Saved version for direct download of the chemlambda gui

It appears that the site which hosts my chemlambda gui is down. Here is a save of the the playall archive for the chemlambda gui. You may use it if the original site is down.  Instructions about how to use it in this video:

UPDATE: The site is up again here  and I made a second video with a gun which shoots in two directions

_______________________________________________

DNA, err… tape replication pictures

Here are the kind of pictures you can get by using the chemlambda visualizer.

UPDATE: Here the first video about it:

Continuing with the post

The first is a screenshot of the initial tape  with bits on it (the tape contains “1010” as an example):

tape_with_bits_0And here is what you get after 6 reductions done by the algorithm:

tape_with_bitsI’ll explain in a moment what I did.

First I wrote the   tape.mol file which represents the initial molecule.

Then I used  bash_main_viral_foe_bubbles.sh  which can be downloaded from the explanations/downloads page of the visualizer.

The script waits me to choose a .mol file,  which I did by writing at the prompter tape.mol.

Then I typed firefox look.html &  (use whatever browser with javascript enabled) to see the results.

UPDATE: Attention, just found out that in some versions of safari there is a problem with working with local files. I suspect, but if you know more then please tell me, that even if safari does handle the file// protocol and opens the look.html, it does not handle well the part where the look.html opens the json files file_0.json … file_10.json.

These json files are produced by the scripts, then they are turned into d3 force graphs by look.html.

So, it may happen that safari opens the file look.html, but when you click on the buttons to see the molecules in action, then safari fails to open the json files which look.html needs, so nothing happens further.

I don’t know yet any solution for this, other than “use firefox” for example. There should be an elegant one.

UPDATE 2: solved!  just download playall.tar.gz .

_____

Now, everything (the scripts, libraries, the file look.html) are available at the said downloads page. This specific .mol file can be saved from the link provided.

I clicked on the “initial” button” and I got a whirling molecule. I let it settle a bit and then I used the click and drag to position some of the atoms in a fashion more understandable if there’s no move, in a picture.

Then I took the screenshot with a generic soft.

The same for the second picture, which shows what you get at step 6.  I combed the two replica of the tape (by click and drag) so that it is obvious that the replication went well.

Took a screenshot again.

And that’s it!

This is not yet part of the gallery of examples,  which I recommend in particular for getting other mol files.

The bit which I used (i.e. the green atoms molecule which is on the “tape” in some places) appears in the example named “the bit propagation“.

__________________________________________________

Varia: updates and preparations

Yesterday I found a bug in one of the programs for the chemlambda visualiser, namely an  unexpected functioning of the priority choice part when applied to a particular mol file (graph).

Today I took it methodically and found two bugs which create that behaviour. One was that the priority choice was not covering all the possibilities in a correct way, the other was a pure programming bug.

So I corrected everything and checked that on the examples from the gallery it works as expected, and also I checked it on many other examples which I have and it works well.

Of course, only to check a program on examples means nothing without a proof that the algorithm works well. I have done that, now the priority choice is indeed well implemented.

What is funny is that by trying to correct the priority choice part I have found the other stupid bug.

OK, so now all the new tar files are marked with 06_10_2014.

And anyway, as everything is open here, you may compare the versions and arrive to your own conclusions.

Mind that in a sense there is still a bug in the main_viral from the “play” archive:  it may happen that at some point the json file which is seen with look.html may be empty. This happens because in the “play” algorithm the loops are erased, and it is possible that a molecule reduces to a collection of loops, hence an empty json file eventually.

No problem with that, by using the “add_new” tar you have an algorithm which does not remove the loops (and also has the FOE node and its new moves). This one works perfectly now.

On a different subject: the artificialagora.wordpress.com  will launch soon. I don’t know yet if chorasimilarity and artificialagora will coexist, or if artificialagora will be the luxury version of chorasimilarity (hope not).

But soon enough we’ll see this.

Chorasimilarity site is still read in a strange way for a blog, because old posts receive comparable hits with new ones. Not all posts are good, for example posts as this one, where I indulge into telling about updates and preparations.

______________________________

Quick and dirty argument for space from chemlambda

One of the least understood ideas of chemlambda is related to this question: which is the space where these artificial molecules live?

There are two different possible applications of chemlambda, each having a different answer for this question. By confusing these two applications we arrive at the confusion about the conception of space in chemlambda.

Application 1 concerns real chemistry and biology. It is this: suppose there exist real chemical molecules which in reaction with real other substances (which play the role of the enzymes for the moves, invisible in chemlambda). Then, from the moment these real molecules and real enzymes are identified, we get *for free* a chemical computer, if we think small. If we think big, then we may hope that the real molecules are ubiquitous in biochemistry and once identified the chemical reactions which represent the chemlambda moves, then we get for free a computational interpretation of big parts of biochemistry. Thinking big, this would mean that we arrive to grasp a fundamental manifestation of computation in biochemistry, which has nothing at all to do with numbers, or bits, or boolean gates, or channels and processes, all this garbage we carry from the experience (very limited historically) we have with computation until now.

In this application 1 space is no mystery, is the well known 3d space, the vessel where real molecules roam. The interest is here not in “what is space”, but “is life in some definite clear way a computational thing?”.

Application 2 resembles more to physics than biochemistry. It aims to answer to the question what is space? Ironically from neuroscience we know that clearly living brains don’t relate with space in any way which involves coordinates and crunching numbers. However, the most fundamental physics never escaped the realm of coordinates and implicit assumptions about backgrounds.

Until now. The idea proposed by application 2 of chemlambda is that space is nothing but a sort of a program.

I try to make this clear by using emergent algebras, and will continue this path, but here is the quick and dirty argument, which appears not to use emergent algebras,  that chemlambda can explain space as a program.

(it does use them but this is a detail, pay attention to the main line.)

OK, so the artificial molecules in chemlambda are graphs. As graphs, they don’t need any space to exist, because everybody knows that a graph can be described in various ways (is a data structure) and only embeddings of a graph in a space need ahem … space.

Just graphs, encoded in .mol files, as used by the chemlambda visualiser I work on these days.

What you see on the screen when you use the visualiser is chemlambda as the main engine and some javascript salt and pepper, in order to impress our visually based monkey brains.

But, you see, chemlambda can do any computation, because it can do combinatory logic. The precise statement is that chemlambda with the reduction strategy which I call *the most stupid” is an universal computer.

That means that for any chain of reductions of a chemlambda molecule, there is another chemlambda molecule whose reductions describe the first mentioned reductions AND the javascript (and whatnot) computation which represent the said first chain of reductions on the screen.

What do you think about this bootstrapping?

__________________________

More input request about the chemlambda gui, thanks

 I get mixed messages from some of those who tried the chemlambda proto-gui. It works for  most, does not work for some of them. I am a mathematician, not a programmer, I learn as I do, I appreciate more input from everybody who tried it. Hope that in a month or so it will be much more evolved. Thanks for  sending private messages with your experience.
Downloads are here.

Visual tutorial for “the soup”

I started here a visual tutorial for chemlambda and it’s gui in the making. I call it a tutorial for the “soup” because it is about a soup of molecules. A living soup.

Hope that in  the  recent future will become THE SOUP. The distributed soup. The decentralized living soup.

Bookmark the page because content will be added on a daily basis!

_____________________________________________________