@alicanter.bsky.social
Interested in microbial evolution and game theory
Does a cell have a 'mind' - say a proto-mind or basal cognition? Although it was once a fringe idea, recent experimental and mathematical works are accumulating in its support. Here is an interesting recent work: www.biorxiv.org/content/10.1... #complexsystem #systemsbiology #sysbio
25.10.2025 09:45 — 👍 3 🔁 3 💬 0 📌 0
OpenBSD 7.8 release artwork, "Terraodontidae".
OpenBSD 7.8 Released!
Featuring parallel TCP input, among numerous other significant improvements and fixes.
www.undeadly.org/cgi?action=a...
Changelog: www.openbsd.org/plus78.html
fans of T4P pili (and 'pili pili') take note 👇
#MicroSky
www.biorxiv.org/content/10.1...
#microsky #phagesky #phage
How can biological systems anticipate future events? In our new paper with @jordiplam.bsky.social, we show how a simple genetic circuit can predict future trends through a simple (and perhaps widespread) mechanism @drmichaellevin.bsky.social @koseskalab.bsky.social www.biorxiv.org/content/10.1...
28.04.2025 22:42 — 👍 96 🔁 28 💬 5 📌 3Bacterial two-hybrid systems evolved: innovations for protein-protein interaction research
#MicroSky 🦠
Overflow metabolism: Why cells waste nutrients—and why it’s not really waste
go.nature.com/4n39Ijw
The landscape of microbial associations in human cancer www.science.org/doi/10.1126/...
TLDR -- most cancers do not have microbiomes...but a few do have consistent microbe associations (i.e., colorectal and oral cancers). Make sense!
Looks interesting: fluorescent proteins being strung together in a fiber as a recording of transcriptional history in cells.
13.09.2025 12:02 — 👍 11 🔁 2 💬 0 📌 0
Abstract: Under the banner of progress, products have been uncritically adopted or even imposed on users — in past centuries with tobacco and combustion engines, and in the 21st with social media. For these collective blunders, we now regret our involvement or apathy as scientists, and society struggles to put the genie back in the bottle. Currently, we are similarly entangled with artificial intelligence (AI) technology. For example, software updates are rolled out seamlessly and non-consensually, Microsoft Office is bundled with chatbots, and we, our students, and our employers have had no say, as it is not considered a valid position to reject AI technologies in our teaching and research. This is why in June 2025, we co-authored an Open Letter calling on our employers to reverse and rethink their stance on uncritically adopting AI technologies. In this position piece, we expound on why universities must take their role seriously toa) counter the technology industry’s marketing, hype, and harm; and to b) safeguard higher education, critical thinking, expertise, academic freedom, and scientific integrity. We include pointers to relevant work to further inform our colleagues.
Figure 1. A cartoon set theoretic view on various terms (see Table 1) used when discussing the superset AI (black outline, hatched background): LLMs are in orange; ANNs are in magenta; generative models are in blue; and finally, chatbots are in green. Where these intersect, the colours reflect that, e.g. generative adversarial network (GAN) and Boltzmann machine (BM) models are in the purple subset because they are both generative and ANNs. In the case of proprietary closed source models, e.g. OpenAI’s ChatGPT and Apple’s Siri, we cannot verify their implementation and so academics can only make educated guesses (cf. Dingemanse 2025). Undefined terms used above: BERT (Devlin et al. 2019); AlexNet (Krizhevsky et al. 2017); A.L.I.C.E. (Wallace 2009); ELIZA (Weizenbaum 1966); Jabberwacky (Twist 2003); linear discriminant analysis (LDA); quadratic discriminant analysis (QDA).
Table 1. Below some of the typical terminological disarray is untangled. Importantly, none of these terms are orthogonal nor do they exclusively pick out the types of products we may wish to critique or proscribe.
Protecting the Ecosystem of Human Knowledge: Five Principles
Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia:
doi.org/10.5281/zeno...
We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
1/n
Synthetic promoters has relied on naturally occurring TFs or Cas9. With de novo designed DNA binding proteins, there are so much potential for synbio, whether it's targeting natural promoters or designing synthetic ones.
12.09.2025 12:01 — 👍 19 🔁 4 💬 0 📌 0Can engineered genetic circuits reveal principles and constraints of biological cognition?
🧬🦠🖥️ #synbio #systemsbiology #cognition
How many chromosomes can an animal have?
In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...
Bio-desulfurization of fossil fuels has been a classic env biotech challenge for decades, but the field became stagnant for a while … until @pglekas.bsky.social et al leveraged SynBio tools to develop superior whole-cell catalysts enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... 😱
12.09.2025 01:07 — 👍 9 🔁 4 💬 1 📌 0
This podcast explores TeselaGen software and its role in revolutionizing cell therapy research and development. Discover how this cutting-edge AI-powered platform helps scientists design, build, and optimize biological products:
www.youtube.com/watch?v=O9HE... #biotech #synbio #AI
First @biorxivpreprint.bsky.social from Eda Deniz Erdem's PhD:
"Selective spread of mobile antibiotic resistance genes in wastewater microbiomes driven by the non-antibiotic pharmaceutical carbamazepine"
www.biorxiv.org/content/10.1...
#AMR #microsky
Deciphering microbial spatial organization: insights from synthetic and engineered communities url: academic.oup.com/ismecommun/a...
10.09.2025 19:45 — 👍 58 🔁 16 💬 0 📌 4
Volatile traits expand the microbial playbook
@cp-trendsmicrobiol.bsky.social Opinion from @laurameredith.bsky.social
www.sciencedirect.com/science/arti...
Our paper presents a mathematical and computational analysis of different circuits implemented by means of gene network motifs, including the problem of mass-spaced learning that was recently shown to be present in non-neural cells @koseskalab.bsky.social @jgojalvo.bsky.social
10.09.2025 17:37 — 👍 7 🔁 2 💬 0 📌 0
Happy to share the published version of our genetic toolbox, EASY-edit, for simple, flexible and efficient targeted editing in E. coli!
Feel free to to try it, we can send strains and plasmids!
academic.oup.com/nar/article/...
The use of evolutionary algorithms offer an interesting advantage for optimising #synbio designs: exploring non-intuitive solutions. We showed this at ALIFE 2023 (paper linked) and will again at #ALIFE 2025 next month! direct.mit.edu/isal/proceed...
10.09.2025 09:49 — 👍 5 🔁 2 💬 0 📌 0![FIG. 3: Time lapse visualizations of a two player coordination game with payo matrix A = [10 5; 510]. The images show the spatial con guration (lattice size L = 256) at t = 0246810 with dt = 005. White corresponds to player 1 and black is player 2. Starting from well mixed initial condition, initial fraction of player 1 is 05, the two players separate into domains whose characteristic length scales (patch size) grow over time.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:pdvoxeret2wq6tzu7gxy7eeh/bafkreieb2n73jcc6srh7s455dc3ztsitbvwe7542vzhjxlc3su3x4l3lpi@jpeg)
FIG. 3: Time lapse visualizations of a two player coordination game with payo matrix A = [10 5; 510]. The images show the spatial con guration (lattice size L = 256) at t = 0246810 with dt = 005. White corresponds to player 1 and black is player 2. Starting from well mixed initial condition, initial fraction of player 1 is 05, the two players separate into domains whose characteristic length scales (patch size) grow over time.
New preprint bubbling up in our group for a while:
"Phase separation and coexistence in spatial coordination games between microbes"
www.biorxiv.org/content/10.1...
Generalizes findings of phase separation in microbes using T6SSs to a broad range of interaction mechanisms.
Li + Steinbach et al.
