The difference--

Did nobody use the headline Alpha Folds

Dan McQuillan@danmcquillan.bsky.social · 5d ago

AlphaFold was always bait-and-switch; now Google confirms it. A hyper-narrow bioinformatrics model with actual science bolted on whose guesses can be experimentally checked was never a licence for socially-applied slop at scale, but it's done its job. Effort transferred to LLMs.

Shultz @beeharpur.bsky.social et al. documented the trajectory of a spontaneous deleterious mutation from its origin in a single queen to its extinction, directly observing how haplodiploidy exposes recessive alleles to immediate purifying selection 🔗 doi.org/10.1093/molbev/msag156 #societyjournal

Open position of Associate Professor in Behavioral ecology and cultural evolution at the @dee-unil.bsky.social! You can toggle the ad to English on top right: wwwfbm.unil.ch/releve/appli...

While these associations do not imply causation. They identify an evolutionary path through which diversity can emerge from a shared developmental foundation. Demonstrating how variation can emerge from a common theme. (8/8) #EvoDevo #Evolution #DevelopmentalBiology #Fish

However, do these genomic changes matter for phenotypic diversity? YES! Across teleosts, variation in the copy numbers of high-turnover network genes was associated with differences in traits including swimming performance and trophic level. (7/8)

This reveals an intriguing pattern. The network’s functional architecture remains conserved, while the number of gene copies within it can change. In other words, evolution modifies the components of a developmental system without disrupting its underlying organisation. (6/8)

But a 'conserved' network doesn't mean an evolutionary static one. Across 133 teleost genomes, genes within the conserved network showed extensive copy-number evolution. High-turnover gene families experienced frequent expansions and contractions. (5/8)

he second partition contained processes that more directly transform the organism, including nervous-system, skeletal, muscular, sensory and physiological development. Together, the two partitions coordinate the post-embryonic transition. (4/8)

This conserved network was divided into two partitions. One contained core cellular processes—such as translation, DNA replication, protein turnover and energy metabolism—that lay the molecular foundation for developmental change. (3/8)

We compared gene-expression trajectories across post-embryonic development in five teleost species spanning ~200 million years of evolution. Despite striking differences in their developmental transitions, we found a shared underlying co-expression network. (2/8)

How can a shared developmental programme generate the extraordinary diversity of teleost fishes? Our study suggests that the answer lies in the combination of conservation of network architecture, coupled with evolutionary flexibility in gene copy number. (1/8) doi.org/10.64898/202...

An evolvable and functionally partitioned network underlies developmental remodelling in teleosts

Comparative embryology has revealed that early animal development is based on highly conserved genetic programs. Beyond embryogenesis however, animals undergo remarkably diverse post-embryonic developmental transitions such as metamorphosis. Whether these transitions are also organised into conserved genetic programs remains largely unexplored. To identify conserved genetic programs underlying post-embryonic development, we examine metamorphic remodelling in five teleost fishes, spanning 200 million years of evolution. By integrating comparative co-expression networks, evolutionary genomics, phylogenetic modelling, and functional data in zebrafish, we uncovered a conserved post-embryonic developmental network. This conserved network comprises components involved in core cellular processes, and involved in development and physiology, both of which are under the control of thyroid hormone during metamorphosis. Despite evolutionary conservation at the coding sequence level, this network exhibits significant turnover in gene family copy number following the teleost-specific whole-genome duplication as well as lineage-specific expansions and contractions. The variation in gene copy numbers is associated with macroevolutionary variation in a number of ecological and morphological traits, including swimming performance and trophic level. Cross-species tissue expression, zebrafish single-cell transcriptomics, and zebrafish perturbation phenotypes placed the implicated genes in biological contexts relevant to these traits. Together, our results provide evidence of an ancient, functionally partitioned post-embryonic developmental network that has diversified throughout teleost evolution. The heterochronic variation in network function, changes in endocrine activity, and gene-family turnover provide potential routes through which a shared developmental architecture contributed to the evolution of phenotypic diversity in teleosts. ### Competing Interest Statement The authors have declared no competing interest. International Human Frontier Science Program Organization, LT0063/2022-L

doi.org

And so people CHANGED THEIR MINDS in the light of NEW DATA regarding the role of the market. Including me! It is profoundly dishonest to present a Jan 2020 take as definitive. Please do better. ▫️6/6

I am sick of some media uncritically repeating Rand Paul's misrepresentation of Fauci's journal about the Huanan market. In late Jan 2020, it was a common commentary that the market may not be the origin of the outbreak, b/c of a Lancet paper on early cases ▫️1/6 www.paul.senate.gov/wp-content/u...

New preprints! 1/3 Spider venom glands are modified salivary glands which have recruited appendage and myogenic programs from other the developmental programs of other organs. Led by Giulia Zancolli, with @yehumoran.bsky.social doi.org/10.64898/202...

📢 preprint update: www.biorxiv.org/content/10.6... 🦀🧬🦐🧬🐝🧬🦋🧬 𝐈𝐧𝐯𝐞𝐬𝐭𝐢𝐠𝐚𝐭𝐢𝐧𝐠 𝐢𝐧𝐝𝐞𝐩𝐞𝐧𝐝𝐞𝐧𝐭 𝐞𝐯𝐨𝐥𝐮𝐭𝐢𝐨𝐧𝐚𝐫𝐲 𝐥𝐢𝐟𝐞 𝐡𝐢𝐬𝐭𝐨𝐫𝐲 𝐭𝐫𝐚𝐧𝐬𝐢𝐭𝐢𝐨𝐧𝐬 𝐭𝐨 𝐦𝐞𝐭𝐚𝐦𝐨𝐫𝐩𝐡𝐢𝐜 𝐝𝐞𝐯𝐞𝐥𝐨𝐩𝐦𝐞𝐧𝐭 𝐚𝐜𝐫𝐨𝐬𝐬 𝐏𝐚𝐧𝐜𝐫𝐮𝐬𝐭𝐚𝐜𝐞𝐚 #phylogenomics #evolution #biodiversity With Giulia Campli, @marcrr.bsky.social, & @chipman-lab.bsky.social

Convergent gene family evolution underpins repeated transitions to metamorphic development across Pancrustacea

Arthropod developmental modes are highly diverse, ranging from direct development with little morphological change between moults to metamorphic life-stage progressions characterised by profound trans...

biorxiv.org

Admitting you have a problem. A horseshoe crab problem. The little fucks are everywhere. In the bathtub, in the crisper. You find their dried up and hollowed out shells tangled in your sheets every morning. You want them gone but they will not take a hint. Perhaps more drastic measures are in order.

Nouveau "Rogatons" ! - "Détente" - 23/07/2026 À lire ici: www.bouletcorp.com/rogatons/202... Ou sur Instagram: www.instagram.com/p/DbJHthSiKT...

But “solving hard problems” has only ever been a proximate goal because it happened to align fairly well with “bring clarity and understanding” for HUMAN mathematicians. AI has broken this correlation: goals set for human minds aren't relevant to them. •13/16

Gro-Tsen@gro-tsen.bsky.social · 2w ago

But OF COURSE we should move the goalposts, because the goals were set for human mathematicians, as a kind of proxy for what we actually care about, which isn't solving conjectures (even if we tricked ourselves into thinking so). •28/38

Free and open-source images, icons, and tools for creating scientific illustrations doi.org/10.59350/5zt... 🧪

Free and open-source images, icons, and tools for creating scientific illustrations

Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics

doi.org

I want to see this award 🤓 xkcd.com/3275

Calibration Nobel

xkcd.com

From the folks complaining about improper interpretation of Greek works: ‘federal agencies “should prioritize foundational research in the biological over the life sciences.”’ Biology, derived from Greek, literally means ‘science of life’. www.nytimes.com/2026/07/22/u...

Disability Pride Month felt quieter this year. A few years ago, organizations regularly reached out to highlight disabled scientists and talk about accessibility in STEM. This year, many of those conversations seemed to disappear. But disabled scientists and accessibility barriers didn't disappear.

Every time I see this on my to-do list, I laugh. Still can't remember why I put it there, but it is now permanent.

I'm still thinking about this and how now "cognitive surrender" is getting laundered properly into the discourse. I have done a couple of deception methods experiments in my day and showing that you can make people incorrect in the lab is simply not a basis for saying they're unable to think now

Cat Hicks@grimalkina.bsky.social · 2w ago

I think this is the paper? it's a preprint osf.io/preprints/ps... The questions are media trivia questions, which aren't exactly judgment questions. Presenting "AI" that's forced to be incorrect basically just tests whether participants trust it to be a lookup tool which I think they do

So, as translation control is getting popular, please note the newly unified nomenclatures: Translons: a single term for translated regions www.nature.com/articles/s41... Peptideins: translated ORFs lacking sufficient evidence for protein-coding gene status www.nature.com/articles/s41...

Translon: a single term for translated regions - Nature Methods

Nature Methods - Translon: a single term for translated regions

nature.com

'Together, our results reveal a conserved venom gland structure among octopuses, squids, and cuttlefish, with a spatially distinct neuromuscular tissue organization indicating venom production and release sites modulated by a network of neuronal agents.' www.biorxiv.org/content/10.1...

Neurons, Muscles, and Venom: Elucidating a Neural-to-Secretory Pathway in Cephalopod Predation

Venom plays a central role in the predatory ecology of coleoid cephalopods (octopuses, squids, and cuttlefish), yet the mechanisms governing venom release from the posterior salivary gland (PSG) are u...

biorxiv.org

I mean, I have interviewed a *lot* of people looking for their first job outside of academia, and really, there cannot be enough articles about this point in particular. It's bafflingly bad how condescending people can be. As if we don't have PhDs and many years of experience out here.

Uma Karmarkar@umakarma.bsky.social · 2w ago

Good advice generally, but this really stuck out: "her job hunt became easier when she started “having conversations with people instead of lecturing them” Uh, YES. Your whole life will get easier if you refrain from lecturing adults *anywhere* outside of a classroom.

Good advice generally, but this really stuck out: "her job hunt became easier when she started “having conversations with people instead of lecturing them” Uh, YES. Your whole life will get easier if you refrain from lecturing adults *anywhere* outside of a classroom.

Nature@nature.com · 2w ago

A postdoc researcher trying to move into an industry role wants help gaining traction and making it past the first interview stage go.nature.com/44Ed0SS