Tag Archives: IoT

Pharma meets the Internet of Things

Pharma meets the Internet of Things, some commented references for this future trend. Use them to understand

[0] After the IoT comes Gaia

There are two realms of computation, which should and will become one: the IT technology and biochemistry.

General stuff

The notion of computation is now well known, we speak about what is computable and about various models of computation (i.e. how we compute) which always turned out to be equivalent in the sense that they give the same class of computable things (that’s the content of the Church-Turing thesis).

It is interesting though how we compute, not only what is computable.

In IT perhaps the biggest (and socially relevant) problem is decentralized asynchronous computing. Until now there is no really working solution of a model of computation which is:
– local in space (decentralized)
– local in time (asynchronous)
– with no pre-imposed hierarchy or external authority which forces coherence

In biochemistry, people know that we, anything living, are molecular assemblies which work:
– local in space (all chemical interactions are local)
– local in time (there is no external clock which synchronizes the reactions)
– random (everything happens without any external control)

Useful links for an aerial view on molecular computing, seen as the biochemistry side of computation:

[1] https://www.britannica.com/technology/DNA-computing

Some history and details provided. Quote from the end of the section “Biochemistry-based information technology”

“Other experiments have shown that basic computations may be executed using a number of different building blocks (for example, simple molecular “machines” that use a combination of DNA and protein-based enzymes). By harnessing the power of molecules, new forms of information-processing technology are possible that are evolvable, self-replicating, self-repairing, and responsive. The possible applications of this emerging technology will have an impact on many areas, including intelligent medical diagnostics and drug delivery, tissue engineering, energy, and the environment.”

[2] http://www.owlnet.rice.edu/~Cyrus.Mody/MyPubs/Molecular%20Electronics.pdf

A detailed historical view (written in 2000) of the efforts towards “molecular electronics”. Mind that’s not the same subject as [1], because the effort here is to use biochemistry to mimic silicon computers. While [1] also contains such efforts (building logical gates with DNA, etc), DNA computing does propose also a more general view: building structure from structure as nature does.

[3] https://www.extremetech.com/tag/molecular-computer

Two easy to read articles about real applications of molecular computing:
– “Microscopic machine mimics the ribosome, forms molecular assembly line”
– “Biological computer can decrypt images stored in DNA”

[4] https://www.technologyreview.com/s/601842/inside-genomics-pioneer-craig-venters-latest-production/

Article about Craig Venter from 2016, found by looking for “Craig Venter Illumina”. Other informative searches would be “Digital biological converter” or anything “Craig Venter”

[5] https://www.ted.com/talks/lee_cronin_print_your_own_medicine/transcript?language=en

Interesting talk by an interesting researcher Lee Cronin

[6] The Molecular Programming Project http://molecular-programming.org/

Worth to be browsed in detail for seeing the various trends and results

Sitting in the middle, between biochemistry and IT:

[1] Algorithmic Chemistry (Alchemy) of Fontana and Buss

Walter Fontana today: http://fontana.med.harvard.edu/www/index.htm

[2] The Chemical Abstract Machine by Berry and Boudol


[3] Molecular Computers (by me, part of an Open Science project, see also my homepage http://imar.ro/~mbuliga/ and the chemlambda github page https://github.com/chorasimilarity/chemlambda-gui/blob/gh-pages/dynamic/README.md )


On the IT side there’s a beautiful research field, starting of course with lambda calculus by Church. Later on this evolved in the direction of rewriting systems, then graph rewriting systems. I can’t even start to write all that’s done in this direction, other than:

[1] Y. Lafont, Interaction Combinators

but see as well the Alchemy, which uses lambda calculus!

However, it would be misleading to reduce everything to lambda calculus. I came to the conclusion that lambda calculus or Turing machines are only two among the vast possibilities, and not very important. My experience with chemlambda shows that the most relevant mechanism turns around the triple of nodes FI, FO, FOE and their rewrites. Lambda calculus is obtained by the addition of a pair of A (application) and L (lambda) nodes, along with standard compatible moves. One might use as well nodes related to a  Turing Machine instead, as explained in


Everything works just the same. The center, what makes things work, is not related to Logic or Computation as they are usually considered. More later.

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:


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.

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.





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.


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

Alife vs AGI

Artificial general intelligence  is, of course, on the top of the mind of some of the best or most interesting researchers. In the post Important research avenues on my mind, Ben Goertzel writes:

1. AGI, obviously … creating robots and virtual-world robots that move toward human-level general intelligence


5. Build a massive graph database of all known info regarding all organisms, focused on longevity and associated issues, and set an AI to work mining patterns from it… I.e. what I originally wanted to do with my Biomind initiative, but didn’t have the $ for…

6. Automated language learning — use Google’s or Microsoft’s databases of text to automatically infer a model of human natural languages, to make a search engine that really understands stuff.  This has overlap with AGI but isn’t quite the same thing…

7. I want to say femtotech as I’m thinking about that a fair bit lately but it probably won’t yield fruit in the next few years…


9. Nanotech-using-molecular-bio-tools and synthetic biology seem to be going interesting places, but I don’t follow those fields that closely, so I hope you’re pinging someone else who knows more about them…

I believe that 9 is far more likely to achieve sooner than 1. Will explain a bit later, after looking a bit at the frame of mind which, I think, constrains this ordering.

AGI is the queen, the graal, something which almost everybody dreams to see. It is an old dream. Recent advances in cognition show that yeah, we, Natural general intelligence beings, are kind of robots with many, many processes going in parallel in the background, all of them giving the feeling of reality. On top of all these processes are the ones related to consciousness and high level functioning of the brain. It is admirable to try to model those, but it is naive, and coming from a old way of seeing things, to believe that the other processes are somehow not as interesting, or not really needed, or simply they are too mechanical, anyway, not something which is a challenge. Reality is that we now know that we even don’t have the right frame of mind to understand how to understand the functioning of those neglected, God given processes.

So, that is why I believe that AGI is not realistic. Unless we concentrate on language, or other really puny aspects of GI, but with lots of traditions.

Btw, have I told you that whatever I write, I am always happy to be contradicted?

The points 5 and 6 look indeed very probable. Will be done by corporations, that is sure. Somehow is the same thing behind, namely that there is an essence of the pyramidal way of thinking, such that with enough means, knowledge will accumulate on top of that pyramid. (For the point 1 intelligence is the top and for 5 and 6 corporations are on top, of course).

As regards the point 7, that starts to be genuinely new, therefore less fashionable. The idea of a single molecule quantum computer springs into mind. Should be known better. [See the comments at this G+ post.]

Several concepts are now under development to make a calculation using a single molecule:
1) to force a molecule to look like a classical electronic circuit but integrated inside the molecule
2) to divide the molecule into “qubits” in order to exploit the quantum engineering developed since several years around quantum computers.
3) to use intramolecular dynamical quantum behavior without dividing molecules into “qubits” leading to Hamiltonian quantum computer

Now, to point 9!

It can be clearly done by a combination of decentralized computing with artificial chemistry. 

In a future post I shall describe with details, by using also previous posts from chorasimilarity, which are the ingredients and what are the arguments in favour of this idea.

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.

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