# New pages of demos and dynamic visualizations of chemlambda moves

The following are artificial chemistry visualizations, made in d3.js. There are two main pages: the first is with demos for #chemlambda   reductions, the second is with dynamic visualizations of the graph rewrites.
Bookmark these pages if you are interested, because there you shall find new stuff on a day-by-day basis.

______________________________________________________

# Living computations

What’s better than a movie? A live performance.

I just started new pages where you can see the last living computations with chemlambda:

• a 20 nodes creature which I qualified previously as a quine, but is not, struggles to survive in a random environment (random reduction method) here
• the reduction of the predecessor function from lambda calculus turned into a chemlambda reduction (random too) here
• the self multplication of the S combinator in random conditions here
• the reduction of Ackermann(2,2) in the  random model here (this is the one used for the video from the last post).
• a complex reduction in chemlamdba. Here is the recipe:
– you can write the Y combinator as an expression in the S,K,I, combinators: Y = S (K (S I I)) (S (S (K S) K) (K (S I I)))
– so take this expression and apply it to the identity I. In combinatory logic this should reduce to something equivalent to YI, which then reduces forever, because it does not have a normal form
-but we do something more funny, namely all this long string of combinators is transformed into a chemlambda molecule, and we add on top of it a node FO which makes all this big thing to self-reproduce.
So, we have a bunch of reductions (from the long expression to YI) in parallel with the self-reproduction of the whole thing.
Now, what you see is this, in a model of computation which uses a random reduction strategy!
See it live here.

The sources are in this github repository.

_______________________________________________________________________

# Mol language and chemlambda gui instead of html and web browsers gives new Net service?

The WWW is an Internet system, based on the following ingredients:

• web pages (written in html)
• a (web) browser
•  a web server (because of the choice of client-server architecture)

Tim Berners-Lee wrote those programs. Then the WWW appeared and exploded.

The force behind this explosion comes from the separation of the system into independent parts. Anybody can write a web page, anybody who has the browser program can navigate the web, anybody who wants to make a web server needs basically nothing more than the program for that (and the  previously existing  infrastructure).

In principle it works because of the lack of control over the structure and functioning.

It works because of the separation of form from content, among other clever separations.

It is so successful, it is under our noses, but apparently very few people think about the applications of the WWW ideas in other parts of the culture.

Separation of form from content means that you have to acknowledge that meaning is not what rules the world. Semantics has only only a local, very fragile  existence, you can’t go too far if you build on semantics.

Leave the meaning to the user, let the web client build his meaning from the web pages he can access via his browser. He can access and get the info because the meaning has been separated from the form.

How about another Net service, like the WWW, but which does something different, which goes to the roots of computation?

It would need:

• artificial molecules instead of web pages; these are files written in a fictional language called “Mol”
• a gui for the chemlambda artificial chemistry, instead of a web browser;  one should think about it as a Mol compiler & gui,
• a chemical server which makes chemical soups, or broths, leaving the reduction algorithm to the users;

This Mol language  is an idea which holds some potential, but which needs a lot of pondering. Because the “language” idea has bad effects on computation.

________________________________________________________

# Walker eating bits and a comment on the social side of research

This post has two parts: the first part presents an experiment and the second part is a comment on the social side of research today.

Part 1: walker eating bits.  In this post I introduced the walker, which has been also mentioned in the previous post.

I made several experiments with the walker, I shall start by describing the most recent one, and then I shall recall (i.e. links to posts and vids) the ones before.

I use the chemlambda gui which is available for download from here.

What I did: first I took the walker and made it walk on a trail which is generated on the fly by a pair A-FOE of nodes. I knew previously that such a pair A-FOE generates a trail of A and FO nodes, because this is the basic behaviour of the Y combinator in chemlambda. See the illustration of this (but in an older version, which uses only one type of fanout nodes, the FO) here.  Part of it was described in the pen-and-paper version in the ALIFE14 article with Louis Kauffman.

OK, if you want to see how the walker walks on the trail then you have to download first the gui and then use the gui with the file walker.mol.

Then I modified the experiment in order to feed the walker with a bit.

A bit is a pair of A-FO nodes, which has the property that it is a propagator. See here the illustration of this fact.

For this I had to modify the mol file, which I did. The new mol file is walker_eating_bit.mol .

The purpose of the experiment is to see what happens when the walker is fed with a bit. Will it preserve its shape and spill out a residue on the trail? Or will it change and degenerate to a molecule which is no longer able to walk?

The answer is shown in the following two screenshots. The first one presents the initial molecule described by the walker_eating_bit.mol.

At the extreme right you see the pair A-FOE which is generating the trail (A is the green big node with two smaller yellow ones and a small blue one and the FOE is the big yellow node with two smaller blue ones and a small yellow one). If you feel lost in the notation, then look a bit at the description in the visual tutorial.

In the middle you see the walker molecule. At the right there is the end of the trail. The walker walks from left to right, but because the trail is generated from right to left, this is seen as if the walker stays in place and the trail at its left gets longer and longer.

OK. Now, I added the bit, I said. The bit is that other pair of two green nodes, at the right of the figure, immediately at the left of the A-FOE pair from the extreme right.

The walker is going to eat this pair. What happens?

I spare you the details and I show you the result of 8 reduction steps in the next figure.

You see that the walker already passed over the bit, processed it and spat it as a pair A-FOE. Then the walker continued to walk some more steps, keeping its initial shape.

GREAT! The walker has a metabolism.

Previous experiments.  If you take the walker on the trail and you glue the ends of the trail then you get a walker tchoo-tchoo going on a circular trail. But wait, due to symmetries, this looks as a molecule which stays the same after each reduction step. Meaning this is a chemlambda quine. I called such a quine an ouroboros. In the post Quines in chemlambda you see such an ouroboros obtained from a walker which walk on a circular train track  made of only one pair.

I previously fed the walker with a node L and a termination node T, see this post for pen and paper description and this video for a more visual description, where the train track is made circular as described previously.

That’s it with the first part.

Part 2: the telling silence of the expert. The expert is no lamb in academia. He or she fiercely protect the small field of expertise where is king or queen. As you know if you read this open notebook, I have the habit of changing the research fields from time to time. This time, I entered into the the radar of artificial chemistry and graph rewriting systems, with an interest in computation. Naturally I tried to consult as many as possible experts in these fields. Here is the one and only contribution from the category theory church.  Yes, simply having a better theory does not trump racism and turf protection.  But fortunately not everything can be solved by good PR only. As it becomes more and more clear, the effect of promotion of mediocrity in academia, which was consistently followed  since the ’70, has devastating effects on the academia itself. Now we have become producers of standardised units of research, and the rest is just the monkey business about who’s on top. Gone is the the trust in science, gone are the funds, but hey, for some the establishment will still provide a good retirement.

The positive side of this big story, where I only offer concrete, punctual examples, is that the avalanche which was facilitated by the open science movement (due to the existence of the net) will change forever the academia in particular. Not into a perfect realm, because there are no such items in the real world catalogue. But the production of scientific research in the old ways of churches and you scratch my back and I’ll scratch yours is now exposed to more eyes than before and soon enough we shall witness a phenomenon similar to the one happened more than 100 years ago in art, where ossified academic art sunk into oblivion and an explosion of creativity ensued, simply because of the exposure of academic painting along with alternative (and, mixed with garbage, much more creative artists) works in the historical impressionist revolution.

______________________________________________

# Chemlambda quines and DNA pairs, speculation

I’m staring at this space view of the walking machine described first in this post:

The .mol file of the walker is available at this link.

What is this: is a walker as described in the ouroboros predecessor post, which walks on a train track generated by a y combinator pair A-FOE.

But the strange thing which makes me stare at the picture is that I see a hexagonal structure connected to a quadrilateral one, or I recall that I have seen such structures, see for example the following crop from this source.

So it’s like the thymine-adenine pair (well, there is no pure adenine side, is only half of it).

Then, I recall seeing all these structures before with the space view, including the one representing the connection between guanine and cytosine, but I have to look at the files to recover them (I have plenty of mol files already, hundreds, I need to classify all the interesting stuff I learned).

Is this a coincidence or not? I don’t know, it is tempting to make the connection between quines in chemlambda, as it is the ouroboros, and self-mantaining molecules like DNA.

______________________________________________

# The new look of the chemlambda gui, new downloads and a video demo of the space view

Here is a short video with a demo of the space view of chemlambda molecules and their interaction.

I would be grateful if as many as possible download it and spread it in as many places, not only google or other clouds.

Please send me a mail, or post a comment here if you did it, thank you! (mind that if it is your first comment then it is moderated, so don’t worry if it does not appear immediately, maybe I sleep or something like that)

It works surely with firefox, I have been told that it does not work with safari or chromium, because, I learned, those browsers don’t allow to open local files.

# The Ackermann function in the chemlambda gui

UPDATE: The Ackermann function, the video:

_______________________

I put this stuff on G+  some days ago and now I can find it only if I look for it on purpose. Older and newer posts, those I can see. I can see colored lobsters, funny nerd jokes, propaganda pro and con legacy publishing, propaganda hidden behind granpa’s way of communicating science, half baked philosophical ideas,  but not my post which I made only two days ago. On my page, I mean, not elsewhere.

Thank you G+ for this, once again. (Note not for humans: this was ironic.)  Don’t forget to draw another box next time when you think about a new algorithm.

A non-ironic thanks though for the very rare occasions when I did met very interesting people and very interesting ideas there.

OK, to the matter, now. But really, G+, what kind of algorithm you use which keeps a lobster on my page but deletes a post about the Ackermann function?

UPDATE: The post is back in sight now. Whew!
The post follows, slightly edited (by adding stuff).
The Ackermann function is an example of a total computable function which is not primitive recursive. It is therefore amusing to try to compute it.
The matter is not what is the value of Ack(m,n), because it grows so fast that very soon the problem of computing it is shadowed by the more trivial problem of storing its values. Instead,  more interesting is to see how your computing device handles the computation itself, things like stacks of calls, etc, because here it is manifest the fact that Ack is not primitive recursive.
To simplify it, the funny thing is to see how you can compute Ack(m,n) without any cheat.
I tried to do this with #chemlambda . I know since a long time that it can be done, as explained (very summary, true) in this old post
https://chorasimilarity.wordpress.com/2013/10/19/a-machine-for-computing-the-ackermann-function-in-graphic-lambda-calculus/
for GLC, not chemlambda (but since chemlambda does with only local moves what GLC does, it’s the same).
I want to show you some pictures about it.
It is about computing Ack(3,2). Everybody will point that Ack(3,2) = 29 and moreover that Ack(3,n) has an explicit expression, but this would be cheating, because I don’t want to use precomputed stuff.
No, what I want to use is a lambda calculus term for the Ackermann function (and one which is not eta reduced, because chemlambda does not have eta reduction!), and I want to apply it to the arguments 3 and 2 written as lambda terms as well (using the Church encoding). Then I want to see if after the reductions performed by the algorithm I have I get 29 as a Church number as well.
During all the algorithm I use only graph reductions!
After all there are no calls, no functions and during the computation the molecules which appear are not even representing lambda terms.
Indeed, lambda calculus does not have operations or concepts like fanin nodes, or FOE nodes, not reductions like FAN-IN or DIST. That’s the amazing point (or at least one of them), that even if it veers outside lambda calculus, it ends where it should (or better, that’s for another time).
I used the programs which are available at the site of the chemlambda gui http://imar.ro/~mbuliga/gallery.html
(which is btw online again, after 2 days of server corruption.)Here are some pictures.The first one is a screenshot of the Ack(3,2) “molecule”, i.e. the graph which is to be reduced according to the chemlambda rules and according to the reduction strategy which I call “viral”.
After almost 200 reductions I get 29, see the second figure, where it appears as the molecule which represents 29 as a Church numeral.
Wow, it really worked!
You can try it for yourself, I’ll give you the mol file to play with, but first some details about it.
I modified a bit the awk script which does the reductions, in the following place: when it introduces new nodes (after a DIST move) it has to invent new names for the new edges. In the script which is available for download the algorithm takes the max over all all ports names and concatenate it with a word which describes where the edge comes from. It is good for being able to track back where the nodes and edges come, but it results into a growth of the ports name which is exponential in the number of iterations of the reduction algorithm. This leads to very big names of some ports, after 200 iterations.
So I modified this part by choosing a naming procedure which is less helpful for tracking but better in the sense that now the growth of names is linear in the number of iterations. It is a quick fix, after all it is as easy to invent naming procedures which result in a logarithmic or almost constant length wrt the number of iterations.
For the Ackermann function the script which is available is just as good, it works well, only that it has this unpleasant feature of long names which enlarges unnecessarily the json files.
Details over, next now.
In the third picture you see the mol file for the Ack(3,2), i.e. the list of nodes and ports of the Ack(3,2) molecule, in the format used by the reduction program.
Btw, do you see in this screenshot the name of the updated script? Right, is foe_bubbles_09_10.awk, instead of foe_bubbles_06_10.awk which is available for download.
I don’t cheat at all, see?
I made some annotations which helps you to see which part corresponds to the Ackermann function (as a lambda term translated into chemlamda), which parts are the arguments “3” and “2”, and finally which part represents the Ackermann function applied to (3,2).
Soon enough, when I’ll be able to show you animated reductions (instead of the steps of reduction only), I think such an example will be very funny to examine, as it grows and then shrinks back to the result.
________________________________________