Chemical Automata

I first came across Chemoton (Chemical Automaton) Theory a few months ago when reading a paper entitledSoftware Replica of Minimal Living Processes, and ever since it has been an inspiration.  At the time, I was trying to figure out how I could possibly build a system that spanned the range of complexity from Chemistry to a minimal Biology.  I was going off of Walter Fontana’s incredible Algorithmic Chemistry work, trying to find a way that his Lambda Calculus approach could become spatial.  It was Ganti’s Chemoton Theory that finally got me there.

Incredibly, the publication of Chemoton Theory in 1971 and subsequent refinement in the early 70′s was practically simultaneous with Maturana and Varela’s Autopoiesis work and Manfred Eigen’s RNA Hypercycles Theory.  Chemoton Theory, unlike Autopoiesis, is based on a very precise model, though simplified, model of chemistry.  In recent years, Ganti has even gone so far as to detail what actual chemical reactions could possibly realize a Chemoton.  Autopoiesis provides no such precision although the work of Pier Luigi Luisi has taken it much further in that direction.

A Chemoton is a network of 3 autocatalytic cycles: the metabolic (energy), template replication (information), and membrane (boundary/dynamics).  Together, they model a minimal living entity as they meet Ganti’s basic criteria of a living system:

• it’s an individual unit
• it performs metabolism
• it’s inherently stable despite constant transformation
• it has an information subsystem that programs the whole
• it’s processes are regulated and controlled

I’m, of course, leaving out a lot of the details so this may not seem like a full definition of a living system.  For the complete explanation, see Ganti’s paper Biogenesis Itself or even better his book The Principles of Life.

What’s most intriguing about the Chemoton from a worldmaking standpoint is it’s fluid nature.  Chemical reactions function best in a fluid environment where spatiality is subsumed by chemical concentrations and statistical tendencies.  There doesn’t need to be a strict spatial ordering for Chemotons to function, just the appropriate chemical concentrations bounded inside a membrane.

Chemoton Theory shows in precise detail how to go from chemistry to a minimal biological unit, but it doesn’t say much about the structure of the membrane or how networks of membranes might form into more complex biological structures.  In the end of Chemoton Theory vol. 1, Ganti speculates about how computers might be built from such objects, but doesn’t link it to Morphogenesis or Topobiology.

http://moniker.name/worldmaking/?p=42

Another view on the Seed Dispersal

Biotic Seed Dispersal

http://database.portal.modwest.com/start.php

The dispersal of seeds can be split up into two major classes: biotic or abiotic dispersal. Abiotic dispersal methods use wind, water, or other abiotic forces to distribute seeds, while biotic dispersal relies on the movements of animals or other organisms for dispersal. The advantages of biotic dispersal are several. Animal movements are predictable and correlated with environmental cues, allowing plants to time seed production to correspond with these movements and environmental changes. Animals can also carry large, heavy seeds with more food for seedling growth thus enhancing the chances for reproductive success of the parent species. Then too, animals have food preferences that impose a sort of consistency on their movements and feeding locations. The presumption here is that if an animal shows a preference for a food type, and the source plant for that food has a selective preference for certain niches, as the animal moves from one location or niche to another in search of that food these locations will be relatively well suited to colonization by the seeds from the plant. And finally, animals can recognize color and odor cues. Mechanisms of animal transport include several different passive methods. In some instances, transport relies on some sort of adhesive (burrs, glues, etc.) to attach seeds to the animal. In other instances, ingestion[섭취] and subsequent off-site defecation[배변] of seeds is the method of dispersal. And finally, fruit hoarding[비축하기], or excess food production satiates[실컷 만족시키다] seed predators. Biotic seed dispersal may inspire a biomimetic systems for the distribution of materials in industrial cycles

Biotic Seed Dispersal

http://database.portal.modwest.com/start.php

The dispersal of seeds can be split up into two major classes: biotic or abiotic dispersal. Abiotic dispersal methods use wind, water, or other abiotic forces to distribute seeds, while biotic dispersal relies on the movements of animals or other organisms for dispersal. The advantages of biotic dispersal are several. Animal movements are predictable and correlated with environmental cues, allowing plants to time seed production to correspond with these movements and environmental changes. Animals can also carry large, heavy seeds with more food for seedling growth thus enhancing the chances for reproductive success of the parent species. Then too, animals have food preferences that impose a sort of consistency on their movements and feeding locations. The presumption here is that if an animal shows a preference for a food type, and the source plant for that food has a selective preference for certain niches, as the animal moves from one location or niche to another in search of that food these locations will be relatively well suited to colonization by the seeds from the plant. And finally, animals can recognize color and odor cues. Mechanisms of animal transport include several different passive methods. In some instances, transport relies on some sort of adhesive (burrs, glues, etc.) to attach seeds to the animal. In other instances, ingestion[섭취] and subsequent off-site defecation[배변] of seeds is the method of dispersal. And finally, fruit hoarding[비축하기], or excess food production satiates[실컷 만족시키다] seed predators. Biotic seed dispersal may inspire a biomimetic systems for the distribution of materials in industrial cycles

Janine Benyus: Biomimicry in action

Interview: Michael Pawlyn on Biomimicry

Why were you drawn to biomimicry?
As a teenager I was torn between studying architecture and biology and eventually chose the former. I was also quite politicized about environmental issues in my early teens after a relative gave me a copy of the Club of Rome’s “Blueprint for Survival”. When I joined Grimshaw to work on the Eden Project, I realized that there was a way to bring these strands together in pursuit of sustainable architecture inspired by nature.

You say we are entering the ecological age. What does that mean exactly?
As I see it, this is the age in which we have the knowledge, technology and imperative to formulate a truly sustainable way of living rather than pursuing approaches that simply mitigate negative impacts.

What are some of the most interesting examples, apart from the Eden Project, of existing architecture that uses biomimicry as its guiding principle?
Pier Luigi Nervi’s Palazzetto dello Sport, an indoor arena in Rome, is a masterpiece of efficiency inspired by giant Amazon water lilies. Many of Nervi’s projects were won in competitions and the secret to his success was his ability to produce the most cost-effective schemes. In a satisfying parallel with the refining process of evolution, the combination of ingenuity and biomimicry led to a remarkable efficiency of resources.

The Eastgate Centre in Harare, Zimbabwe by Mick Pearce, is based on termite mounds. It manages to create comfortable conditions for the people inside without air-conditioning in a tropical environment.

What species in nature are you most in awe of and why?
Camel’s nostrils are miracles of heat exchange and water recovery engineering. We are currently looking at cuttlebone(오징어 뼈) and bird skulls(두개골) to help design more efficient concrete structures for office buildings. The combustion(연소) chamber in the abdomen(하복부) of a bombardier beetle mixes two high explosives from fuel tanks with valves that open and close 200 times a second—it is being studied in order to develop needle-free medical injections, more efficient fuel injection systems and more effective fire extinguishers.

Not everything in nature is innocuous. Which are the species you would not want to “mimic”?
There are quite a few species that have been studied by defense industries in order to develop sophisticated weapons using parasites, natural toxins, germ warfare and the like. This is why some people make a distinction between “biomimicry” (which is specifically about developing sustainable solutions) and the more general term of “biomimetics”.

You have said that environmentally sustainable architecture tends to focus on mitigation, when it should be regenerative and restorative. How achievable is this?
Humans are accustomed to engineering things to maximize one goal, whereas ecosystems have evolved towards an optimized overall system. We are only slowly embracing the benefits of designing the kind of synergistic systems like the Cardboard to Caviar project (a closed-loop scheme which takes restaurant waste, turns it into horse bedding, feeds it to worms who in turn are fed to fish whose caviar eventually ends up back on the plates of the restaurant) and the Sahara Forest project.

It is also partly down to conventional economics, which externalizes issues such as pollution, liquidation of natural capital and so on. If we were to shift some taxation away from employment and towards the use of resources it would reward resource efficiency.

How would the construction industry have to change?
We need to get better at procuring the built environment in a way that delivers the maximum long-term value for the minimum long-term cost. At the moment, progress is hampered by short-term thinking, conventional economics and collaboration that do not lead to optimized results.

Why is getting something like the Sahara Forest project off the ground so slow? It seems like this is innovation with few downsides.
The powerful vested interests of oil and motor companies—both of which provide extensive funding to political parties—are a major impediment.

Short term ways of thinking also tend to favor solutions that produce quick profits at the expense of long-term loss. I think this occurred in the late ’80s and early ’90s when developers were fairly brazen about saying that they weren’t interested in anything with a payback period. We now need to create investment models that allow people to invest in longer term projects that deliver value far into the future.

What other projects are you working on at the moment?
I’m working on a concept study for a biomimetic office building—essentially using biomimicry to completely rethink the workplace with the aim of producing a scheme that is as far as possible self-heating, self-cooling and self-ventilating, entirely day-lit and a net producer of energy. Plants will also be incorporated to boost human productivity. A radical new approach to designing IT servers that delivers a factor-10 reduction in carbon emissions is possibly on the cards as well.

Via The Economist