On the way to the physical principles of biological evolution. Continuation
Abridged translation of an article by M. Katznelson, J. and E. Wolf Kunin
Towards Physical Principles of Biological evolution
Mikhail I. The Katsnelson, Yuri I. The by Wolf, Eugene V. The Koonin
arxiv.org/abs/1709.00284
→ Previous Section
Other famous Schrödinger's statement that 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 better understand the nature of entropy and the second law of thermodynamics, so that such a view of Schrödinger is possible and necessary to clarify. 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', one can say 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, this 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.
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
Crosspost
Towards Physical Principles of Biological evolution
Mikhail I. The Katsnelson, Yuri I. The by Wolf, Eugene V. The Koonin
arxiv.org/abs/1709.00284
→ Previous Section
Other famous Schrödinger's statement that 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 better understand the nature of entropy and the second law of thermodynamics, so that such a view of Schrödinger is possible and necessary to clarify. 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', one can say 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, this 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.
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
Bibliography
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2. Dobzhansky T: Genetics and the origin of species, 2nd edn. New York: Columbia University Press; 1951.
3. Dobzhansky T: Nothing in biology makes sense except in the light of evolution. The American Biology Teacher 1973, 35, 125-129.
4. Koonin EV: The Logic of Chance: The Nature and Origin of Biological 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 CondensMatter Phys 2011, 2, 375-399.
7. Sella G, Hirsh AE: The application of statistical physics to evolutionary biology. Proc Natl Acad Sci U S A 2005, 102(27), 9541-9546.
8. Ao P: Emerging of Stochastic Dynamical Equalities and Steady State Thermodynamics from Darwinian Dynamics. Commun Theor Phys 2008, 49(5), 1073-1090.
9. Barton NH, Coe JB: On the application of statistical physics 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 evolutionary genetics to human immunology: how selection shapes host defence genes. Nat Rev Genet 2010, 11(1), 17-30.
12. Seppala O: Natural selection on quantitative immune defence 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 U S A 2010, 107(43), 18545-18550.
14. Casas-Selves M, Degregori J: How cancer shapes evolution, and how evolution shapes cancer. Evolution (N Y) 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 U S A 2013, 110(8), 2910-2915.
16. McFarland CD, Mirny LA, Korolev KS: Tug-of-war between driver and passenger mutations in cancer and other adaptive processes. Proc Natl Acad Sci U S A 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 U S A 2000, 97(1), 28-31.
20. Laughlin RB, Pines D, Schmalian J, Stojkovic BP, Wolynes P: The middle way. Proc Natl Acad Sci U S A 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, and the Pace of Life in Organisms, Cities, Economies, and Companies. New York: Penguin Press; 2017.
21
25. Schroedinger E: What is Life? The Physical 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.
29. Koonin EV: Why the Central Dogma: on the nature of the great biological exclusion principle. Biol Direct 2015, 10, 52.
30. Prigogine IR, Stengers I: Order Out of Chaos. London: Bantam; 1984.
31. Lemon E, Stewart DW, Shawcroft RW: The Sun's Work in a Cornfield. Science 1971, 174(4007), 371-378.
32. Toussaint O, Schneider ED: The thermodynamics and evolution of complexity in biological systems. Comp Biochem Physiol A Mol Integr Physiol 1998, 120(1), 3-9.
33. Pascal R, Pross A, Sutherland JD: Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics. Open Biol 2013, 3(11), 130156.
34. Gell-Mann M: The Quark and the Jaguar: Adventures in the Simple and the Complex New York: St. Martin's Griffin; 1995.
35. Adami C, Ofria C, Collier TC: Evolution of biological complexity. Proc Natl Acad Sci U S A 2000, 97(9), 4463-4468.
36. McShea DW, Brandon RN: Biology's First Law: The Tendency for Diversity and Complexity to Increase in Evolutionary Systems. Chicago: Univ Chicago Press; 2010.
37. Adami C: What is complexity? Bioessays 2002, 24(12), 1085-1094.
38. Koonin EV: A non-adaptationist perspective on evolution of genomic complexity or the continued dethroning of man. Cell Cycle 2004, 3(3), 280-285.
39. Koonin EV: The meaning of biological information. Philos Trans A Math Phys Eng Sci 2016, 374(2063).
40. Heim NA, Payne JL, Finnegan S, Knope ML, Kowalewski M, Lyons SK, McShea DW, Novack-Gottshall PM, Smith FA, Wang SC: Hierarchical complexity and the size limits of life. Proc Biol Sci 2017, 284(1857).
41. Egelman E (ed.): Comprehensive Biophysics. New York: Academic Press; 2012.
42. Bohr N: The Atomic Theory and the Description of Nature. Oxford: Ox Bow Press; 1934.
43. Fisher RA: The Genetical Theory of Natural Selection. London & New York: Oxford University Press; 1930.
44. Gavrilets S: Fitness Landscapes and the Origin of Species. Princeton: Princeton University Press; 2004.
45. Gavrilets S, Gravner J: Percolation on the fitness hypercube and the evolution of reproductive isolation. J Theor Biol 1997, 184(1), 51-64.
46. Gravner J, Pitman D, Gavrilets S: Percolation on fitness landscapes: effects of correlation, phenotype, and incompatibilities. J Theor Biol 2007, 248(4), 627-645.
47. Shannon CE, Weaver W: The Mathematical Theory of Communication. Chicago: University of Illinois Press; 1949.
48. Lynch M: The origins of genome archiecture. Sunderland, MA: Sinauer Associates; 2007.
49. Lynch M, Conery JS: The origins of genome complexity. Science 2003, 302(5649), 1401-1404.
50. Lynch M: The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A 2007, 104 Suppl 1, 8597-8604.
51. Lynch M: The origins of eukaryotic gene structure. Mol Biol Evol 2006, 23(2), 450-468.
2. Dobzhansky T: Genetics and the origin of species, 2nd edn. New York: Columbia University Press; 1951.
3. Dobzhansky T: Nothing in biology makes sense except in the light of evolution. The American Biology Teacher 1973, 35, 125-129.
4. Koonin EV: The Logic of Chance: The Nature and Origin of Biological 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 CondensMatter Phys 2011, 2, 375-399.
7. Sella G, Hirsh AE: The application of statistical physics to evolutionary biology. Proc Natl Acad Sci U S A 2005, 102(27), 9541-9546.
8. Ao P: Emerging of Stochastic Dynamical Equalities and Steady State Thermodynamics from Darwinian Dynamics. Commun Theor Phys 2008, 49(5), 1073-1090.
9. Barton NH, Coe JB: On the application of statistical physics 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 evolutionary genetics to human immunology: how selection shapes host defence genes. Nat Rev Genet 2010, 11(1), 17-30.
12. Seppala O: Natural selection on quantitative immune defence 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 U S A 2010, 107(43), 18545-18550.
14. Casas-Selves M, Degregori J: How cancer shapes evolution, and how evolution shapes cancer. Evolution (N Y) 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 U S A 2013, 110(8), 2910-2915.
16. McFarland CD, Mirny LA, Korolev KS: Tug-of-war between driver and passenger mutations in cancer and other adaptive processes. Proc Natl Acad Sci U S A 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 U S A 2000, 97(1), 28-31.
20. Laughlin RB, Pines D, Schmalian J, Stojkovic BP, Wolynes P: The middle way. Proc Natl Acad Sci U S A 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, and the Pace of Life in Organisms, Cities, Economies, and Companies. New York: Penguin Press; 2017.
21
25. Schroedinger E: What is Life? The Physical 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.
29. Koonin EV: Why the Central Dogma: on the nature of the great biological exclusion principle. Biol Direct 2015, 10, 52.
30. Prigogine IR, Stengers I: Order Out of Chaos. London: Bantam; 1984.
31. Lemon E, Stewart DW, Shawcroft RW: The Sun's Work in a Cornfield. Science 1971, 174(4007), 371-378.
32. Toussaint O, Schneider ED: The thermodynamics and evolution of complexity in biological systems. Comp Biochem Physiol A Mol Integr Physiol 1998, 120(1), 3-9.
33. Pascal R, Pross A, Sutherland JD: Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics. Open Biol 2013, 3(11), 130156.
34. Gell-Mann M: The Quark and the Jaguar: Adventures in the Simple and the Complex New York: St. Martin's Griffin; 1995.
35. Adami C, Ofria C, Collier TC: Evolution of biological complexity. Proc Natl Acad Sci U S A 2000, 97(9), 4463-4468.
36. McShea DW, Brandon RN: Biology's First Law: The Tendency for Diversity and Complexity to Increase in Evolutionary Systems. Chicago: Univ Chicago Press; 2010.
37. Adami C: What is complexity? Bioessays 2002, 24(12), 1085-1094.
38. Koonin EV: A non-adaptationist perspective on evolution of genomic complexity or the continued dethroning of man. Cell Cycle 2004, 3(3), 280-285.
39. Koonin EV: The meaning of biological information. Philos Trans A Math Phys Eng Sci 2016, 374(2063).
40. Heim NA, Payne JL, Finnegan S, Knope ML, Kowalewski M, Lyons SK, McShea DW, Novack-Gottshall PM, Smith FA, Wang SC: Hierarchical complexity and the size limits of life. Proc Biol Sci 2017, 284(1857).
41. Egelman E (ed.): Comprehensive Biophysics. New York: Academic Press; 2012.
42. Bohr N: The Atomic Theory and the Description of Nature. Oxford: Ox Bow Press; 1934.
43. Fisher RA: The Genetical Theory of Natural Selection. London & New York: Oxford University Press; 1930.
44. Gavrilets S: Fitness Landscapes and the Origin of Species. Princeton: Princeton University Press; 2004.
45. Gavrilets S, Gravner J: Percolation on the fitness hypercube and the evolution of reproductive isolation. J Theor Biol 1997, 184(1), 51-64.
46. Gravner J, Pitman D, Gavrilets S: Percolation on fitness landscapes: effects of correlation, phenotype, and incompatibilities. J Theor Biol 2007, 248(4), 627-645.
47. Shannon CE, Weaver W: The Mathematical Theory of Communication. Chicago: University of Illinois Press; 1949.
48. Lynch M: The origins of genome archiecture. Sunderland, MA: Sinauer Associates; 2007.
49. Lynch M, Conery JS: The origins of genome complexity. Science 2003, 302(5649), 1401-1404.
50. Lynch M: The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A 2007, 104 Suppl 1, 8597-8604.
51. Lynch M: The origins of eukaryotic gene structure. Mol Biol Evol 2006, 23(2), 450-468.
Crosspost