A New Biology: A Modern Perspective on the Challenge of Closing the Gap between the Islands of Knowledge

Abstract

Abstract. This paper discusses the rebirth of the old quest for the principles of biology along the discourse line of machine-organism disanalogy and within the context of biocomputation from a modern perspective. It reviews some new attempts to revise the existing body of research and enhance it with new developments in some promising fields of mathematics and computation. The major challenge is that the latter are expected to also answer the need for a new framework, a new language and a new methodology capable of closing the existing gap between the different levels of complex system organization.

On some recent insights in Integral Biomathics

“…Following previous studies carried out in the INBIOSA project 17 (Simeonov et al, 2011;Simeonov et al 2012a/b,) and the follow-up activities such as this special issue of JPBMB, we are suggesting an innovative multi-layer approach for qualitative modeling and simulation of living systems based on the integration of three complementary approaches:…”

Stepping beyond the Newtonian Paradigm in Biology

“…Thus, just as the Scientific Revolution provided us with physics-based mathematics that made possible the investigation of whole new realms of science, so can we expect the development of a biology-based mathematics, Integral Biomathics (Simeonov, 2010a/b;Simeonov et al, 2011), to have equally far-reaching and revolutionary effects. Since we have to think about biological systems in all of these ways in order to model them, and since biological processes are intrinsically carried out in these integrated ways by Nature itself, it seems logical that real and useful connections must exist within the mathematical formulations of these natural processes as well.…”

A quantum model of exaptation: Incorporating potentiality into evolutionary theory

“…Representations of the underlying laws of how new traits, species, and cultural artifacts come into existence are outside the scope of current evolutionary biology. It is increasingly recognized that to capture the causal dynamics of biological systems there is a need for a general theory of biocomputation and novel mathematical formalisms capable of incorporating the multiple interacting facets of complex living systems (Simeonov et al, 2011). One central and fascinating feature of evolutionary change in need of a formal theoretical framework is exaptation: the retooling or co-option of existing organs, appendages, or other evolved structures for new functions, possibly after further modification.…”

“…A physics-inspired model may seem like a strange move given the position (as stated in the introduction to this special issue) that biology is 'broken' in large part because it has adopted the abstractions of Newtonian physics (Simeonov et al, 2011). However, the formalism we use does not come from Newtonian physics; indeed it arose through recognition of the limitations of Newtonian physics.…”