Oscar Silva

The other ~15% is about ploidy and Mike Lynch's stuff.

Photo of young JMS and RCL. Both are wearing shirts and tie.

John Maynard Smith and Richard Lewontin at the University of Sussex, 9 March 1972.

Gaza es Rio de Janeiro. Gaza es el mundo entero

"Dicen narcotraficantes con la misma insensibilidad que nombran palestinos, mapuche o mayas. Se trata sólo de excusas. De argumentos para clases medias urbanas. Pero la historia reciente nos dice que están creando laboratorios para el genocidio."

1/5
🦖 Michael Crichton’s Jurassic Park (1990) turns 35 in November. In a new preprint, I argue that it was a prescient meditation on evolutionary genetics, complexity, & control. I also examine analogous efforts of today (e.g. “de-extinction.")

Select points below:
ecoevorxiv.org/repository/v...

¿Qué demonios pasó en Río de Janeiro?

Science is intertwined with eugenics; eugenic ideologies continue to negatively impact #Indigenous communities to this day.

In the October issue of #GENETICS, @jazlynmooney.bsky.social and colleagues offer a timely and important reminder on the perils of eugenics. buff.ly/1Q5r3XF

Figure 3A from Bruttel et al. describes “How to make SARS2” by adding and removing restriction sites. This is the “synthetic fingerprint” hypothesis.

Claim 1: 11 "synthetic-looking" sites “unlikely to have evolved from [SARS-CoV-2’s] close relatives”

Bruttel et al. identified 11 sites they suspected were modified because they didn't match relatives like RmBANAL52.

50 years ago, King & Wilson published a foundational paper that underlies the cis-regulatory paradigm (CRP) of #DevoEvo #EvoDevo, i.e., that *almost* all morphological evolution is driven by mutations in regulatory elements, rather than proteins, and it all arose from simple misunderstanding 🧪 🧵

We have an open PhD position (application deadline 9 January 2026) in "Theory of fitness landscapes" at @unibe.ch 🤓⛰️📊👩‍💻🎓: banklab.github.io/positions/

Please share widely!

#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED

Jack DeJohnette, acclaimed jazz drummer who worked with Miles Davis, dies at 83 Acclaimed jazz drummer Jack DeJohnette has died at 83. He is perhaps best known for collaborating with Miles Davis on the 1970 fusion album “Bitches Brew.”

Acclaimed jazz drummer Jack DeJohnette has died at 83. He is perhaps best known for collaborating with Miles Davis on the 1970 fusion album “Bitches Brew.”

Protein Structure Evolution (ProSe) Seminar is now on BlueSky! Every 2nd Tuesday, 4PM GMT.

Sign-Up: tinyurl.com/prose-seminar2

Organized by Claudia Alvarez Carreño, Zachary Ardern, Lars Eicholt, Carolina Sanchez-Rocha,
Sergio Romero Romero and Md. Hassan Uz-Zaman.

Ancient origin of an urban underground mosquito Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...

How does life evolve to adapt to modern cities?

Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.

🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515

Networks: The Visual Language of Complexity Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Netwo...

Excited to be in Valencia this week for my annual master’s seminar at the Master’s Degree in Bioinformatics, coinciding with the publication of our new book chapter based on course notes.
Thanks to @julipereto.bsky.social for the ongoing collaboration!

📚 link.springer.com/chapter/10.1...

Proud of the latest edition of my free intro biostats book.

gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/

Not complete but at a good point to take a break, and I think its quite usable

dm me with comments , ideas etc

Simple scaling laws control the genetic architectures of human complex traits Genome-wide association studies have revealed that the genetic architectures of complex traits vary widely. This study shows that differences in architectures of highly polygenic traits arise mainly f...

Why do complex traits differ in their genetic architecture?
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.

Thread:
journals.plos.org/plosbiology/...

Three schematic diagrams. The first illustrates selective publishing of internal resection, the second selective causal focus, and the third selective access and funding for researchers.

1. We ( @jbakcoleman.bsky.social, @cailinmeister.bsky.social, @jevinwest.bsky.social, and I) have a new preprint up on the arXiv.

There we explore how social media companies and other online information technology firms are able to manipulate scientific research about the effects of their products.

A general model for genomic traits evolution https://www.biorxiv.org/content/10.1101/2025.10.22.684021v1

Infographic on the mole. One mole is the amount of substance that contains exactly 6.022 x 10^23 atoms, molecules or ions. This number is also known as Avogadro's number. Using moles makes it easier to talk about amounts of substances involved in reactions by relating the mass of a substance to its atomic or molecular mass. Amount of substance (moles) = mass (grams) divided by the mass of 1 mole (grams per mole). One mole contains a different mass for different substances.

I'm a bit late with the customary #MoleDay infographic this year, but better late than never!

The mole makes it easier to describe the huge numbers of atoms, molecules, or ions that participate in chemical reactions.

More in this graphic: www.compoundchem.com/2014/10/23/m...

#ChemSky 🧪

Sexual selection and speciation: a meta-analysis of comparative studies Abstract. Understanding the drivers of biodiversity is a central goal in evolutionary biology. In particular, sexual selection has long been proposed as a

Does #SexualSelection fuel #Speciation?

Our new #meta-analysis of comparative studies finds support for a positive relationship, but the rather moderate global effect suggests it’s not necessarily a dominant force.

doi.org/10.1093/evle...

Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...

One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.

www.biorxiv.org/content/10.1...

Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor - Nature Ecology & Evolution Phylogenetic and biochemical analyses show a diversity of components of the DNA replication machinery in different Asgard archaea that contributed to the eukaryotic DNA replication machinery.

Phylogenetic and biochemical analyses show a diversity of components of the DNA replication machinery in different Asgard archaea that contributed to eukaryotic DNA replication machinery. 🧪

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

Aaaannnddd I messed up the link. Here it is.

doi.org/10.1101/2025...

I’m excited to announce the launch of my lab at EPFL in Jan 2026 🎉. We’ll combine evolution & synthetic biology to study and (re)engineer bacterial communication.
I’m recruiting PhD students to start in the first semester of 2026.
Apply via EPFL PhD programs by Nov 1
drive.google.com/file/d/1cm-t...

#PhD Position: Interested in the evolutionary and ecological impacts of whole genome duplication?

Join Dr. Tia-Lynn Ashman @drtialynn.bsky.social
and I at the U. of Pittsburgh, to test what drives the competitive outcomes between diploids and #polyploids

Details: shorturl.at/nQ8UW

La actividad de la CIA contra el chavismo resucita el intervencionismo de EE UU en América Latina Las operaciones encubiertas de la agencia, que Trump ha confirmado esta semana, remiten a los golpes, intentos de magnicidio e insurgencias apoyados o ejecutados por Washington en la región durante el...

"Las operaciones encubiertas de la agencia, que Trump ha confirmado esta semana, remiten a los golpes, intentos de magnicidio e insurgencias apoyados o ejecutados por Washington en la región durante el siglo XX"

elpais.com/internaciona...

Lo peor de todo es que sí estoy a favor de ese impuesto; pero los argumentos empleados por el gobierno federal me parecen absurdos (y todo por tenerle a la reforma fiscal).

Dimensionality reduction usually loses information.

- PCA loses the non-linear cycling.

- t-SNE distorts the distances between the three populations

-- Diffusion maps compress the early state cells and lose the cycling.

Fig. 2e from nature.com/articles/s41...

Polyploidy Webinar Speaker Signup 25-26

The #PolyploidyWebinar series is back for another season! 🧬 Join us for talks at 9AM Pacific on the second Thursday of each month. Are you working on something exciting in polyploidy? We'd love to have you speak! Sign up for open dates at the link below. Looking forward to the great research ahead!

Loss of macroevolutionary species fitness explains the rise and fall of clades - Nature Ecology & Evolution The interplay between speciation and extinction rates shapes clade diversity dynamics. Using a novel phylogenetic model that includes living and fossil lineages, the authors estimate speciation and ex...

Excited to share our new paper where we find that the rise, decline and fall of clades is not explained by the usual suspects (diversity-dependence, ecological opportunities) but rather by species' insidious loss of macroevolutionary fitness: www.nature.com/articles/s41... 1/3

The Quarterly Review of Biology: QRB 100th Anniversary

The Quarterly Review of Biology turns 100! We are celebrating our anniversary with free-to-read articles from the archives, through 2026. Learn more: ow.ly/xXli50X7Z5B