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Topic: Autocatalytic sets

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	Autocatalytic set - Wikipedia, the free encyclopedia
		An autocatalytic set is a collection of entities, each of which is able to catalyze the creation of others within the set, such that as a whole, the set is able to catalyze its own replication.
		Autocatalytic sets were originally and most concretely defined in terms of entities which are replicating molecules, but have more recently been metaphorically extended to the study of systems in sociology and economics.
		Such studies make autocatalytic sets candidates for a theoretical explanation of the very early origin of life, but are empirically unsupported in real chemistry.
	en.wikipedia.org /wiki/Autocatalytic_set (535 words)

	Read about Autocatalytic set at WorldVillage Encyclopedia. Research Autocatalytic set and learn about Autocatalytic set ... (Site not responding. Last check: 2007-09-18)
		Therefore, several models of the origin of life are based on the notion that life may have arose through the development of an molecular autocatalytic set.
		Several models that are based on autocatalytic set include Stuart Kauffman and others.
		Formally, it is difficult to treat molecules as anything else but unstructured entities, since the set of possible reactions (and molecules) would become infinite.
	encyclopedia.worldvillage.com /s/b/Autocatalytic_set (524 words)

	Autocatalytic set -- Facts, Info, and Encyclopedia article (Site not responding. Last check: 2007-09-18)
		In this way the set as a whole is said to be (Click link for more info and facts about autocatalytic) autocatalytic.
		Autocatalytic sets were originally and most concretely defined in terms of entities which are replicating ((physics and chemistry) the simplest structural unit of an element or compound) molecules, but have more recently been metaphorically extended to the study of systems in sociology and economics.
		Several models that are based on autocatalytic set include (Click link for more info and facts about Stuart Kauffman) Stuart Kauffman and others.
	www.absoluteastronomy.com /encyclopedia/a/au/autocatalytic_set.htm (192 words)

	[No title]
		An autocatalytic set is a network of catalyzed chemical reactions with nonlinear feedback: pre-replicator metabolisms.
		First via their generality, and then via their stability, life has gobbled up all the amino and nucleic acids that once were found in autocatalytic sets.
		Even better, these replicators may have extended the scope of those autocatalytic sets from incestuous cannibals to the ability to manufacture new nucleic and amino acids out of even simpler building blocks.
	www.etext.org /Politics/Extropy.Institute/szabo.052693 (688 words)

	Stark Reality -- Genes: Maintaining Order
		Autocatalytic sets of reactions can appear even without a genome, a set of instructions for building a new set of reactions.
		The set of catalysts that comprises the autocatalytic collection is uniquely captured in a code comprised of a sequence of nucleotide bases.
		This allows the whole set to not only be copied but also to be copied with great fidelity, and to be altered slightly from one generation to the next yet still remaining collectively autocatalytic.
	members.aol.com /starkreal/Personal/newspersonal/genes.htm (2934 words)

	Gabora: Fabric of Reality
		An autocatalytic system is a set of molecules which, as a group, catalyze their own replication.
		An autocatalytic set: A catalyses the formation of B, and B catalyses the formation of A. Thick fl arrows represent catalyzed reactions.
		For ease of visualization, the set of nested hypercubes representing the space of possible memes is shown as a set of concentric circles, where deeper circles store deeper layers of abstraction (lower dimensional hypercubes).
	www.vub.ac.be /CLEA/liane/FabricOfReality (10863 words)

	At Home in the Universe. (Stuart Kauffman).
		Autocatalytic set theory is an absolute simple model with absolutely non-trivial properties.
		And further: the fortunate set of proteins becoming an autocatalytic set, is a random subset of all possible autocatalytic sets [2].
		However, the theory of autocatalytic sets is a law, albeit a statistical law.
	home.planet.nl /~gkorthof/kortho32.htm (3394 words)

	Autocatalytic Closure in a Cognitive System
		The second probing of memory activates a slightly different set of locations, which evoke the abstract category ‘container’, the class of objects that are concave and impermeable, and for which the attributes bumpy and striped are irrelevant.
		The original set of polymers from which an autocatalytic set emerges is referred to as the ‘food set’.
		Since autocatalytic sets appear to be a predictable, emergent outcome in any sufficiently complex set of polymers, the theory suggests that life is an expected outcome rather than a lucky long-shot.
	www.vub.ac.be /CLEA/liane/ACCS (13759 words)

	NOEMA > IDEAS
		Autocatalytic sets possess the property whereby each member’s formation is catalyzed by one or more members, so that its own high concentration is maintained.
		The set is collectively autocatalytic by virtue of reflexive catalysis among its members.
		Autocatalytic sets exhibit the emergent property of holism.
	www.noemalab.org /sections/ideas/ideas_articles/wittig_landcape_data.html (2104 words)

	'Ideas are Not Replicators but Minds Are' by L. Gabora (Site not responding. Last check: 2007-09-18)
		Such a set is autocatalytically closed because although none of the polymers can catalyze its own replication, each polymer can catalyze the replication of some other polymer in the set, and likewise, its own replication is catalyzed by some other member of the set.
		It is commonly believed that the primitive self-replicating set was enclosed in a small volume (such as a coascervate or liposome) to permit the necessary concentration of reactions (Oparin 1971; Morowitz 1992; Cemin and Smolin 1997).
		We saw that, like autocatalytic sets of polymers, worldviews do not evolve with the efficiency of a symbolic code, but in a piecemeal manner, largely through the expression, assimilation, and accommodation of cultural entities in the course of social interaction.
	www.vub.ac.be /CLEA/liane/papers/replicator.html (7984 words)

	Evolution of genetic evolution
		We have seen that an autocatalytic set is a group of proteins in a watery environment that collectively reproduces itself.
		If a set has a tendency to separate into different parts too readily and too often, it risks breaking up effective arrangements and producing daughter sets that are not competitive.
		The limited ability of autocatalytic sets to discover new proteins was overcome once RNA began to manage autocatalytic sets to form proto cells.
	users.tpg.com.au /users/jes999/9.htm (9562 words)

	Autocatalytic set - Encyclopedia, History, Geography and Biography
		Most of these models which have emerged from the studies of complex systems predict that life arose not from a molecule with any particular trait (such as self-replicating RNA) but from an an autocatalytic set.
		This can be formulated by a closure over a generating subset of M. Formally, cl(S) denotes the smallest subset Y of M that contains S such that for each reaction (A,B)
		Autocatalytic set, Formal definition, Probability that a random set is autocalytic, Formal limitations and External links.
	www.arikah.com /encyclopedia/Autocatalytic_sets (646 words)

	Psycoloquy 9(67): Autocatalytic Closure in a Cognitive System:
		AUTOCATALYTIC SET: A catalyses the formation of B, and B catalyses the formation of A. Thick fl arrows represent catalyzed reactions.
		Kauffman's response is: if we can show that autocatalytic sets emerge for a wide range of hypothetical chemistries (i.e., different collections of catalytic molecules), then the particular details of the chemistry that produced life do not matter so long as it falls within this range.
		The autocatalytic origin of life theory circumvents the chicken-and-egg problem by positing that the same collective entity is both code and decoder.
	www.cogsci.ecs.soton.ac.uk /cgi/psyc/newpsy?9.67 (13968 words)

	Some Remarks on Autocatalysis and Autopoiesis
		This usage depends on the existence of a large set of distinct molecules (which can thus carry ``information'' via their distinctions) but which are all individually autocatalytic, thus allowing for the generation of informational ``copies'' for distribution to offspring.
		The idea here is to consider sets of molecular species such that none of them need be individually autocatalytic (which may be an unfeasible requirement), but where production of every element of the set is effectively catalysed by at least one other member of the same set.
		It is clear that the notion of an autocatalytic set is closely related to the first element of the definition of autopoiesis.
	www.eeng.dcu.ie /~alife/bmcm9901/html-single (5534 words)

	CEPTUAL INSTITUTE: nuc_com002 (Oct 1997) Chaotic Autocatalysis
		Autocatalytic sets are envisioned as being real world expressions of this mathematical process.} The principle dynamic they are trying to evaluate is the process by which complex systems arise so naturally and pervasively when thermodynamic laws do not allow for or expect such events.
		This is exactly identical with "autocatalytic sets", thirty years before becoming institutionally popular, to explain dynamically stable metabolic plateaus that build complexity in opposition to perceived "general entropy".
		The interpretation of that previous statement is that Kauffman et al., are saying that autocatalytic biochemistry establishes the environment and the force to arise complexity.
	www.ceptualinstitute.com /nuc/nuc_com002.htm (1455 words)

	Quantum Evolution, Johnjoe McFadden. Chapter 4
		The sets could even replicate whenever a few drops of the soup containing one autocatalytic set splashes into another pool to start a new cycle.
		The autocatalytic set would have become enclosed within membranes and the first living cell was born.
		My guess is that the spontaneous emergence of autocatalytic sets is only feasible in computers, where each set can be isolated from the jumble of reactions going on around them.
	www.geneticengineering.org /evolution/mcfaddenc4.html (1593 words)

	Citations: Autocatalytic sets of proteins - Kauffman (ResearchIndex) (Site not responding. Last check: 2007-09-18)
		where autocatalytic sets emerge automatically we setup a system with fixed but very large catalytic network which has to be explored by the population: Using an ordered set of 1000 secondary structures as phenotypes, a catalytic network of about 420 random hypercycles of size 3 to 7, and about 18.
		The main idea is that of the so called autocatalytic set, namely a set of chemicals in which each member is the product of at least one reaction catalyzed by at least one other member.
		Such a set al..lows in principle at least for the development of a fortuitous cycle or catalytic closure....
	citeseer.lcs.mit.edu /context/406/0 (1746 words)

	Ideas on NumEconomy as a self-organizing information system
		Autocatalytic sets may be identified as cycles in the transactions graphs which can be considered similar to chemical reaction graphs.
		Autocatalytic sets, by definition will react at greater rates given sufficient inputs.
		These sets can then be used as if it were that prime number.
	www.redfish.com /research/webEconomyIdeas (746 words)

	Psycoloquy 10(007): Joining the Dots: Extending the Autocatalytic Picture
		This is done by changing the unit of replication from a concept to a path consisting of a series of concepts, where each concept in the path has a tendency to cause the next to be recalled into the stream of thought.
		Coherence is the property that there will not be different sections of the population of paths that tend to be mutually exclusive; in Gabora's picture it is possible for two or more separate autocatalytic sets to emerge (although the probability of this could be a function of the connectiveness of the concepts).
		In this way, once an autocatalytic process has occurred so as to stimulate a continuous stream of thought, an evolutionary process acting on paths will tend to develop this into a pervasive and coherent system -- one that might be meaningfully called a `world-view'.
	www.cogsci.ecs.soton.ac.uk /cgi/psyc/newpsy?10.007 (1320 words)

	Origin of life - Wikipedia, the free encyclopedia
		It is therefore hypothesized that such systems may be able to evolve into autocatalytic sets of self-replicating, metabolically active entities that would predate the life forms known today.
		The experiment as performed, produced a relatively small yield of dipeptides (0.4–12.4%) and a smaller yield of tripeptides (0.003%) and the authors note that: "under these same conditions dipeptides hydrolysed rapidly." Another criticism of the result is that the experiment did not include any organomolecules that would most likely cross-react or chain-terminate.
		More abstract and theoretical arguments for the plausibility of the emergence of metabolism without the presence of genes include a mathematical model introduced by Freeman Dyson in the early 1980s, and Stuart Kauffman's notion of collectively autocatalytic sets discussed later in that decade.
	en.wikipedia.org /wiki/Origin_of_life (3496 words)

	Untitled Document
		An autocatalytic set is a collection of molecules which catalyze each other’s reactions—help bring each other into existence, so to speak.
		Even so, as the diversity of the molecules in the pool increases, at some point an autocatalytic set emerges all by itself.
		Suddenly there's a shift from a simple pool of reacting organic molecules to a pool of organic molecules, a small set of which is now able to reproduce itself exponentially, given a requisite flow of food molecules.
	www.mgtaylor.com /mgtaylor/jotm/summer97/complexity.htm (2557 words)

	Citebase - Autocatalytic Sets and the Growth of Complexity in an Evolutionary Model (Site not responding. Last check: 2007-09-18)
		Autocatalytic Sets and the Growth of Complexity in an Evolutionary Model
		We consider the population dynamics of a set of species whose network of catalytic interactions is described by a directed graph.
		The relationship between the attractors of this dynamics and the underlying graph theoretic structures like cycles and autocatalytic sets is discussed.
	citebase.eprints.org /cgi-bin/citations?id=oai%3AarXiv%2Eorg%3Aadap%2Dorg%2F9809003 (1180 words)

	Power HD:Stan:web:html:kauffman.html (Site not responding. Last check: 2007-09-18)
		Kauffman argues that such autocatalytic sets are to be expected to occur via natural self-organizational processes.
		Arguing from the expected appearance of such autocatalytic sets, Kauffman contends that life didn't evolve from self-replicating molecules, as is the common belief (see Christian de Duve's Vital Dust, 1994).
		Though the genomes are identical in the muscle cells and neurons of an individual organism, the sets of active genes are not.
	www.msci.memphis.edu /~franklin/kauffman.html (1858 words)

	6.1 Alchemy
		Reactions are deliberately specified to occur under flow conditions--so that particular sets of molecular species can continue to inhabit the reactor on an ongoing basis only if they (collectively) regenerate themselves.
		Briefly, if the possibility of individually autocatalytic molecules is allowed (the ``Level 0'' experiments) then reactors quickly become dominated either by one such species, or a co-operative network of such species.
		A further set of experiments (``Level 2'') considers the results of ``mixing together'', in one reactor, collectively autocatalytic sets that have first emerged in independent reactors.
	www.eeng.dcu.ie /~alife/bmcm9901/html-multi/6_1_Alchemy.html (449 words)

	Stuart Kauffman - Wikipedia, the free encyclopedia
		Kauffman rose to prominence through his association with the Santa Fe Institute (a non-profit research institute dedicated to the study of complex systems, where he was one of the faculty in residence from 1986 to 1997) and through his work on models in various areas of biology.
		These included autocatalytic sets in origin of life research, gene regulatory networks in developmental biology and fitness landscapes in evolutionary biology.
		In 1996 Kauffman started the BIOS Group, a Santa Fe, New Mexico-based for-profit company that employs complex systems methodology to attempt to solve business problems.
	en.wikipedia.org /wiki/Stuart_Kauffman (297 words)

	Citebase - Formation and Destruction of Autocatalytic Sets in an Evolving Network Model (Site not responding. Last check: 2007-09-18)
		The resultant fully autocatalytic graph, whose probability of forming by pure chance is very small, nevertheless forms in this model in an average time that grows only logarithmically with the size of the system.
		The model is analytically tractable: two theorems are proved which determine the set of nodes with least relative population in the attractor, for any given graph.
		Jain, S. and Krishna, S. (1998) Autocatalytic sets and the growth of complexity in an evolutionary model, Phys.
	citebase.eprints.org /cgi-bin/citations?id=oai%3AarXiv%2Eorg%3Anlin%2F0403050 (3044 words)

	Dispatches Weblog
		During the course of the lecture, I was reminded of the concept of collectively autocatalytic sets, which I've tried to apply to entrepreneurship.
		In matters of economic development, the norm is to (a) declare a "chicken or the egg" problem, (b) throw up our hands in exasperation, and (c) allocate resources politically.
		If we can identify the components and processes of a collectively autocatalytic set for technology commercialization, for example, we can have a roadmap for identifying which links and/or components are missing and acting to fill the gaps.
	radio.weblogs.com /0111718/2002/11/10.html (252 words)

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