Tag Archives: bootstrapping

The replicant

This is a molecular machine designed as a patch which would upgrade biological ribosomes. Once it attaches to a ribosome, it behaves in an almost similar ways as the synthetic ribosome Ribo-T, recently announced in  Nature 524,119–124(06 August 2015) doi:10.1038/nature14862  [1].  It thus enables an orthogonal genetic system, (i.e., citing from the mentioned Nature letter “genetic systems that could be evolved for novel functions without interfering with native translation”).

The novel function is designed for is more ambitious than specialized new proteins synthesis. It is, instead, a  two-ways translation device, between real chemistry and programmable artificial chemistry.

It behaves like a bootstrapper in computing. It is itself simulated in chemlambda, an artificial chemistry which was recently proposed as a means towards molecular computers [2].  The animation shows one of the first successful simulations.

 

spiral_boole_construct2_orig_in

 

With this molecular device in place, we can program living matter by using living cells themselves, instead of using, for example, complex, big 3D DNA printers like the ones developed by Craig Venter.

The only missing step, until recently, was the discovery of the basic translation of the building blocks of chemlambda into real chemistry.

I am very happy to make public a breakthrough result by Dr. Eldon Tyrell/Rosen, a genius who went out of academia some years ago and pursued a private career. It appears that he got interested early in this mix of lambda calculus, geometry and chemistry and he arrived to reproduce with real chemical ingredients two of the chemlambda graph rewrites: the beta rewrite and one of the DIST rewrites.

He tells me in a message  that he is working on prototypes of replicants already.

He suggested the name “replicant” instead of a synthetic ribosome because a replicant, according to him, is a device which replicates a computer program (in chemlambda molecular form) into a form compatible with the cellular DNA machine, and conversely, it may convert certain (RNA) strands into chemlambda molecules, i.e. back into  synthetic form corresponding to a computer program.

[1] Protein synthesis by ribosomes with tethered subunits,  C. Orelle, E. D. Carlson, T. Szal,  T. Florin,  M. C. Jewett, A. S. Mankin
http://www.nature.com/nature/journal/v524/n7563/full/nature14862.html

[2] Molecular computers, M Buliga
http://chorasimilarity.github.io/chemlambda-gui/dynamic/molecular.html

[This post is a reply to +Yonatan Zunger  post
https://plus.google.com/u/0/+YonatanZunger/posts/6a3C5Nm5fNS
where he shows that the INCEPT DATE of the Blade Runner replicant Roy Batty appears to be 8 Jan, 2016.
So here is a replicant, in the inception phase 🙂 ]

PS: The post appeared as well in the chemlambda collection:

https://plus.google.com/+MariusBuliga/posts/jQTh741YYdP

Artificial chemistry suggests a hypothesis about real biochemistry

What is the difference between a molecule encoded in a gene and the actual molecule produced by a ribosome from a copy of the encoding?

synthetic_bigpred

Here is a bootstrapping hypothesis based on the artificial chemistry chemlambda.

This is a universal model of computation which is supposed to be very simple, though very close to real chemistry of individual molecules. The model is implemented by an algorithm, which uses as input a data format called a mol file.

The language use does not matter, although there may be more elegant versions than mine, like the one by +sreejith s  (still work in progress though) [1].

Since the model is universal it implies that the algorithm and the mol data structure can be themselves turned into an artificial molecule which reacts with the usual invisible enzymes from the model and does the computation of the reduction of the original molecule.

The boostrapping hypothesis is that the original molecule is like the synthetized molecule and that the mol file format turned into a molecule is the stored version of the molecule.

In the post there  is mentioned a previous post [2], where this was tried by hand for a molecule called the 20 quine, but now there are new scripts in the chemlambda repository which allow to do the same for any molecule (limited by the computer and the browser of course).

The final suggestion is that the hypothesis can be continued along these lines, by saying that the “enzymes” which do the rewrite are (in this boostrapping sense) the rewriting part of the algorithm.

[1] Chemlambda-py

[2] Invisible puppeteer

https://plus.google.com/+MariusBuliga/posts/2XMSyKJrPPW

Synthetic stuff. Now there is a script which allows to synthetize any chemlambda molecule, like in the previous Invisible puppeteer post.
Look in the chemlambda repository, namely at the pair synthetic.sh and synthetic.awk from this branch of the repository (i.e. the active branch).
In this animation you see the result of the “synthetic” bigpred.mol (which was the subject of the recent hacker news link).

What I did:
– bash synthetic.sh and choose bigpred.mol
– the output is the file synt.mol
– bash quineri.sh and choose synt.mol (I had a random evolution, with cycounter=150, time_val=5 (for safari, but for chromium I choose time_val=10 or even 20).
– the output is synt.html
– I opened synt.html with a text editor to change a bit some stuff: at lines 109-110 I choose a bigger window         var w = 800,   h = 800; and smaller charges and gravity (look for  and modify to .charge(-10)
.gravity(.08) ).

Then I opened the synt.html with safari. (Also worked with chromium). It’s a hard time for the browser because the initial graph has more than 1400 nodes (and the problem is not coming from setTimeout because, compared with other experiments, there are not as many, but it comes from an obscure problem of d3.js with prototypes; anyway this makes firefox lousy, which is a general trend at firefox, don’ know why, chromium OK and safari great. I write this as a faithful user of firefox!).
In this case even the safari had to think a bit about life, philosophy, whatnot, before it started.

I made a screencast with Quicktime and then sped it up progressively to 16X, in order to be able to fit it into less than 20s.

Then I converted the .mov screencast to .gif and I proudly present it to you!

It worked!

Now that’s a bit surprising, because, recall, what I do is to introduce lots of new nodes and bonds, approx 6X the initial ones, which separate the molecule which I want to synthetize into a list of nodes and a list of edges. The list of edges is transformed into a permutation.

Now during the evolution of the synt molecule, what happens is that the permutation is gradually applied (because if randomness) and it will mix with the evolution of the active pieces which start already to rewrite.

But it worked, despite the ugly presence of a T node, which is the one which sometimes may create problems due to such interferences if the molecule is not very well designed.

At the end I recall what I believe is the take away message, namely that the mol file format is a data structure which itself can be turned into a molecule.