On the way to the physical principles of biological evolution. Continuation

Abridged translation of the article by M. Katsnelson, Y. Wolf and E. Kunin
Towards physical principles of biological evolution
Mikhail I. Katsnelson, Yuri I. Wolf, Eugene V. Koonin
arxiv.org/abs/1709.00284

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Another well-known statement by Schrödinger that organisms use “negative entropy” (or negentropy, a term that Schrödinger obviously liked but was not picked up by researchers) is potentially deceptive. Strikingly, during the time of Schrödinger, it seemed widespread, albeit uncertain, the view that such complex systems as living beings sometimes violate the second law of thermodynamics, and that such an apparent “violation” requires a special explanation [30].

Now we understand better the nature of entropy and the second law of thermodynamics, so that such a point of view of Schrödinger is possible and necessary to be clarified. Obviously, the biosphere and the Earth as a whole are not closed systems, but rather open to a constant flow of energy, mostly from the Sun (other sources of relatively lesser environmental significance include the radioactive decay of heavy elements in the interior of the Earth).

Earthly life uses this flow of energy through photosynthesis, carried out by photo autotrophs (organisms that use light energy to biosynthesis of cell components), which function, to a certain extent, like photochemical machines. Of course, when considering the Sun-Earth system, even the appearance of a violation of the second law of thermodynamics is absent. Each individual organism, population, or ecosystem is also thermodynamically open systems. And more appropriate would be the statement that organisms mainly consume energy along with chemical building blocks, rather than 'negentropy', according to Schrödinger's bizarre statement.

However, with regard to Schrödinger's current motivation in the presentation of 'negentropy', it can be said that this correlates with some of the most fundamental and complex problems of biology, namely, the emergence and preservation of a surprising order and gigantic complexity in living organisms. Complexity is undoubtedly one of the most problematic concepts in all of science; it confronts all-encompassing definitions [34]. In fact, the most used definitions of complexity are context dependent. In biology, complexity is significant, at least at the level of genomes, organisms, and ecosystems [35, 36].

The complexity of the genome can be clearly interpreted through the number of nucleotide sites that are selected and thus carry biologically significant information [37-39], although the detailed definition does not take into account other important sources of complexity at the genome level, such as alternative transcription initiation and alternative splicing in eukaryotes (alternative splicing in eukaryotes). Complexity in relation to the organism and ecology is usually perceived as the number of individual constituent parts and / or hierarchy levels in the respective systems [40]. Regardless of the exact definitions, it seems clear that a consistently maintained, ever-increasing level of complexity is an exceptional characteristic feature of life and a major challenge for theoretical constructs.

The most traditional means of interaction between physics and biology is biophysics, which studies the properties of the structure and dynamics of biological macromolecules, as well as the structure of cells and organisms, together with their functions, through the approaches adopted in physics. Various areas of biophysics have proven to be productive and successful for several decades [41]. However, it is, after all, a separate additional area of ​​interaction between physics and biology, whereby physical theory is used to describe, model and analyze biological processes, in particular, evolution at the population level.

Already, Bohr attached particular importance (as part of the general discussion on the complementarity principle) of complementarity between the purely physical, structural approach to organisms and the “whole” nature as living beings [42]. The principle of drawing analogies between thermodynamics and statistical mechanics, on the one hand, and population genetics, on the other hand, was first proposed by the famous statistician and founder of the theory of population genetics, Ronald Fisher in the 1920s [43], and in subsequent years development of a theoretical approach to this process [7, 9, 10].

In various forms, the theoretical formalism (mathematical models for describing a theory) from statistical mechanics was increasingly used to substantiate the model of biological evolution. Among other similar mathematical models, the use of percolation theory for analyzing evolution in adaptive landscapes [44-46] finds significant use. The main goal of such penetration of physics into evolutionary biology is rather ambitious: it is nothing more than the development of a physical theory of biological evolution, or even the transformation of biology into a part of physics [5, 6]. Obviously, such a comprehensive program, even a feasible in principle, cannot be implemented in one fell swoop. Only progress is possible at one of the stages at a given time by simulating a diverse evolutionary process using the ideas and mathematical apparatus of theoretical physics in the hope that in the end it will be possible to combine such models into a harmonious theoretical justification.

In this article, we discuss several aspects of biological evolution, where theoretical considerations, originating initially from condensed physical concepts, seem possible. We propose for consideration the statement that physical theory is capable of making a non-trivial contribution to the current understanding of evolution, and the latest theoretical developments in physics itself will probably be in demand with full consideration of the phenomenon of the emergence and evolution of the complexity level, which is characteristic of biological systems.

To be continued


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