Dissipative Structure and Non-Equilibrium
The biological concept of autopoiesis is not separated from the study of thermodynamic processes and dissipative structures, as described by Ilya Prigogine, the Russian-born chemist and physicist. He was Nobel Laureate and professor of physical chemistry at the Free University of Brussels.
If the Santiago theory focuses on the organizational closure in the description of the pattern of life in an autopoietic network, Prigogine elaborates on the structure of a living system in openness to the glow of energy and matter. The living organism or structure exists in a boundary region between order and disorder (entropy), reaching point of instability or bifurcation through the external influence of the environment; they move toward the emergence of new differentiated order, adaptation, system’s change, and new structure.
A theory of dissipative structures is the first and most influential description of living self-organizing organisms far from equilibrium, maintaining their life process under conditions of nonequilibrium. For example, when the liquid is heated from below, a constant heat flux is established, moving from the bottom to the top. As the temperature difference increases through the continual flow of heat between the top and bottom, it reaches a certain critical point of instability in which the heat flux is replaced by heat convection.
At this point, a pattern of hexagonal cells emerges like an ordered honeycomb. A spectacular example of self-organization emerges in the ordered pattern of hexagonal convection cells (the Bénard cells) at the critical point of instability or disorder far from equilibrium. This experiment refers to the emergence of dissipative structures, which can be also seen in other natural phenomena (vortex, tornado or hurricane) or even social political events (risk, crisis, change, and revolution).
Catalytic Reaction and Complex Systems
Dissipative structures go through new instabilities and transform themselves into new structures of increased complexity through fluctuation, reacting at the bifurcation very sensitively to small or random fluctuations in the environment. Complex biochemical systems generate catalytic loops leading to instabilities and produce new structures of higher order. We cannot know or predict the future path of the system (indeterminacy). The self-organizing process (far from equilibrium) is irreversible, indeterminate, and unpredictable.
A change in structure implies epistemological rupture (nonequilibrium, nonlinearity, instability, indeterminacy) from the deterministic view, while heralding the living structures in reproducing and evolving in their dependence on their previous develops and continual flows of energy and resources from environment.
For example, in a living system of cells we observe the cycles in their metabolic processes, because a cell far from equilibrium may develop through multiple feedback loops into forms of ever-increasing complexity. Every molecule in the cell has its formation which is catalyzed by other molecules in the cell. In an autocatalytic DNA replication cycle mRNA (a copy of DNA) acts as a messenger between DNA and ribosomes (the sites of mRNA and protein synthesis, or translation).
In ribosome (a definite structure), one of cytoplasmic organelles, both proteins (involved in the formation of structures) and the enzymes (specific types of the proteins) are made. The cytoplasm is gel-like fluid between the nucleus and cell membrane, in which distinctive structures (organelle) can operate as the medium for chemical reaction.
GIven the system of complexity at a cellular level, Stuart Kaufmann articulates a phase transition to collectively autocatalytic sets of polymers. They are capable of exhibiting heritable variation, evolving without harvoring a genome (The Origins of the Order, 287-8, 330).
For the autocatalytic behavor, the system is necessary to be open to the flux of matter and energy outside in the thermodynamic sense. It requires a sustained metabolic flux from exgeneous food set as linked to an endergonic reaction (like photosynthesis). This factor of the food set is higher than Darwinian fitness, since co-evolution of autocatalytic sets would occur.
For instance, enzyme catalytic function can be seen in Glucose (blood sugar), which is the final substrate at the cellular level; it comes from the food, and the blood carries glucose to all of body cells.
Enzymes are the biological catalysts for chemical reaction working in a network of the enzyme-substrate complex. In such catalytic reactions mechanism to environment and temperature, substrate (key) should bind into the empty active site (lock).
Allosteric Mechanism: Conformational Ensemble
Allostery (other from the Greek allo) and stere (meaning solid) implies that proteins have two kinds of interaction in terms of the catalytic function as well as the regulatory one. Allostery, a chemical model (known as the discovery of the second secrete life), demonstrates how a molecular switch operates within functional regulatory sites of interaction (The Plausibilty of Life, 129).
Enzymes and substrates are compared to locks and keys fitting together. In the catalytic reaction, the enzyme is induced to fit more closely around the substrate (the induced fit), strengthening the attractions between the substrate and the active site. Several enzymes are inhibited by molecules that looked nothing like their substrates.
Enzymes at the beginning of a biosynthetic pathway are often inhibited by chemical entities of molecules that look nothing like their substrates; these are produced at the end of the pathway, while many steps removed. Therefore, the whole process is charactersitic of feedback inhibition.
The end product of a pathway did not generally fit the substrate, which is used by the enzyme of the first step. Regulatory control is exerted at an alternative or “allosteric” site. The feedback inhibition implies that the primary binding site of the enzyme (the catalytic site) is independent of the regulatory site. If the regulatory site can be constructed to interact with anything in regulatory relevance, much of evolution involves in connecting conserved core processes in new ways; the regulatory part evolving in unconstraied manner separates itself from the functional part of a protein.
Enzyme regulation works in the feedback inhibition, promoting all metabolic processes, ever-releasing products of the different molecules (substrates), and regulating the production. The power of the protein in its regulatory part communicate signals across very different pathways; these are ranged from cell proliferation to protein synthesis, from metabolism to heart rate, and from inflammation to cell death.
The power of proteins is to integrate new regulatory connections in a simple way, fueling much of their change in multicellular evolution. according to the development of regulatory connections (ibid., 130). Allostery is typically seen in its regulatory function relying on conformational ensembles to describe and control enzyme function, while transmitting long range binding information to modulate and control catalysis.
Catalytic function is in mutual formation among the enzymes in complexity, while metabolic substrates are used to produce energy (mainly glucose) and synthesize larger molecules (amino acids from foods used by all living things for protein synthesis). There occurs conformational change, or shape change in the enzyme by the catalytic reaction, finally converting a substrate reactant to numerous products from the active site.
The active site is free to take a new substrate molecule after releasing the numerous products from itself. This aspect implies collectively auto-catalytic sets of molecules to emerge, obviously as seen in the enzyme-substrate relationship in terms of diversity and complexity. DNA repair enzymes, as seen in histone modifications in the chromatin, recognize and correct physical damage in DNA, alleviating loss of genetic information and preventing the mutations.
At this juncture, it is helpful to combine the auto-catalytic set regulatory function in light of allosteric mechanism, which is involved in signal transduction, metabolism, enzyme acticvation, and gene regulation. The allostery model features the cellular network as autopoietic system of life.
Allosteric Ensemble and Novely of Organism
The protein functions as a molecular switch, which has active and inactive states regarding enzymatic activity. The protein oscillates between the two conformations. In the case of allosteric enzymes (homoglobin), the two states aew different bith in their catalytic activity and in their ability to bind the regulator.
Allostery implies that there is a change in the “solid” shape of a protein, thus the protein had alternative conformations or two states. If the inactive conformation binds the regulator more tightly, the regulator becomes an allosteric inhibitor; it holds the protein in its inherently inactive state. If the regulator binds more tightly to the active state of the enzyme, it is an allosteric activator; it holds the protein in the active state.
There are conserved and constrained mechanisms in allostery protein, which facilitate variation around them. An allosteric protein is highly constrained, having thousands of weak chemical interactions, capable of weak linkage. These interactions enable extensive deconstraint in the evolution of regulatory connections abd sites which can be almost anywhere on the protein surface.
In the workings of this form of physiology, two-state proteins are significant going beyond metabolic control. The core mechanism lies in allostery in the case of switch-like molecules, which communicate much of the information for control of cell growth and cell differentiation, communicating information from signals outside the cell to internal pathways, which leads to cell proliferation.
Allosteric core mechanism cuts through the limitations of collective autocatalytic sets of polymers, which are related only to the emergence of a connected metabolism through a web of transformations, which links exogonic reaction to endergonic reaction, as harnessed by the organism (The Origins of the Order, 343).
By contrast, the greatest novelty evolved in multicellular organisms based on two conformations takes place due to the passage of information. It is not merely based on the chemical rendering of metabolic intermediates. Allostery promotes weak linkage by separating regulationary part from functionary part, facilitating the generation of phenotypic variation and deconstraining the selection for new functions and new regulatory connections. These collectively regulatory mechabism involve procedure from the synthesis of the amino acids to the synthesis of RNA and its translation (ibid.,132-4).
According to Stuart Kaufmann, the system is greater than the sum of its parts through its catalytic function in complex genetic systems and exhibits self-organized structural and dynamic properties in a spontaneous crystallization of generic order out of complex systems. “The system shows spontaneous self-organization and produces global, emergent structures” with no role of Darwinian natural selection. (Depew and Weber, Darwinism Evolving, 431. 437).
Given this, chemical instabilities do not automatically appear, but require the presence of catalytic loops, which regulates the system and brings it to the point of instability through repeated self-amplifying feedback which involves chemical reactions, oscillation, and diffusion in nonlinear and irreversible process. (Prigogine and Stengers, Order out of Chaos, 144).
Complex systems dynamics utilizes a term for phase space through regions of which systems travel, called attractors. As a system moves on to a stable point, it settles down to a point attractor, since a pendulum stops swinging owning to friction.
In a point attractor there is no further change occurring in phase space. Inappropriately compressed into point attractors or limit cycles, however, many different patterns of order at or near the edge of chaos emerge out of chaotic dynamics, its house of chaotic attractors. Insofar as complex systems demonstrate the distinctive feature of self-organization and adaptability, the adaptation takes place near the edge of chaos by virtue of selective feedback processes (Depew and Weber, Darwinism Evolving, 438-9. 443).
Be that as it may, allosteric ensemble modulates and controls enzime catalysis, and its regulatory mechanism vary in different environs at organism level, evolving to adapt to their envioronment. Allosteric-catalytic combination helps better to undersrand an emergence of novelty in the evolution of dissipative structure.
The Emergent Creativity and Religious Naturalism
The emergent approach to co-evolution is concerned with life’s inherent tendency to creativity and complexity in the process of survival, adaptation, and propagation to create novelty and new order. This refers to an autopoietic, yet collectively autocatalytic system which drives the complexity of the living system and its diversity upward through molecule’s complex interaction.
In a collectively autocatalytic set, a complex web of producers is seen in the case of rainforests; likewise, the human body is a walking ecosystem in autocatalytic collective network, which is compared to a melting pot of niches, co-option, and interdependencies.
This complex web of co-creation is true of our social, political, economic, cultural, and technological systems within which subsystems emerges by creating space for something new like social media, education, academia, and arts. In the emergent complexity, evolution cannot be a brutal race for the survival of genes any longer.
The role of organisms is not reducible to work merely as the vehicles to carry the ‘selfish gene’ to be selected, as seen in sociobiology. This reductionist position undermines a role of organisms in co-creating together in their networking of life symbiosis. Self-organization refers to a property of complex genetic systems, which is characterized by order for free out there; it has no need for natural selection or any other external force of selection (Darwinism Evolving, 431).
A symbiotic co-creation implies religious naturalism, which is imbued with the complexity of a living organism and emergence of its creativity. The network of collective autocatalysis enables living systems to accumulate and constitute systems in space (structure) or order (boundary) against the increase in entropy in closed space; this might degrade them in the sense of irreversibility (the gear moving downhill from hotter objects to colder objects).
An idea of co-creation in the emergent frame features the autopoiesis in complexity of living organism in the long history of life; it has religious meaning, which leads us to live in the face of mystery, “a fully natural God,” who is “the very creativity of the universe.” (Kaufmann, Reinventing the Sacred, 6).
God is the source of gifts of creativity and meaning which can be applied to the symbolic material realm. This position argues that creativity in evolution transpires foremost in the self-organization prior to natural selection and chance, by which we are not capable of explaining all the creativity in evolution.
(Haught, Science and Religion, 158).