Just migrated to @eurosky.social. I guess all my data is in EU servers now. Everything else looks the same: network, apps, etc.
06.03.2026 13:20
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Just migrated to @eurosky.social. I guess all my data is in EU servers now. Everything else looks the same: network, apps, etc.
Can we engineer the resilience of fragile ecosystems? In this paper with @vmaull.bsky.social @lizashpilkina.bsky.social & @vdlorenzo.bsky.social, we discuss "Emergent Bioengineering" bringing together complexity, #synbio and ecology across scales www.preprints.org/manuscript/2...
(5/5) Based on our knowledge of NOT gates, can we design a larger circuit? Oh, yes! We designed a YES gate by coupling two NOT functions. We designed the best gate that would work in Pf-5. The model also said that gate would not work in KT2440 Guess what? That is what happened (fourth result).
(4/5) A good example is parameter g. This is in charge of digital performance i.e. how clear the two states (on/off) are defined. We tested gates that only differed in the RBS (that is basically g in the model). Third result: Pf-5 is more digital tan KT2440. Let that sink in :-)
(3/5) Each of the four new parameters had a very specific impact on NOT gate performance (arrows in figure). This is the core of the comparison. Second result: the four parameters that explained each NOT gate in a chassis built a fingerprint. Their value told as a lot.
(2/5) We compared NOT gates against the (also soil!) chassis Pseudomonas putida KT2440. But hey, we needed math models to run this comparison. Overfitting enters the game. First result: we turned full mechanistic models (A) into models with clustered rates (B). Bye, bye overfitting!
(1/5) As promised, here a short thread about this work.
Why Pseudomonas protegens Pf-5? It is a key environmental host with unique interactions with soil’s biotic and abiotic compounds. Thus great for our Lab’s goal: ecosystems computing. We needed to know how this host interacts with circuits.
Good luck! We'll miss you. Amazing years indeed.
Thanks!
Latest paper out! This piece was a challenge: logic, predictability, decidability, non-model organisms, design... Kudos to @juanricomol.bsky.social & Pablo Japón #syntheticbiology #synbio #biocomputation (I'll post more on this next week) www.sciencedirect.com/science/arti...
Back at the lab after a week in Copenhagen for @aliceworkshop.org! A brilliant week—full of ideas and enthusiastic colleagues. So many things to discuss with the lab now. Kudos to the organizers, and thanks for bringing this energy to #ALIFE topics.
On my way to Copenhagen for the ALICE workhsop @aliceworkshop.org! Discussions around #ALIFE topics for a full week — looking forward. I'll be talking about cellular computing (what else? :-)
New tech adventure: co-founded Newton Biotwins together with @mirobueno.bsky.social. We're building #DigitalTwins for the lab — starting with a flow cytometry twin. Turning #biology into an information science! newtonbiotwins.com/en/home_en/
Next in Lab's conference agenda: AI, Engineering Biology and beyond. It starts today in Bristol hosted by @chofski.bsky.social. Looks great: aiebab.github.io. From our side, @lewisgrozinger.bsky.social will be talking about our approach to the use of evolutionary algorithms for biocomputation.
Just published our workflow for genotyping transposon libraries. All methods, files, scripts... are open source and publicly available.
🔗 link.springer.com/article/10.1...
The biological messiness, as the quantum weirdness, as a source of (unconventional) computing.
The team: @crislaineksr.bsky.social, @angeles-hg.bsky.social, @loraleja.bsky.social, @juanricomol.bsky.social and Paula Múgica.
New paper out!📢 Exploring the computing power of microbes that shapes the environment.
In this short review we talk about the "complexity gap", the distance between bottom-up genetic circuits and microbial information processes. Key questions to improve #biocomputation.
🔗 doi.org/10.1016/j.mi...
Bacteria do compute and can be reprogrammed for new capacities—but not exactly by following Turing’s rules. Evolution, context dependence, and the soft-matter nature of living hardware redefine what computation means in biology. From @angelgm.bsky.social Lab 👉🏻 www.sciencedirect.com/science/arti...
Side story: NAND gates where one input deals directly with growth control, and it is the actual physical body doing the computation. This is our initial approach to morphological computing in living cells. #biocomputation #alife
Our new strain KT-TTX is truly fascinating. Feedback welcome!
Preprint of our work tuning bacterial growth, something that changes context for genetic circuits and therefore, their behaviour. Very interesting observations from both experimental results and a model describing it in this piece of work with @mirobueno.bsky.social and @angelgm.bsky.social! :)
Preprint out! By controlling growth, via RNAP, we control the entire cellular machinery, and tune the cellular context into distinct, stable states. See how NOT gates behave! Kudos to @angeles-hg.bsky.social and @mirobueno.bsky.social
🔗https://www.biorxiv.org/content/10.64898/2025.12.19.695408v1
🔔 Exciting News from the ALIFE Community 🔔
We are pleased to share that the proceedings of ALIFE 2025, the 2025 edition of the premier conference on artificial life, held in Kyoto are now published and accessible - direct.mit.edu/isal/proceed...
This book is brilliant. Impossible to read without current scenarios in mind...
Huge news for #biocomputation! In a major call (€30M total) for AI proposals, Spain just funded an initiative for implementing AI with living matter using #synbio as the programming tool. The 'AI in vivo project' is a massive, official recognition of biocomputation as a leading field in computing.
2⃣ equipos #CNB participan en nuevos proyectos de investigación en #InteligenciaArtificial
'GRAINS', coordinado desde la @uc3m.es, y 'AI en vivo', coordinado por @upm.es
➡️Iniciativas subvencionadas en la convocatoria de la #AEI ( @cienciagob.bsky.social)
www.cnb.csic.es/nuevos-proye...
@csic.es
The CSIC @csic.es Doctoral Programme in #SyntheticBiology is currently offering 10 PhD positions on a number of projects. Good opportunities!
syntheticcell.eu/synbio-csic-...
El disco de Ana Crismán es alucinante! Como aficionado al flamenco me ha encantado. Muy valiente, muy bonito. Como guitarrista me he quedado un poco descolocado 😅 arpaflamenca.es
Our #ALIFE2025 paper is out! 🎉 We show that even when two circuits produce the same output, their evolutionary potential can differ greatly. #Evolution at the smallest scale.
“Parameter Evolvability in Gene Expression Models Drives Phenotypic Adaptation”
🔗 direct.mit.edu/isal/proceed...
