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The eighth day of creation: makers of the revolution in biology
No full textThe eighth day of creation: makers of the revolution in biolog
The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli.
No full textThe incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli
Heiraten (Giftas)
No full textHeiraten (Giftas)
http://gutenberg.spiegel.de/strindbe/heiraten/toc.htm
http://www.gutenberg.org/browse/authors/s#a160
Functional cartography of complex metabolic networks
No full textFunctional cartography of complex metabolic networks
Care has to be taken with equation one; the 2L in it can be very misleading. When implementing the measure I first ended up with very strange results and only looking through the references (esp. Newman, Fast algorithm for detecting community structure in networks) helped. It becomes clearer when you think about the statement "A good partition of a network into modules must comprise many within-module links and as few as possible between-module links. Equation (1) addresses this diffiulty by imposing that M=0 if nodes are placed at random into modules or if all nodes are in the same cluster.".
The latter is not true if you naively implement this as putting the whole network into one module leads to: l_s = d_s implying [l_s / L - (d_s / 2L)^2]= [1 - 1/4 * 1]= 0.75
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Handbook of Graphs and Networks - From the Genome to the Internet
No full textHandbook of Graphs and Networks - From the Genome to the Interne
Reducing the Dimensionality of Data with Neural Networks
No full textReducing the Dimensionality of Data with Neural Network
Self-Organization In Living Systems
No full textSelf-Organization In Living Systems
-According to Prigogine, in a steady state situation the system is stable (i.e. damps out rate changes in irreversible processes) with respect to environmental perturbations (changes in flow rates). It minimizes its dissipation (due to irreversible processes). This is the MINIMUM DISSIPATION RULE.
However, Prigogine shows that as the input flow rates increase, a critical threshold is approached. Beyond this threshold a catastrophe occurs. The system will rapidly dissipate energy and material and enter a new more ordered steady state. Just which new state is entered is determined by which flow rate exceeds its critical threshold first.
-First, the second law of thermodynamics is the only physical law with a time sense and hence must be intimately linked to any discussion of the temporal phenomena, organization. Second, environmental fluctuations are required for the emergence of organization; and third, as systems evolve there is an increase in entropy production per component.
-"The second law of thermodynamics prescribes that all irreversible chemical processes increase the overall randomness of matter-energy in the universe. Whereas this is a disordering directive, it is not necessarily disorganizing. I have tried to show that the evolution of molecular organization is, in fact, a natural consequence of the operation of this law. Molecular organization is achieved through chemical bonding. Chemical bonding, in turn, provides a means through which the randomization of matter and energy can occur." (Wicken, 1978, p.202).
If one accepts that, in a pre-biotic soup such as found on Earth before life began, the generation of complex molecular forms is mandated by the second law, then Wicken argues that one would expect the eventual emergence of "quasi-stable, self perpetuating patterns of information flow, of catalytic cycles ..."(Wicken, 1980, p.16) that would guarantee the degradation of the flow of high quality energy. If these patterns and cycles could evolve and stabilize sufficiently to form systems which are self-maintaining, reproduce and continue to operate (i.e. degrade energy) in the face of environmental fluctuations, then one would have a permanent organization for satisfying the second law\u27s requirement that the high quality energy flux to the system be continually degraded. One would also have life.
-Consider a chemical soup bombarded with solar energy. Wicken\u27s work suggests that the second law [10] of thermodynamics dictates the emergence of chemical factories in this soup. The factories would degrade (i.e. increase the entropy of) the solar energy impinging on the earth. Degradation would be accomplished largely by utilizing the available molecules and energy to form new more complex molecules. The process of formation of new molecules could degrade the available potential energy by transforming it into bond, translational, and vibrational energy, and into heat. Many different types of processes and molecular forms should emerge as the larger their number the more thoroughly degraded the incoming solar energy becomes.
As time goes on, these systems (the chemical factories) should become STABLE. That is they would evolve mechanisms to stabilize their internal chemical processes and to maintain the functioning of the system in the face of environmental changes. The degradation of the incoming solar energy, as required by the second law, would then be assured. This expectation would be justified by the second law alone, but is reinforced by Prigogine\u27s findings regarding the emergence of stable dissipative structures.
Suppose, for now, that the physical environment is homogeneous. As stated, the emergence of primary producers who would use the incoming solar energy to produce complex molecules and stored energy is expected. These primary producers would be expected to degrade into lower quality forms as much of the incoming energy as possible. They would only produce as much stored potential energy (via for example photosynthesis) as is required to fuel the processes necessary for the internal stability of the system. The stored potential energy of the primary producers could be further degraded if it is used by other chemical factories to fuel more production of complex molecules. Chains of such systems, each system feeding on the stored potential energy of another system, would emerge in accordance with Prigogine\u27s order through fluctuations scenario. The characteristics of these chains is that they would degrade as much of the incoming energy as possible per unit production of complex molecules. Such chains will be referred to as ENERGY DEGRADING CHAINS.
If only energy degrading chains existed, they would quickly run out of material to be used as inputs. Thus we should expect the emergence of consumers who would use the complex molecules and stored energy of the energy degrading chains, as inputs to processes which simplify the complex molecules. The existence of such MATTER SIMPLIFYING chemical factories would guarantee the supply of simple molecules to be used by the primary producers. These consumers would be expected to simplify the molecules as much as possible per unit of energy flow.
-The number of different solutions possible in any given supersystem is large and the details of specific solutions unpredictable. This leads to the expectation that there would be many different forms of life
Rechnender Raum
No full textRechnender Raum
Note that the link provided gives you the English translation: Calculating Space, MIT Technical Translation AZT-70-164-GEMIT, MIT (Proj. MAC), Cambridge, Mass. 02139, Feb. 1970