Suppose this. What then?

 I want to understand how a single molecule interacts with others, chemically. You have to agree that this is a worthy goal.
What I say is this. By using a collection of made up molecules and made up chemical reactions, I proved that by the stupid deterministic algorithm I can do anything and by experiment that it seems that if I design well the initial molecule then I can do anything I proposed myself doing, with the stupid random algorithm (a molecule which encounters randomly enzymes which rewrite it by chemical reactions). For me, the molecule is not the process, it is just a bunch of atoms and bonds. But I proved I can do anything with it, without any lab supervision.Which is relevant because any real cell does that. It has no supervision, nor goals, nor understanding, is nothing else than a collection of chemicals which interact randomly.

My hypothesis is the following. There is a transformation from the made up chemlambda molecules, which TRANSFORMS:
– node into real molecule
– port into real molecule
– bond into real molecule

and some other real molecules called here “enzymes”, one per any type of graph rewrite

such that

– graph rewrite G which replaces this configuration LT of two nodes and 1 bond  into that  RT configuration TRANSFORMS into  the chemical reaction between enzyme G and the transformation of LT into real chemicals, which gives the transformation of RT into real chemicals and the enzyme G (perhaps carrying away some other reaction products, to have conservation of # atoms)

The argument for that hypothesis is that the rewrites are so simple, compared with real chemistry of biomolecules, that there have to exist such reactions.

This is explained in the Molecular computers
http://chorasimilarity.github.io/chemlambda-gui/dynamic/molecular.html

Suppose that the hypothesis is confirmed. Either by identifying the TRANSFORM from scratch (i.e. by using chemistry knowledge to identify classes of reactions and chemicals which can model chemlambda), or by finding the enzymes G and the real molecules corresponding to node, port and bond in some fundamental biochemical processes (that would be even more wonderful).

Suppose this. What then?

Then, say I have the goal to design a molecule which does something inside a cell, when injected in the body. It does it by itself, in the cell medium. What it does can always (or in principle) be expressed as an algorithm, as a computation.

I use chemlambda and TRANSFORM to design the molecule and check that once I have it, it does the job. It is of course a problem to build it in reality, but for this I have the printer of Craig Venter, the digital biological converter https://youtu.be/DVL1nL3SU6I .

So I print it and that’s all. When injected in the body, once arrived in the cell, it does the job.

Other possibilities would open in the case some formalism like chemlambda (i.e. using individual molecules and rewrites, along with trivial random algorithms) is identified in real biochemistry. This would help enormously the understanding of biochemical processes, because instead of working empirically, like now when we work at the level of functions of molecules (knowing well that the same molecule does different things in different contexts and that molecule-function association is very fragile in biology), we might work inversely, from using functions as black boxes to being able to build functions. Even to go outside functions and understand chemistry as computation directly, not only as a random medium for encoding our theoretical notions of computation.

See more about this at the chemlambda index
http://chorasimilarity.github.io/chemlambda-gui/index.html

_________________________________________________________________

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s