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@calcharp.bsky.social @agporto.bsky.social @anujkarpatne.bsky.social I managed to fail to successfully find everyone prior to posting this, but here are the bluesky tags of everyone...

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We welcome feedback, questions, and critiques.

"Drawing on ideas from Representation Learning, Representational Measurement Theory, and abductive reasoning...we then establish...the ways DCMs “think” differently from human biologists...we lay out a practical toolbox for addressing these differences and supporting meaningful inference with DCMs"

"If neural networks—often criticized as opaque blackboxes—have their greatest interpretive difficulties when the underlying biology would most benefit from their ability to represent complexity, how can we expect DCMs [deep comparative methods] to possibly improve the situation?"

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Caleb spent a ton of time on how to communicate these ideas with co-authors Anuj Karpatne & Arthur Porto, and with the Imageomics institute. I'm really proud of the synthesis and road map he produced. We ask what the benefit of deep learning is in biodiversity science and comparative methods.

On the Promise (and Practice) of Deep Comparative Methods: Expressivity, Limitations, and Design

New preprint led by grad student Caleb Charpentier that I'm very excited about! This is a hefty review & perspective on how we can close the gap in trust between new "Deep comparative methods", and the biological meaning & inferences that systematists want. ecoevorxiv.org/repository/v...

ecoevorxiv.org

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Josef Uyeda @pseudacris.bsky.social · 28/09/2026

If you're submitting a reference letter for a PRFB, I was surprised to not see any option for deleting and reuploading, which contradicts the info provided in the email requesting it. In fact, as soon as you select the file it is uploaded and you can't change it. Was fine for me, but beware.

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Josef Uyeda @pseudacris.bsky.social · 26/09/2026

Depauperon? More like Depaupewrong!!!

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Josef Uyeda @pseudacris.bsky.social · 23/09/2026

also ecology in general. Every planet has a single biome.

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Josef Uyeda @pseudacris.bsky.social · 23/09/2026

the last four episodes of clone wars are one of the best star wars movies of all time

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Josef Uyeda @pseudacris.bsky.social · 17/09/2026

I have a cartilage to pick with this taxonomy

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Reposted by Josef Uyeda

Society for the Study of Evolution @sse-evolution.bsky.social · 11/09/2026

Applications are now open for the International Travel Stipends to attend #Evol2027! Funds cover registration, travel, meals, and lodging. The application deadline is earlier this year: November 1st! www.evolutionsociety.org/content/soci... @evolmtg.bsky.social

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Josef Uyeda @pseudacris.bsky.social · 10/09/2026

This has been central to all R propaganda for ages, benefits to the working class by any means other than helping business/the rich will make you lose anyway. Best I can tell, this is a homogenous internalized world view of R's and Inds. But no one is going to activate that argument now? Hm.

Josef Uyeda @pseudacris.bsky.social · 10/09/2026

I see 2 or 3 responses from the left about Trump's $5000 dividend. It's bribery for votes, he's not going to do it, don't be a sucker. But if a Dem proposed anything of the sort, the immediate R response would be its inflationary and would increase the deficit, and this attack seems to always work.

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So we don't think it's a major crisis in the field, but there are problems to solve, and excitingly, lumpability may give efficient ways of navigating the vast possibilities of character construction alternatives to find biologically plausible and evolutionarily justified representations of traits

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More importantly, we view the rules of lumpability as a way to navigate model space and identify biologically plausible hypotheses about diversification and trait evolution. Hidden state models are cool because they are essentially a joint inference of character construction & evolutionary process.

That is to say, there are problems. But at the same time, model selection with so-called "irreducible models" is a reasonable solution. It doesn't guarantee that model is the one that best maps onto the real biological process that happened, but it does address the statistical issues of congruence.

Furthermore, we don't count hidden states as extra parameters, only transition rates, which leads to inadequate penalization of the degrees of freedom these models have and consistent mistakes in model inference across congruence classes using information criteria such as AIC.

A lot of what we found requires a balanced reaction: In hidden state modeling of trait evolution and diversification, there are large congruence classes that emerge as we increase the number of hidden states. Because of these congruence classes, there are statistical and interpretational issues.

Michael Hobbes @michaelhobbes.bsky.social · 31/08/2026

Reposted by Josef Uyeda

A 76-year-old green card holder with stage 4 cancer was arrested at his citizenship application interview and has been held by ICE for two months. www.seattletimes.com/seattle-news...

Loreto Javar, a green card holder who’s lived in the United States for over three decades and is being treated for Stage 4 prostate cancer, has been held at the Northwest ICE Processing Center in Tacoma for more than two months.

A 76-year-old retired hotel worker who lives in Fife with his wife and daughter, Javar was detained by Immigration and Customs Enforcement officials June 23 during an interview for his U.S. citizenship application in Tukwila. He was receiving ongoing cancer treatment when he was taken into ICE custody, his family said, and has missed several medical appointments since his arrest.

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Reposted by Josef Uyeda

Casey Dunn @caseywdunn.bsky.social · 25/08/2026

My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore.

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Josef Uyeda @pseudacris.bsky.social · 24/08/2026

Spot on, but for the more pickle brained signatories I suspect that not only is it demonstrating their priorities, but the positive feedback between their priorities and their algorithm. I could easily believe they mostly don't know what's happened whereas this was a defcon1 event in their feeds.

Carl T. Bergstrom @carlbergstrom.com · 24/08/2026

Reposted by Josef Uyeda

Because if you didn't say a word about DOGE eliminating every federal grant with any element that Grok thought had anything to do with LGBTQ health, climate change, health disparities, and most of all DEI? I don't think you give a shit about academic freedom. I think you're just a racist.

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Josef Uyeda @pseudacris.bsky.social · 21/08/2026

you are a phylophygophile after all.

Josef Uyeda @pseudacris.bsky.social · 17/08/2026

I don't think you should worry, tech companies have proven them very trustworthy at designing algorithms that maximize human flourishing.

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Josef Uyeda @pseudacris.bsky.social · 14/08/2026

It has a great thought experiment on PKU as a genetic disorder that breaks down how we define "normal" and "disorder" and how genes affect phenotypes. Has led to some great discussions.

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Josef Uyeda @pseudacris.bsky.social · 14/08/2026

I teach a freshman seminar on "The stories we tell about genetics and ancestry". In addition to reading chapters from @adamrutherford.bsky.social 's A Brief History of Everyone Who Ever Lived, I really like this chapter from Virginia Tech emeritus Richard Burian: research.ebsco.com/c/5drqht/sea...

research.ebsco.com

Shibboleth Authentication Request

Aramati Casper @aramaticasper.bsky.social · 13/08/2026

Reposted by Josef Uyeda

Why is there "no consensus" about sex in biology? Turns out, we're using seven different concepts. In "Evolution, development and the incoherence of sex" we name & elucidate these concepts. With Karen Warkentin and Jay Falk @jjinsing.bsky.social @sicbjournals.bsky.social doi.org/10.1093/icb/...

The cover of the article, in Integrative and Comparative Biology. The image caption is "Examples of seven biological phenomena sometimes called sex and the evolutionary relationships among them. The seven sex concepts are depicted with images: 0) horizontal gene transfer, 1) meiosis and syngamy, 2) anisogamy, 3) the gametes produced by an individual, 4) traits often associated with gamete production, 5) processes that bring gametes in proximity to facilitate syngamy, 6) processes/behaviors/traits derived from sex5.

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Reposted by Josef Uyeda

International Journal of Plant Sciences @ijpsjournal.bsky.social · 12/08/2026

AOP @ijpsjournal.bsky.social Comparative Evolution of Photosynthetic Light Response Curves: Approaches and Pitfalls in Phylogenetic Modeling of a Function-Valued Trait Rebekah Evelyn Davis, @plantevoecophys.bsky.social, Eric Goolsby www.journals.uchicago.edu/doi/10.1086/... #PlantScience

journals.uchicago.edu

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We like to think of our terminology as fundamental building blocks from which all biological variation can be described, but it is not and we essentialize a biased typology of "normal" in biology at the cost of clarity and understanding, and a great byproduct of harm to real human communities.

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In other words, using their definitions, a term like "to fertilize" blends together sex1 with sex2 (and maybe sex4 & sex5) in ways that are unnecessary, promote confusion, and often fail when confronted with biological diversity.

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My favorite example: There is no isogamous version of the verb "to fertilize" that doesn't imply actor-receiver, i.e. mutual causation over syngamy. The fact this key biological concept is described by a word with constitutive asymmetry, despite the biology not needing it, shows the depth of bias.

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The authors understandably use placeholders for the distinct concepts for each concept of sex/sexes (e.g. sex0, sex1, sex2). That we don't have words for these yet in biology is frankly embarrassing, especially when we have so many dizzying and barely pronounceable terms in sex biology.

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Biologists need to get this right because our words and authority get weaponized in the public sphere. Interrogate your usage and beliefs to see whether you can justify collapsing your definitions; 1) is it biologically accurate? 2) does doing so cause harms? 3) What can we do to better teach facts?

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