Tag Archives: chemical computing

Molecular computers in real life

A molecular computer [1]  is a single molecule which transforms into a predictable another one, by a cascade of random chemical reactions mediated by a collection of enzymes, without any external control.

composite_2

We could use the artificial chemistry chemlambda to build real molecular computers. There is a github repository [2] where this model is implemented and various demos are available.

By using molecular bricks which can play the role of the basic elements of chemlambda we can study the behaviour of real molecules which suffer hundreds or thousands of random chemical reactions, but without having to model them on supercomputers.
A molecule designed like this will respect for a while the chemlambda predictions… We don’t know for how much, but there might be a window of opportunity which would allow a huge leap in synthetic biology. Imagine instead of simple computations with a dozen of boolean gates, the possibility to chemically compute with recursive but not primitive recursive functions.

More interesting, we might search for chemlambda molecules which do whatever we want them to do. We can build arbitrarily complex molecules, called chemlambda quines, which have all the characteristics of living organisms.

We may dream bigger. Chemlambda can unite the virtual and the real worlds… Imagine a chemical lab which takes as input a virtual chemlambda molecule and outputs the real world version, much like Craig Venter’s printers. The converse is a sensor, which takes a real chemical molecule, compatible with chemlambda and translates it into a virtual chemlambda molecule.

Applications are huge, some of them beneficial and others really scary.

For example, you may extend your immune system in order to protect your virtual identity with your own, unique antibodies.

As for using a sensor to make a copy of yourself, at the molecular level, this is out of reach in the recent future, because the real living organism works by computations at a scale which dwarfs the human technical possibilities.

The converse is possible though. What about having a living computer, of the size of a cup, which performs at the level of the whole collection of computers available now on Earth? [3]

References:

[1] this is the definition which I use here, taken from the articles Molecular computers and Build a molecular computer (2015)

[2] https://github.com/chorasimilarity/chemlambda-gui/blob/gh-pages/dynamic/README.md

[3] The internet can be your pet

Improve chemical computing complexity by a 1000 times factor, easily

That is, if autonomous computing molecules are possible, as described in the model shown in the Molecular computers.

To be exactly sure about about the factor, I need to know the answer for the following question:

What is the most complex chemical computation done without external intervention, from the moment when the (solution, DNA molecule, whatnot) is prepared, up to the moment when the result is measured?

Attention, I know that there are several Turing complete chemical models of computations, but they all involve some manipulations (heating a solution, splitting one in two, adding something, etc).

I believe, but I may be wrong, depending on the answer to this question, that the said complexity is not bigger than a handful of boolean gates, or perhaps some simple Turing Machines, or a simple CA.

If I am right, then compare with my pet example: the Ackermann function. How many instructions a TM, or a CA, or how big a circuit has to be to do this? 1000 times is a clement estimate. This can be done in my proposal easily.

So, instead of trying to convince you that my model is interesting because is related with lmbda calculus, maybe I can make you more interested if I tell you that for the same material input, the computational output is way bigger than in the best model you have.

Thank you for answering to the question, and possibly for showing me wrong.

___________________________