Permutation-replication-composition all-in-one

This is the permutation cycle 1 – > 2 – > 3 – > 4 – > 5 – > 6 – > 7 – > 8 – > 1 which is replicated and composed with itself in the same time.

pwheel_8_compo

Done with pwheel_8_compo.mol from the chemlambda repo, and with quiner.sh, in the deterministic variant (all weights set to 0. The result is a pair of cycles 1 – > 3 – > 5 – > 7 – > 1  and 2 – > 4 – > 6 – > 8 – > 2.

See other plays with permutations in the

https://plus.google.com/collection/UjgbX

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The mesh is the computer

The article

The mesh is a network of microtubule connectors that stabilizes individual kinetochore fibers of the mitotic spindle

announces the discovery of a new structure in the cell: the mesh.

From the abstract:

Kinetochore fibers (K-fibers) of the mitotic spindle are force-generating units that power chromosome movement during mitosis. K-fibers are composed of many microtubules that are held together throughout their length.
Here, we show, using 3D electron microscopy, that K-fiber microtubules (MTs) are connected by a network of MT connectors. We term this network ‘the mesh’.
The K-fiber mesh is made of linked multipolar connectors. Each connector has up to four struts, so that a single connector can link up to four MTs.  […]
Optimal stabilization of K-fibers by the mesh is required for normal progression through mitosis.
We propose that the mesh stabilizes K-fibers by pulling MTs together and thereby maintaining the integrity of the fiber. “

My speculation is that the mesh has not only the role of a scaffold for the microtubule structure.

Together with the microtubules and with some other (yet undiscovered or, on the contrary, very well known) parts, this is the computer.

 

F1.large

DNA, which fascinates us, is more like a memory device.

But the computation may be as in  chemlambda. The dynamical reorganization of the mesh-microtubule-other proteins structure is very much resembling to a chemlambda molecule (or even to a chemlambda quine.

20_20_hyb

 

Mentioned this here, because there is an evocative image

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Inceptionism: an AI built on pragmatic principles turns out to be an artificial Derrida

Not willing to accept this, now they say that the artificial neural network dreams. Name: Google Deep Dream.

The problem is that the Google Deep Dream images can be compared with dreams by us humans.  Or in the general case of an automatic classifier of big data there is no term of comparison.  How can we, the pragmatic scientists, know that the output obtained from data (by training a neural network on other data) is full of dreamy dog eyes or not?

If we can’t trust the meaning obtained from big data, by pragmatic means, then we might as well renounce at analytic philosophy and turn towards continental (so called) philosophy.

That is seen as not serious, of course, which means that the ANN dreams, whatever that means. With this stance we transform a  kick in the ass of our most fundamental beliefs into a perceived progress.

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The inner artificial life of a cell, a game proposal

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.

For example:
– 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.

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Artificial life which can be programmed

Artificial life

3_27_quine_huge_short

which can be programmed

ttttt

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An apology of molecular computers and answers to critics

This is how a molecular computer would look like, if seen with a magically powerful microscope. It is a single molecule which interacts randomly with other molecules, called “enzymes”, invisible in this animation.

molecular_computer_new

There is no control over the order of the chemical reactions. This is the idea, to compute without control.

The way it works is like this: whenever a reaction happens, this creates the conditions for the next reaction to happen.

There is no need to use a supercomputer to model such a molecule, nor is it reasonable to try, because of big number of the atoms.

It is enough instead to find real molecular assemblies for nodes, ports and bonds, figured here by colored circles and lines.

The only computations needed are those for simulating the family of rewrites – chemical reactions. Every such rewrite involves up to 4 nodes, therefore the computational task is handy.

Verify once that the rewrites are well done, independently of the situation where you want to apply them, that is all.

Once such molecular compounds are found, the next task is to figure out how to build (by chemical reactions) such molecules.

But once one succeeds to build one molecule, the rest is left to Nature way of computing: random, local, asynchronous.

From this stage there is no need to simulate huge molecules in order to know they work. That is something given by the chemlambda formalism.

It is so simple: translate the rewrites into real chemistry, they are easy, then let go the unneeded control from that point on.

This animation is a screencast of a part of the article Molecular computers
http://chorasimilarity.github.io/chemlambda-gui/dynamic/molecular.html
and everything can be validated (i.e. verified by your own) by using the chemlambda repository
https://github.com/chorasimilarity/chemlambda-gui/tree/gh-pages/dynamic

Now I’ll pass to a list of critics which, faced with the evidence, they look uninformed:
1. Chemlambda is one of those rewriting systems everybody knows. Ignorant claim, while it is true that some rewrites appear all over the place, from string theory to knot theory to category theory to geometry of interaction, the family of graphs considered is not the same, because those graphs are purely combinatorial object and they don’t need a global embedding, like all other formalism do, in a schematic space-time. Moreover, the choice of the rewrites is such that the system works only by local rewriting and no global control on the cascade of rewrites. No other formalism from the family does that.

2.  Is well known that all this is already done in the category theory treatment of lambda calculus.

False, if one really reads what they do in category theory with lambda calculus, then one figures quick that they can’t do much for untyped lambda beta calculus, that is without eta reduction. This is mentioned explicitly in Barendregt, for example, but the hype around categories and lambda calculus is so pervasive that people believe more than what actually is.

3.  Chemical computing is old stuff: DNA computing, membrane computing, the chemical abstract machine, algorithmic chemistry.

Just because it is chemical computing, it does not mean that it is in the family mentioned.

The first name of chemlambda was “chemical concrete machine” and there there are comparison with the chemical abstract machine
http://arxiv.org/abs/1309.6914
(btw I see that some people discover now “catalysts” without credits in the written papers)
The cham is a formalism working with multisets of molecules, not with individual ones, and the computation is done by what corresponds to lab operation (splitting a solution in two, heating, cooling, etc)
The membrane computing work is done around membranes which enclose containers of multisets of molecules, the membrane themselves being some abstract concepts, of a global nature, whil ein reality, as well as in chemlambda, everything is a molecule. Membranes exist in reality but they are made of many molecular compounds.
DNA computing is an amazing research subject, which may be related to chemlambda if there is a realization of chemlambda nodes, ports and bonds, but not otherwise, because there is not, up to my knowledge, any model in DNA computing with the properties: individual molecules, random reactions, not lab operations.
Algorithmic chemistry is indeed very much related to chemlambda, by the fact that it proposes a chemical view on lambda calculus. But from this great insight, the paths are very different. In algorithmic chemistry the application operation from lambda calculus represents a chemical reaction and the lambda abstraction signals a reactive site. In chemlambda the application and lambda abstraction corresponds to atoms of molecules. Besides, chemlambda is not restricted to lambda calculus, only some of the chemlambda molecules can be put in relation with lambda terms, but even for those, the reactions they enter don’t guarantee that the result is a molecule for a lambda term.

Conclusion: if you are a chemist, consider chemlambda, there is nothing like it already proposed. The new idea is to let control go and instead chain the randomly appearing reactions by their spatial patterns, not by lab operations, nor by impossibly sophisticated simulations.
Even if in reality there would be more constraints (coming from the real spatial shapes of the molecules constructed from these fundamental bricks) this would only influence the weights of the random encounters with the enzymes, thus not modifying the basic formalism.
And if it works in reality, even for only situations where there are cascades of tens of reactions, not hundreds or thousands, even that would be a tremendous advance in chemical computing, when compared with the old idea of copying boolean gates and silicon computers circuits.

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Appeared also in the chemlambda collection microblog

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What if… it can be done? An update of an old fake news post

In May 2014 I made a fake news post (with the tag WHAT IF) called Autodesk releases Seawater. It was about this big name who just released a totally made up product called Seawater.

“SeaWater is a design tool for the artificial life based decentralized Internet of Things.”

In the post it is featured this picture

[source]

scoop-of-water-magnified-990x500… and I wrote:

“As well, it could be  just a representation of the state of the IoT in a small neighbourhood of you, according to the press release describing SeaWater, the new product of Autodesk.”

Today I want to show you this:

3_27_quine

or better go and look in fullscreen HD this video

The contents is explained in the post from the microblogging collection chemlambda

27 microbes. “This is a glimpse of the life of a community of 27 microbes (aka chemlambda quines). Initially the graph has 1278 nodes (atoms) and 1422 edges (bonds). There are hundreds of atoms refreshed and bonds made and broken at once.”

Recall that all this is done with the most simple algorithm, which turns chemlambda into an asynchronous graph rewrite automaton.

A natural development would be to go further, exactly like described in the Seawater post.

Because it can be done :)

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