Problematization: Autopoiesis and Epigenetic World
Francisco Varela gives account of the concept of autopoiesis in terms of the biological cell. A cell, the smallest living system, 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.
For instance, the cell nucleus contains the genetic material of the DNA molecules, which carry 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. This refers to the central dogma of molecular biology about the informational processes, maintaining an exclusive role of the gene expression in a unilateral way through replication, transcription, and protein synthesis.
Against this central dogma, however, enzymes are the catalysts in a network of catalytic reactions promoting all cellular or metabolic processes and producing enzymes. In the metabolic process of replication, transcription, and translation (DNA-RNA-Protein/enzymes), catalytic reactions are central operative through the complex activity of histone modifications after translation.
In fact, their posttranslational modifications are undertaken in transcriptional activation, chromosome packaging, and DNA damage/repair and make change in gene expression without mutations. A group of special enzymes in the chromatin (a mixture of DNA and histones proteins) form the 46 chromosomes.
The new histones are made in the cytoplasm during the S phase of the cell cycle in parallel with the DNA replication from its chromosomal DNA. They are transported into the nucleus, while the old histones are reassembled into nucleosomes. The histones package and wrap the massive amount of DNA in a genome on string structure (nucleosomes), while involved in the repair of damaged components of DNA, mutation.
When DNA replication begins during the interphase (S phase), the cell duplicates its chromosomes, making them ready for cell division. It is unzipped by the enzyme helicase at the replication fork. Moving down the entire length of the molecule, the helicase unwinds the double stranded nature of the molecule, which separates the DNA helices in an anti-parallel direction (semiconservative replication).
A type of enzyme (DNA polymerase—many pieces enzyme) is involved attaching many pieces of DNA, yet working in one leading direction continuously. During the elongation stage, RNA primers are created by the enzyme primes and are used in the lagging strand (5’-3’ direction opposite to the replication fork); it is synthetized in short stretches (Okazaki fragments), solving the opposition direction in the double stranded DNA.
This process continues until the entire complement of an organism’s DNA is replicated. The DNA long string (about 1.5m long) is folded into and organized in a chromatin loop, which plays a dynamic role in gene expression and regulation, while facilitating DNA repair.
Catalytic Circulation and Epigenetic World
This catalytic circulation and feedback reinforce an epigenetic position, which cuts through limitation of the central dogma of molecular biology underlying gene-determinism. A theory of autopoiesis remains incomplete without taking seriously a structural role of epigenetic world, which remains central in regulating gene information and expression and healing its mutation.
The boundary of the cell is a membrane, which encloses the cell fluid (cell nutrients) of the cytoplasm like ocean; out of them the cell builds its structure. The membranes separate some organelles (the nucleus and mitochondria) from the cytoplasm. The membrane again is a process that limits diffusion and thus preserves the internal network of production that produces the membrane. The energy carriers (coming from the food we eat) are broken down in energy network (mitochondrion), thus substrate for the enzyme. Cell’s self-organization entails a symbiotic life, as well as the epigenetic world.
In Varela’s view, this self-organizing system emphasizes the core of autonomy in terms of operational closure, though open to the flow of energy and matter. The autonomy and autopoiesis of biological systems come to terms with their operational closure as established by the system itself. The results of systemic operations are once more systemic operations independent of the imposition of the environment.[1]
Given this reasoning, there is insufficient consideration of a structural operation of epigenetic world which regulates the whole process of cell autopoiesis through collective complex catalytic function. The Santiago theory of cognition identifies living systems as cognitive systems, emphasizing a process of living and cognition. In the continual interaction between system and its environment, perturbations or problems can be resolved through the functional differentiation of the system according to its adaption to the environment.
On the contrary, we cannot relativize a basic insight in which the catalytic function underlays a new emergence. A symbiotic life recognizes a unique place of the other within the cellular organism. This perspective remains crucial at the social cultural realm, along with differentiation and adaption. Furthermore, there is a common structure of life-world, which is transmitted through history, culture, and language, while influencing human cognition, critical thinking, and proleptic consciousness—structure underlying life and cognition in process.
[1] Varela, “Autopoiese, strukturelle Kopplung und Therapie. Fragen an Francisco Varela.” In Lebende Systeme, ed. F. B. Simon [148–64] (Frankfurt/Main: Suhrkamp, 1997), 149.