User:Jtwsaddress42/Darwin's Program/Somatic Selection Systems

Somatic Selection Systems - Population thinking

Introduction To Somatic Selection Systems

Pre-existing Diversity is the Engine of Adaptive Creativity "It is clear from both evolutionary and immunological theory that in facing an unknown future, the fundamental requirement for successful adaption is preexisting diversity." Gerald M. Edelman (1978) Edelman saw the immune system as an ideal model for the study of how population dynamics shape somatic evolution within a population. But, the immune system is just one of many systems in the vertebrate body comprised of a multitude of variant cell populations acting in a coordinated manner as somatic selection systems. The vertebrate immune system, because of it's dissociated nature and distinctively variant antibody idiotypes, has been historically the easiest to study as a somatic selection system but, much of what we have learned about the immune system can be applied to other systems in the body. Similarly, we could treat the developing embryo or nervous system. Very few, if any, neurons in the vertebrate nervous system act solo. Most individual neurons undergo somatic selection during embryogenesis and ultimately find themselves a member of a neuronal group, array, or ensemble, whether that be in the form of ganglia, nuclei, or laminae. Like organisms in the environment, neurons are born into a population of other cells and find themselves members of a community or group. For these neurons, their group is their ecology - and, natural selection operates as usual but in a somatic context.

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Variation In Biological Systems - Degeneracy, Complexity, Robustness, and Evolvability

The Ubiquity of Degeneracy in Biological Systems "Degeneracy, the ability of elements that are structurally different to perform the same function or yield the same output, is a well known characteristic of the genetic code and immune systems. Here, we point out that degeneracy is a ubiquitous biological property and argue that it is a feature of complexity at genetic, cellular, system, and population levels. Furthermore, it is both necessary for, and an inevitable outcome of, natural selection." Gerald M. Edelman & Joseph A, Gally (2001) Edelman, Gerald M.; Gally, Joseph A. (2001). "Degeneracy and Complexity in Biological Systems". Proceedings of the National Academy of Sciences, USA 98 (24): 13763–13768. doi:10.1073/pnas.231499798. PMID 11698650. PMC 61115. //www.ncbi.nlm.nih.gov/pmc/articles/PMC61115/.  The Ubiquity of Degeneracy in Biological Systems Relationships between degeneracy, complexity, robustness, and evolvability. The degeneracy of the genetic code buffers biological systems from the effects of random mutation. A large number of degenerate sidechain residue combinations form the tertiary structures that make the protein globular. Antibody chains with variable regions constitute a pre-existing pool of diversity within a degenerate population. The more we deviate from an ideal form, the more we are tempted to describe the deviations as imperfections. Edelman, on the other hand, explicitly acknowledges the structural and dynamic variability of the nervous system. Degeneracy, and its relationship to variation, is a key concept in the population biology dynamics employed by Edelman in the development of Neural Darwinism. He likes to contrast the difference between redundancy within an engineered system to the degeneracy within a biological system. He argues that the "noise" that plagues computational and algorithmic approaches is actually a beneficial feature for somatic selection systems by providing a wide, and degenerate, array of potential response elements. Edelman's argument is that in an engineered system, a known problem is confronted, a logical solution is devised an artifice is constructed to implement the resolution to the problem. To insure the robustness of the solution, critical components are replicated as exact copies. Redundancy provides a fail-safe backup in the event of catastrophic failure of an essential component but it is the same response to the same problem once the substitution has been made. If the problem is predictable and known ahead of time, redundancy works optimally. But biological systems face an open and unpredictable arena of spacetime events of which they have no foreknowledge of. It is here where redundancy fails - when the designed answer is to the wrong problem... Variation fuels degeneracy - and degeneracy provides somatic selective systems with more than one way to solve a problem; as well as, the ability to solve more than one problem the same way. This property of degeneracy has the effect of making the system more adaptively robust in the face of unforeseen contingencies, such as when one particular solution fails unexpectedly - there are still other unaffected pathways that can be engaged to result in the comparable final outcome. Early on, Edelman spends considerable time contrasting degeneracy vs. redundancy, bottom-up vs. top-down processes, and selectionist vs. instructionist explanations of biological phenomena.

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Population Thinking – From the bottom up

The Requirements of a Selection Theory "[T]he abstract general requirements on any selection theory are (1) a source of diversification leading to variants, (2) a means for effective encounter with or sampling of an independent environment that is not initially categorized in any absolute or predetermined fashion, and (3) a means of differential amplification over some period of time of those variants in a population that have greater adaptive value." Gerald M. Edelman (1987) Darwin's theory of Natural Selection put population dynamics at the center of biology and distinguished it from the other sciences in its epistomology. Edelman points out that population thinking freed biologists from the formalism of Platonic Essentialism, or typology that other sciences relied upon. For Edelman, "population thinking states that evolution produces classes of living forms from the bottom up by gradual selective processes over eons of time." He points out that biology is somewhat unique in its particular "mode of thought" vis a vis most of the other physical sciences. By applying the principles of selection theory to a population of degenerate elements, one can analyze the system as a somatic selective system. The following primary features of a somatic selective system are: A degenerate population of elements, A mechanism of selection, Differential amplification of adaptive elements in the next generation. Selective systems can take many forms, not only at the inter-organismal level but also within organismal structures that are constructed of "sub"-organisms, i.e. cells and cell populations within a multicellular organism, or organelles within an cells... enzymes and macromolecular structures within the biochemistry of the cell, et cetera. These systems operate in terms of response amplification or suppression under historically contingent circumstances, where there is a population of potential response networks from which a particular response network is selected and strengthened upon realization of threshold conditions, thereby differentially amplifying that particular system potential in response to similar future events.

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Recognition & Memory In Somatic Selection Systems

Recognition and Memory in the Immune and Nervous Systems "[I]t is not difficult to see that both the brain and the immune system are recognition systems. Both can recognize and therefore distinguish positively among different objects in a set (in the one case via sensory signals, in the other via molecular complementarity between the shapes of antigens and the combining sites of antibodies). By positive recognition I mean that they do not merely exclude an object by subjecting it to a match with a fixed pattern, but rather that they can name or tag an object uniquely. This is a much more powerful kind of recognition than the exclusive one embodied, say, in the construction of a combination lock. Furthermore, both systems have the capacity to store a recognition event ("memory" and "immunological memory") as well as the capacity to forget." Gerald M. Edelman (1975) Edelman, Gerald M. (1975). "Molecular Recognition in the Immune and Nervous Systems". In Worden F.G., Swazey J.P., Adelman G.. The Neurosciences: Paths of Discovery. Boston: I. Birkhäuser. 1990. doi:10.1007/978-1-4684-6817-5_4. ISBN 978-1-4684-6817-5. https://link.springer.com/chapter/10.1007/978-1-4684-6817-5_4.  Edelman lists the evolutionary emergence of four distinct types of biological memory systems that are based upon somatic selection: Hereditary – DNA provides a stable molecular substrate for replication. Immunological – differential amplification of adaptive lymphocytes within a population. Reflexive – phylogenetically constrained and deeply experiential canalized neural transduction pathways. Recategorical – neuronal group selection within reentrant topobiological maps. Recognition links cognition to memory and serves as the basis for evolutionary and developmental learning in a somatic system. Memory in a Somatic Selection System "Each memory reflects a system property within a somatic selection system. And each property serves a different function based upon the evolution of the appropriate neuroanatomical structure. These higher-order systems are selective and are based on the responses to environmental novelty of populations of neuronal groups arranged in maps. They are recognition systems." Gerald M. Edelman (1992) Edelman, Gerald M. (1992a). Bright Air, Brilliant Fire - On the Matter of the Mind. Basic Books, Inc.. ISBN 0-465-05245-2. https://www.hachettebookgroup.com/titles/gerald-m-edelman/bright-air-brilliant-fire/9780465007646/.

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