Stuart Kauffman (notes on others)
number of cell types = sq root of number of genes
i don’t see anything in self emergent sytems that is diff from natural selection (i.e.nat selection is about creation ofmultiple competing sustems, selfemergence is about merging of indiv systems into a symbiotic whole.
“in The Origins of Order  Kauffman calculates the minimum complexity (threshold) of a closed autocatalytic set as 6165 different molecules under favourable conditions and 34 million under unfavourable conditions. It’s a pity that he did not mention these results in At Home in the Universe. Because the simplest free-living organism, Mycoplasma genitalium, has only 468 genes! ”
Information theory and molecular biology”
by Hubert Yockey
An autonomous agent is something that can both reproduce itself and do at least one thermodynamic work cycle.
“There is a chance that there are general laws. I’ve thought about four of them. One of them says that autonomous agents have to live the most complex game that they can. The second has to do with the construction of ecosystems. The third has to do with Per Bak’s self-organized criticality in ecosystems. And the fourth concerns the idea of the adjacent possible. It just may be the case that biospheres on average keep expanding into the adjacent possible. By doing so they increase the diversity of what can happen next.
biospheres, as a secular trend (kauffman has an annoying habit of using ’secular’ instead of long term), maximize the rate of exploration of the adjacent possible. If they did it too fast, they would destroy their own internal organization.
“Normally, when we think about a bacterium swimming upstream in a glucose gradient we say that the bacterium is going to get food. That is to say, we talk about the bacterium teleologically, as if it were acting on its own behalf in an environment.”
This is because we view things the wrong way round.
living things are autonomous agents
an autonomous agent can reproduce and do one work cycle
this requires an open thermodynamic system (it is an idea rather than a thing - a whirlpool rather than the water in a whirlpool at any one time)
“cells do thermodynamic work to build a structure called the membrane, which in turn manipulates constraints on reactions, meaning that cells do work at constructing constraints that manipulate constraints. ” hmm
“cannot do a work cycle at equilibrium, meaning that the concept of an autonomous agent is inherently a non equilibrium concept.”-sameas opensystem really.
“Peter Atkins gives a definition of work that I find congenial. He says that work itself is a thing—the constrained release of energy.”- i.e. directed information
Th ediff between a whirlpool and life is that the whirlpool merely reproduces itself,it doesn’t (necessarily) create some directed work.
Also - why is kauffman obsessed with maxwell’s demon. The paradox goes away if information is real (and that all that varies is the efficiency of ts storage).
An NK automaton is an autonomous random network of N Boolean logic elements. Each element has K inputs and one output. The signals at inputs and outputs take binary (0 or 1) values. The Boolean elements of the network and the connections between elements are chosen in a random manner. There are no external inputs to the network. The number of elements N is assumed to be large.
If k is large (=N) behaviour is random(i.e. state 2 bears no relation to 1)
(this is key to an information form of darwinism)
[The "programs" are very sensitive to minimal disturbances (a minimal disturbance is a change of an output of a particular element during an automaton operation) and to mutations (changes in Boolean element types and in network connections). The attractor lengths L are very large: L ~ 2N/2 . The number of attractors M is of the order of N.] - what does this mean?
At K ~ 2 the network behavior changes drastically. The sensitivity to minimal disturbances is small. The mutations create typically only slight variations an automaton dynamics. Only some rare mutations evoke the radical, cascading changes in the automata “programs”. The attractor length L and the number of attractors M are of the order of N1/2.
(k= 2 is like a pair breeding sexual reproduction environment)
“if we compare the number of automaton attractors M at K = 2 (calculated for given number of genes N) with the number of different kind of cells ncells in biological organisms at various evolutionary levels, we find similar values; for example, for a human we have (N ~ 105): M = 370, ncells = 254″
same as square root thing above
to model darwinism:
work cycle =inheritance
mutation = ? (change in wiring - input or output?)
name: Per Bak