Cellosophical Explorations #1

My first foray into @atproto.science via biology; if you are reading this and you know people I should talk to or handles I should follow on Bluesky (or elsewhere in the ATmosphere), let me know!

All links to articles are to their @semble.so page - I am hoping that those pages will be able to host the full text of the article at some point and once that's available, Semble could also host discussions of said article.

While Cellosophy is meant to be a deep dive into unicellular cognition, I'm aware that the ATmosphere isn't exactly teeming with ideas about how to study cognition in bacteria :) Forget that niche topic; my investigations so far haven't revealed as much biology on the ATmosphere as I might have expected.

Am I not working hard enough?

In any case, I am taking upon myself the responsibility to curate some of the best work in biology that I see being reported in the ATmosphere, and then figure out ways in which the science - not just the reporting of it - can come on ATProto. There are some new developments in synthetic biology that:

I find fascinating irrespective of what they mean for my main project.

Bonus: are relevant to studying unicellular cognition.

Intuitively, it feels obvious that synthetic biology will have a lot to contribute to the study of cognition in micro-organisms. Studying the human mind went hand in hand with studying artificial intelligence; shouldn't studying unicellular cognition should go hand in hand with synthesizing microorganisms who perform specific cognitive functions?

I am trying to learn synthetic biology on the fly as I also try to learn cell biology on the fly. Multiplying two domains of ignorance feels more reasonable than tackling them one by one.

The most interesting new development in synthetic biology that came to my attention is the SpudCell, reported here by @quantamagazine.bsky.social. SpudCell (developed by Kate Adamala and colleagues at the University of Minnesota) represents a landmark advance in synthetic biology because it is the first synthetic cell constructed entirely from scratch using non-living chemical components that completes an entire cell cycle. Here is what makes SpudCell unique:

Bottom-Up Synthesis: Unlike top-down minimal cells (such as JCVI-syn3.0/3A), which rely on stripping down pre-existing, living host bacteria, SpudCell is assembled entirely bottom-up from defined, non-living biochemical parts (lipids, cell-free PURE system, DNA, and enzymes).

Integrated Life Behaviors: While previous bottom-up experiments reconstituted isolated cellular processes (such as transcription or membrane growth), SpudCell links the complete dynamic cycle: active nutrient feeding, membrane growth, internal genome replication, genetically encoded division, and competitive selection.

Complete Schematics: Because every single molecular component of SpudCell is known and defined, there are no mystery genes of unknown function (unlike the ~149 uncharacterized genes in top-down minimal strains).

These are the novelties I understand - there are other unique features I am still struggling to grasp, like the fact that the SpudCell's genome is distributed rather being in a single contiguous chromosome as it is in evolved life: what does that mean informationally? Does the shift in physics mean a difference in information processing?

BTW, there's a @spudcell.bsky.social account, but it hasn't posted anything, so I don't know if the account is going to post about progress in creating Spudcells or something else altogther.

These are the types of questions I would like to explore in future Cellosophical essays. Meanwhile, if you know interesting takes on the Spudcell or other aspects of Synthetic Biology on the ATmosphere do let me know!