Life emerged because the cellular membrane separated inside from outside. It constrained the diffusion of molecules inside and excluded others from coming inside. A clear boundary was created. When the molecules inside happened to make a network and a part of the network had a replication system, the membrane defined the unit of replication. Thus, this is the unit of life.
This created the first definition of Self. Everything required for replication is called Self. All Self were encoded in the DNA sequence, one-dimensional information of four nucleotides. Self is something that is necessary for replication, including survival. The first Self emerged because of the first replication of the biochemical networks within a membrane, not by any intention but simply by chance. When the first replication occurred in its environment, it kept replicating. Not all components within the membrane are required for replication. The first accidental replication created the logic for replication in the network.
The logic separated the biochemical networks into two classes: the part of the replication network and outside of it—the first exclusion. The peptides are encoded on DNA as sequences. Initially, the randomly polymerized DNA sequences were classified as the sequences necessary for replication and not. The first genes and non-coding sequences.
The membrane defines the inside and outside. The first exclusion, but there is no logic here yet. Then, the accidental replication of a membranous unit creates the first logic and definition of self and non-self. The first logic is a retrospective narrative for the first unintentional replication of the membranous unit encapsulating the networks of biochemical reactions.
There was one long list of many participants at the beginning. Then, suddenly, they are split into players and non-players, assigned based on the accidental replication event. As far as a copy of this long list is available, the replication happens again in the same environment. Simultaneously, a whole long list is unnecessary because the list of non-players is not required for replication. Non-players have three categories. The ones helping players, disturbing players or doing nothing. Importantly, however, they are not defined categories but are highly dependent on their environment – context-dependent. As far as staying in one context/environment, players, helpers, disturbers, or observers will be consistent. However, if they move out from the original context, their requirements in replication drastically change. It is possible that a disturber suddenly becomes an elite player or vice versa.
Life is a system that recognizes self and non-self based on its need for replication within its environment. Replication is not the purpose or goal but keeps happening as far as staying in the same environment. DNA carries the instructions for replication as its sequences. A cell carries the instruction of biochemical reactions as the self-organized geometry of molecules and organelles. As two combined, a cell carries all the necessary information for replication as a whole. This is the organism. In other words, once it starts, there is no way to stop it. Unless a cell leaves the environment or the environment changes, replication continues because everything is environment-dependent.
The fidelity of DNA replication is not high. Anything not essential for replication is mutated and could be deleted. If errors occur in the essential sequence, cellular replication is failed. If the extra sequence accidentally increases the fidelity, it will be added as a new essential for successful replication in fluctuating environments, providing robustness to the system stretching its limit. Through this process, an organism can expand its livable environment. Robustness allows organisms to live in a more hostile environment than the original one, reducing the dependency on the original environment.
In prokaryotes, the non-Self is solely defined based on DNA sequences. There are two types of non-self-detection strategies, either restriction enzymes or CRISPR. The balancing point of replication error frequency that accidentally creates the recognition site in its own genome and non-self-sensitiveness sets the organism's genome size. For example, 4 bp recognition is more sensitive to recognizing non-self than 6 bp recognition. Still, the risk of accidentally creating the 4 bp recognition site (1/256, the risk of cutting the own genome) is much higher than 6 bp recognition (1/4096). Inversely, the risk of exogenous sequences like viruses sneaking into the genome would increase in the 6 bp recognition system. Having a larger genome size keeps opportunities for increasing robustness to stretch livable niches, although it does not necessarily have advantages for staying in the current niche.
Interestingly, in animal cells that have their own DNA in the nucleus, non-self is primarily defined by innate immunity. Various properties unique to bacteria and viruses are recognized as specific receptors. Before entering a cell, they are identified and eliminated by phagocytic cells, like macrophages. Even if they successfully enter a cell,
DNA in the cytoplasm is recognized as foreign. It will be shredded. Self DNA is stored in membranous structures, the nucleus and mitochondria. Self/non-Self in a cell is not defined by the DNA sequence but by its location. Therefore, it became possible to carry a larger genome. As I mentioned above, the larger genome has a chance to increase robustness. In addition, the diploid life cycle also increases the robustness. The division of roles, germ cells and somatic cells, was another great innovation for continuity of life. Somatic cells are disposable and serve to support germ cells. Germ cells are essential for life continuity. This division of roles created another robustness, permitting the organism to explore previously unoccupied niches.
Robustness creates adaptability. There are two types of adaptation. The one with the expense of variation – this is often called selection. The other is with robustness – this is often called plasticity. There are two distinct concepts in the word ‘adaptability.’
When the variation in a population is used for adaptation (i.e. selection), the diversity in a population decreases. If selection occurs, we do not know how diversity will be restored.
On the other hand, robustness looks like internally absorbing external changes. The individuals, as well as the population, do not appear to have changed. The diversity in a population never declines but increases with increasing the variation of robustness.
Robustness prepares the organism to overcome the limit of a livable niche set by the threshold of intrinsic lethal deficiency. Robustness provides plasticity to survive in the previous non-livable niche. There is no competitive selection, but the livable niche expands, and so does diversity. Retrospectively, this appears the environment selected the one can survive. Indeed. However, this is not what Darwin meant and neo-Darwinian theory implicated. This new environment was not in the context, not in the part of equations, and was not realized as an environment. The new niche/environment is only recognized after the emergence of the one that can survive.
The increase in robustness permits the exploration of new niches through the increased plasticity. Using the robustness, the threshold for lethal deficiency becomes lower, enabling the organism to take the place considered too harsh for living. In other words, the environment contributes to the threshold for lethal deficiency. Robustness can provide options to overcome this threshold.
Adaptation based on selection is one-dimensional. This view demands the concept of fitness and the direction of better as if winning logic or adaptation strategies exist. Adaptation becomes a competition, and fitness matrices become available.
On the other hand, robustness has no dimension because no one knows what will happen in the future and what will be helpful. To continue as life, lower the risk of lethal deficiency with the hope that their robustness allows them to survive through an unpredictable future.
In a uniform, consistent and closed environment, robustness is useless, meaningless and inefficient. In the only consistent closed condition humans have been building, the survival of the fittest exists. Competition and fairness emerge in this condition and are weighed with high value. However, if the environment is multilocal, inconsistent, or open, competition is not essential anymore; it is meaningless. Adaptability to unpredictability is only crucial for continuity. Robustness only permits this in unpredicted ways.
Biological evolution is the increase of robustness. On the other hand, human societies have been aiming to increase consistency towards the future. Consistency creates vested interests. Uniform, consistent, and closed conditions are required to protect and expand vested interests. Therefore, our history shows inevitable competition and fighting over and over. Imperialism was unavoidable because you want everyone to follow your rules and fitness values.
Interestingly, economic activities fluctuate between these two conditions, often called blue and red oceans. There is no real red ocean in nature because no organism recognizes the future and does not demand consistency. A new niche starts from a blue ocean, and then the ocean will be stabilized at green between blue and red. Without human involvement, the ocean will never turn to be red.
The current various issues in the world are all matters of vested interests. Everyone focuses on maximizing and protecting their vested interests. The vested interests are potential benefits for the future, based on the current consistency. In other words, ‘exclusiveness of others.’ To secure future benefits, everyone must follow the current consistency. Capitalism has developed the mechanisms to suck up the future wealth under the name of investments. A stable society with a massive division in the allocation of world wealth has self-enforcing power to maintain that in the participants. No winner wants real innovation. Someone’s wealth is the amount of ‘exclusion of others.’ We keep encouraging excluding others with logic, common sense and values. Logically justified diversity or inclusion is hypocritical bullshits for me because logic is the one creating exclusion. When did we start trusting logic this much? Where is healthy critical skepticism against the context? Why can we not tolerate other contexts, common sense or values? Where are we heading to?