A solution for the “Amazon’s war on publishers”

I spent some time thinking about the “Amazon’s war on publishers” (learned via +Tim O’Reilly post https://plus.google.com/u/0/+TimOReilly/posts/WhyyNx7PYnt ) and now I believe that I have a solution.

The publishers and Amazon could behave maturely and use the method of scientific publishers with the researchers!

Step 1.  Amazon should hire some prominent authors or publishing managers

Step 2.  Amazon should ask the publishers to renounce at their rights, should they want their creation to appear on Amazon site

Step 3. The hired prominent authors and managers should make clear to any publisher and author that if their work is not on Amazon then it is probably crap.

You see, scientists are the most clever people, so if they are happy with this system, then  everybody should be happy too!

[There is a false assumption in this text, which is, unfortunately, a pamphlet.]

________________________________________________

Zipper logic appeared in math.CO (combinatorics)

Today,  a week after the submission, the article Zipper Logic   arXiv:1405.6095 appeared in math.CO , math GT, and not in math.LO , math.GT.

Actually, combinatorics, especially lately, is everywhere, being probably one of the most dynamic research fields in mathematics.

There is a small world connection of zipper logic with combinatorics,   because zipper logic is a variant of chemlambda, which is a variant of GLC, which has an emergent algebra sector  arXiv:1305.5786 section 5 , which is a sort of approximate algebraic structure, alike, but not the same as the approximate groups arXiv:1110.5008 .

____________________________________

 

Morlocks and eloi in the Internet of Things

For any fan of Neal Stephenson and Cory Doctorow,  the contents of the following opinion piece on goals and applications of the Internet of Things (IoT) should be no great surprise.

I am using the post Technical Machine – Designing for Humans as a study case.

[ Technical Machine is the company which builds  the Tessel. This is a product with a great potential! I wish I could use tessels for   the purpose explained in the post Experimental alife IoT with Tessel .  ]

This nice post is interesting in itself, but it is also an example of the shifting of the ideology concerning the Internet of Things.

I extract two contradictory quotes from the post and then I discuss them (and explain why they seem to me contradictory).

(1) ” A completely interactive tool, one that seamlessly incorporates humans as a piece of the system, is a tool that people don’t even think about. That’s the end goal: Ubiquitous Computing as Mark Weiser imagined it. Every object is an embedded device, and as the user, you don’t even notice the calm flow of optimization.
The Nest thermostat is a good example of this sort of calm technology. The device sits on your wall, and you don’t spend much time interacting with it after the initial setup. It learns your habits: when you’re home, when you’re not, what temperatures you want your house to be at various points in the day. So you, as the user, don’t think about it. You just live in a world that’s better attuned to you.”

_______

(2) “I think that one of the most interesting things we’ll see in the near future is the creation of non-screen interfaces. Interacting with technology, we rely almost solely on screens and buttons. But in the physical world, we use so many other interfaces. […] there’s a lot of fascinating work going on to receive outputs from humans. […] The implications there are amazing: you can wire up your own body as an electrical input into any electrical system– like a computer, or a robot, or whatever else you might build. You can control physical and digital things just by thinking really hard or by twitching your fingers.”

_______________

Now the discussion. Why are (1) and (2) contradictory?

I shall explain this by using the morlocks/eloi evocative oversimplification.

From historical reasons maybe the morlocks (technical nerds) are trained/encouraged/selected to hate discussions, human exchanges and interactions in general. Their dream technology is one like in (1), i.e. one which does not talk with the humans, but quietly optimize (from the morlock pov) the eloi environment.

On the contrary, the eloi love to talk, love to interact one with the others. In fact the social Net is a major misuse of morlock technology by eloi. Instead of a tool for fast and massive share of data, as the morlocks designed it, the Net became a very important (most important?) fabric of human interactions, exchanging lolcats images and sweet little nonsenses which make the basis of everyday empathic interaction with our fellow humans. And much more: the eloi prefer to use this (dangerous) tool for communicating, even if they know that the morlocks are sucking big data from them. They (the eloi) would prefer by far to not be in bayesian bubbles, but that’s life, they are using opportunistically things they don’t understand how they work, despite being told to be more careful.

The quote (2) show that people start to think about the IoT as an even more powerful tool of communication. OK, we have this nice technology which baby-sits us and we live calm lives because quietly the machine optimizes the little details without asking us. But, think that we can use the bit IoT machine for more than conversations. We can use it as the bridge which unites the virtual and the meat spaces, we can make real things  from discussions and we can discuss about real objects.

This is a much more impressive application of the IoT than the one which optimizes our daily life. It is something which would allow to make our dreams come true, literary! And collaboratively.

I have argued before about that, noticing that “thing” means both an assembly and a discussion (idea taken via Kenneth Olwig) and object is nothing but the result,  or outcome of a discussion, or evidence for a discussion. See the more at the post Notes for Internet of Things not Internet of objects.

It’s called “Internet of Things” and not “Internet of Objects” and it seems that morlocks start to realize this.

_________________________________________

 

 

 

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.

 

_______________________________________________

 

 

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.

__________________________________________________
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.

__________________________________________________

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.

__________________________________________________
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.

__________________________________________________
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.

__________________________________________________
Q6. What would happen in your dream world?

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

__________________________________________________

 

 

 

Zipper logic and RNA pseudoknots

UPDATE: compare with the recent Chemlambda strings (working version).

Zipper logic is a variant of chemlambda, enhanced a bit with a pattern identification move called CLICK.

Or, chemlambda is an artificial chemistry.  Does it have a natural, real counterpart?

It should. Finding one is part of the other arm of the research thread presented here, which aims to unite (the computational part of) the real world with the virtual world, moved by the same artificial life/real life basic bricks. The other arm is distributed GLC.

A lot of help is needed for this, from specialists!Thank you for pointing to the relevant references, which I shall add as I receive them.

Further is a speculation, showing that zipper graphs can be turned into something which resembles very much with RNA pseudoknots.

(The fact that one can do universal computation with RNA pseudoknots is not at all surprising, maybe with the exception that one can do functional style programming with these.)

It is a matter of notation changes. Instead of using oriented crossings for denoting zippers, like in the thread called “curious crossings” — the last  post is Distributivity move as a transposition (curious crossings II) — let’s use another, RNA inspired one.

rna_2

So:

  • arrows (1st row) are single stranded RNA pieces. They have a natural 5′-3′ orientation
  • termination node (2nd row) is a single strand RNA with a “termination word on it”, figured by a magenta rectangle
  • half-zippers are double strands of RNA (3rd and 4th rows). The red rectangle is (a pair of antiparallel conjugate) word(s) and the yellow rectangle is a tag word.

Remark that any (n) half-zipper can be transformed into a sequence of (1) half-zippers, by repeated applications if the TOWER moves, therefore (n) half-zippers appear in this notation like strings of repeated words.

Another interesting thing is that on the 3rd row of the figure we have a notation for the lambda abstraction node and on the 4th row we have one of the application  node form chemlambda. This invites us to transform the other two nodes — fanin and fanout — of chemlambda into double stranded RNA. It can be done like this.

rna_3

On the first two rows of this picture we see the encoding of the (1) half-zippers, i.e. the encoding of the lambda abstraction and application, as previously.

On the 3rd row is the encoding of the fanout node and on the 4th row the one of the fanin.

In this way, we arrived into the world of RNA. The moves transform as well into manipulations of RNA strings, under the action of (invisible and to be discovered) enzymes.

But why RNA pseudoknots? It is obvious, as an exercise look how the zipper I and K combinators look in this notation.

rna_4

We see hairpins.

___________________________________

Conclusion:  help needed for chemistry experts. Low hanging fruits here.

___________________________________

Chemlambda at ALIFE 14

Good news for chemlambda, our article

M. Buliga, L. H. Kauffman, Chemlambda, universality and self-multiplication, arXiv:1403.8046 [cs.AI]

has been accepted in the ALIFE 14 conference:

ALIFE 14: The Fourteenth International Conference on the Synthesis and Simulation of Living Systems,

July 30th – Aug 2nd, New York

Louis Kauffman will give the talk. I shall not be there, but for anybody interested in chemlambda, who will also be in New York then, this is a good occasion to meet and discuss more there, live.

______________________________

How is different signal transduction from information theory?

They look different.

“Signal transduction occurs when an extracellular signaling[1] molecule activates a specific receptor located on the cell surface or inside the cell. In turn, this receptor triggers a biochemical chain of events inside the cell, creating a response.[2] Depending on the cell, the response alters the cell’s metabolism, shape, gene expression, or ability to divide.[3] The signal can be amplified at any step. Thus, one signaling molecule can cause many responses.[4]

Signal transduction involves the binding of extracellular signalling molecules and ligands to cell-surface receptors that trigger events inside the cell. The combination of messenger with receptor causes a change in the conformation of the receptor, known as receptor activation. This activation is always the initial step (the cause) leading to the cell’s ultimate responses (effect) to the messenger. Despite the myriad of these ultimate responses, they are all directly due to changes in particular cell proteins. Intracellular signaling cascades can be started through cell-substratum interactions; examples are the integrin that binds ligands in the extracellular matrix and steroids.[13]

[wiki source]

 

It seems that signal transduction involves:

  • messenger molecule
  • receptor molecule
  • the messenger reacts with the receptor, which changes conformation (receptor activation)
  • receptor activation triggers other chemical reactions

Let’s condense further:

  • molecule M (messenger) binds to molecule R (receptor)
  • the complex MR changes shape (a spatial notion, in a generalized sense)
  • which triggers other reactions between (the new) R with other neighboring molecules.

It is interesting for me because that is how distributed GLC works:

  • the actor M reacts with the actor R
  • after interaction both molecules may change, the one which belongs to the actor M and the one which belongs to the actor R,
  • but also the actors adjacencies may change as well, due to the reductions involving the reaction between M and R (this corresponds to the receptor activation)
  • which triggers other interactions between GLC actors.

 

Information theory, on the other side, concerns a sender, a channel and a receiver. The sender sends messages through the channel to the receiver.

Completely different frames.

One may, of course, partially ignore the mechanism (signal transduction) and look instead at the environment as a sender, to the cell as a receiver and to the cell’s membrane as a channel (just an example).

But sender, channel and receiver look (to me) as mind constructs which are useful for the human trying to make a sense of what is happening, from outside. What is happening though,  is signal transduction.

_________________________________

 

 

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.

______________________________

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

Distributivity move as a transposition (curious crossings II)

It looks that there is a connection of the following with the research on DNA topology, but I shall comment on this in a future post, mainly because I am learning about this right now. (But another main reference is Louis Kauffman.)

Let’s see.

If I am using this encoding of chemlambda nodes with crossings

 

ccdeco_1

which is a variant of the encoding from Curious crossings   then, as in the mentioned post,   the beta move becomes a CLICK between “sticky ends” which are marked with dashed lines, followed by R2b move, and also the FAN-IN move becomes a CLICK between sticky ends, followed by a R2a move.

What about the DIST moves? Let’s take the DIST move which involves an application node and a fanout node. The move looks like this:

ccdeco_surgery_1(Click on the picture to make it bigger.)

In the right column we see the DIST move with chemlambda drawing conventions. In the left column there is the translation with crossings and sticky ends.

What do we see? The strings 1-5 and 6-3 are transposed by the DIST move and a new string appears, which crosses them.

I can draw the same move like this:

ccdeco_surgery_2In this figure, the left column is as before, but the right column has changed. I just kept the order, from left to right, of the strings 6-3 and 1-5, and I wiggled the string 2-4 for this.

This is starting to look interestingly alike some other pictures from  DNA topology.

 

___________________________________________

 

Curious crossings

I’m coming back to  the post   Halfcross way to pattern recognition (in zipperlogic)    and I am going to modify the drawings a bit.

Instead of this convention of transforming chemlambda nodes into half-crossings

halfcross_1

I draw this mapping from chemlambda nodes to crossings:

cdeco_1

Remark that at the left we have now crossings. At the right we have the chemlambda nodes, each with a dashed half-arrow attached, so now the nodes become 4-valent locally planar ones.

As usual (here at chorasimilarity) the crossing diagrams are only locally planar!

Look closer: there are two kinds of oriented crossings, right? To each kind corresponds a colour (green or red) of a chemlambda node.

This is no longer a dictionary, there is no longer a bijective correspondence, because for each oriented crossing there are two possible chemlambda nodes, depending on where is the dashed half-arrow! That is the meaning of the wiggling blue arrow from right to left, it’s uni-directional.

OK then, instead of drawing this interpretation of the beta move

halfcross_2

we get the following one

cdeco_2

where the arrows are drawn like that in order to see what transforms into what (otherwise there is no need for those convoluted arrows in the formalism).

Likewise, instead of this

halfcross_3

I draw this:

cdeco_3

Funny, what could that mean?

________________________________________