All posts by chorasimilarity

can do anything

How does a zipper logic zipper zip? Bonus: what is Ackermann goo?

Zipper logic is an alternative to chemlambda, where two patterns of nodes, called half-zippers, appear.

It may be more easy to mimic, from a molecular point of view.

Anyway, if you want to have a clear image about how it works then there are two ways to play with zippers.

1. Go to this page and execute a zip move. Is that a zipper or not?

2. Go to the lambda2chemlambda page and type this lambda term

(\h.\g.\f.\e.\d.\c.\b.\a.z) A B C D E F G H

Then reduce it. [There is a difference, because a, b, … h do not occur in A B C D E F so the parser adds a termination node to each of them, so when you reduce it the zipper will zip and then will dissappear.]

You can see here the half-zippers



which are the inspiration of the zippers from zipper logic.

In chemlambda you can also make FI-zippers and FOE-zippers as well, I used this for permutations.

BONUS: I made a comment at HN which received the funny reply “Thanks for the nightmares! 🙂“, so let me recall, by way of this comment, what is an Ackermann goo:

A scenario more interesting than boundless self-replication is Ackermann goo [0], [1]. Grey goo starts with a molecular machine able to replicate itself. You get exponentially more copies, hence goo. Imagine that we could build molecules like programs which execute themselves via chemical interactions with the environment. Then, for example, a Y combinator machine would appear as a linearly growing string [2]. No danger here. Take Ackermann(4,4) now. This is vastly more complex than a goo made of lots of small dumb copies.





Robert Hermann on peer review

The gossip blog “Not even wrong”, not a friend of Open Science, has an update of the post Robert Hermann 1931-2020. Following the update to an older post, the reader is led to some very relevants quotes from Robert Hermann on peer review.

For those who are not aware, Robert Hermann was far ahead of his time not only in the understanding of the geometrical structure of topics in modern physics, but also in his efforts concerning research sharing.

I reproduce the quotes here,  copy-pasted from the sources in the linked comments.

Before that, some very short answers to potential questions you may have:

  • I don’t think bad about American mathematics or physics, on the contrary, the point is that if bad things happen in that strong research community, then it is expected the same or worse in other communities. I believe these opinions of Hermann apply everywhere in the research community, today.
  • Peer review is better than no peer review, but it is worse than validation.
  • Peer reviews are opinions, with  good and bad sides. They are not part of the scientific method.
  • By comparison, the author who makes all the work available (i.e. Open Science) opens the way to the reader to independently validate the said work. This is the real mechanism of the scientific method.

The quotes, from the sources:

[source] … consider these quotes from two letters he published in his 1979 book “Cartanian Geometry, Nonlinear Waves, and Control Theory: Part B”:
“… I am not the only one who has been viciously cut down because I tried to break out of the rigid shell and narrow grooves of American mathematics. … My proposal was to continue my … work with … Frank Estabrook and Hugo Wahlquist of the Jet Propulsion Laboratory. … I most deeply resent the arrogance of the referee #3 toward their work … typical … arrogance of Referee #3 is his blather about the “prematureness” of our work … Now, we are working in a field – nonlinear waves – which is moving extremely rapidly and which has the potential for the most important applications, ranging from … Josephson junction to … fusion … and I am supposed to sit back and wait for Professor Whosits to tell me when he thinks problems are “mature”…
I sent the papers he mentions to very few people … I am also interested to note that he did look at them, since there is considerable overlap in methodology with a recent paper by one of his students, with no mention of my papers in his bibliography …
any money spent by NSF on a Mathematics Research Institute would be down the proverbial rat hole – it would only serve to raise Professor Whosits’ salary and make him ever more arrogant. It would do more good to throw the money off the Empire State Building: at least there is a chance it would be picked up and used creatively by a poor, unemployed mathematician …
This issue transends my own personal situation …
Most perversely, the peer review system … works as a sort of Gallup poll to veto efforts by determined individuals … As budgets have tightened, the specialists fight more and more fiercely to keep what little money is available for their own interests. Thus, people with a generalist bent are driven out …”.

[source] … Hermann said in letters published in his 1979 book “Cartanian Geometry, Nonlinear Waves, and Control Theory: Part B”:
“… In 1975 … I had essentially quit my academic job at Rutgers (so I could do my research full time), and my main support came from Ames Research Center (NASA) for my work on control theory. I was also starting a publishing company, Math Sci Press, writing books for it to hold out the hope that, some day, I would get off this treadmill of endless grant proposals. (Unfortunately, it is still [March 1979] at best bearly breaking even.) …
Ever since I lost my ONR grant in 1970, thanks to Senator Mansfield, I have been trying to persuade NSF … that my work on the differential geometric foundations of engineering and physics is worthy of their support … I see my colleagues who stay within the disciplinary “clubs” receiving support much more readily … Thanks to Freedom of Information, I finally see what the great minds of my peers object to, and I see nothing but vague hearsay, bitchiness, and plain incompetence in reviewing … specialized cosed shops that blatantly discriminate against the sort of … work that I do.”


Parser gives fun arrow names

Not yet released with modifications, but the lambda2chemlambda parser can be made to give fun arrow names. Like for example the term

((\g.((\x.(g (x x))) (\x.(g (x x))))) (\x.x))

which is the Y combinator applied to id, becomes the mol

FROUT [^L [((\g. [((\g [((\^L [((\g.((\x. [((\g.((\x [((\g.((\^FO [((\g [((\g.((\x.(g [((\g.((\x.(g*^A [((\g.((\x.(g [((\g.((\x.(g@( [((\g.((\x.(g@^FO [((\g.((\x [((\g.((\x.(g@(x [((\g.((\x.(g@(x*^A [((\g.((\x.(g@(x [((\g.((\x.(g@(x@x [((\g.((\x.(g@(x@^Arrow [((\g.((\x.(g@(x* [((\g.((\x.(g@(x@x^Arrow [((\g.((\x.(g@(x@ [((\g.((\x.(g@(^Arrow [((\g.((\x.(g@ [((\g.((\x.(^Arrow [((\g.((\x.( [((\g.((\x.^Arrow [((\g.((\ [((\g.((^A [((\g.(( [((\g.((\x.(g@(x@x)))@( [((\g.((\x.(g@(x@x)))@^L [((\g.((\x.(g@(x@x)))@(\x. [((\g.((\x.(g@(x@x)))@(\x [((\g.((\x.(g@(x@x)))@(\^Arrow [((\g.((\x.(g* [((\g.((\x.(g@(x@x)))@(\x.(g^A [((\g.((\x.(g@(x@x)))@(\x.(g [((\g.((\x.(g@(x@x)))@(\x.(g@( [((\g.((\x.(g@(x@x)))@(\x.(g@^FO [((\g.((\x.(g@(x@x)))@(\x [((\g.((\x.(g@(x@x)))@(\x.(g@(x [((\g.((\x.(g@(x@x)))@(\x.(g@(x*^A [((\g.((\x.(g@(x@x)))@(\x.(g@(x [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x [((\g.((\x.(g@(x@x)))@(\x.(g@(x@^Arrow [((\g.((\x.(g@(x@x)))@(\x.(g@(x* [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x^Arrow [((\g.((\x.(g@(x@x)))@(\x.(g@(x@ [((\g.((\x.(g@(x@x)))@(\x.(g@(^Arrow [((\g.((\x.(g@(x@x)))@(\x.(g@ [((\g.((\x.(g@(x@x)))@(\x.(^Arrow [((\g.((\x.(g@(x@x)))@(\x.( [((\g.((\x.(g@(x@x)))@(\x.^Arrow [((\g.((\x.(g@(x@x)))@(\ [((\g.((\x.(g@(x@x)))@(^Arrow [((\g.((\x.(g@(x@x)))@ [((\g.(^Arrow [((\g.( [((\g.^Arrow [((\ [((^A [(( [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@( [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@^L [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@(\x. [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@(\x [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@(\^Arrow [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@(\x [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@(\x.x^Arrow [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@(\x.x [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@(\x.^Arrow [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@(\ [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@(^Arrow [((\g.((\x.(g@(x@x)))@(\x.(g@(x@x)))))@ [(^Arrow [( [

Recall that the parser is part of the landing page for all chemlambda projects.

So, if you write in the parser:

(\x.a) b

which is the pattern for a beta rewrite, then the relevant part of the mol (with funny arrow names) and the rewrite will have the form:



Biography of Sci-Hub creator Alexandra Elbakyan

I found today Alexandra Elbakyan biography, written by herself.

This link is to the original (in Russian) and this link is the google translate into English.

I think this is a very interesting read. You can get a really first hand description of the context and motivations of the creation of Sci-Hub. It is also a glimpse into the mind of a special individual who was born and lived in a middle of nowhere and who changed the world.

Some quotes, which I particularity resonate with:

“What is this misfortune?” I thought “again they see in me not a man, but a programmer”


“It was 2012, and I turned 24. I was a patriot and supported Putin’s policies. And I was also the creator of the Sci-Hub service, which, according to numerous reviews, incredibly helped Russian science.

But no one called and wrote to me like that.
No one invited me to participate in any scientific projects.
Every day I went in a cold, crowded train from Odintsovo, where the HSE hostel was located – to the university and back.”


Especially this I can’t understand. For anyone creative it would be a privilege to participate in a scientific project with Elbakyan.

Beta and dist are emergent, just like Reidemeister 3 and Hamiltonian mechanics

The title says all 🙂 This is a time tag announcement. The computing with space project is essentially finished. The last piece was discovered today.

I still have to write all down though. It would be helpful to make me do it quicker by making me give talks or something like that.

It is beautiful.

All goes well!

The “attack” on my institute web, or whatever that was, seems to have a solution. So now all pages go well (Feb 10 2020).

In conclusion, you may use:

I can be found at:

EDIT: some words about the revived collection. There are 264 posts/animations, which is a bit more than 1/2 of the original collection. Now there is the possibility to rerun in js the simulation, because whenever possible there is a mol file attached to the animation, which can be reduced in js. Some numbers now. In verifiedMol.js there are 500 mol files, but some are duplications, in order to manually enhance the automated  matching of posts with mols, so say there are about 490 mol files. If they are too big to be used without stalling the js reduction, this is signaled by the message “mol too big” in the post. If there is no mol which matches, this is signaled as “mol unavailable”. Of all 264 posts, 36 of them fall in the “mol too big” category, 46 in the “mol unavailable” and there are 6 posts which don’t have a chemlambda simulation inside. So this leaves 264-88=176 posts which have matching mol files to play with. Finally, there are two situations where the matching mol-post is not perfect: (1) when in the original simulation is used a mol file which contains nodes of a busy-beaver Turing machine (of the kind explained here), (2) when in the original is used a .mola file (a mol with actors). In both cases the js reduction does not know how to do this.

Pure See, emergent beta, Heisenberg

Some updates, for things to come and plans.

1. Pure See is a relative of lambda calculus, in the sense that it is Turing universal, is very simple, but it does not use abstraction, application, let as primitives. It is a programming language built over  commutative emergent algebras, i.e. those with the shuffle trick, or equivalently with the algebraic properties of em-convex (but mind that em-convex still uses lambda and application operations; these are not needed).

I plan to make a parser for Pure See very soon.

2. This means that Pure See is as commutative as lambda calculus. Or, the general theory that I have in mind is non-commutative. And emergent, in the sense of emergent algebras.

Before going full non-commutative, one has to realize the beta rewrite as emergent. This is true, in the same way as associativity is emergent in the equational theory of emergent algebras, or the way to realize Reidemeister 3 rewrite from R1 and R2 (and a passage to the limit). The fact that beta is emergent is what makes Pure See to work and answers to the question: do emergent algebras compute? Yes, they do, because in the most uninteresting situation, the commutative one, we can implement lambda calculus with commutative emergent algebras.

3. The first non-coomutative case is the Heisemberg group, described as a non-commutative emergent algebra. I have since a long time the description. The shuffle trick becomes something else. Means that beta rewrite and DIST rewrites change into something more interesting. The whol eformalism actually becomes something else.

I thought that the general non-commutative case is in principle far more complex than the Heisenberg case. It was also unsatisfying that I had no explanation for the reason why Heisenberg groups appear in physics. What’s special about them?

Now I know, they are logically unavoidable (again in the frame of emergent algebras).

So I still play with this new point of view and I wonder what to do next.

The wise thing would be to carefully explain, in a legacy way, all this body of work. My initial plan was to base this explanations on a backbone of openly communicated programs and demos, so that the article versions would be a skin of the whole description. Who wants to read betdime stories has the article. Who wants more has the programs. Who wants all thinks about all this.

With the DDOS or whatever is it,  it becomes harder to use independent ways of sharing.

Or should I jump directly to the non-commutative case?

Or somebody really started to make molecular computers?  If so,  it would be, short time span, the most interesting thing.