http:// https://en.wikipedia.org/wiki/Marc_Kirschner
Cell Network and Complex Mechanism
A cell, the smallest living system, is a dissipative structure, which reproduces itself (DNA replication), developing, and differentiating. A living system is an organization that preserves itself as a result of its organization, because it produces components that produce components in self-differentiation.
This systemic stance differs from a central dogma of molecular biology (Francis Crick and James Watson) with a unilateral information process. The genetic material of the DNA molecules carries the genetic information in its replication. The RNA molecules are made by the DNA (transcription) to deliver instructions to ribosomes located in the cytoplasm, in which the cell’s proteins are produced as well as the enzymes. Information does not flow the other way around, downplaying the cellular network and feedback loops.[1]
The DNA centered view is expressed in a controversial way: “The genes hold culture on a leash. The leash is very long, but inevitably values will be constrained in accordance with their effects on the human gene pool.”[2] A genetic determinism is imbued with the ultra Darwinian fundamentalism, in so doing, “the organism is only DNA’s way of making more DNA.”[3] The gene occupies the driver’s seat dictating and determining the physiology of organisms and their phenotypic variations.
By contrast, in Varela’s cognitive science, the organism (phenotype) precedes the genotype, bringing forth the world of culture. The self-organizing system emphasizes the core of autonomy in terms of operational closure, though open to the flow of energy and matter from the environment.
The autopietic systemic operations are interconnected within the open network regulating gene expression. The cellular network holds the genes on a leash. Thus, I argue that there is no organism without an environment, so no environment without an organism. “The environment of an organism is the penumbra of external conditions that are relevant to it because it has effective interactions with those aspects of the outer world.”[4]
Dialectical Linkage: Conserved Core Processes and Epigenetics
An ecological-systemic approach to the autopoietic network is undertaken in connection with the physiology of organisms. I find it indispensable to incorporate a theory of conserved core process and social epigenetics into a phenomenology of lifelines.
According to Marc Kirschner and John Gerhart, there are hundreds of behaviors or activities at cellular life involving conserved core processes in cell organization, in which function and protein structure are reserved. Kirschner and Gerhart utilize a theory of punctuated equilibrium, which views long periods of stasis as punctuated by bursts of innovation.
The history of cellular innovation is featured by both conservation and diversification of organisms (economy). Core processes imply the punctuated part, which is mainly unchanged until the present (an equilibrium or stasis).
The novel deployment of cell behaviors or activities continually produces new phenotypes. Construction of the core processes is to facilitate phenotypic variation.[5] The conserved components and processes are integrated into functioning pathways and circuits; thus, any enzymes of metabolism are components of some of the core processes.
Seen in this regard, I understand a major number of epigenetic studies as indispensable components of the conserved core process. An epigenetic approach focuses on the interaction of DNA sequence-specific transcription factors, repressors, and RNA polymerases. This interaction is performed by histone proteins, chromatin compaction, and looping, regulating gene expression.
Indeed, the DNA code itself is wound around the histones, marked by an epigenetic signature into the organism. Its mechanisms are known at the molecular level by histone modification and chromatic remodeling. Histone modification refers to methylation of cytosine bases, as controlled by interaction with the tails of histones. Therefore, the process of methylation and control modulates gene expression.
Complexity of metabolism must arise through the multiple use of a relatively few conserved elements and their diverse combinations with differing consequences. Conservation works along with the economy in combinations for diversification.[6]
Epigenetic marks or signatures imply changes in DNA methylation or histone modifications. A sociological study of epigenetics researches the extent to which social economic adversity or polluted environments can lead to later negative outcomes of public health through epigenetic mechanisms. Molecular modifications regulate gene activity through changes in the DNA methylation without changing its sequence.
Sociological studies of DNA methylation in various genes concern a mediating index in explicating the relation between social exposure and disease outcomes. The social environment problems become crucial in terms of safety concerns, lack of food availability, or exposure to environmental toxicants. They research transgenerational epigenetic inheritance in analyzing the impact of the environment on epigenetic marks or the epigenome.[7]
In this cellular network and process, genes as DNA molecules are modified and eliminated and edited in the regulating system. The genes are controlled by the cells and tissue. This process refers to downward causation by modulating how frequently the genes should be transcribed and when to cease. This network view is opposed to a ‘bottom-up’ gene causal reductionism.[8]
I make the case for locating natural selection within an ecological landscape, grounding evolutionary variation upon somatic variation of the organism. Organisms can move in physiological plasticity, interacted dynamically with environmental response and evolutionary (genetic) modification.
The organism plays an import role in undertaking the somatic adaptability of the core processes in generating different cell types and different cell behaviors. The somatic core of adaptability and process has capacity to produce and respond to diverse signals. It retrieves varied information from the genome, generating multiple combinations of cell behaviors.
In genetic accommodation, gene frequency changes increase fitness and heritability, but the phenotypic change is not necessarily under genetic control.[9] This ecological systemic view of novelty is framed within somatic adaptability. It better facilitates comprehension of histone modification in reference to methylation of cytosine bases. A process of methylation is controlled by interaction through the tails of histones, a docking site of encountering outside elements (diets, drugs, pollutants), modulating gene expression.
The aspect of multiplicity becomes crucial in explaining the origin of complex phenotypic variations and novelties in a nonlinear state of innovation and diversification “far from equilibrium.” The ecological systemic position, as conceptualized in nonlinear thermodynamics, reinvigorates a punctuated equilibrium approach to a dialectical relation between the conserved core process and the somatic adaptability core process. This epistemic structure facilitates a heuristic explanation in delving into evolutionary adaptation shaping natural selection.
In a nutshell, “somatic adaptability provides for only certain types of facilitated phenotypic variation.”[10] The eco-systems view of the adaptive core process facilitates a theory of autopoiesis, a conserved core process, taking into account a structural role of an organism in an ecological background and epigenetic mechanism.
New phenotypes are crafted and fabricated in the evolutionary process, replacing a genetic change with an environmental condition. This underlays the adaptive core process in the state of nonlinear equilibrium. Such multiple realities enable a favorable condition for the emergence of phenotypic variation, its diversification, and innovative novelty.
An autopoietic system is operative in regulatory linkage, set within a symbiotic rhythm and catalytic modulation and collaboration at multiple levels. This implies how information is passed from one component to another at the molecular level. Signals may come from outside the cell or the organism, passing through a chain of command until a response is made in an appropriate manner. In turn, that response could affect the environment or the organism.[11]
This biological position of multiplicity and modulation helps an attempt to combine the autopoietic network with a theory of lifelines. In so doing, I elaborate on a dialectics of punctuated equilibrium in dealing with the relation between the cellular core process of conservation and the somatic adaptability core process of organisms.
[1] Nobel, The Music of Life, 18.
[2] Wilson, On Human Nature, 167.
[3] Wilson, Sociobiology, 3.
[4] Lewontin, The Triple Helix, 48-9.
[5] Kirschner and Gehart, The Plausibility of Life, 45. 68.
[6] Ibid, 110.
[7] Deichmann, “The social construction of the social epigenome and the larger biological context.” Epigenetics & Chromatin (2020) 13:37.
[8] Nobel, The Music of Life, 18.
[9] Kirschner and Gerhart, The Plausibility of Life, 82.
[10] Ibid., 74.
[11] Ibid., 110.