Alicia
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alicanter.bsky.social
Alicia
@alicanter.bsky.social
55 followers 94 following 5 posts
Interested in living computation, microbial evolution and game theory.
Posts Replies Media Videos
Reposted by Alicia
binomicalabs.org
Apparently an engineering issue with Springer Nature platform is inflating citations for their online journal articles through circular citation links. They were informed by the preprint authors months ago, but nothing's happened so far.

🧪

arxiv.org/abs/2511.01675
Incorrect Citation Association for Articles in Online-Only Springer Nature Journals
We show that citation metrics of journal articles in many of the online-only Springer Nature journals and associated ones are distorted, going back to articles from 2001. We find that most likely due ...
arxiv.org
November 12, 2025 at 7:04 PM
Reposted by Alicia
ricardsole.bsky.social
How “intelligent” is a slime mold? When it solves mazes, it might not be thinking:it’s obeying physics. Our new paper with
@jordiplam.bsky.social shows how it follows a least action principle,letting physics do the job arxiv.org/pdf/2511.08531
@drmichaellevin.bsky.social @docteur-drey.bsky.social
November 12, 2025 at 4:17 AM
Reposted by Alicia
ricardsole.bsky.social
Sunday morining at @sfiscience.bsky.social
November 9, 2025 at 8:20 PM
Reposted by Alicia
drmichaellevin.bsky.social
New preprint:

arxiv.org/abs/2510.19976

"Morphological computational capacity of Physarum polycephalum"

Suyash Bajpai, Aviva Lucas-DeMott, @msahsorin.bsky.social, Philip Kurian
Morphological computational capacity of Physarum polycephalum
While computational capacity limits of the universe and carbon-based life have been estimated, a stricter bound for aneural organisms has not been established. Physarum polycephalum, a unicellular, mu...
arxiv.org
November 10, 2025 at 2:16 PM
Reposted by Alicia
bruceslieberman.bsky.social
If you're a #teacher interested in a great #openaccess write up on reading #phylogenetic trees, check out www.digitalatlasofancientlife.org/learn/system... created by @jonhendricks.bsky.social and Elizabeth Hermsen.
2.1 Reading Trees
Chapter contents: Systematics — 1. Taxonomy — 2. Phylogenetics —— 2.1 Reading trees ← —— 2.2 Building trees —— 2.3 Character mapping —— 2.4 Phylogenetic trees and classificationParts of a tree A phylo...
www.digitalatlasofancientlife.org
November 11, 2025 at 10:05 PM
Reposted by Alicia
biplabbose.bsky.social
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
Engineering Basal Cognition: Minimal Genetic Circuits for Habituation, Sensitization, and Massed–Spaced Learning
Cognition is often associated with complex brains, yet many forms of learning—such as habituation, sensitization, and even spacing effects—have been observed in single cells and aneural organisms. The...
www.biorxiv.org
October 25, 2025 at 9:45 AM
Reposted by Alicia
stcmicrobeblog.bsky.social
fans of T4P pili (and 'pili pili') take note 👇
#MicroSky
October 13, 2025 at 9:47 PM
Reposted by Alicia
emmseveri.bsky.social
www.biorxiv.org/content/10.1...

#microsky #phagesky #phage
Phages communicate across species to shape microbial ecosystems
Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX ex...
www.biorxiv.org
October 14, 2025 at 6:52 AM
Reposted by Alicia
ricardsole.bsky.social
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...
April 28, 2025 at 10:42 PM
Reposted by Alicia
bstevensonlab.bsky.social
Bacterial two-hybrid systems evolved: innovations for protein-protein interaction research
#MicroSky 🦠
geiselbiofilm.bsky.social George O'Toole (he/him/his) @geiselbiofilm.bsky.social · Sep 16
JB Editor's Choice: Richardson & Pascal do a deep dive into the many iterations of bacterial two-hybrid systems and their uses in bacteria - a must read for those looking at protein-protein interactions.
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology
September 16, 2025 at 12:14 PM
Reposted by Alicia
pierremillard.bsky.social
Overflow metabolism: Why cells waste nutrients—and why it’s not really waste

go.nature.com/4n39Ijw
Overflow metabolism: Why cells waste nutrients—and why it’s not really waste
Cells often appear to waste nutrients by releasing them as useless, and sometimes toxic, by-products—a phenomenon known as overflow metabolism. Far from being mere waste, these molecules also play vit...
go.nature.com
September 14, 2025 at 7:59 PM
Reposted by Alicia
gibbological.bsky.social
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!
The landscape of microbial associations in human cancer
Differences between cancer types, infectious disease, and potential prognostic markers are uncovered by studying microbes within cancer DNA.
www.science.org
September 12, 2025 at 7:40 PM
Reposted by Alicia
chenxinli2.bsky.social
Looks interesting: fluorescent proteins being strung together in a fiber as a recording of transcriptional history in cells.
Figure 1 of the preprint (part)
September 13, 2025 at 12:02 PM
Reposted by Alicia
olivia.science
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
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
September 6, 2025 at 8:13 AM
Reposted by Alicia
chenxinli2.bsky.social
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.
September 12, 2025 at 12:01 PM
alicanter.bsky.social
Can engineered genetic circuits reveal principles and constraints of biological cognition?
🧬🦠🖥️ #synbio #systemsbiology #cognition
ricardsole.bsky.social Ricard Solé @ricardsole.bsky.social · Sep 10
Can a single cell learn? Even without a brain, some microbes show simple forms of cognition. Can this basal cognition be engineered? Check our new paper with @jordiplam.bsky.social on the minimal synthetic circuits & their cognitive limits. @drmichaellevin.bsky.social www.biorxiv.org/content/10.1...
September 12, 2025 at 11:07 AM
Reposted by Alicia
charlottewright.bsky.social
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...
Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly
The genome of the Atlas blue butterfly contains ten times more chromosomes than most butterflies, and more than any other known diploid animal. Wright et al. show that this extraordinary karyotype is ...
tinyurl.com
September 11, 2025 at 3:22 PM
Reposted by Alicia
vdlorenzo.bsky.social
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/... 😱
Boosting Dibenzothiophene Biodesulfurization Through Implantation of a Refactored DBT Pathway in a Tailored Pseudomonas putida Chassis
This study engineered a Pseudomonas putida strain to efficiently remove sulfur from dibenzothiophene (DBT) by reordering and optimising the dsz operon from Rhodococcus qingshengii IGTS8, enhancing ca...
enviromicro-journals.onlinelibrary.wiley.com
September 12, 2025 at 1:07 AM
Reposted by Alicia
teselagen.bsky.social
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
Revolutionizing Cell Therapy with AI
YouTube video by TeselaGen Biotechnology, Inc.
www.youtube.com
September 9, 2025 at 6:25 PM
Reposted by Alicia
ulikluemper.bsky.social
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
Selective spread of mobile antibiotic resistance genes in wastewater microbiomes driven by the non-antibiotic pharmaceutical carbamazepine
Carbamazepine (CBZ), a widely used anticonvulsant, is a persistent aquatic micropollutant that withstands biodegradation and accumulates in wastewater-impacted environments. While non-antibiotic pharm...
www.biorxiv.org
September 10, 2025 at 8:45 AM
Reposted by Alicia
yschaerli.bsky.social
Deciphering microbial spatial organization: insights from synthetic and engineered communities url: academic.oup.com/ismecommun/a...
Deciphering microbial spatial organization: insights from synthetic and engineered communities
Abstract. Microbial communities are frequently organized into complex spatial structures, shaped by intrinsic cellular traits, interactions between communi
academic.oup.com
September 10, 2025 at 7:45 PM
Reposted by Alicia
evolvedbiofilm.bsky.social
Volatile traits expand the microbial playbook

@cp-trendsmicrobiol.bsky.social Opinion from @laurameredith.bsky.social

www.sciencedirect.com/science/arti...
September 11, 2025 at 6:19 AM
Reposted by Alicia
ricardsole.bsky.social
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
September 10, 2025 at 5:37 PM
Reposted by Alicia
mlejars.bsky.social
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/...
EASY-edit: a toolbox for high-throughput single-step custom genetic editing in bacteria
Abstract. Targeted gene editing can be achieved using CRISPR–Cas9-assisted recombineering. However, high-efficiency editing requires careful optimization f
academic.oup.com
September 10, 2025 at 1:02 PM
Reposted by Alicia
angelgm.bsky.social
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...
Computational evolution of gene circuit topologies to meet design requirements
Abstract. The design and implementation of synthetic gene regulatory networks that compute is a central effort to synthetic biology. Genetic components are arranged into circuits to perform pre-define...
direct.mit.edu
September 10, 2025 at 9:49 AM