Towards the physical principles of biological evolution
Abridged translation of the article by M. Katsnelson, Y. Wolf and E. Kunin
An article suggestive of such reflections, I became interested in the presentation of the astrophysicist and popularizer of science Sergei Popov. In one of his reviews of preprints, an article with an intriguing title was mentioned, and among the authors was Yevgeny Kunin. I began to read the book of this author, "The Logic of Case" ... Of course, only separate sections. Engineering education, doing technical translations, reading popular science articles - all this brought me to a seditious thought - to perform a brief translation of an article written by Evgeny Kunin in collaboration with Mikhail Katsnelson and Yury Wolf.
Physical Principles of Towards Biological evolution
Mikhail I. The Katsnelson, Yuri I. The by Wolf, Eugene V. The Koonin
arxiv.org/abs/1709.00284
Biological systems achieve complex organization, which significantly exceeds the complexity of any of the known inanimate objects. Biological entities, of course, are subject to the laws of quantum physics and statistical mechanics. However, is modern physics enough to adequately describe the model and explain the evolution of biological complexity?
This article provides a detailed analysis of the analogies between statistical thermodynamics and the population-genetic theory of biological evolution. Based on the presented analogies, we outline new perspectives in relation to theoretical approaches in biology and major transitional periods of evolution, and also offer a biological equivalent of thermodynamic potential, which reflects the propensity for changes in the evolving population.
It is assumed that there are deep analogies: between the properties of biological entities and the processes in them on the one hand, and non-equilibrium states in physics, for objects such as glass. Such systems are characterized by a violation whereby a local state with a minimum of free energy conflicts with a global minimum, resulting in “nascent qualities”. We disseminate such analogies through the study of manifestations of nascent qualities, such as, for example, between different levels of selection in biological evolution. Such frustration effects appear as drivers in the evolution of biological complexity.
Next, we turn to evolution in multidimensional adaptive landscapes, considering them from the point of view of percolation theory (percolation), and assume that percolation at a level above the critical threshold causes a tree-like type of evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology mean that the construction of a meaningful physical theory of biological evolution cannot be a futile attempt. However, it would not be realistic to expect such a theory to be created by “one scooping”; even if we move towards this, this can only happen through the integration of various physical models of evolutionary processes.
What is the difference between living organisms and inanimate matter? There is an obvious answer to this question when defining in terms of chemical composition and structure. (At least, because the only suitable case, namely, life on Earth, refers to this). But when it comes to the basic processes of the evolution of life, the difference becomes less obvious. In the Darwinian tradition, it is tempting to argue that life is determined by evolution through the survival of the fittest [1–4]. However, the uniqueness of this process can be questioned, since the entire history of the Universe consists of changes that withstand the most stable (adapted) structures. Moreover, the process of replication (reproduction) is not in itself unique and exists not only in biology: crystals also replicate. On a macroscopic scale of time and space, however, life is undoubtedly a clear phenomenon. For an objective determination of the characteristic features by which life differs from other phenomena existing in the Universe, it is important to investigate key processes of biological evolution within the framework of theoretical physics [5, 6].
Perhaps the main feature that distinguishes modern physics from other areas of human exploratory activity is the obvious link between theory and experiment, in which research programs are formed by verifiable theoretical predictions. In a general sense, modern biology is not a science based on theory, in the sense in which physics is interpreted. But there is a significant exception, namely - population genetics (a formalized section of biology, which is effectively structured as a field of theoretical physics), similar mainly to statistical thermodynamics [7-10].
At the same time, mathematical models of population genetics are highly effective in immunology [11, 12] and biological oncology [13–16], which, perhaps, suggests that further penetration of theory into biology could turn out to be real and productive. Modern theoretical physics is an area with many strong links in which the most diverse subdivisions of physics are intertwined. At present, population genetics or some other direction of theoretical biology is not part of such a network. It is possible to argue that this separation is not optimal, since many sections of theoretical physics would provide information and stimulate theoretical developments in biology.
And yet there is still such a landmark question: is modern physics sufficiently filled to serve (provide support) for biology? A similar question, in various formulations (in particular, “whether biology is reducible to physics”), has a long and very dramatic history (for example, [17, 18]).
Without going into details of a historical or philosophical plan, we reject any assumption that life may follow some special laws of “biological” physics instead of the general ones that exist. For example, quantum mechanics, in general, is quite effective and applicable to living organisms, just like any other form of matter. The problem is that this strong theory, to a certain extent, can be considered as a “theory of everything”, as it introduces little in explaining biological phenomena [19, 20]. Of course, quantum-mechanical calculations can be useful in analyzing biochemical reactions, but they can not help us in understanding evolution. Therefore, it is assumed that the physical concept, which could be the main one in the theoretical description of biological phenomena, is the appearance (or the appearance, emergency), that is, the collective behavior of large aggregates, which is qualitatively different from the behavior of their components. “More is different” is so anphoristically formulated by Anderson [19-24].
In his book containing fruitful ideas “What is life? The physical aspect of the living cell "Schrodinger made several basic points that even after 70 years remain at the heart of many discussions about the significance of physics for biology [25]. Probably the most significant is the characterization (at that time hypothetical) of molecular carriers of heredity as “aperiodic crystals”. Schrödinger was inaccurate in such a definition of an aperiodic crystal, and so far this metaphor covers the basic properties that were later discovered (not without the influence of Schrödinger) of biological information carriers, DNA and RNA [26-28].
Molecules of nucleic acids, in particular DNA, combine the uniformity (and periodicity) of the spatial structure with the effectiveness of multiple diversity (aperiodicity) of the main sequence. The combination of these distinctive features makes nucleic acids the only known molecules suitable for storing and transmitting digital information [29], in full accordance with Schrödinger's prediction. As for modern physics, biological “aperiodic crystals” are sometimes referred to as “glasses” [19, 20]. In fact, there are deep analogies, at various levels, between the state of glass and biological structures and the phenomena discussed below. At the same time, it will be shown that there are significant differences: in a certain sense, the glasses exhibit excessive confusion.
To be continued
Bibliography
1. Darwin C: On the Origin of Species; 1859.
2. Dobzhansky T: Genetics and the origin of the species, 2nd edn. New York: Columbia University
Press; 1951.
3. Dobzhansky T: Nothing in biology makes it different from the light of evolution. The American
Biology Teacher 1973, 35, 125-129.
4. Koonin EV: The Logic of Evolution: Upper Saddle
River, NJ: FT press; 2011.
5. Goldenfeld N, Woese C: Biology's next revolution. Nature 2007, 445 (7126), 369.
6. Goldenfeld N, Woese CR: Life is Physics: Evolution as a Collective Phenomenon Far From
Equilibrium. Annu Rev Condens Matter Phys 2011, 2, 375-399.
7. Sella G, Hirsh AE: The application of statistical economics to evolutionary biology. Proc Natl Acad
Sci USA 2005, 102 (27), 9541-9546.
8. Ao P: Emerging of Thermodynamics from
Darwinian Dynamics. Commun Theor Phys 2008, 49 (5), 1073-1090.
9. Barton NH, Coe JB: On the application of statistical economics to evolutionary biology. J Theor Biol
2009, 259 (2), 317-324.
10. de Vladar HP, Barton NH: The contribution of statistical physics to evolutionary biology. Trends
Ecol Evol 2011, 26 (8), 424-432.
11. Barreiro LB, Quintana-Murci L: From the
selection of the host defense of the genes. Nat Rev Genet 2010, 11 (1), 17-30.
12. Seppala O: natural selection on quantitative immune defense traits: a comparison between
theory and data. J Evol Biol 2015, 28 (1), 1-9.
13. Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S, Karchin R, Kinzler KW, Vogelstein B, Nowak
MA: Accumulation of driver and passenger mutations during tumor progression. Proc Natl
Acad Sci USA 2010, 107 (43), 18545-18550.
14. Casas-Selves M, Degregori J.
Evolution (NY) 2011, 4 (4), 624-634.
15. McFarland CD, Korolev KS, Kryukov GV, Sunyaev SR, Mirny LA: Impact of deleterious passenger
mutations on cancer progression. Proc Natl Acad Sci USA 2013, 110 (8), 2910-2915.
16. McFarland CD, Mirror LA, Korolev KS: Tug-of-War
: Proc Natl Acad Sci USA 2014, 111 (42), 15138-15143.
17. Polanyi M: Life's irreducible structure. Science 1968, 160, 1308-1312.
18. Rosenberg A: Darwininan Reductionism, Or, How to Stop Worrying and Love MoOlecular
Biology Chicago: Univ Chicago Press; 2006.
19. Laughlin RB, Pines D: The theory of everything. Proc Natl Acad Sci USA 2000, 97 (1), 28-31.
20. Laughlin RB, Pines D, Schmalian J, Stojkovic BP, Wolynes P: The middle way. Proc Natl Acad Sci USA 2000, 97 (1), 32-37.
21. Anderson PW: More is different. Science 1972, 177 (4047), 393-396.
22. Laughlin RB: A Different Universe: Reinventing Physics From The Bottom Down. New York:
Basic Books; 2008.
23. Anderson PW: More and Different: Notes from a Thoughtful Curmudgeon. Singapour: World
Scientific Publishing Company; 2011.
24. West G: Scale: The Universal Laws of Growth, Innovation, Sustainability
, Cities, Economies, and Companies. New York: Penguin Press;
25. Schroedinger E: What is Life? Aspect of the Living Cell. Dublin: Trinity College
Press; 1944.
26. Watson JD, Crick FH: Molecular structure of nucleic acids; a structure for deoxyribose nucleic
acid. Nature 1953, 171 (4356), 737-738.
27. Watson JD, Crick FH: Genetical implications of the structure of deoxyribonucleic acid. Nature
1953, 171 (4361), 964-967.
28. Frank-Kamenetskii MD: Unraveling Dna: The Most Important Molecule Of Life, 2nd edn. New
York: Basic Books; 1997.
Crosspost 7i.7iskusstv.com/2018-nomer5-lesov
Is convergence of physics and biology possible?
An article suggestive of such reflections, I became interested in the presentation of the astrophysicist and popularizer of science Sergei Popov. In one of his reviews of preprints, an article with an intriguing title was mentioned, and among the authors was Yevgeny Kunin. I began to read the book of this author, "The Logic of Case" ... Of course, only separate sections. Engineering education, doing technical translations, reading popular science articles - all this brought me to a seditious thought - to perform a brief translation of an article written by Evgeny Kunin in collaboration with Mikhail Katsnelson and Yury Wolf.
Physical Principles of Towards Biological evolution
Mikhail I. The Katsnelson, Yuri I. The by Wolf, Eugene V. The Koonin
arxiv.org/abs/1709.00284
annotation
Biological systems achieve complex organization, which significantly exceeds the complexity of any of the known inanimate objects. Biological entities, of course, are subject to the laws of quantum physics and statistical mechanics. However, is modern physics enough to adequately describe the model and explain the evolution of biological complexity?
This article provides a detailed analysis of the analogies between statistical thermodynamics and the population-genetic theory of biological evolution. Based on the presented analogies, we outline new perspectives in relation to theoretical approaches in biology and major transitional periods of evolution, and also offer a biological equivalent of thermodynamic potential, which reflects the propensity for changes in the evolving population.
It is assumed that there are deep analogies: between the properties of biological entities and the processes in them on the one hand, and non-equilibrium states in physics, for objects such as glass. Such systems are characterized by a violation whereby a local state with a minimum of free energy conflicts with a global minimum, resulting in “nascent qualities”. We disseminate such analogies through the study of manifestations of nascent qualities, such as, for example, between different levels of selection in biological evolution. Such frustration effects appear as drivers in the evolution of biological complexity.
Next, we turn to evolution in multidimensional adaptive landscapes, considering them from the point of view of percolation theory (percolation), and assume that percolation at a level above the critical threshold causes a tree-like type of evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology mean that the construction of a meaningful physical theory of biological evolution cannot be a futile attempt. However, it would not be realistic to expect such a theory to be created by “one scooping”; even if we move towards this, this can only happen through the integration of various physical models of evolutionary processes.
Introduction
What is the difference between living organisms and inanimate matter? There is an obvious answer to this question when defining in terms of chemical composition and structure. (At least, because the only suitable case, namely, life on Earth, refers to this). But when it comes to the basic processes of the evolution of life, the difference becomes less obvious. In the Darwinian tradition, it is tempting to argue that life is determined by evolution through the survival of the fittest [1–4]. However, the uniqueness of this process can be questioned, since the entire history of the Universe consists of changes that withstand the most stable (adapted) structures. Moreover, the process of replication (reproduction) is not in itself unique and exists not only in biology: crystals also replicate. On a macroscopic scale of time and space, however, life is undoubtedly a clear phenomenon. For an objective determination of the characteristic features by which life differs from other phenomena existing in the Universe, it is important to investigate key processes of biological evolution within the framework of theoretical physics [5, 6].
Perhaps the main feature that distinguishes modern physics from other areas of human exploratory activity is the obvious link between theory and experiment, in which research programs are formed by verifiable theoretical predictions. In a general sense, modern biology is not a science based on theory, in the sense in which physics is interpreted. But there is a significant exception, namely - population genetics (a formalized section of biology, which is effectively structured as a field of theoretical physics), similar mainly to statistical thermodynamics [7-10].
At the same time, mathematical models of population genetics are highly effective in immunology [11, 12] and biological oncology [13–16], which, perhaps, suggests that further penetration of theory into biology could turn out to be real and productive. Modern theoretical physics is an area with many strong links in which the most diverse subdivisions of physics are intertwined. At present, population genetics or some other direction of theoretical biology is not part of such a network. It is possible to argue that this separation is not optimal, since many sections of theoretical physics would provide information and stimulate theoretical developments in biology.
And yet there is still such a landmark question: is modern physics sufficiently filled to serve (provide support) for biology? A similar question, in various formulations (in particular, “whether biology is reducible to physics”), has a long and very dramatic history (for example, [17, 18]).
Without going into details of a historical or philosophical plan, we reject any assumption that life may follow some special laws of “biological” physics instead of the general ones that exist. For example, quantum mechanics, in general, is quite effective and applicable to living organisms, just like any other form of matter. The problem is that this strong theory, to a certain extent, can be considered as a “theory of everything”, as it introduces little in explaining biological phenomena [19, 20]. Of course, quantum-mechanical calculations can be useful in analyzing biochemical reactions, but they can not help us in understanding evolution. Therefore, it is assumed that the physical concept, which could be the main one in the theoretical description of biological phenomena, is the appearance (or the appearance, emergency), that is, the collective behavior of large aggregates, which is qualitatively different from the behavior of their components. “More is different” is so anphoristically formulated by Anderson [19-24].
In his book containing fruitful ideas “What is life? The physical aspect of the living cell "Schrodinger made several basic points that even after 70 years remain at the heart of many discussions about the significance of physics for biology [25]. Probably the most significant is the characterization (at that time hypothetical) of molecular carriers of heredity as “aperiodic crystals”. Schrödinger was inaccurate in such a definition of an aperiodic crystal, and so far this metaphor covers the basic properties that were later discovered (not without the influence of Schrödinger) of biological information carriers, DNA and RNA [26-28].
Molecules of nucleic acids, in particular DNA, combine the uniformity (and periodicity) of the spatial structure with the effectiveness of multiple diversity (aperiodicity) of the main sequence. The combination of these distinctive features makes nucleic acids the only known molecules suitable for storing and transmitting digital information [29], in full accordance with Schrödinger's prediction. As for modern physics, biological “aperiodic crystals” are sometimes referred to as “glasses” [19, 20]. In fact, there are deep analogies, at various levels, between the state of glass and biological structures and the phenomena discussed below. At the same time, it will be shown that there are significant differences: in a certain sense, the glasses exhibit excessive confusion.
To be continued
Bibliography
1. Darwin C: On the Origin of Species; 1859.
2. Dobzhansky T: Genetics and the origin of the species, 2nd edn. New York: Columbia University
Press; 1951.
3. Dobzhansky T: Nothing in biology makes it different from the light of evolution. The American
Biology Teacher 1973, 35, 125-129.
4. Koonin EV: The Logic of Evolution: Upper Saddle
River, NJ: FT press; 2011.
5. Goldenfeld N, Woese C: Biology's next revolution. Nature 2007, 445 (7126), 369.
6. Goldenfeld N, Woese CR: Life is Physics: Evolution as a Collective Phenomenon Far From
Equilibrium. Annu Rev Condens Matter Phys 2011, 2, 375-399.
7. Sella G, Hirsh AE: The application of statistical economics to evolutionary biology. Proc Natl Acad
Sci USA 2005, 102 (27), 9541-9546.
8. Ao P: Emerging of Thermodynamics from
Darwinian Dynamics. Commun Theor Phys 2008, 49 (5), 1073-1090.
9. Barton NH, Coe JB: On the application of statistical economics to evolutionary biology. J Theor Biol
2009, 259 (2), 317-324.
10. de Vladar HP, Barton NH: The contribution of statistical physics to evolutionary biology. Trends
Ecol Evol 2011, 26 (8), 424-432.
11. Barreiro LB, Quintana-Murci L: From the
selection of the host defense of the genes. Nat Rev Genet 2010, 11 (1), 17-30.
12. Seppala O: natural selection on quantitative immune defense traits: a comparison between
theory and data. J Evol Biol 2015, 28 (1), 1-9.
13. Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S, Karchin R, Kinzler KW, Vogelstein B, Nowak
MA: Accumulation of driver and passenger mutations during tumor progression. Proc Natl
Acad Sci USA 2010, 107 (43), 18545-18550.
14. Casas-Selves M, Degregori J.
Evolution (NY) 2011, 4 (4), 624-634.
15. McFarland CD, Korolev KS, Kryukov GV, Sunyaev SR, Mirny LA: Impact of deleterious passenger
mutations on cancer progression. Proc Natl Acad Sci USA 2013, 110 (8), 2910-2915.
16. McFarland CD, Mirror LA, Korolev KS: Tug-of-War
: Proc Natl Acad Sci USA 2014, 111 (42), 15138-15143.
17. Polanyi M: Life's irreducible structure. Science 1968, 160, 1308-1312.
18. Rosenberg A: Darwininan Reductionism, Or, How to Stop Worrying and Love MoOlecular
Biology Chicago: Univ Chicago Press; 2006.
19. Laughlin RB, Pines D: The theory of everything. Proc Natl Acad Sci USA 2000, 97 (1), 28-31.
20. Laughlin RB, Pines D, Schmalian J, Stojkovic BP, Wolynes P: The middle way. Proc Natl Acad Sci USA 2000, 97 (1), 32-37.
21. Anderson PW: More is different. Science 1972, 177 (4047), 393-396.
22. Laughlin RB: A Different Universe: Reinventing Physics From The Bottom Down. New York:
Basic Books; 2008.
23. Anderson PW: More and Different: Notes from a Thoughtful Curmudgeon. Singapour: World
Scientific Publishing Company; 2011.
24. West G: Scale: The Universal Laws of Growth, Innovation, Sustainability
, Cities, Economies, and Companies. New York: Penguin Press;
25. Schroedinger E: What is Life? Aspect of the Living Cell. Dublin: Trinity College
Press; 1944.
26. Watson JD, Crick FH: Molecular structure of nucleic acids; a structure for deoxyribose nucleic
acid. Nature 1953, 171 (4356), 737-738.
27. Watson JD, Crick FH: Genetical implications of the structure of deoxyribonucleic acid. Nature
1953, 171 (4361), 964-967.
28. Frank-Kamenetskii MD: Unraveling Dna: The Most Important Molecule Of Life, 2nd edn. New
York: Basic Books; 1997.
Crosspost 7i.7iskusstv.com/2018-nomer5-lesov