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Neurons improved. Along the idea that the network is the computation. I used the mol file neuron_10X10_2_S.mol which will be available after updates of the library of chemlambda molecules [1].

[1] Library of chemlambda molecules
https://github.com/chorasimilarity/chemlambda-gui/tree/gh-pages/dynamic/mol

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The Seed, later. Continuation of the post "CryptNet's true desire is the Seed" [1]. If you look in the chemlambda repo [2], there is a folder "test", containing a variant of the (deterministic) program which spits out molecules (mol files) instead of js animations. This can be used for quickly advance to later states of the evolving molecule.

The original use of the test folder is for comparisons of my version with chemlambda-hask [3], i.e a Haskell version done by synergistics.

[1] CryptNet's true desire is the Seed
https://plus.google.com/u/0/+MariusBuliga/posts/6zKCN4fM7jp

[2] Chemlambda repository (the active branch)
https://github.com/chorasimilarity/chemlambda-gui/tree/gh-pages/dynamic

[3] Chemlambda-hask (by synergistics)
https://github.com/synergistics/chemlambda-hask
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Mother of dodecahedra uses the same molecule as [1]. While in that simulation you can clearly see the 4 dodecahedra generated, here is another random reduction with space constraints, along the line of [2] or [3].

[1] Dodecahedra
https://plus.google.com/u/0/+MariusBuliga/posts/aTwA8EnFDcp

[2] Polyribosome, first attempt
https://plus.google.com/u/0/+MariusBuliga/posts/UQZ82FaiEuU

[3] Infected tape duplication
https://plus.google.com/u/0/+MariusBuliga/posts/5635raGKZvE
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Aggressive growth obtained from a 6 nodes molecule called stree.mol, with minimal effects postprocessing, because some applications of chemlambda may be worrying, see [1].

This molecule is related to the S combinator applied to itself. It will be added to the library of chemlambda molecules [2], along with the more recent molecules, at the next update.

[1] Pharma meets the IoT
https://plus.google.com/u/0/+MariusBuliga/posts/SA2t4bvSoiu

[2] Library of chemlambda molecules
https://github.com/chorasimilarity/chemlambda-gui/tree/gh-pages/dynamic/mol
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Pharma meets the Internet of Things, some commented references for this future trend. Use them to understand

[0] After the IoT comes Gaia
https://chorasimilarity.wordpress.com/2015/10/30/after-the-iot-comes-gaia/



There are two realms of computation, which should and will become one: the IT technology and biochemistry.

General stuff

The notion of computation is now well known, we speak about what is computable and about various models of computation (i.e. how we compute) which always turned out to be equivalent in the sense that they give the same class of computable things (that's the content of the Church-Turing thesis).

It is interesting though how we compute, not only what is computable.

In IT perhaps the biggest (and socially relevant) problem is
decentralized asynchronous computing. Until now there is no really working solution of a model of computation which is:
- local in space (decentralized)
- local in time (asynchronous)
- random (no pre-imposed hierarchy or external authority which forces coherence)

In biochemistry, people know that we, anything living, are molecular assemblies which work:
- local in space (all chemical interactions are local)
- local in time (there is no external clock which synchronizes the reactions)
- random (everything happens without any external control)


Useful links for an aerial view on molecular computing, seen as the biochemistry side of computation:

[1] https://www.britannica.com/technology/DNA-computing

Some history and details provided. Quote from the end of the section "Biochemistry-based information technology"

"Other experiments have shown that basic computations may be executed using a number of different building blocks (for example, simple molecular “machines” that use a combination of DNA and protein-based enzymes). By harnessing the power of molecules, new forms of information-processing technology are possible that are evolvable, self-replicating, self-repairing, and responsive. The possible applications of this emerging technology will have an impact on many areas, including intelligent medical diagnostics and drug delivery, tissue engineering, energy, and the environment."



[2] http://www.owlnet.rice.edu/~Cyrus.Mody/MyPubs/Molecular%20Electronics.pdf

A detailed historical view (written in 2000) of the efforts towards "molecular electronics". Mind that's not the same subject as [1], because the effort here is to use biochemistry to mimic silicon computers. While [1] also contains such efforts (building logical gates with DNA, etc), DNA computing does propose also a more general view: building structure from structure as nature does.

[3] https://www.extremetech.com/tag/molecular-computer

Two easy to read articles about real applications of molecular computing:
- "Microscopic machine mimics the ribosome, forms molecular assembly line"
- "Biological computer can decrypt images stored in DNA"



[4] https://www.technologyreview.com/s/601842/inside-genomics-pioneer-craig-venters-latest-production/

Article about Craig Venter from 2016, found by looking for "Craig Venter Illumina". Other informative searches would be "Digital biological converter" or anything "Craig Venter"

[5] https://www.ted.com/talks/lee_cronin_print_your_own_medicine/transcript?language=en

Interesting talk by an interesting researcher Lee Cronin


[6] The Molecular Programming Project http://molecular-programming.org/

Worth to be browsed in detail for seeing the various trends and results





Sitting in the middle, between biochemistry and IT:




[1] Algorithmic Chemistry (Alchemy) of Fontana and Buss
http://fontana.med.harvard.edu/www/Documents/WF/Papers/alchemy.pdf

Walter Fontana today: http://fontana.med.harvard.edu/www/index.htm


[2] The Chemical Abstract Machine by Berry and Boudol

http://www.lix.polytechnique.fr/~fvalenci/papers/cham.pdf

[3] Molecular Computers (by me, part of an Open Science project, see also my homepage http://imar.ro/~mbuliga/ and the chemlambda github page https://github.com/chorasimilarity/chemlambda-gui/blob/gh-pages/dynamic/README.md )

http://chorasimilarity.github.io/chemlambda-gui/dynamic/molecular.html





On the IT side there's a beautiful research field, starting of course with lambda calculus by Church. Later on this evolved in the direction of rewriting systems, then graph rewriting systems. I can't even start to write all that's done in this direction, other than:

[1] Y. Lafont, Interaction Combinators
http://iml.univ-mrs.fr/~lafont/pub/combinators.ps

but see as well the Alchemy, which uses lambda calculus! 

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Middle of a neural network computation, detail. 
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Maturana, chemlambda quines and the no-semantics point of view In this collection there are many examples of chemlambda quines, which are my proposal for living organisms (ex. [2] where I explain how I discovered the first quine from a lambda term). The following are quotes from [1] which support the views that chemlambda quines are living systems in the sense of Maturana and the "no-semantics" point of view advocated many times, see for ex. [3].

The image, taken from [3], shows a 28-quine with only the bonds which have "meaning" visible. All this changes in time and there is no global semantic decoration (nor DAGs covering all the bonds).


"... if there were a system that is isomorphic to a molecular
autopoietic system but with a different kind of components, that
system would be like a living system in the domain of its components.
Yet, at the same time I think that for that to happen the components
involved would have to operate in the way that molecules operate, and if that were the case then that autopoietic system would operate as a living system"



"The meaning of a word is not in its sound or form, but in the way we
use it as we language it. At the same time processes or entities do
not have meaning in themselves; a particular substance is not a
nutrient but we say it is a nutrient when it participates in some
metabolic process in a cell, and some particular behavior is not
adaptive in itself, but we say as observers that it is adaptive when
we see it to participate in a particular kind of processes that we call
adaptive. When one does not understand this one expects that processes should have meaning or should make relational sense by themselves, and in doing so one confuses domains. Sense and meaning belong to the domain of the commentaries and reflections that an observer makes about what he or she sees."



"Purpose, meaning, value, utility, advantage, importance, regulation,
cause, control … are reflexive commentaries that an observer makes
about what happens in the human sensory-operational-relational space, and are not features or characteristics of any process."

The notions of ultrastability and of dissipative systems do not add to
the understanding of the constitution or of the operation of living
systems. They are interesting notions but even though living systems
may operate as ultrastable and dissipative systems, it is not
ultrastability or dissipative processes which makes them living, it is
their continuous self production as discrete self producing
dynamically closed molecular entities: that is, molecular autopoiesis.



[1] Ultrastability ... Autopoiesis? H.R. Maturana, Cybernetics and Human Knowing. Vol. 18, nos. 1-2, pp. 143-152
https://froese.files.wordpress.com/2013/01/maturana-11-ultrastability-e280a6-autopoiesis-reflexive-response-to-tom-froese-and-john-stewart.pdf

[2] Nothing vague in the "no-semantics" point of view
https://chorasimilarity.wordpress.com/2015/05/04/nothing-vague-in-the-no-semantics-point-of-view/

[3] Ouroboros, the first quine
https://plus.google.com/u/0/+MariusBuliga/posts/Y73GVD2Wt3h
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"CryptNet’s true desire is the Seed —a technology that, in their diabolical scheme, will one day supplant the Feed, upon which our society and many others are founded. Protocol, to us, has brought prosperity and peace—to CryptNet, however, it is a contemptible system of oppression. They believe that information has an almost mystical power of free flow and self-replication, as water seeks its own level or sparks fly upward— and lacking any moral code, they confuse inevitability with Right. It is their view that one day, instead of Feeds terminating in matter compilers, we will have Seeds that, sown on the earth, will sprout up into houses, hamburgers, spaceships, and books—that the Seed  will develop inevitably from the Feed, and that upon it will be founded a more highly evolved society." [Neal Stephenson, The Diamond Age]

The image is a part of the computation of a double exponential.
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Is Gource better? Check out this awesome visualization of the Linux Kernel Development [1], which is made by using Gource [2] [3]. I put it here because it looks that we could use Gource instead of D3.js.

Gource clearly looks like a graph rewrite visualization tool. It is used to show the history of contributions to a project. Instead it could be the history of rewrites, as given by one of the chemlambda programs [4]. Much beter though, because in Gource we can see icons representing the people who made contributions, with the contributions made represented as laser beams from the icon of the contributor to the node which is the contribution. This mechanism could be used to visualize the enzymes from chemlambda!

Anybody willing to give a try? Let me know!



[1] Linux Kernel Development, 1991-2015 (from min 48)
https://youtu.be/5iFnzr73XXk?t=48m30s

[2] gource.io
http://gource.io/

[3] Gource repository
https://github.com/acaudwell/Gource

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

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Disorder from a very regular state. Like the last two animations of random healing grids [1] [2] this is  initially a regular web made of pairs of nodes. This time the randomness of reductions explodes the regular grid.

It happens gradually though, because the pair of nodes are FO and A. The application node A is duplicated by FO (of another pair) and it produces FOE nodes too. These fresh FOE nodes in turn duplicate the FO nodes as well.

You can see in the animation that I "nailed" four nodes from the corners of the initial grid. This is possible because the animation is done from the result of the simulation, which is a javascript file, which we can play with, as explained in [3].

[1] Bigger healing grid
https://plus.google.com/+MariusBuliga/posts/VAX3Wh66Pwf

[2] Random healing grid
 https://plus.google.com/u/0/+MariusBuliga/posts/d1VJP3FtPMi

[3] Playing with a quine while it reduces
https://plus.google.com/+MariusBuliga/posts/dxSQLMsoYHt
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