"Emergence of Genome: Generalization and Use of Environmental Information by Cell"
A cell dynamics is considered to be driven by environment - in geological timeframe. Accordingly, the response structures get gradually built up in cell and become its current genome. In this process, repeated environmental signals are generalized by spatial superposition and form a central core of the cell, a nucleus. Likewise, the novelty signals form the peripheral components of the cell – cytoplasm, mitochondria, etc. This is a differential encoding, specifically a space-division multiplexing. So, a cell – its structure and functions – is a mechanism to accumulate, generalize and use the environmental information to build its responses to the environment Its genome emerges as a compressed model of the long-term (geological timeframe) history of the environment. So, the genome is incrementally updated by novelty in the environment, and the cellular structures and functions also get built up incrementally rather than from scratch. From this viewpoint, a cell is a novelty encoder using the space-division multiplexing. With no novelty in the environment, there is no growth, the cell is in balance with the environment. The same model is applicable to organs, organisms, populations. The flexible controlling substrate in a cell is identified. This is a lattice of hydrogen atoms in the H-bonds of the nucleotide base pairs. In fact, the nucleotide sequence determines the positions of H atoms in the H-bonds (Watson-Crick model); however, not uniquely. The reason is that these H atoms are indeed in metastable state (double-well potential) and are able to change their position under environmental control – thus changing the complementarity relations. So metastable H atoms in the H-bonds of the base pairs are critical for immediate (adaptive) response to environment. When a cell is divided, the H-bond based adaptivity resource is roughly doubled thus increasing the adaptation options. The novelty stimulus gets integrated in a stimuli-response (SR) pair which is a structural and functional unit of responding to the environment. The response component of a SR pair contains all the protein-synthesizing (expression) circuits. In multi-cellular environments such as tissue or organ, novelty is created by the immediate as well as external environment, and so the growth is driven by this mixed novelty. In particular, in an organ, a “central core” is a response base for generalized, repeated stimuli and the peripheral (cortical) layers – for novel stimuli. A computer model based on these principles demonstrates the basic mechanisms discussed including emergence of an artificial genome under control of highly dynamic environment. The model builds up the stimulus-response patterns from different stimuli and generalizes them by spatial superimposition. With the permanent components in the stimulation stream, the genome develops a central core, whereas the variable components develop fine peripheral structures.