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David Castellano @castellanoed.bsky.social · 1d

Working link: academic.oup.com/mbe/advance-...

Interpreting supervised machine learning inferences in population genomics using haplotype matrix permutations

Abstract. Supervised machine learning methods, such as convolutional neural networks (CNNs), that use haplotype matrices as input data have become powerful

academic.oup.com

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David Castellano @castellanoed.bsky.social · 1d

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This project reminded me that science often begins with process, not plans — a casual “what if” in a lab meeting can lead to methods that help us see the field in a new light.

🧠 Authors: @lntran.bsky.social @ryangutenkunst.bsky.social
#PopGen #MachineLearning #Interpretability

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David Castellano @castellanoed.bsky.social · 1d

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We developed a systematic permutation approach that progressively scrambles features (LD, haplotype structure, allele frequencies) in haplotype matrices to see how each affects model performance.

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David Castellano @castellanoed.bsky.social · 1d

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Supervised ML methods like CNNs are now powerful tools for demographic and selection inference.
But they’re often black boxes — we rarely know which population-genetic features actually drive their predictions.

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David Castellano @castellanoed.bsky.social · 1d

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Excited to share our new paper in Molecular Biology & Evolution!
👉 [https://doi.org/10.1093/molbev/msaf250]
It started as a lab-meeting sanity check for another project — and ended up turning into a new way to interpret machine-learning models in population genomics.

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Reposted by David Castellano

Dr Paul Dorfman @drpauldorfman.bsky.social · 5d

#Solar becomes main source of electricity in the #EU for first time. More than half of the EU’s #electricity in the second quarter of 2025 came from #RenewableEnergy
www.independent.co.uk/tech/solar-p...

Solar becomes main source of electricity in the EU for first time

More than half of the EU’s electricity in the second quarter of 2025 came from renewable energy

www.independent.co.uk

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Reposted by David Castellano

POPGROUP59 @popgroup2026.bsky.social · 9d

Exciting news!
The next #PopGroup meeting will take place in Lille 🍟, France, 7–9 January 2026 – just 1 hour by train from London, Brussels, and Paris.

This year, PopGroup will also host ALPHY, the annual meeting of Evolutionary Genomics.

More info: populationgeneticsgroup.org.uk

See you there !

Population Genetics group 59

populationgeneticsgroup.org.uk

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Reposted by David Castellano

Marshall Abrams @marshall0i.bsky.social · 9d

Mathematician Hilda Geiringer was born OTD 9/28/1893. In philosophy of science, best known for translating and adding to her husband Richard von Mises' books on probability and statistics, in biology for seminal work on genetic linkage. www.bbc.com/future/artic... #philsci #evobio #probability #math

The woman who reshaped maths

She fled the Nazis, only to face a new challenge: being accepted in academia.

www.bbc.com

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Reposted by David Castellano

JazzReads📚 @jazzreads.bsky.social · 10d

So exhausting..

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Reposted by David Castellano

Dr. Jey McCreight 🧬🏳️‍⚧️ @jeymccreight.bsky.social · 14d

Proud to announce the project I've been working on 🏳️‍⚧️🧬

Had hoped to have more ready, but the events of the last week stressed the importance of speaking up against fascism NOW

I'd appreciate your support in spreading the word, esp if you work in life sciences research, healthcare, or biotech

Beyond X&Y @beyondxandy.bsky.social · 14d

It's the scientific community's duty to fight misinformation, bioessentialism, and eugenics

That's why we're launching Beyond X&Y, an educational campaign combating the rise of unscientific political propaganda used to attack trans and intersex people

Subscribe to our newsletter at beyondxandy.org

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Reposted by David Castellano

Tatsuya Amano @tatsuya-amano.bsky.social · 19d

Women, non-native English speakers & those form low-income countries are disadvantaged in science but by how much? We found that women with non-English first languages from low-income countries publish up to 70% fewer in English than their counterparts. 1/5
doi.org/10.1371/jour...
#languagebarriers

Scientific productivity gap based on English-language peer-reviewed papers. Shown are the maximum % differences in the number of peer-reviewed papers published by female native English speakers from a high-income country (-45%), female non-native English speakers from a high-income country (-60%), and female non-native English speakers from a lower-middle income country (-70%), compared to male native English speakers from a high-income country (red flag).

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David Castellano @castellanoed.bsky.social · 20d

@adameyrewalker.bsky.social Nice to see you here!

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Reposted by David Castellano

Yogi Jaeger @yoginho.spore.social.ap.brid.gy · 21d

Giving a little boost to this appendix to #beyondtheageofmachines:

"Limitations of Mathematical Modeling"

https://expandingpossibilities.org/a4-limitations-of-mathematical-modelling.html

It starts with static network models, then shows how to include dynamics […]

[Original post on spore.social]

Quote from the appendix:

"But this is not the main insight we gain from our survey of methods. Its central message, instead, is this: we do not have any modelling formalism able to capture the full behavioural and evolutionary potential of any living system. Life always goes beyond formalisation. This is not to say that we cannot model aspects of living systems and their evolution. In fact, the above modelling formalisms give us a powerful toolkit to do just that. Rather, we are saying that none of these formalisms are able to capture the future behaviour and evolution of a living system completely. We said it before: life, and the large world it exists in, will always surprise us! Every once in a while, at least. And this fact really matters: a machine world can be formalised in its entirety. There is no surprise, but also no relevance or meaning in such a world.

The machine kills life. That is why we must move beyond it. This does not mean that we should no longer be using the tools we’ve introduced above. Quite the contrary: we use them more wisely, and more effectively, if we are aware of their nature and limitations as tools. Our models are means to a better understanding. But they are not our world. The world, after all, is not a set."

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Reposted by David Castellano

Jonathan Basile @jonothingeb.bsky.social · 23d

I'm excited to share with you all a conference I'm planning Oct. 10-12: Dialectical Biology Today: Legacies of Richard Lewontin.

It will be hybrid in Toronto and on zoom, so please join us however you can! Register for zoom link here: ihpst.utoronto.ca/events/diale...

Conference title: Dialectical Biology Today: Legacies of Richard Lewontin, and image of Lewontin in Black and White with intense expression in front of a chalkboard holding up a fist,
When and Where
Friday, October 10, 2025 11:30 am to Sunday, October 12, 2025 2:00 pm
Music Room (218)
Goldring Student Centre
150 Charles St W, Toronto, ON M5S 1K5 | and online via Zoom

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Reposted by David Castellano

Ryan Gutenkunst @ryangutenkunst.bsky.social · 23d

With two months to go, @alwaysrong.bsky.social is dominating the Genomic History Inference Strategies Tournament leaderboards. Jump into the competition to help dethrone Stephen! Glory, money, and authorship are all on the line! ghi.st

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Reposted by David Castellano

Yogi Jaeger @yoginho.spore.social.ap.brid.gy · 27d

Chapter 12 of #beyondtheageofmachines is out!

"Was lange währt, wird endlich gut"
we'd say in German.

It's called "The World is Not a Set."

https://www.expandingpossibilities.org/12-the-world-is-not-a-set.html

Diagram showing two processes co-constructing each other's states S by the output Y of one entering as input X into the other.

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Reposted by David Castellano

Richard Lenski @relenski.bsky.social · 27d

Curious to hear thoughts from #popgen, #humangenetics, #genomics folks on recent paper:

www.pnas.org/doi/10.1073/...

"Directed mutation" in specific human pop'ns seems unlikely to me. DM didn't stand up as proposed in bacteria, but there are hot spots shaped by past selection. Plausible here?

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Reposted by David Castellano

Jeffrey Ross-Ibarra @jrossibarra.bsky.social · Sep 3

Save the date! #PEQG26 June 9-12 2026 in Asilomar, CA. Happens only every 2yrs, but is my favorite conference. Full website coming soon, and registration and abstract submission opens November 14, but I'm allowed to tease that keynotes will be @jnovembre.bsky.social @jennytung.bsky.social and me!

Homepage - Population, Evolutionary, and Quantitative Genetics Conference

Visit our website to learn more.

genetics-gsa.org

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Reposted by David Castellano

PlantEvolution 🌱🌾 @plantevolution.bsky.social · Sep 3

Biology never ceases to amaze!

Alejandro Montenegro @aemonten.bsky.social · Sep 3

I've read the abstract 3 times and I still don't understand the phenomenon

www.nature.com/articles/s41...

One mother for two species via obligate cross-species cloning in ants - Nature

In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...

www.nature.com

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Reposted by David Castellano

EvolDir @evoldir.bsky.social · Sep 3

The SMBE 2026 Annual Meeting in Copenhagen is open for symposium proposals from Sept 1 to Oct 15, 2025. Details at https://smbe2026.org/symposia/. Looking forward to your submissions! #conference

Symposia - SMBE 2026 - Copenhagen Denmark

SMBE 2026 Symposia Check deadlines and important dates below. Days Hours Minutes Seconds Conference Symposia We are now accepting proposals for symposium for the 2026 Annual meeting taking place in Copenhagen, Denmark. Selection of proposals will prioritize the interests of SMBE members, emphasizing innovative scientific developments while ensuring geographic and gender diversity among the participants. […]

smbe2026.org

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Reposted by David Castellano

Mike Barker @barkerms.bsky.social · Sep 2

Our latest preprint led by @conjustover.bsky.social with fantastic undergraduate Sam Gibbon and @ryangutenkunst.bsky.social! Read Justin's thread below for more information on this fun project diving into mutation-selection balance in tetraploids! #polyploidy 🧪

Justin Conover @conjustover.bsky.social · Sep 2

New Preprint! This one led by Sam Gibbon, an outstanding undergrad I've worked with for the past year. We take a look at whether segregation patterns in tetraploids (disomic v polysomic) affects mut-sel dynamics. We found some surprising results, and some subtleties: www.biorxiv.org/content/10.1...

Bistable Mutation-Selection Equilibria and Violations of Fisher's Theorem in Tetraploids: Insights from Nonlinear Dynamics

Polyploidy and whole genome duplication (WGD) are widespread biological phenomena with substantial cellular, meiotic, and genetic effects. Despite their prevalence and significance across the tree of ...

www.biorxiv.org

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Reposted by David Castellano

Justin Conover @conjustover.bsky.social · Sep 2

New Preprint! This one led by Sam Gibbon, an outstanding undergrad I've worked with for the past year. We take a look at whether segregation patterns in tetraploids (disomic v polysomic) affects mut-sel dynamics. We found some surprising results, and some subtleties: www.biorxiv.org/content/10.1...

Bistable Mutation-Selection Equilibria and Violations of Fisher's Theorem in Tetraploids: Insights from Nonlinear Dynamics

Polyploidy and whole genome duplication (WGD) are widespread biological phenomena with substantial cellular, meiotic, and genetic effects. Despite their prevalence and significance across the tree of ...

www.biorxiv.org

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Reposted by David Castellano

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Sep 2

SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution https://www.biorxiv.org/content/10.1101/2025.09.01.673541v1

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Reposted by David Castellano

Saganism @sagan.bsky.social · Aug 21

When Ted Turner asked Carl Sagan if he was a socialist, Sagan gave the answer America keeps failing to learn.

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Reposted by David Castellano

Flo Débarre @flodebarre.bsky.social · Aug 22

Next ESEB meeting will have an innovative format, across four hubs.
The aim is to make it easier to avoid plane travel, and to diversify the locations that can host a meeting
#ESEB2025 #ESEB2027

Photo of the presentation of the next meeting
Text:
ESEB
Hub Congress 2027
Istanbul
16-20 August 2027
www.eseb2027.org
London
Munchen
Göteborg
Why a Hub Congress?
> Plane travel to and from ESEB events contributes >90% of their carbon emissions.
> ESEB is pioneering the organisation of a Hub congress:
> To act as a role model amongst scientific societies,
> To demonstrate that as a scientific community we are proactive and innovative in our response to the climate crisis.
Advantages of the format?
> Favours local participation and climate-friendly, shorter travel to the nearest hub.
> Increases the involvement of organizers from diverse countries and universities.

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