Tag Archives: what if

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

After the IoT comes Gaia

They say that sneakernet does not scale. If you think about the last product of Amazon, the AWS Import/Export Snowball, this clumsy suitcase contains less than a grain of pollen.

Reason from these arguments:

  • the Internet of Things is an extension of the internet, where lots of objects in the real world will start to talk and to produce heaps of data
  • so there is a need for a sneakernet solution in order to move these data around,  because the data are only passive evidence and they need to be processed,
  • compared though with biology, this quantity of data is tiny
  • and moreover biology does not function via signal transmission, it functions via signal transduction, a form of sneakernet,

you’ll get to the unavoidable conclusion that the IoT is only a small step towards a global network which works with chemical like interactions, transports data (which are active themselves) via signal transduction and it extends the real world biology.

After the IoT comes Gaia. A technological version, to be clear.

Some time in the future, but not yet when we could say that the Gaia extension appeared, there will still be a mixture of old ways IoT and new ways biological like. Maybe there will be updates, say of the informational/immunity  OS, delivered via anycasts issued from  tree like antennas, which produce pollen particle. The “user” (what an ugly reductionistic name) breaths them and the update start to work.

The next scene may be one which describes what happens if somebody find out that some antennas produce faulty grains. Maybe some users have been alerted by their (future versions of) smartwatches that they inhaled a possible terminal vector.

The faulty updates have to be identified, tracked (chemically, in real world) and anihilated.

The users send a notification via the old internet that something is wrong and somewhere, perhaps on the other side of the planet, a mechanical turk identifies the problem, runs some simulations of the real chemistry with his artificial chemistry based system.

His screen may show something like this:

mask_of_anarchy_new_short

Once a solution is identified, the artificial chemistry solution is sent to a Venter printer close to the location of the faulty antenna and turned real. In a matter of hours the problem is solved, before the affected users metabolisms go crazy.

Experimental alife IoT with Tessel

Here is an idea for testing the mix between the IoT and chemlambda.  This post almost qualifies as an What if? one but not quite, because in principle it might be done right now, not in the future.

Experiments have to start from somewhere in order to arrive eventually to something like a Microbiome OS.

Take Tessel.

Tessel is a microcontroller that runs JavaScript.
It’s Node-compatible and ships with Wifi built in.

Imagine that there is one GLC actor per Tessel device. The interactions between GLC actors may be done partially via the Wifi.

The advantage is that one may overlap the locality of graph rewrites of chemlambda with space locality.

 

Each GLC actor has as data a chemlambda molecule, with it’s in and out free arrows (or free chemical bonds) tagged with names of other actors.

A bond between two actors form, in the chemlambda+Tessel world, if the actors are close enough to communicate via Wifi.

Look for example at the beta move, done via the behaviour 1 of GLC actors. This may involve up to 6 actors, namely the two actors which communicate via the graphic beta move and at most 4 other actors which have to modify their tags of neighbouring actors names as a result of the move. If all are locally connected by Wifi then this becomes straightforward.

What would be the experiment then? To perform distributed, decentralized computations with chemlambda (in particular to do functional programming in a decentralized way) which are also sprawled over the physical world.  The Tessel devices involved in the computation don’t have to be all in possible Wifi connections with the others, on the contrary, only local connections would be enough.

Moreover, the results of the computations could as well have physical effects (in the sense that the states of the actors could produce effects in the real world) and as well the physical world could be used as input for the computation (i.e. the sensors connected to Tessel devices could modify the state of the actor via a core-mask mechanism).

That would play the role of a very primitive, but functional, experimental ancestor of a Microbiome OS.

 

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Autodesk releases SeaWater (another WHAT IF post)

[ This is another  WHAT IF  post  which  responds to the challenge formulated in  Alife vs AGI.  You are welcome to suggest another one or to make your own.]

The following is a picture of a random splash of sea water, magnified 25 times [source]

scoop-of-water-magnified-990x500

As well, it could be  just a representation of the state of the IoT in a small neighbourhood of you, according to the press release describing SeaWater, the new product of Autodesk.

“SeaWater is a design tool for the artificial life based decentralized Internet of Things. Each of the tiny plankton beings which appear in the picture is actually a program, technically called a GLC actor. Each plankton being has it’s own umwelt, it’s own representation of the medium which surrounds it. Spatially close beings in the picture share the same surrounding and thus they can interact. Likewise, the tiny GLC actors interact locally one with another,  not in real space, but on the Net. There is no real space in the Net, instead, SeaWater represents them closer when they do interact.

Sea Water is a tool for Net designers. We humans are visual beings. A lot of our primate brains powers can be harnessed for designing the alife decentralized computing which form the basis of the Internet of Things.

It improves very much the primitive tools which give things like this picture [source]

ack_6

 

 

Context. Recall that IoT is only a bridge between two worlds: the real one, where life is ruled by real chemistry and the artificial one, based on some variant of an artificial chemistry, aka  chemlambda.

As Andrew Hessel points out, life is a programming language (chemically based),  as well as the virtual world. They are the same, sharing the same principles of computation. The IoT is a translation tool which unites these worlds and lets them be one.

This is the far reaching goal. But in the meantime we have to learn how to design this. Imagine that we may import real beings, say microbes, to our own unique Microbiome OS.  There is no fundamental difference between synthetic life, artificial life and real life, at least at this bottom level.

Instead of aiming for human or superhuman artificial intelligence, the alife decentralized computing community wants to build a world where humans are not treated like bayesian units by  pyramidal centralized constructs.  There is an immense computing power already at the bottom of alife, where synthetic biology offers many valuable lessons.

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UPDATE.  This is real: Autodesk Builds Its Own Virus, as the Software Giant Develops Design Tools for Life Itself.

Microbes take over and then destroy the HAL 9000 prototype

Today was a big day for the AI specialists and their brainchild, the HAL 9000. Finally, the decision was made to open the isolation bubble which separated the most sophisticated artificial intelligence from the Net.  They  expected that  somehow their brainchild will survive unharmed  when exposed to the extremely dynamic medium of decentralized, artificial life based computation we all use every day.

As the video made by Jonathan Eisen shows,  in about 9   seconds after the super-intelligence was taken out of the quarantine and relayed to the Net “microbes take over and then destroy the” HAL 9000 prototype.

After the experiment, one of the creators of the HAL 9000 told us: “Maybe we concentrated too much on higher level aspects of the mind. We aim for understanding intelligence and rational behaviour, but perhaps we should learn this lesson from Nature, namely that real life is a wonderful, complex tangle of local, low level interactions, and that rational mind is a very fragile epiphenomenon. We tend to take for granted the infrastructure of life which runs in the background.”

“I was expecting this result” said a Net designer. “The strong point of the Alife decentralized functioning of the Net is exactly this: as the microbes, the Net needs no semantics to function. This is what keeps us free from the All Seeing Eye, corporation clouds based Net which was the rule some years ago. This is what gives everybody the trust to use the Net.”

 

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This is another post  which  respond to the challenge from Alife vs AGI.  You are welcome to suggest another one or to make your own.

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Microbiome OS

Your computer could be sitting alone and still be completely outnumbered for your operating system  is home to  millions of tiny passengers – chemlambda molecules.

The programs making the operating system of your computer are made up of around ten million code lines, but you harbour a hundred million artificial life molecular beings. For every code line in your ancient windows OS, there are 100 virtual bacterial ones. This is your ‘microbiome’ OS and it has a huge impact on your social  life, your ability to  interact with the Internet of Things and more. The way you use your computer, in turn, affect them. Everything from the forums we visit  to the way we use the Internet for our decentralized computations  influences the species of bacteria that take up residence in our individual mocrobiome OS.

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Text adapted from the article Microbiome: Your Body Houses 10x More Bacteria Than Cells, which I found by reading this G+ post by Lacerant Plainer.

This is a first example of a post which would respond to the challenge from Alife vs AGI. For commodity of the reader I reproduce it further:

In  this post I want to propose a challenge.  What I have in mind, rather vague  but might be fun, would be to develop through exchanges a “what if” world, where, for example, not AI is the interesting thing when it comes about computers, but artificial biology. Not consciousness, but metabolism, not problem solving, but survival. Also related to the IoT which is a bridge between two worlds. Now, the virtual world could be as alive as the real one. Alive in the Avida sense,  in the sense that it might be like a jungle, with self-reproducing, metabolic artificial beings occupying all virtual niches, beings which are designed by humans, for various purposes. The behaviour of these virtual creatures is not limited to the virtual, due to the IoT bridge.  Think that if I can play a game in a virtual world (i.e. interact both ways with a virtual world) then why not a virtual creature can’t interact with the real world? Humans and social manipulations included.

If you start to think about this possibility, then it looks a bit like this. OK, let’s write such autonomous, decentralized, self sustained computations to achieve a purpose. May be any purpose which can be achieved by computation, be it secure communications, money replacements, or low level AI city management. What stop others to write their creatures, one for example for the fun of it,  of writing across half of the world the name Justin by building at right GPS coordinates sticks with small mirrors on top, so that from orbit all shine the pixels of that name.  Recall the IoT bridge and the many effects in the real world which can be achieved by really distributed, but cooperative computations and human interactions. Next: why don’t write a virus to get rid of all these distributed jokes of programs which run low level in all phones, antennas and fridges? A virus to kill those viruses. A super quick self-reproducer to occupy as much as possible of the cheap computing  capabilities. A killer of it. And so on. A seed, like in Neal Stephenson, only that the seed is not real, but virtual, and it does not work on nanotechnology, but on any technology connected to the net via IoT.

Stories? Comics? Fake news? Jokes? Should be fun!

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