, 11 min of joy, h/t @danlarremore.bsky.social
Adventures in State Space
YouTube video by 2swap
youtube.com
you have been visited by "Le Boulanger Quebecois" repost to receive his blessing
🦠🌿🐦🧪 How can biodiversity monitoring help global efforts in disease surveillance? With ✨ fantastic ✨ colleagues from @viralemergence.org and the @geobon.org working group on One Health, we try to identify three key lessons for the future. 🧵 A short thread! academic.oup.com/bioscience/a...
Biodiversity science and biosurveillance are fellow travelers
The failure to meet the Aichi targets to alleviate global biodiversity decline (Nature 2020) was a wake-up call to the biodiversity monitoring community (T
academic.oup.com
Poor as a mouse every morning Rich as a cat every night
An update from the team on the uncertain future of our program and the impact of NSF budget cuts. Please share and reach out 🦠
One week until Blitz the Gap (www.blitzthegap.org) starts - a Canada-wide event to fill biodiversity data gaps with iNaturalist! @laura-pollock.bsky.social
Blitz the Gap 2025
blitzthegap.org
There were no new ways to understand the world, only new days to set our understanding against.
🐾 #CSEE2025 Workshop Highlight 🐾 "Interpretable machine learning for species distribution modelling" 💻 Discover how to use reproducible ML tools to tackle diverse ecological questions! 🔗 Register here: event.fourwaves.com/scee2025/reg...