The inner life of a cell is an excellent, but passive window
It is also scripted according to usual human expectations: synchronous moves, orchestrated reactions at a large scale. This is of course either something emergent in real life, or totally unrealistic.
As you know, I propose to use the artificial chemistry chemlambda for making real, individual molecular computing devices, as explained in Molecular computers.
But much more can be aimed at, even before the confirmation that molecular computers, as described there, can be built by us humans.
Of course that Nature builds them everywhere, we are made of them. It works without any external control, not as a sequence of lab operations, asynchronously, in a random environment, and it is very hard to understand if there is a meaning behind the inner life of a living cell, but it works nevertheless without the need of a semantics to streamline its workings.
So obvious, however so far from IT way of seeing computation.
Despite the huge and exponential advances in synthetic biology, despite the fact that many of these advances are related to IT, despite that more and more ways to control biological workings, I believe that there has to be a way to attack the problem of computations in biology from the basis. Empirical understanding is great and will fuel for some time this amazing synthetic biology evolution, but why not thinking about understanding how life works, instead of using biological parts to make functions, gates and other components of the actual IT paradigm?
As a step, I propose to try to build a game-like artificial life cell, based on chemlambda. It should look and feel like the Inner life of a cell video, only that it would be interactive.
There are many bricks already available, some molecules (each with its own story and motivation) are in the chemlambda repository, other are briefly described, with animations, in the chemlambda collection.
– a centrosome and the generated microtubules like in
– kinesins as adapted walkers like in
– molecules built from other ones like RNA from DNA
– programmed computations (mixing logic and biologic)
– all in an environment looking somehow like this
Like in a game, you would not be able to see the whole universe at once, but you could choose to concentrate to this part or that part.
You could build superstructures from chemlambda quines and other bricks, then you could see what happens either in a random environment or in one where, for example, reductions happen triggered by the neighbourhood of your
mouse pointer (as if the mouse pointer is a fountain of invisible enzymes).
Videos like this, about the internal working of a neuron
would become tasks for the gamer.