iiinova — where your digital self keeps evolving

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Jacob Garbe 💀 @logodaedalus.bsky.social · 28/07/2026

This is very well-written and made me very sad: kirwinhampshire.substack.com/p/the-dark-n...

kirwinhampshire.substack.com

The Dark Night of Mathematics

What are we really doing?

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Met Office - weather and climate @metoffice.gov.uk · 28/07/2026

Major wildfires continue in parts of Europe🔥 Satellite imagery shows widespread smoke across Portugal, Spain and near to Bordeaux. There's little prospect of any rain relief and the heat will even intensify for some, with temperatures of over 40°C possible in places📈

A satellite image of France, Spain and Portugal showing plumes of smoke on the afternoon of Monday 27 July 2026

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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 08/07/2026

This puzzle is in my first book (the one no one reads), and I know Claude ate my books (bc I got part of that copyright settlement against Anthropic), so here's Claude's answer, from my book. The whole chapter is about this puzzle basically, builds answer using covariance genetics.

3.4.5 What is r?
We’vecomefarenoughnowthatwecanspelloutmoreclearly
what the r in Hamilton’s rule is and is not.
r is not Pr(A|A). It is also easy to see from Equations 3.7
and3.8thatr ismostdefinitelynot thechancethattherecip-
ient has a given allele, given that the donor has it. This com-
mon mis-definition of r arises from a basic misunderstanding.
The recipient and donor can be alike simply because the al-
lele is common in the population (p is large). Instead, r is
the increased similarly of the donor and recipient relative to
the population mean. Only in extreme cases, as when p ≈0
and pi = 1, will r = E(pj|pi).
r is the extent to which actor’s genotype predicts re-
cipients’ genotypes. We showed a fairly standard deriva-
tion of r as a regression coeﬃcient, as Hamilton presented it.
The slopes of the lines in Figure 3.3 are measures of r. In
calculus-speak, r is the partial derivative of pj with respect to
pi, ∂pj/∂pi: the rate of change in recipients’ genotypes as a
function of actors’ genotypes. One important consequence of
this interpretation is that negative relatedness is possible. If
being an altruist predicts that the recipient is less likely than
chancetohavethealtruismallele, theslopeofthebest-fitline
will be negative. You might think this is a weird and unlikely
circumstance, but it might be important in some cases.

Figure 3.3: How positive assortment relates to the regression of
recipient’s genotype (pj) on actor’s genotype (pi). The size of the
white circles represents the number of pairs at each combination
of pi and pj. The black circles in each plot represent the mean
genotype of actors and recipients, which is p in each case. The
dashed lines are the regressions of pj on pi. The slopes of these
lines are the beta coeﬃcients important in Expression 3.6.

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BCBHubCSIC @bcbhubcsic.bsky.social · 01/06/2026

#BCBToolsSeminars Join the next session on June 3 at 11h with Miguel Alvarez Herrera (I2SYSBIO-CSIC) & David San León (CNB-CSIC), presenting VIPERA & MIPERA and FLYCOP. Live streaming available! 👉 goo.su/2WCzwt @i2sysbio.es @cnb-csic.bsky.social Don´t miss it!

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Aparna Nair @disabilitystor1.bsky.social · 02/05/2026

I find it incredibly telling when men like Dawkins are convinced that the LLMs are ‘intelligent’ because it ‘agrees’ with them or tells them how insightful or clever they are

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Haiku Fortuito @haiku-fortuito.bsky.social · 07/04/2026

Haiku fortuito nº 544 Todo el mundo a pedir su prórroga de alquileres

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Miguel 💻🧬 @ahmig.es · 05/04/2026

acabo de migrar mis datos a un PDS europeo! hola desde @eurosky.social :)

pds.ls screenshot of at://ahmig.es displaying the PDS eurosky.social

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FirerMcFirer @aradfirer.bsky.social · 02/04/2026

I made it my life mission to reference this as many times as I can

A tweet by @Llama In a Tux (dated Sep. 10, 2022):
Don't you understand? The human race IS an endless number of monkeys. And every day we produce an endless number of words. And one of us already wrote Hamlet

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Miguel 💻🧬 @ahmig.es · 02/04/2026

Our preprint on the first reconstruction of the core metabolic network of Xylella fastidiosa is now available! Using this model, we were able to design defined minimal media and guide our hypotheses about how this bacterium assimilates acetate and produces polyamines, with in vitro validation 🧪👀👇

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AEMET @aemet.es · 30/03/2026

🧵El planeta Dune, también conocido como Arrakis no solo ha fascinado a los lectores de Frank Herbet, también a los científicos, que han tratado de simular el clima de este mundo cubierto de arena. En este artículo nuestro compañero David Quintero os cuenta más sobre Dune aemetblog.es/2026/03/30/c...

aemetblog.es

Clima en el planeta «Dune»

¿Cumple este planeta las leyes de la física? Descúbrelo en #AEMETBlog

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PathoGenOmics Lab @pathogenomics.bsky.social · 11/03/2026

Happy Bioinformatics Day!🧬💻Celebrate the power of data for understanding life at every level. In @pathogenomics.bsky.social we combine experiments with bioinformatics to understand bacterial evolution, virulence, and infection dynamics. #SoyBioinformatica @paururo.bsky.social @ahmig.es @i2sysbio.es

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Miguel 💻🧬 @ahmig.es · 10/03/2026

Sharing my entry for @i2sysbio.es's BioVision 2026! "MTB 20:02" is a night photograph of the metabolic network of M. tuberculosis hovering near our building at night (made in Blender, based on iEK1011) methods 🤓👉 tangled.org/ahmig.es/biovision2026 #b3d

3D rendering of a glass-like sculpturecof a metabolic network over a night photograph of a building

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Eric Ravenscraft @lordravenscraft.bsky.social · 05/03/2026

"you need to learn how to use gAI or you'll get left behind!" counterpoint! the absolute fastest way to render yourself unemployable is to build your skillset around a tool that does your thinking for you, that everyone has access to, and that one company can change or take away at any time

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Miguel 💻🧬 @ahmig.es · 03/03/2026

🥈🥈🥈🗣️🗣️‼️

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I2SysBio @i2sysbio.es · 24/02/2026

🎖️ El #I2SysBio ha sido reconocido como el segundo instituto más sostenible del @csic.es 🟢Este logro es fruto del trabajo constante de nuestra Comisión de Sostenibilidad, impulsando iniciativas ambientales, sociales y económicas.

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Ana Conesa @anaconesa.bsky.social · 28/02/2026

Euphoric for my institute @i2sysbio.es receiving the 2nd @csic.es Sustainability Prize. Proud of the tireless & impactful work of our Committee. Especially happy to share recognition with friends from IDAEA & @geo3bcn-csic.bsky.social. Congrats @icmabcsic.bsky.social and @ibmb-csic.bsky.social

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CSIC @csic.es · 28/02/2026

2️⃣ Desde el @i2sysbio.es presentan sus medidas y, entre ellas, su trabajo para obtener las certificaciones internacionales de investigación sostenible

youtu.be

Distintivo de Sostenibilidad del CSIC. Segundo puesto I2SysBio

Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.

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Letters of Note @lettersofnote.com · 12/02/2026

Happy birthday to one of my favourite haters, Charles Darwin

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Miguel 💻🧬 @ahmig.es · 17/11/2025

VIPERA v1.3.0 is out!! 🐍🐍🐍 under the hood: visualization decoupled from computation, faster allele freq distance calculations using a custom tool (afwdist) and improved performance on the user side: same inputs and outputs, a few options removed or renamed, clearer docs and a prettier report 🧪👇

github.com

GitHub - PathoGenOmics-Lab/VIPERA: A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis

A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis - PathoGenOmics-Lab/VIPERA

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Miguel 💻🧬 @ahmig.es · 30/07/2025

VIPERA v1.2.2 is out!! 🐍 now you can swap in different stats (useful for non-linear allele freq trends). also: new Docker images on release, containerized CI, updated envs, and minor bug fixes for smoother, reproducible intra-patient SARS-CoV-2 analyses 🧪👉 github.com/PathoGenOmics-Lab/VIPERA

github.com

GitHub - PathoGenOmics-Lab/VIPERA: A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis

A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis - PathoGenOmics-Lab/VIPERA

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David Rankin @asteroiddave.bsky.social · 02/07/2025

FACT THREAD on New Interstellar Object #A11pl3Z This story unfolded pretty fast yesterday for a few reasons. The object was discovered on July 1st UTC by the Asteroid Terrestrial-impact Last Alert System, or ATLAS team. A #NASA funded survey at the University of Hawaii. atlas.fallingstar.com 🔭🧪

Orbit diagram of interstellar object A11pl3Z

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astrafoxen @astrafoxen.bsky.social · 02/07/2025

So uh, there's a new interstellar object discovered at Chile yesterday. Name is A11pl3Z, has a hyperbolic trajectory of eccentricity 14±4 (WTF). Currently appmag 18, 4 AU away from Earth, and coming to 2 AU perihelion this October. (tagging🔭☄️) Observing it with remote scope rn, calling astronomers..

projectpluto.com

Pseudo-MPEC for A11pl3Z

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I2SysBio @i2sysbio.es · 26/06/2025

On June 20, #I2SysBio (@csic.es - @uv.es) hosted Alva Saa from association PRISMA, who shared ten key measures to foster #LGTBIQA+ 🏳️‍🌈 inclusion in #science. The talk addressed actions like staff training, safe reporting channels, and collective visibility in research. 🌐 i2sysbio.es/communicatio...

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Miguel 💻🧬 @ahmig.es · 30/06/2025

VIPERA v1.2.1 is here!! 🐍🐍🐍 Our workflow for SARS-CoV-2 intra-patient evolution analysis now fully supports Snakemake 8/9 (with dedicated CI tests), BIONJ trees, richer reports, added config parameters, modular Snakefiles and more! 🧪👉 github.com/PathoGenOmics-Lab/VIPERA

github.com

GitHub - PathoGenOmics-Lab/VIPERA: A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis

A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis - PathoGenOmics-Lab/VIPERA

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Miguel 💻🧬 @ahmig.es · 20/05/2025

Just back from MCEB 2025 in Granada! I presented our year-long work expanding VIPERA🐍 to help us better track pathogen evolution, here at @pathogenomics.bsky.social - @i2sysbio.bsky.social. I learned so much and returned full of ideas! Thanks to @bcbhubcsic.bsky.social for funding my attendance! 🧪

A photo of a group of people with the Alhambra in the back

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Mikel López Iturriaga @mikeliturriaga.bsky.social · 15/05/2025

Gentes de Bluesky, firmad esto que es importante: iniciativa ciudadana europea para prohibir las "terapias" de conversión de personas LGTBIQ+. NO es un change.org, puede suponer un cambio legal real. Y no lo dejéis para luego, que se acaba el sábado. eci.ec.europa.eu/043/public/#...

eci.ec.europa.eu

European Citizens' Initiative

Give your support !

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Delegación CSIC Comunitat Valenciana - Casa de la Ciència @dicv.csic.es · 02/04/2025

Un equipo liderado por el @i2sysbio.bsky.social publica una investigación que halla errores en las secuencias genéticas del #coronavirus incluidas en la mayor base de datos mundial. También participan @ibv-csic.bsky.social y el IIS La Fe. delegacion.comunitatvalenciana.csic.es/hallan-error...

Un equipo multidisciplinar liderado por el Instituto de Biología Integrativa de Sistemas (I2SysBio), centro mixto del Consejo Superior de Investigaciones Científicas (CSIC) y la Universitat de València (UV), acaba de publicar un estudio que descubre una nueva perspectiva sobre la capacidad del virus SARS-CoV-2 para mutar e infectar a los humanos. Mediante una revisión de la base de datos genéticos del virus más utilizada durante la pandemia, el equipo de investigación halló ‘falsos positivos’ en su capacidad de reparación de las deleciones, un proceso que restaura secciones del genoma viral que afecta la capacidad del virus para replicarse o evadir el sistema inmunológico del huésped. En el trabajo, publicado en la revista Virus Evolution, participan investigadores del Instituto de Biomedicina de Valencia (IBV) del CSIC y del Instituto de Investigación Sanitaria La Fe (IIS-La Fe).

El trabajo liderado por el grupo de Patogenómica del I2SysBio en colaboración con el grupo de Biología Viral del mismo instituto ofrece una perspectiva innovadora sobre ciertos cambios genéticos raros en la proteína spike del SARS-CoV-2, la ‘llave’ que utiliza el coronavirus para infectar nuestras células. La investigación se centró en los llamados eventos de reparación de deleciones en esta proteína, en los que el virus aparenta corregir su genoma.

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I2SysBio @i2sysbio.es · 03/04/2025

By mining GISAID, researchers from I2SysBio uncover sequencing artifacts in SARS-CoV-2. Many repair mutations in the spike protein were due to errors in data processing. #covid19 #viruses #microsky🧪🦠💻🧬 More info: www.i2sysbio.es/communicatio... ⬇️

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Miguel 💻🧬 @ahmig.es · 03/04/2025

happy to share our new study! 🧪 while exploring how often #sars-cov-2 "repairs" deletions in BA.1, we found significant genome artifacts in GISAID 🤯 we compared with raw reads from ENA + tested the effects in vitro. turns out, data processing matters a lot 📉 check it out!! doi.org/10.1093/ve/v...

doi.org

Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein

Abstract. Mutations within the N-terminal domain (NTD) of the spike (S) protein are critical for the emergence of successful SARS-CoV-2 viral lineages. The

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I2SysBio @i2sysbio.es · 25/03/2025

Oferta de beca de investigación en nuestro instituto con la excelente supervisora Mireia Coscollá @pathogenomics.bsky.social . Proyecto enfocado en bioinformática, tema patógenos 🧪🦠🧫🧬🖥👩‍🔬

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I2SysBio @i2sysbio.es · 27/02/2025

Our institute hosts the exhibition “Train the feminist gaze”, promoted by the City Council of Valencia @ajuntament-vlc.bsky.social to highlight the inequalities between women and men present in everyday life and in areas such as art or science 🧪 www.i2sysbio.es/communicatio... #WomenInSTEM 👩‍🔬

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I2SysBio @i2sysbio.es · 20/11/2024

Our research institute I2SysBio🇪🇸 has created a starter pack for researchers in systems biology, everybody is welcome, write us if you want to be added 🔬🧫🧬🖥🦑🦠🌱🦟🪳🪸🌾

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Miguel 💻🧬 @ahmig.es · 18/10/2024

Had a great time sharing an exciting new direction for VIPERA🐍 at the I congress of the Spanish Society of Bioinformatics and Computational Biology (SEBiBC)! Can't wait for the next one 🗣️🗣️

a picture taken during my flash talk about large-scale data analysis based on our tool, VIPERA (Viral Intra-Patient Evolution Reporting and Analysis), at the I SEBiBC congress

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