Concepts: the ideas, in the order to learn them
The map has eight strands, and the order is an argument. Each strand asks a question that can't be asked sensibly until the one before it has an answer.
We start with Orientation because "do cells think?" is a bad first question. Before it, you need to decide what a cell is doing in an explanation, what kind of explanation you want, and how strong a claim has to be before you'd bet on it. Then comes Life at cell scale, because a bacterium lives in a world of diffusion, noise and constant energy bills, and none of what it does makes sense without that. Its first real stake lives here too: the cell has to keep itself going, and that gives "better" and "worse" a meaning that doesn't borrow anything from us.
With the physics and the stakes in hand, Sensing and action can describe the smallest loop worth calling behavior: receptor, signal, motor, move. Memory and learning asks what that loop carries from one moment to the next. Collectives asks what changes when many cells do it together. By now we have capacities on the table, and only now do we ask whether to call them cognition. That's the Cognition debates strand, kept late on purpose so the arguments have evidence to chew on.
The last two strands turn from describing cells to testing and making. Whole-cell program is about how a claim survives rival models and hard experiments. Design is about imagining cells that don't exist yet, and building the ones we can, because a theory you can only read is a theory you've only half tested.
Could the ladder run in a different order?
Maybe. We could have put Cognition debates first and fought over definitions for a hundred pages. We chose to earn the word before arguing about it, and we may be wrong. If you'd order it differently, tell us.
- AOrientationWhat counts as an answer?
- BLife at cell scaleWhat does a cell live in?
- CSensing and actionWhat is the smallest loop of behavior?
- DMemory and learningWhat does the loop carry forward?
- ECollectivesWhat changes with company?
- FCognition debatesWhat should we call all this?
- GWhole-cell programHow does a claim survive?
- HDesignWhat can we build?
A Orientation
B Life at cell scale
- B1 Scale, diffusion, and life at low Reynolds number draft
- B2 Noise and limits of molecular sensing draft
- B3 Nonequilibrium maintenance and energetic cost draft
- B4 Boundary, metabolism, and self-production draft
- B5 Viability and organism-relative normativity draft
- B6 The cell-relative environment draft
C Sensing and action
D Memory and learning
E Collectives
F Cognition debates
- F1 Competing criteria for minimal cognition draft
- F2 Adaptivity, valence, and natural agency draft
- F3 Representation, computation, and dynamical alternatives draft
- F4 Cognition, subjectivity, sentience, and consciousness draft
- F5 Pre-neural cellular capacities draft
- F6 The emergence and diversification of nervous systems draft
G Whole-cell program
- G1 Organism-relative environment, stakes and available action draft
- G2 Actual and possible: the modal status of a claim draft
- G3 Whole-cell modeling draft
- G4 Synthetic tests of whether a retained state matters for viability draft
- G5 Rival models and discriminating interventions draft
- G6 A cumulative cycle of modeling, experiment and rival theory draft
H Design
- H1 Counterfactual biological imagination draft
- H2 Designing organisms and their environments together draft
- H3 Constraints, tradeoffs, and realizability draft
- H4 Inventing observables and experimental worlds draft
- H5 Comparing alternative implementations draft
- H6 Speculative natural history and discovery draft
- H7 Iterative whole-cell design and research proposal draft