Self-Organization and Genomic Causality in Models of Morphogenesis

Contrasting philosophical and scientific views in the long history of studying the generation of form in development

Focusing on the opposing ways of thinking of philosophers and scientists to explain the generation of form in biological development, I show that today's controversies over explanations of early development bear fundamental similarities to the dichotomy of preformation theory versus epigenesis in Greek antiquity. They are related to the acceptance or rejection of the idea of a physical form of what today would be called information for the generating of the embryo as a necessary pre-requisite for specific development and heredity. As a recent example, I scrutinize the dichotomy of genomic causality versus self-organization in 20th and 21st century theories of the generation of form. On the one hand, the generation of patterns and form, as well as the constant outcome in development, are proposed to be causally related to something that is "preformed" in the germ cells, the nucleus of germ cells, or the genome. On the other hand, it is proposed that there is no pre-existing form or information, and development is seen as a process where genuinely new characters emerge from formless matter, either by immaterial "forces of life," or by physical-chemical processes of self-organization. I also argue that these different ways of thinking and the research practices associated with them are not equivalent, and maintain that it is impossible to explain the generation of form and constant outcome of development without the assumption of the transmission of pre-existing information in the form of DNA sequences in the genome. Only in this framework of "preformed" information can "epigenesis" in the form of physical and chemical processes of self-organization play an important role.

Self-Organisation of Prediction Models

Living organisms are active open systems far from thermodynamic equilibrium. The ability to behave actively corresponds to dynamical metastability: minor but supercritical internal or external effects may trigger major substantial actions such as gross mechanical motion, dissipating internally accumulated energy reserves. Gaining a selective advantage from the beneficial use of activity requires a consistent combination of sensual perception, memorised experience, statistical or causal prediction models, and the resulting favourable decisions on actions. This information processing chain originated from mere physical interaction processes prior to life, here denoted as structural information exchange. From there, the self-organised transition to symbolic information processing marks the beginning of life, evolving through the novel purposivity of trial-and-error feedback and the accumulation of symbolic information. The emergence of symbols and prediction models can be described as a ritualisation transition, a symmetry-breaking kinetic phase transition of the second kind previously known from behavioural biology. The related new symmetry is the neutrally stable arbitrariness, conventionality, or code invariance of symbols with respect to their meaning. The meaning of such symbols is given by the structural effect they ultimately unleash, directly or indirectly, by deciding on which actions to take. The early genetic code represents the first symbols. The genetically inherited symbolic information is the first prediction model for activities sufficient for survival under the condition of environmental continuity, sometimes understood as the "final causality" property of the model.

Mathematical Modeling in Systems Biology

Mathematical modeling is a key tool used in the field of systems biology to determine the mechanisms with which the elements of biological systems interact to produce complex dynamic behavior [...].