The more I learn about biological computing, like, in a random order, about:
- Milner’s bigraphs, or this,
- Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models,
- kappa language,
- Interaction combinators, where you see in figure 2, at page 9, one DIST move and some LOC PRUNING moves,
the more it seems that the chemical concrete machine fits naturally into this. Yes, it is partly a garage lab version of this thread of research, but on the other side it has certain advantages, mainly the following one. It is a “pure” graph rewriting system, freed from any 1D thinking conventions. It is true that in order to compute with it on a silicon computer one needs to rewrite it by adding lots of things on top (for example bigraphs may be a way to formalize a model of computation with graphs, in silico, where we need to manage reaction sites, labels of input and output arrows), not because they are natural, but because of the need to make a humanly comprehensive discourse about that (which brings all the effects of the cartesian disease, see the conclusion of this post) .
Soon, after the start of the academic year, an article will be available on arxiv (and submitted to publication, although I am more and more skeptical about this way of research communication, starting with the ’90s) . There are so many directions of development for the chemical concrete machine, also in parallel with graphic lambda calculus, and also with the initial path, computing with space (i.e. the computational content of emergent algebras).
I don’t feel anymore that what I write here is too abstract for the “applied” researchers in biological computing. No, it turns out some of you have already seen this kind of stuff. The only question is: “does the chemical concrete machine brings anything new”? I think it does, because, as nature, is geometrical and not discourse based.
In conclusion, I look forward for collaborations, academic or not. As you might have noticed, I spend a lot of time with this open notebook/blog for trying to stir open, free share of ideas in fundamental research, which might be also very concretely relevant for the real world. Needless to say I shall benefit from such collaborations, but the converse is also true, if you excuse my self-promotional impulse (again, I heard that the net is not subtle, which I doubt, but let’s suppose so). The idea is that if I can do it alone, then imagine what could we do together.
UPDATE: What do you think about this logo for the chemical concrete machine?