# More about chemical transactions

There is much more about these chemical transactions and their proofs. First is that transactions are partially independent on the molecules. The blockchain may be useful only for having a distributed database of transactions and proofs, available for further use. But there’s more.

Think about this database as one of valid computations, which can then be reused in any combination or degree of parallelism. Then, that’s the field of several competitions.

The same transaction can have several proofs, shorter or longer. It can have big left pattern therefore costly to use it in another computation. Maybe a transaction goes too long and therefore it is not useful to use in combination with others.

When there is a molecule to reduce, the application of a transaction means:
– identify a subgraph isomorphic with the left pattern and pick one such subgraph
– apply the transaction to this particular subgraph (which is equivalent with: reduce only that subgraph of the molecule, and freeze the rest of the molecule, but do it in one step because the sequence of reductions is already pre-computed)

Now, which is more convenient, to reduce the molecule by using the random algorithm and the available graph rewrites, or to use some transactions which fit, which is fast (as concerns step 2) but costly (as concerns step 1), moreover it may be that there is a transaction with shorter proof for that particular molecule, which mixes parts of several available precomputed transactions.

Therefore the addition of transactions and their proofs (needed to be able to validate them) into the database should be made in such a way which profit from this competition.

If I see the reduction of a molecule (which may be itself distributed) as a service then besides the competition for making available the most useful transactions with the shortest proofs, there is another competition between brute force reducing it and using the available transactions, with all the time costs they need.

If well designed, these competitions should lead to the emergence of clusters of useful transactions (call such a cluster a “chemlisp”) and also to the emergence of better strategies for reducing molecules.

This will lead to more and more complex computations which are feasible with this system and probably fast enough they will become very hard to understand by a human mind, or even by using IT tools on a limited part of the users of the system.

# Tay has been retired, Blade Runner style

It is always unexpected when fiction becomes real. Tay, the adolescent AI, survived for about 24 hrs on Twitter. She turned into something socially unacceptable. Then she has been retired. See Gizmodo story.

Almost two years ago I posted Microbes take over and then destroy the HAL 9000 prototype. I gave 9 seconds as an estimate for the chance of life of an AI in the real world, where there is no control and faced with  the “extremely dynamic medium of decentralized, artificial life based computation we all use every day“(that post suggests an artificial life, not AI version of the future internet).

Now, the story of Tay seems unbelievably close to the Blade Runner world. The genius of Philip K. Dick manifests here because  he mixes AI with synthetic life with real life.

Real people socially hacked Tay. Virtual microbes destroy HAL 9000. The common themes are: in a decentralized environment and AI vs life (real or virtual).

Not many people understand that today obsessions with security, control, privacy are all lost battles.

# What if… it can be done? An update of an old fake news post

In May 2014 I made a fake news post (with the tag WHAT IF) called Autodesk releases Seawater. It was about this big name who just released a totally made up product called Seawater.

“SeaWater is a design tool for the artificial life based decentralized Internet of Things.”

In the post it is featured this picture

[source]

… and I wrote:

“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.”

Today I want to show you this:

or better go and look in fullscreen HD this video

The contents is explained in the post from the microblogging collection chemlambda

27 microbes. “This is a glimpse of the life of a community of 27 microbes (aka chemlambda quines). Initially the graph has 1278 nodes (atoms) and 1422 edges (bonds). There are hundreds of atoms refreshed and bonds made and broken at once.”

Recall that all this is done with the most simple algorithm, which turns chemlambda into an asynchronous graph rewrite automaton.

A natural development would be to go further, exactly like described in the Seawater post.

Because it can be done 🙂

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# Separation of form from content, no semantics

One of the principles which make the net possible, as stated by Tim Berners-Lee,

separation of form from content: The principle that one should represent separately the essence of a document and the style with which it is presented.

Applied to decentralized computing, this means no semantics.

[One more confirmation of my impression that logic is something from the 21st century disguised in 19th century clothes.]

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# Distributed GLC discussion

This is my contribution to a discussion about the distributed GLC model of computation and about the associated gui.

Read carefully.  It has a fractal structure.

Basics about chemlambda graphs and the GUI

The chemlambda graphs (molecules) are not flowcharts. One just has to specify certain (known) graphs with at most 4 nodes and how to replace them with other known simple graphs. That is all.

That means that one needs:

– a file which specifies what kind of graphs are used (by giving the type of nodes and arrows)

– a file which specifies which are the patterns (i.e. graphs) and which are the rewrite moves

– and a program which takes these files as input and a graph and does things, like checking if the graph is of the kind described in file 1, if there are any patterns from the file 2 and do the rewrite in a place where the user wants, do a sequence of rewrites until it forks, if the user wants, take as input a lambda expression given by the user and transform it into a graph.

– then there is the visualization of the graphs program(s), that is the hard part, but it is already done in multiple places. Means that one has to write only the possible conversions of file formats from and to the viz tool.

That is the minimal configuration.

Decorations

There are various reasons why one wants to be able to decorate the graphs, locally, as a supplementary thing, but in no way is this needed for the basic process.

Concerning decorations, one needs a file which specifies how to decorate arrows and which are the relations coming from nodes. But this is not part of the computation.

If we want to make it more powerful then it gets more complex because if we want to do symbolic computations of decorations (like elimination of a relation coming from a node) then probably it is better to output a file of decorations of arrows and relations from nodes and input it in a symbolic soft, like mathematica or something free, there is no need to reinvent the wheel.

After the graph rewrite you loose the decoration, that’s part of the fun which makes decorations less interesting and makes supposedly the computation more secure.

But that depends on the choice of decoration rules.

For example, if you decorate with types then you don’t loose the decoration after the move. Yes, there are nodes and arrows which disappear, but outside of the site where the move was applied, the decorations don’t change.

In the particular case of using types as decorations, there is another phenomenon though. If you use the decoration with types for graphs which don’t represent lambda terms then you will get relations between types, relations which are supplementary. a way of saying this is that some graphs are not well typed, meaning that the types form an algebra which is not free (you can’t eliminate all relations). But the algebra you get, albeit not free, is still an interesting object.

So the decoration procedure and the computation (reduction) procedure are orthogonal. You may decorate a fixed graph and you may do symbolic algebraic computations with the decorations, in an algebra generated by the graph, in the same way as a know generates an algebra called quandle. Or you may reduce the graph, irrespective of the decorations, and get another graph. Decorations of the first graph don’t persist, a priori, after the reduction.

An exception is decoration with types, which persists outside the place where the reduction is performed. But there is another problem, that even if the decoration with types satisfies locally (i.e. at the arrows of each node) what is expected from types, many (most) of the graphs don’t generate a free algebra, as it would be expected from algebras of types.

The first chemical interpretation

There is the objection that the reductions can’t be like chemical reactions because the nodes (atoms) can’t appear or disappear, there should be a conservation law for them.

Correct! What then?

The reduction, let’s pick one – the beta move say – is a chemical reaction of the graph (molecule) with an enzyme which in the formalism appears only with the name “beta enzyme” but is not specified as a graph in chemlambda. Then, during the reaction, some nodes may disappear, in the sense that they bond to the beta enzyme and makes it inactive further.

So, the reduction A –>beta B appears as the reaction

A + beta = B + garbage

How moves are performed

Let’s get a bit detailed about what moves (graph rewrites) mean and how they are done. Every move says replace $graph_1$ with $graph_2$ , where $graph_1$, $graph_2$ are graphs with a small number of nodes and arrows (and also “graph” may well be made only by two arrows, like is the case for $graph_2$ for the beta move).

So, now you have a graph G. Then the program looks for $graph_1$ chunks in G and adds some annotation (perhaps in an annotation file it produces). Then there may be script which inputs the graph G and the annotation file into the graph viz tool, which has as effect, for example, that the $graph_1$ chunk appears phosphorescent on the screen. Or say when you hover with the mouse over the $graph_1$ chunk then it changes color, or there is an ellipse which encircles it and a tag saying “beta”.

Suppose that the user clicks, giving his OK for performing the move. Then on the screen the graph changes, but the previous version is kept in the memory, in case the user wants to go back (the moves are all reversible, but sometimes, like in the case of the beta move, the $graph_2$ is too common, is everywhere, so the use of both senses of some moves is forbidden in the formalism, unless it is used in a predefined sequence of moves, called “macro move”).

Another example would be that the user clicks on a button which says “go along with the reductions as long as you can do it before you find a fork in the reduction process”. Then, of course it would be good to keep the intermediate graphs in memory.

Yet another example would be that of a node or arrow of the graph G which turn out to belong to two different interesting chunks. Then the user should be able to choose which reduction to do.

It would be good to have the possibility to perform each move upon request,

plus

the possibility to perform a sequence of moves which starts from a first one chosen by the user (or from the only one available in the graph, as is the case for many graphs coming from lambda terms which are obtained by repeated currying and nesting)

plus

the possibility to define new, composed moves at once, for example you notice that there is a chunk $graph_3$ which contains $graph_1$ and after reduction of $graph_1$ to $graph_2$ inside $graph_3$, the $graph_3$ becomes $graph_4$; $graph_4$ contains now a chunk $graph_1$ of another move, which can be reduced and $graph_4$ becomes $graph_5$. Now, you may want to say: I save this sequence of two moves from $graph_3$ to $graph_5$ as a new move. The addition of this new move does not change the formalism because you may always replace this new move with a sequence of two old moves

Practically the last possibility means the ability to add new chunks $graph_3$ and $graph_5$ in the file which describes the moves and to define the new move with a name chosen by the user.

plus

Finally, you may want to be able to either select a chunk of the input graph by clicking on nodes and arrows, or to construct a graph and then say (i.e. click a button) that from now on that graph will be represented as a new type of node, with a certain arity. That means writing in the file which describes the type of nodes.

You may combine the last two procedures by saying that you select or construct a graph G. Then you notice that you may reduce it in an interesting way (for whatever further purposes) which looks like this:

– before the chain of reduction you may see the graph G as being made by two chunks A and B, with some arrows between some nodes from chunk A and some nodes from chunk B. After the reduction you look at the graph as being made by chunks C, D, E, say.

– Then you “save” your chunks A, B, C, D, E as new types of nodes (some of them may be of course just made by an old node, so no need to save them) and you define a new move which transforms the chunk AB into the chunk CDE (written like this only because of the 1D constraints of writing, but you see what I mean, right?).

The addition of these new nodes and moves don’t change the formalism, because there is a dictionary which transforms each new type of node into a graph made of old nodes and each new move into a succession of old moves.

How can this be done:

– use the definition of new nodes for the separation of G into A, B and for the definition of G’ (the graph after the sequence of reductions) into C,D,E

– save the sequence of moves from G to G’ as new composite move between G and G’

– produce a new move which replaces AB with CDE

That’s interesting how should work properly, probably one should keep both the move AB to CDE and the move G to G’, as well as the translations of G into AB and G’ into CDE.

We’re getting close to actors, but the first purpose of the gui is not to be a sandbox for the distributed computation, that would be another level on top of that.

The value of the sequence of moves saved as a composite move is multiple:

– the $graph_3$ which is the start of the sequence contains $graph_1$ which is the start of another move, so it always lead to forks: one may apply the sequence or only the first move

– there may be a possible fork after you do the first reduction in $graph_3$, in the sense that there may be another chunk of another move which could be applied

GLC actors

The actors are a special kind of decoration which transform (some) moves (at the choice of the user) into interaction devices.

You decorate the nodes of a graph G with actors names (they are just names, for the moment, at your choice). As a convention let’s say that we denote actor names by :a , :b , etc

You also decorate arrows with pairs of names of actors, those coming from the decorations of nodes, with the convention that (:a, :a) is identified (in the user mind) with :a (nothing surprising here, think about the groupoid over a set X, which is the set of “arrows” $X \times X$ and X appears as the set of objects of the groupoid and it identifies with the set of pairs (x,x) with $x \in X$).

Now, say you have a move from $graph_1$ to $graph_2$. Then, as in the boldfaced previous description, but somehow in the opposite sense, you define graphs A, B such that $graph_1$ is AB and graphs C,D such that $graph_2$ is CD.

Then you say that you can perform the reduction from $graph_1$ to $graph_2$ only if the nodes of A are all decorated with :a and the nodes of :b are decorated with :b, a different name than :a.

After reduction you decorate the nodes of C with :a and the nodes of D with :b .

In this way the actors with identities :a and :b change their state during the reduction (i.e. the graph made by the nodes decorated with :a and the arrows decorated with (:a,:a) change, same for :b).

The reduction can be done for the graph G only at chunks $graph_1$ which are decorated as explained.

To explain what actor :Bob is doing it matters from which point of view. Also, what is the relation between actors and the chemical interpretation, how they fit there?

So let’s take it methodically.

The point of view of the GUI

If we discuss from the point of view of playing with the gui, then the user of the gui has global, God’s view over what happens. That means the the user of the gui can see the whole graph at one moment, the user has a clock which is like a global notion of time. So from this point of view the user of the gui is the master of space and time. He sees the fates of :Bob, :Alice, :Claire, :Dan simultaneously. The user has the right in the gui world to talk about parallel stuff happening (i.e. “at the same time”) and sequential stuff happening (to the same actor or actors). The user may notice that some reductions are independent, in the sense that wrt to the user’s clock the result is the same if first :Bob interacts with :Alice and then :Claire interacts with :Dan or conversely, which makes the user think that there is some notion more general than parallelism, i.e. concurrency.

If we discuss from the point of view of :Bob, it looks different. More later.

Let’s stay at the user of the gui point of view and think about what actors do. We shall use the user’s clock for reference to time and the user’s point of view about space (what is represented on the screen via the viz tool) to speak about states of actors.

What the user does:

– he defines the graph types an the rules of reduction

– he inputs a graph

– he decorates it with actors names

– he click some buttons from time to time ( deus ex machina quote : “is a plot device whereby a seemingly unsolvable problem is suddenly and abruptly resolved by the contrived and unexpected intervention of some new event, character, ability or object.” )

At any moment the actor :Bob has a state.

Definition: the state of :Bob at the moment t is the graph formed by the nodes decorated with the name :Bob, the arrows decorated by (:Bob, :Bob) and the arrows decorated by (:Bob, :Alice), etc .

Because each node is decorated by an actor name, it follows that there are never shared nodes between different actors, but there may be shared arrows, like an arrow decorated (:Bob, :Alice), which is both belonging to :Bob and :Alice.

The user thinks about an arrow (:Bob, :Alice) as being made of two half arrows:

– one which starts at a node decorated with :Bob and has a free end, decorated with :Alice ; this half arrow belongs to the state of :Bob

– one which ends at a node decorated with :Alice and has a free start, decorated with :Bob ; this half arrow belongs to the state of :Alice

The user also thinks that the arrow decorated by (:Bob, :Alice) shows that :Bob and :Alice are neighbours there. What means “there”? Is like you, Bob, want to park your car (state of Bob) and the your front left tyre is close to the concrete margin (i.e. :Alice), but you may consider also that your back is close to the trash bin also (i.e :Elvis).

We may represent the neighboring relations between arrows as a new graph, which is obtained by thinking about :Bob, :Alice, … as being nodes and by thinking that an arrow decorated (:Bob, :Alice) appears as an arrow from the node which represents :Bob to the node which represents :Alice (of course there may be several such arrows decorated (:Bob, :Alice) ).

This new graph is called “actors diagram” and is something used by the gui user to put order in his head and to explain to others the stuff happening there.

The user calls the actors diagram “space”, because he thinks that space is nothing but the neighboring relation between actors at a moment in time (user’s time). He is aware that there is a problem with this view, which supposes that there is a global time notion and a global simultaneous view on the actors (states), but says “what the heck, I have to use a way to discuss with others about what’s happening in the gui world, but I will show great caution and restraint by trying to keep track of the effects of this global view on my explanation”.

Suppose now that there is an arrow decorated (:Bob, :Alice) and this arrow, along with the node from the start (decorated with :Bob) and the node from the end (decorated with :Alice) is part of the $graph_1$ of one of the graph rewrites which are allowed.

Even more general, suppose that there is a $graph_1$ chunk which has the form AB with the sub-chunk A belonging to :Alice and the sub-chunk B belonging to Bob.

Then the reduction may happen there. (Who initiates it? Alice, Bob, the user’s click ? let’s not care about this for a moment, although if we use the user’s point of view then Alice, Bob are passive and the user has the decision to click or not to click.)

This is like a chemical reaction which takes into consideration also the space. How?

Denote by Alice(t) and Bob(t) the respective states of :Alice and :Bob at the moment t. Think about the states as being two chemical molecules, instead of one as previously.

Each molecule has a reaction site: for Alice(t) the reaction site is A and for Bob(t) the reaction site is B.

They enter in the reaction if two conditions are satisfied:

– there is an enzyme (say the beta enzyme, if the reduction is the beta) which can facilitate the reaction (by the user’s click)

– the molecules are close in space, i.e. there is an arrow from A to B, or from B to A

So you see that it may happen that Alice(t) may have inside a chunk graph which looks like A and Bob(t) may have a chunk graph which looks like B, but if the chunks A, B are not connected such that AB forms a chunk which is like the $graph_1$ of the beta move, then they can’t react because (physical interpretation, say) they are not close in space.

The reaction sites of Alice(t) and Bob(t) may be close in space, but if the user does not click then they can’t react because there is no beta enzyme roaming around to facilitate the reaction.

If they are close and if there is a beta enzyme around then the reaction appears as

Alice(t) + Bob(t) + beta = Alice(t+1) + Bob(t+1) + garbage

Let’s see now who is Alice(t+1) and Bob(t+1). The beta rewrite replaces $graph_1$ (which is AB) by $graph_2$ (which is CD). C will belong to Alice(t+1) and D will belong to Bob(t+1). The rest of Alice(t) and Bob(t) is inherited unchanged by Alice(t+1) and Bob(t+1).

Is this true? What about the actors diagram, will it change after the reaction?

Actually $graph_1$, which is AB, may have (and it usually does) other arrows besides the ones decorated with (:Bob, :Alice). For example A may have arrows from A to the rest of Alice(t), i.e. decorated with (:Alice, :Alice), same for B which may have others arrows from B to the rest of B(t), which are decorated by (:Bob, :Bob).

After the rewrite (chemical reaction) these arrows will be rewired by the replacement of AB by CD, but nevertheless the new arrows which replace those will be decorated by (:Alice, :Alice) (because they will become arrows from C to the rest of Alice(t+1)) and (:Bob, :Bob) (same argument). All in all we see that after the chemical reaction the molecule :Alice and the molecule :Bob may loose or win some nodes (atoms) and they may suffer some internal rewiring (bonds), so this looks like :Alice and :Bob changed the chemical composition.

But they also moved as an effect of the reaction.

Indeed, $graph_1$, which is AB, may have other arrows besides he ones decorated with (:Bob, :Alice) , (:Bob, :Bob) or (:Alice, :Alice). The chunk A (which belongs to Alice(t)) may have arrows which connect it with :Claire, i.e. there may be arrows from A to another actor, Claire, decorated with (:Alice, :Claire), for example.

After the reaction which consist in the replacement of AB by CD, there are rewiring which happened, which may have as effect the apparition of arrows decorated (:Bob, :Claire), for example. In such a case we say that Bob moved close to Claire. The molecules move this way (i.e. in the sense that the neighboring relations change in this concrete way).

Pit stop

Let’s stop here for the moment, because there is already a lot. In the next message I hope to talk about why the idea of using a Chemical reaction network image is good, but still global, it is a way to replace the user’s deus ex machina clicks by random availability of enzymes, but still using a global time and a global space (i.e. the actors diagrams). The model will be better also than what is usually a CRN based model, where the molecules are supposed to be part of a “well stirred” solution (i.e. let’s neglect space effects on the reaction), or they are supposed to diffuse in a fixed space (i.e let’s make the space passive). The model will allow to introduce global notions of entropy.

Such a CRN based model deserves a study for itself, because it is unusual in the way it describes the space and the chemical reactions of the molecules-actors as aspects of the same thing.

But we want to go even further, towards renouncing at the global pov.

# FAQ: chemlambda in real and virtual worlds

Q1. is chemlambda different than previous models, like the algorithmic chemistry of Fontana and Buss, or the CHAM of Berry and Boudol?

A1. Yes. In chemlambda we work with certain graphs made of nodes (atoms) and bond (arrows), call such a graph a  molecule.  Then:

• (A) We work with individual molecules, not with populations of molecules. The molecules encode information in their shape, not in their number.
• (B) different from algorithmic chemistry, the application and abstraction are atoms of the molecules.
• (C) There are no variables in chemlambda and there is no need to introduce one species of molecules per variable, like in the previous models.
• (D) chemlambda and it’s associated computing model (distributed GLC)  work well in a decentralized world, there is no need for having a global space or a global time for the computation.

There is a number of more technical differences, like (non exhaustively):

• (E)  molecules  are not identified with their functions. Technically, chemlambda rejects eta reduction, so even for those molecules which represent lambda terms, they are not identified (as happens when we use eta reduction) with their function. This calls for an “extreme” functional programming style.
• (F) only a small part of the chemlambda molecules correspond to lambda terms (there is a lambda calculus “sector”).
• (G) there is no  global semantics.

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Q2.  is chemlambda a kind of computing with chemical reaction networks (CRNs)?

A2. No. Superficially, there are resemblances, and really one may imagine CRNs based on chemlambda, but this is not what we are doing.

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Q3. Why do you think chemlambda has something to tell about the real or even about the living world?

A3. Because the real world, in it’s fundamental workings, does not seem to care about 1D language based constructs which we cherish in our explanation. The real and especially the living world seems to be based on local, asynchronous interactions which are much more like signal transductions and much less like information passing. (See How is different signal transduction from information theory? )
Everything happens locally, in nontrivial but physical ways, leading to emergent complex behaviours. Nature does not care about coordinates and names of things or abstractions, unless they are somehow physically embodied. This is the way chemlambda functions.

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Q4. Why do you think chemlambda has something to say about the virtual  world of the Net?

A4. Because it puts the accent on alife instead of AI, on decentralization instead of pyramidal constructs.  A microbial ecology like internet is much more realistic to hope to realize than one based on benevolent pyramidal AI constructs (be them clouds, or other corporations constructs). Because real and virtual worlds are consistent only locally.

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Q5. What about the Internet of Things?

A5. We hope to give to the IoT the role of the bridge which unites two kinds of computations real-virtual, under the same chemistry.

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Q6. What would happen in your dream world?

A6. There are already some (fake) news about it here: what if

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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]

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]

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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