All posts by chorasimilarity

can do anything

I deleted the Google+ chemlambda collection

This 400 posts collection, 60 000 000 views,  was as much a work of research popularization as a work of art. Google cannot be trusted with keeping high density data (scientific, art, etc). Read here about this.


It pained me to delete it, but it had to be done. It was harder than when I quit Facebook, Twitter.

The collection and richer material exist, I have them. Still, the Github repository is available, as well as the demos. For example, the dodecahedron multiplication animation used as background for a conference site of was made from a screencast of a d3.js which can be seen  here.


Mail me for access to more material. I have to think what I am going to do with them, long term. Meanwhile look for updates at my professional homepage or the alternative page.


John Baez’ Applied Category Theory 2019 post uses my animation without attribution [updated]

The post, dated Oct 2, appears at John Baez Azimuth blog. Here is what I see today Oct 4th:


UPDATE: now there is a link to the chemlambda repository, but see also the comments, there and here. The real problem is related to the attitude concerning  Open Science. Link to archived post.

This is the gif which illustrates the chemlambda github repository.

The original animation appeared for the first time in the chemlambda collection post Metabolism as failed replication. The later post (Sept 2016) contains more about this idea and useful links.

[ UPDATE: Recently, I deleted the chemlambda collection. The content of it will become public again in a new form. Meanwhile mail me for access. However, the github repo, libraries, demos and articles are public.]

The chemlambda molecule which is used is available at the chemlambda library of molecules, as tape_long_4653_2.mol . You can download the simulation itself (which was used to make the animation) from the Chemlambda collection of simulations at Figshare, the file tape_long_4653_2.js.

The last time when one of my animations was used withot attribution, the situations was quickly solved.  I explained then that the chemlambda project is an Open Science project and that correct attribution is what is fair to do.

Now, I would expect from an academic researcher more.

Anyway, again the magic of chemlambda strikes. Let me tell you what the animation is really about. Metabolism and replication are two fundamental ingredients of life. Which came first? Are these independent?  I prepared the molecule and experimented with it to show that (in the artificial toy chemistry chemlambda) metabolism and replication may be related, in the sense that metabolism may appear as failed replication.

The molecule in question is a “tape”, topologically the same as a DNA loop. On the tape there is a very small part which triggers the duplication of the tape molecule. The duplication works perfectly, there are several examples in the chemlambda collection. But this time I took a tape which duplicates without problems and I modified it in a single place. The result is a failed duplication which is spectacular in the sense that the tape molecule produces a number of disconnected graphs (i.e. other molecules), some of them are quines.




Torsor rewrites

With the notation conventions from em-convex, there are 3 pairs of torsor rewrites.  A torsor, figured by a fat circle here, is a term T of type  T: E \rightarrow E \rightarrow E \rightarrow E

with the rewrites:




Finally, there is a third pair of rewrites which involve terms of the form \circ A for A: N


The rewrite T3-1 tells that the torsor is a propagator for \circ A, the rewrite T3-2 is an apparently weird form of a DIST rewrite.

Now, the following happen:

  • if you add the torsor rewrites to em-convex then you get a theory of topological groups which have a usual, commutative smooth structure, such that the numbers from em-convex give the structure of 1-parameter groups
  • if you add the torsor rewrites to em, but without the convex rewrite then you get a more general theory, which is not based on 1-parameter groups,  because the numbers from em-convex give a structure more general
  • if you look at the emergent structure from em without convex, then you can define torsor terms whch satisfy the axioms, but of course there is no em-convex axiom.

Lots of fun, this will be explained in em-torsor soon.



Authors: hodl your copyright or be filtered

For me this is the only sane reaction to the EU Copyright Directive. The only thing to do is to keep your copyright. Never give it to another. You can give non-exclusive rights of dissemination, but not the copyright of your work.

So: if you care about your piece of work then hodl copyright, if you don’t care about it (produced it to satisfy a job demand, for example) then proceed as usual, is trash anyway.

For my previous comments see this and this.

If you have other ideas then share them.


The second Statebox Summit – Category Theory Camp uses my animation

with attribution.

UPDATE: the post was initially written as a reaction to the fact that the Open Science project chemlambda needs attribution when some product related to it is used (in this case an animation obtained from a dodecahedron molecule which produces 4 copies; it works because it is a Petersen graph). As it can be seen in the comments everything was fixed with great speed, thank you Jelle. Here’s the new page look

Screenshot from 2018-09-09 15:18:06.png

Wishing the best to the participants, I’d like to learn more about Holochain in particular.

The rest of the post follows. It may be nice because it made me think about two unrelated little facts: (1) I was noticed before about the resemblance between chemlambda molecules and the “vajra chains” (2) well, I CHING hexagrams structure and rewrites are close to the two families of chemlambda rewrites, especially as seen in the “genes” shadow of a molecule. So putting these two things together, stimulated to find an even more halucinatory application of chemlambda, I arrived to algorithmic divination. Interested? Write to me!


I hope they’ll fix this, the animation is taken probably from the slides I prepared for TED Chemlambda for the people (html+js).

Here’s a gif I made from what I see today Saturday 20:20 Bucharest time.


Otherwise I’m interested in the subject and open to discussions, if any which is not category theory PR, but of substance.

UPDATE: second thoughts

  • the halucinatory power of chemlambda manifests again 🙂
  • my face is good enough for a TED conference (source), now my animation is good for a CT conference, but not my charming personality and ideas
  • here is a very lucrative idea, contact me if you like it,  chemlambda OS research could be financed from that: I was notified about the resemblance between chemlambda molecules and the vajra chains of awareness, therefore what about making an app which would use chemlambda as a divination tool? Better than a horoscope, if well made, huge market. I can design some molecules and the algorithm for divination.

The mistery of dissipation and hamiltonian who share the same mathematical formalism

I love so much the  “Transparency is better than trust” idea  that I put it on the top of my page.  Like I did for em, I want to announce the start of a new draft where is formulated a general mathematical treatment which aims to solve a growing collection of coincidences between dissipation as treated in convex analysis and the hamiltonian formalism.

This form of dissipation function, discovered by De Saxce, called by him “bipotential”, shares some very intriguing features with hamiltonians. In past articles about the mathematical treatment of bipotentials these features were noted as curiosities (for example the ressemblance between convex lagrangian covers (remark 6.1 here) and lagrangian fibrations from quantization).

But with formalism from the draft, which extends the one from arXiv.1807.10480, indeed dissipation will be treated with the same mathematical formalism as hamiltonians (from a stochastic point of view).

I don’t say that dissipation is a sort of hamiltonian, mind you, I say that once again nature likes to repeat a winning pattern, in a different context.

So follow that link from time to time, because I am going to update it until it reaches the final form.

Comments welcome!

On the origin of artificial species

I read Newton but not Darwin’s On the origin of species, until now. Chance was that, looking for new things to read in the tired landscape of libraries, I felt on a translation of Darwin’s famous book. Is wonderful.

While reading it I was striken by the fact that genetics was unknown to him, Though, what a genius. I’m almost a professional reader (if you understand what I mean) and I passed by Newton, as I said, in original, by some of the ancient greek philosophers (an even greater experience). Now, as I’m reading Darwin in a translation, I am aware of the translation limitations but I can’t stop to think that, before reading it, I lived this experience.

The main gain of the chemlambda project was for me the building of a world which undoubtedly has an autonomous existence, whatever your opinions may be. In my dreams, as I read Darwin, I see a rewrite of this book based on the observations of the chemlambda’s 427 valid molecules (eliminate from the chemlambda library of molecules those from this list, what you get are all valid molecules).

What I don’t see, perhaps because of my ignorance, is that the logical last implication of Darwin’s work is that the theory of evolution refutes any semantics, in particular the semantics of species.

It is in probabilities the possible blend of individual evolution and species evolution into a new theory which is not unlike the evolution theory, but as much as different as possible from any actual political theory. A dream, of course, a Hari Seldon dream 🙂 because probabilities look as much as semantics as space.

Who really knows? Funding bodies, especially these private high risk takers, don’t seem to have the balls to risk in the field of fundamental research, the most riskier activity ever invented. Who knows? I may know, if this little cog in the evolution machine ever had a chance to.