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Evgeny Kunin - The logic of chance. On the nature and origin of biological evolution. Evgeny Kunin, "the logic of chance" Introduction. Towards a New Synthesis of Evolutionary Biology

Evgeny Kunin

case logic. On the nature and origin of biological evolution

The Logic of Chance. The Nature and Origin of Biological Evolution»

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©The electronic version of the book was prepared by LitRes

The news that a group of enthusiasts, self-organized through LiveJournal, began work on the translation of this book was a complete surprise for the author, of course, a pleasant one. In the 21st century, the question of the need to translate scientific literature from English into any other languages is, to put it mildly, ambiguous. Scientific texts are now published in English, and the ability to read them in this language is an elementary requirement of professional fitness. Popular science literature is, of course, a completely different matter. This book is not popular, but it is not a typical specialized monograph either. Ideally, this text is intended for a wide range of scientists in various specialties, including graduate and undergraduate students. It would, of course, be great if all this readership could freely read the original, but so far this is hardly realistic. The most important argument in favor of the translation was for the author the very fact that a considerable team of translators gathered in a matter of days. In this situation, the author considered it his honorable duty to read and edit the entire text of the translation, of course, following first of all the actual accuracy.

The original of this book was published in autumn 2011, two years before the Russian edition. Biological research is progressing at an unprecedented pace in our time, and over the years, of course, many important new results have accumulated and many serious articles have been published that shed light on the fundamental problems of evolutionary biology discussed in the book. Of course, new considerations, only partially published, also appeared in the author's work. Moreover, many readers, including translators, and the author himself, when editing the translation, noted inaccuracies and ambiguities in the presentation (fortunately, as far as the author knows, none of them can be considered a serious mistake). It was impossible to take all this into account in the Russian translation, but the author made an attempt to reflect the most important clarifications and some of the most interesting scientific news in the notes to the Russian edition. As a result, there were much more such new notes than expected at the beginning of work on editing the translation (and there could have been even more - the author spoke only when he could not keep silent at all). The author is very pleased with this, because it clearly illustrates the speed of progress in modern evolutionary biology. A few notes relate rather to the translation, explaining those places in the text where the English pun could not be accurately conveyed in Russian. Of course, these notes cannot claim to make the book a “second edition”, it is a translation, but still the author hopes that these small additions increase its value.

From the author's point of view, the main ideas of the book so far stand the test of time (albeit short in astronomical terms, but not negligible, given the astonishing rate of accumulation of new data); in any case, the need for a radical revision has not yet arisen. Moreover, the author believes that the past tense has only increased the need for a conceptual generalization of information about the diversity of organisms and their genomes and about evolutionary processes. A new evolutionary synthesis based on data from genomics and systems biology seems important and relevant as never before. Without such a generalization, it becomes simply impossible to comprehend the sea of observations in any way.

Of course, it is important to emphasize that this book can by no means claim to be such a new synthesis. This is just a sketch, an attempt to guess the contours of the future building. Even leaving aside the fundamental openness of science and assuming that some stages of completion and summarizing it really exist, in the author's opinion, the completion of a new synthesis of evolutionary biology is a matter for at least two scientific generations. Too much remains unclear, and too much needs to be done to fit the gigantic data sets produced by genomics and systems biology into coherent and valid theories and concepts. Perhaps the main task of this book was to identify those areas of evolutionary biology where traditional ideas do not work, to outline possible paths to solutions, and only in some cases to offer the solutions themselves, of course, preliminary ones. To what extent all this has been achieved is for the reader to judge.

Acknowledgments to teachers, staff, and numerous colleagues with whom I have had the opportunity to discuss the issues discussed in the book are given at the end of the book. Here it is also a pleasant duty of the author to express sincere gratitude to Georgy Yuryevich Lyubarsky for the idea of a collective translation and its organization, to all translators and editors of the publishing house for working on the Russian version, and personally to one of the translators, Valery Anisimov, for valuable comments, largely taken into account in the author's notes. to translation.

To my parents

Introduction. Towards a New Synthesis of Evolutionary Biology

The title of this work is associated with four remarkable books: Paul Auster's novel The Music of Chance (Auster, 1991), Jacques Monod's famous treatise on molecular biology, evolution and philosophy Chance and Necessity (Monod, 1972), François Jacob's book The Logic of Life (Jacob, 1993) and, of course, Charles Darwin's On the Origin of Species (Darwin, 1859). Each of these books, in its own way, touches on the same all-encompassing theme: the relationship of arbitrariness and order, chance and necessity in life and evolution.

It was only after this work was completed and was already in the final stages of editing that I learned about the book of John Venn, the eminent logician and philosopher from Cambridge, who in 1866 published The Logic of Chance: An Essay on the Foundations and Structure of the Theory of Probability ( Venn, 1866). In this work, Venn introduces the frequency interpretation of probability, which remains the basis of probability theory and statistics to this day. Most of all, John Venn is known, of course, for the ubiquitous diagrams he invented. I am embarrassed that I did not know about Venn's work when I started this book. On the other hand, it is difficult for me to imagine a more worthy predecessor.

The main impetus for writing this book was my conviction that now, 150 years after Darwin and 40 years after Monod, we have collected enough data and ideas to develop a deeper and probably more satisfactory interpretation of the crucial relationship between case and necessity. My main thesis is that randomness, limited by various factors, lies at the very basis of the whole history of life.

Many events prompted the author to write this book. The most immediate impetus for describing the emerging new view of evolution was the revolution in genome research that began in the last decade of the 20th century and continues to this day. The ability to compare nucleotide sequences in the genomes of thousands of organisms of a wide variety of species has qualitatively changed the landscape of evolutionary biology. Our conclusions about extinct, ancestral life forms are no longer the vague guesses they used to be (at least for organisms whose fossils have not been found). Comparison of genomes reveals the diverse genes conserved in major groups of living beings (in some cases even all or most of them), and thus brings us a hitherto unimaginable wealth of reliable information about ancestral forms. For example, it is no exaggeration to say that we have a fairly complete understanding of the basic genetic makeup of the last common ancestor of all bacteria, which probably lived about 3.5 billion years ago. More ancient ancestors are seen less clearly, but certain features are deciphered even for them. The genomic revolution has not only enabled the confident reconstruction of the gene sets of ancient life forms. More importantly, it literally reversed the central metaphor of evolutionary biology (and perhaps all of biology), the tree of life (TL), by showing that the evolutionary trajectories of individual genes are incompatiblely different. The question of whether JJ should be revived and, if so, in what form, remains the subject of fierce debate, which is one of the important topics of this book.

US National Institutes of Health campus in Bethesda. Against the backdrop of the building of the National Medical Library, which, in particular, houses the National Center for Biotechnology Information (NCBI) - Yuri Volf (employee of E.K.), Evgeny Kunin, David Lipman (founder and director of NCBI), Mikhail Gelfand and Kira Makarova ( collaborator E.K.) A few years ago, we did a fairly large bibliometric study in the laboratory - we did not have access to citation data, but we looked at which of the bioinformaticians co-authored with whom and about what. For various accidental reasons, his results remained unpublished, but one of them I will now tell. We ranked all keywords (MESH terms in the PubMed database) by how their use varies from year to year. The word is “fashionable” (vogue) if the frequency of its use is steadily increasing, or “vintage” (vintage) - this terminology was introduced so as not to offend anyone (it will be clear who exactly in a couple of sentences). Accordingly, it is possible to classify authors because they write on fashionable or vintage topics.

And it turned out that among the “world experts” (as Yevgeny Kunin is recommended on the cover of his book The Logic of Chance) — the bioinformaticians with the largest number of citations, with the longest lists of articles and Hirsch indices — he is the only vintage author (for colleagues I will mention that the most following fashion and, perhaps, partly shaping it are Mark Gerstein and Per Bork). I think this is a very important observation. It shows that even in today's hectic biology, it is not necessary to chase fashion, rushing from epigenetics to metagenomics and from neural networks to networks of protein interactions, in order to become one of the most influential and respected members of the community. It also explains why only Kunin could write such a book. I don’t know if he admits to himself, but I’m sure that in the depths of his soul he uttered the classic phrase: “But shouldn’t we take a swing at William our Shakespeare?” Well, that is, our Charles Darwin and half a dozen other classics from Fisher and Wright to Mayr and Gould.

The content of the book and the unusual history of its translation into Russian have already been described in the reviews of Denis Tulinov and Georgy Lyubarsky, so I will try to talk about what I was missing - about the notes of the translators and the scientific editor. In addition to a couple of little things that should be corrected (see Appendix to the article below), and mentioning the latest results (partly the author himself does this in the notes to the translation), this would provide an opportunity for dialogue - the way it is done in the journal biology direct, one of the founders of which is Kunin. In this journal, the decision to publish is made by the author himself, and the article can be published even with negative feedback from reviewers - but reviews and answers to them will also be published. The author decides which of the members of the editorial board to invite to write a review, and Kunin, who often publishes in biology direct his articles, chooses such reviewers that reading the controversy is no less instructive than the article itself. So, desiderata.

In many places, and even in a special appendix, Kunin tries to discuss biological evolution from a physical point of view. At the same time, he completely neglects linguistic analogies. The degree of their depth could be different, but it is strange to ignore the fact that language is another evolving information system, and many problems in its description and study coincide almost verbatim with problems in the study of genome evolution. Offhand: the boundaries of the language - what are different languages, and what are dialects (cf. species definition); the divergence of a single language into a group of related ones (the origin of the Romance languages from Latin is a convincing argument in table conversations with creationists demanding "to show an intermediate view between a cat and a dog"); the gradual evolution of language by changing the frequencies of words and other phenomena (cf. the synthetic theory of evolution) and, conversely, the relatively rapid restructuring of language systems, from phonological to syntactic (cf. the theory of punctuated equilibrium); hybridization and creole languages, borrowings (not only of words, but also of syntactic constructions) and horizontal transfer of genes and operons along with regulators; reconstruction of proto-languages; coexistence in the language of different codes; the opposition "language and speech" (cf. genome and epigenome, or possibly genotype and phenotype); finally, the problem of problems is the origin of language and the origin of life (where some stages can be imagined, but colossal holes remain, to explain which Kunin resorts to the anthropic principle and the theory of multiple universes). Of course, there are important differences both in the systems themselves and in their understanding (say, we seem to have a better understanding of the systemic nature of the language than the systematicity of how the genome functions); in linguistics there is a concept of "meaning", which is difficult to imagine in biology, etc. - but, it seems to me, it would be very instructive to discuss it. It seems that in bioinformatics, as in mathematics, there are two ways to think: physical and linguistic (I will refer to my interviews with Yu.I. Manin and V.A. Uspensky, published in TrV-Nauka, and to the article by Yu.I. Manin "Languages of Mathematics or Mathematics of Languages").

In the book, there is practically no discussion of the connection between evolution and development - evo-devo - and in general, there is little to say about the evolution of regulation. Of course, this is due to the author's own scientific interests and also to the fact that the success of bioinformatics in this area is small: the little that we know about the evolution of regulation in eukaryotes mainly comes from experimental work. But the swing was not for self-review, but for the "third evolutionary synthesis"! One might think that it is the rapid evolution of regulatory networks, especially those operating at the early stages of ontogeny, that leads to drastic changes in morphology, which are, in particular, the basis of traditional taxonomy. In this connection - and in the context of the discussion of the tree of life - it would be instructive to discuss what reality the taxonomic levels correspond to. Clearly not degrees of sequence difference, but do they exist at all? Formally, if we project the tree of life onto the time axis, will we observe the condensation of internal nodes? If so, then the corresponding branches determine the levels of the family, order, class, etc. It seems that in some cases this is the case: for example, difficulties in determining the relationship of mammalian orders associated with short branch lengths at the base of the class prove the reality of both the class and the detachments. On the other hand, if branching occurs uniformly in time, then the entire taxonomy is largely a convention arising from the arbitrary selection of some internal nodes as defining taxa. A related topic, discussed in detail in the book, but in a different context, is matching sets of genes. The existence of a large number of genes specific to, say, chordates proves the reasonableness of separating them into a taxon. It would be especially instructive to consider the evolution of bacteria from these points of view, which should be close to the author. Fruiting body of the myxobacterium Myxococcus stipitatus The fruiting body of the slime mold Dictyostelium discoideum Speaking about models of evolution, it would be interesting to touch on the controversy about the existence of group selection, that is, selection that operates at the level of not individual individuals, but groups of related individuals. This theory is intended to explain, in particular, the emergence of altruistic behavior, but is it possible to do without it? A good model is the altruistic behavior of unicellular organisms, for which there are several classical examples. Individual cells in starving colonies of myxobacteria and slime molds crawl together and form fruiting bodies (see photos), after which those who are in the "hat" form spores and scatter in search of a better life, and those who remain in the stem die ( By the way, myxobacteria are bacteria, and slime molds are eukaryotes, so this is also a good example of convergent evolution, especially since cAMP is the signaling molecule in both cases). Similarly, in some sporulating bacilli, part of the starving colony commits suicide to serve as a breeding ground for another part and give them time to go into sporulation. In this case, the fate of the cell depends on the concentration of a single protein, which varies greatly in genetically identical individuals for random reasons (cf. the discussion in the book of the role of noise in evolution and the story about the toxin-antitoxin systems - again, in a slightly different context). In other bacteria, similar mechanisms regulate the formation of biofilms, luminescence, virulence, degradation of cellulose, etc. But in unicellular bacteria, this behavior can be easily explained at the level of individual genes due to the clonal origin of colonies from one ancestral cell (genetically identical individuals, from the point of view of a selfish gene , anyway, that one individual, which is affected by selection). To what extent this carries over to the level of multicellular organisms is a very interesting question.

In conclusion, the main thing must be said. Kunin's book is required reading not only for bioinformaticians and evolutionists, but, I think, for all biologists. In fact, it declares a research program, the depth of which is comparable to classical works. Even those who are well acquainted with Kunin's work and already know most of the facts and considerations presented in the book will find a lot of instructive information in it, even if only in the way these considerations are assembled into a single picture, in the style of writing and in the structure of the text. Those who come across it for the first time will discover a new way of thinking about biology that will undoubtedly affect their own research. The book will be of interest to non-biologists as well, because it shows the cutting edge, the frontier of the science of evolution.

Evgeny Kunin. case logic. M.: Tsentrpoligraf, 2014.
Denis Tulinov. The evolution of the theory of evolution. TrV-Nauka No. 149, 03/11/2014.
George Lubarsky. Third evolutionary synthesis. Chemistry and Life No. 5, 2014, see also http://ivanov-petrov.livejournal.com/1 870 801.html.
Yuri Manin: “We do not choose mathematics as our profession, but it chooses us.” TRV-Science № 13, 30.09.2008 .
V.A.Uspensky: “Mathematics is a humanitarian science.” TRV-Science № 146, 28.01.2014 .
Yuri Manin. Languages of mathematics or mathematics of languages. TRV-Science № 30, 09.06.2009.

Appendix

As in any review, you can not do without minor corrections and comments. Here are the most significant ones.

Page 43: " Zuckerkandl and Pauling… proposed the concept of the molecular clock: they predicted that the rate of evolution of a certain protein sequence would be constant (allowing for possible fluctuations) over long time intervals in the absence of functional changes". The real story seems to be a bit more complicated and controversial. Here is a quote from Emil Zuckerkandl's article "The Evolution of Hemoglobin" (collection "Molecules and Cells", M: Mir, 1966, original - in the journal Scientific American): «… In addition to these three postulates, I would like to put forward a fourth, much more controversial one. I assume that in those modern organisms that differ little from their ancestors, polypeptide chains apparently predominate, very similar to those of their ancestors. Such organisms, a kind of “living fossil”, include the cockroach, the horseshoe crab, the shark, and, among mammals, the lemur. Apparently, very many polypeptide molecules synthesized by these organisms differ only slightly from the polypeptide chains synthesized by their ancestors millions of years ago. What is the contradiction of this postulate? It is often said that evolution lasted equally long for organisms that seem to differ little from their ancestors, and for those organisms that have changed a lot. From this, scientists conclude that in terms of their biochemical properties, all these “living fossils” should also differ sharply from their distant ancestors. From my point of view, it is unlikely that morphological characters are preserved in the process of selection, but the underlying biochemical properties change.". However, part of Zuckerkandl's further reasoning, such as estimates of the time of divergence of homologous (now we would say "paralogous") chains of hemoglobin, really relies on the constancy of velocities. But not all: to build phylogenetic trees, he uses the principle, which later became known as the “maximum economy principle”: “ One of the principles of chemical paleogenetics is as follows: when postulating an ancestral amino acid residue, one should proceed from the assumption of the smallest number of mutations in the genome that led to its replacement in the polypeptide chain of descendants».

Page 73: " The typical time for the disappearance of sequence similarity in homologous genes is comparable to the time of the existence of life on Earth". It seems to me that there is an assurance bias here: if some proteins changed faster, we are simply not able to establish their relationship; this is indicated, in particular, by a large number of proteins that have the same spatial structure, but the sequences are similar at the random level. On the other hand, for homologues whose divergence happened very early, we can still observe differences in the rates of evolution, and, therefore, their similarity will disappear at different times.

Page 120, about the distribution of degrees of vertices: " Random graphs have a bell-shaped Poisson distribution, while for biological networks the distribution is described by a power function". In fact, several papers have shown that the power-law distribution does not describe biological networks well. The point is that, until recently, there were no statistical tests to test the hypothesis of a power-law distribution, and statements were made by eye — by the presence of a rectilinear segment in the distribution function constructed in double logarithmic coordinates (cf. Table 4−1, lower right graph). But double logarithmic coordinates are a very tricky thing; almost any arbitrarily drawn monotonically decreasing function with a monotone derivative will have such a visually straight segment (unless this function is specifically constructed to refute this assertion).

In the discussion of the endosymbiotic origin of cellular organelles (Chapter 7), it might be worth mentioning that, unlike mitochondria, chloroplasts arose at least twice: the amoeba has a primary chloroplast. paulinella, and it is absent from its closest relatives and, apparently, arose independently of the chloroplast of the ancestor of red and green algae. It appears that an early state of impending chloroplast acquisition is observed in euglena, which may or may not have a symbiotic intracellular cyanobacterium: when dividing, the cyanobacterium remains in one of the daughter cells, and the second becomes a predator until it acquires a new (previously free-living) cyanobacterium . Even more interesting is the question of the boundary between organelles and intracellular bacterial endosymbionts of sucking insects, which can have a very small genome, comparable in size to the genome of organelles (say, the genome Carsonella ruddii, endosymbiont of psyllid Pachypsylla Venusta, encodes a total of 182 proteins, and the genome Tremblaya princeps, one of the endosymbionts of the mealybug Planococcus citri, - 121 proteins, however, inside Tremblaya princeps another endosymbiont lives - Moranella endobia with 406 proteins). I think that the export to the organelle of proteins encoded in the nuclear genome can serve as a criterion.

Page 234: " The only archaea with more than 5,000 genes are found among mesophiles(namely, some Methanosarcina) , and up to 20 percent of these genomes contain genes of relatively recent bacterial origin". Indeed, the proportion of bacterial genes in methanosarcines is greater than in other archaea, but this estimate seems to be overestimated. It is taken from old papers (beginning of the millennium), and the reason for this error is that at that time the number of sequenced archaeal genomes was small. Accordingly, database searches revealed bacterial but not archaeal homologues for many genes. Reproducing the procedure used in these works, if it were applied to data banks that change over the years, shows that the proportion of bacterial genes in methanosarcins decreases monotonically (see figure). A more accurate procedure of building phylogenetic trees for "suspicious" genes results in an estimate of 6% (Garushyants & Gelfand, submitted).

The horizontal axis is the GenBank year. The vertical axis is an estimate of the proportion of genes of bacterial origin that are horizontally transferred into genomes Methanosarcina(green) and Methanosarcinales (red)

Dias BG, Ressler KJ. Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat Neurosci. 2014; 17(1): 89-96.
Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury JM, Wincker P, Roudier F, Jansen RC, Colot V, Johannes F. Mapping the epigenetic basis of complex traits. Science. 2014; 343(6175): 1145-1148.
Gapp K, Jawaid A, Sarkies P, Bohacek J, Pelczar P, Prados J, Farinelli L, Miska E, Mansuy IM. Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice. Nat Neurosci. 2014; 17(5): 667-669.

In this ambitious book, Evgeny Kunin highlights the intertwining of the random and the regular that underlies the very essence of life. In an attempt to gain a deeper understanding of the mutual influence of chance and necessity that drives biological evolution forward, Kunin brings together new data and concepts, while charting a path that leads beyond the synthetic theory of evolution. He interprets evolution as a stochastic process based on pre-contingencies, limited by the need to maintain cellular organization, and guided by a process of adaptation. To support his conclusions, he combines many conceptual ideas: comparative genomics, which sheds light on ancestral forms; a new understanding of the patterns, modes, and unpredictability of the evolutionary process; advances in the study of gene expression, protein abundance, and other phenotypic molecular characteristics; the application of methods of statistical physics to the study of genes and genomes; and a new look at the probability of the spontaneous appearance of life generated by modern cosmology.

The logic of chance demonstrates that the understanding of evolution that has been developed by 20th century science is outdated and incomplete, and outlines a fundamentally new approach - challenging, sometimes contradictory, but always based on solid scientific knowledge.

The Logic of Chance. The Nature and Origin of Biological Evolution»

Author's preface to the Russian translation

The Logic of Chance. The Nature and Origin of Biological Evolution»

©The electronic version of the book was prepared by Litres (www.litres.ru)

Author's preface to the Russian translation

The author is very pleased with this, because it clearly illustrates the speed of progress in modern evolutionary biology. A few notes relate rather to the translation, explaining those places in the text where the English pun could not be accurately conveyed in Russian. Of course, these notes cannot claim to make the book a “second edition”, it is a translation, but still the author hopes that these small additions increase its value.

To my parents

Introduction. Towards a New Synthesis of Evolutionary Biology 1
The translation of the title of this introduction presented serious difficulties. The English original was towards a postmodern synthesis . This is, of course, a play on words: on the one hand, postmodern simply means "after Modern Synthesis ”(what is usually called in Russian literature the synthetic theory of evolution, STE), and on the other hand, “postmodernist”. How to convey this in Russian is not at all obvious. Worse, this simple pun is repeatedly played up in later chapters. No way to cope with this difficulty, except for writing this note, neither the translators nor the author came to mind (author's note to the Russian edition hereinafter in italics).

I see the fall of JJ as a "meta-revolution", a major change in the entire conceptual structure of biology. Clearly at the risk of incurring the ire of many for being associated with a harmful cultural trend, I nevertheless refer to this major change as a transition to a postmodern biological view of life. 2
In many ways, these ideas are based on the publications of the greatest modern evolutionist Ford Doolittle, which are cited in the relevant chapters..

In essence, this transition reveals the multiplicity of patterns and processes of evolution, the central role of unpredictable events in the evolution of living forms [evolution as tinkering] and, in particular, the collapse of pan-adaptationism as a paradigm of evolutionary biology. Despite our unwavering admiration for Darwin, we must relegate the Victorian view of the world (including its updated versions that flourish in the 20th century) to the venerable museum halls where it belongs, and examine the consequences of a paradigm shift.

This revolution in evolutionary biology has another plan. Comparative genomics and evolutionary systems biology (for example, the comparative study of gene expression, protein concentration, and other molecular characteristics of the phenotype) have revealed several common patterns that appear in all cellular life forms from bacteria to mammals. The existence of such universal patterns suggests that relatively simple molecular models, similar to those used in statistical physics, can explain important aspects of biological evolution; some similar models with significant predictive power already exist. The notorious "physicist envy" that seems to bother many biologists (myself included) can be quenched by recent and forthcoming theoretical developments. The complementary relationship between general tendencies and the unpredictability of particular evolutionary outcomes is central to biological evolution and the current revolution in evolutionary biology—another key theme of this book.

Another reason for the outline of a new synthetic evolutionary theory that is proposed in this book is specific, to some extent personal. I received a higher education and completed my postgraduate studies at Moscow State University (back in the days of the USSR), in the field of molecular virology. My PhD work involved the experimental study of the reproduction of poliovirus and related viruses, whose tiny genome is represented by an RNA molecule. I never knew how to work properly with my hands, and the place and time were not the best for experiments, because even the simplest reagents were difficult to get. Immediately upon completion of my Ph.D. thesis, my colleague Alexander Evgenievich Gorbalenya and I set about a different direction in research, which at that time seemed completely unscientific to many. It was "sequence looking"—an attempt to predict the functions of the proteins encoded in the tiny genomes of viruses (these were the only complete genomes available at the time) from the sequence of their amino acid building blocks. Today, anyone can easily perform such an analysis using convenient software tools that can be downloaded free of charge from the Internet; Naturally, a meaningful interpretation of the result will still require thought and skill (nothing has changed much here since then). In 1985, however, there were practically no computers or programs. And yet, with the help of our fellow programmers, we managed to develop some rather useful programs (we then stuffed them on punched cards). The lion's share of the analysis was done manually (or, more accurately, by eye). Despite all the difficulties and despite some missed opportunities, our efforts over the next five years were quite successful. We have been able to turn the functional maps of those tiny genomes from largely unexplored territories into very rich genomic maps of biological functions. Most of the predictions were subsequently confirmed experimentally, although some of them are still in progress: laboratory experiments take much more time than computer analysis. I am sure that our success was due to the early recognition of a very simple but surprisingly powerful basic principle of evolutionary biology: if a distinct motif in a protein sequence persists over long evolution, then it is functionally important, and the more conservative it is, the more important the function. This principle, essentially derived from simple common sense, but of course strictly following from molecular evolutionary theory, has served our purposes admirably and, I am sure, made me an evolutionary biologist for the rest of my days. I am inclined to paraphrase the famous dictum of the great evolutionary geneticist Theodosius Dobzhansky: “Nothing in biology makes sense except in the light of evolution” (Dobzhansky, 1973) in an even more direct way: biology is evolution.

In those early days of evolutionary genomics, Sasha and I often talked about the possibility that our favorite RNA viruses are direct descendants of the oldest life forms. After all, they are small and simple genetic systems using only one kind of nucleic acid, and their replication is directly related to expression through the translation of genomic RNA. Of course, these were evening conversations, not at all connected with our daytime attempts to map the functional domains of viral proteins. Today, 25 years later, with hundreds of different virus and host genomes studied, the idea that viruses (or virus-like genetic elements) could have been central to the early evolution of life has grown from nebulous assumptions into a concept compatible with a vast body of experimental data. . In my opinion, this is the most promising line of thought and analysis in early life evolution studies.

These are the various lines of thought that, unexpectedly for me, have converged in the growing realization that our understanding of evolution, and with it the very nature of biology, has forever moved away from the views that prevailed in the 20th century, which today look rather naive and rather dogmatic. At a certain point, the desire to weave these lines into a kind of coherent picture became irresistible, and hence this book appeared.

Some of the impetus for writing this book came not from biology at all, but from the astonishing achievements of modern cosmology. These discoveries not only raised cosmology to the level of real physics, but also completely turned our ideas about the world, and especially about the nature of chance and necessity. When it comes to the frontiers of biology, such as the problem of the origin of life, this new way of looking at the world is impossible to ignore. Physicists and cosmologists are increasingly posing the question of why there is something in the world and not nothing, not only as a philosophical but also as a physical problem, and explore possible answers in the form of certain physical models. It's hard not to ask the same question about the biological world, and on more than one level: why does life exist, and not just solutions of ions and small molecules? And if life exists, why are there palm trees and butterflies, cats and bats, and not just bacteria? I am sure that these questions can be posed in a direct scientific way, and it seems to me that plausible, albeit preliminary, answers are already appearing on them.

Recent advances in high-energy physics and cosmology have inspired this book in more than just the scientific sense. Many leading theoretical physicists and cosmologists have proven to be gifted writers of popular and popular science books (which makes one wonder about the connection between top-level abstract thinking and literary talent) that convey the excitement of the latest discoveries about the structure of the universe with delightful clarity. , grace and fervor. The modern wave of such literature, coinciding with the revolution in cosmology, began with Stephen Hawking's classic A Brief History of Time (Hawking, 1988). Since then, dozens of different excellent books have appeared. One of them that changed my own view of the world more than others was Alexander Vilenkin’s excellent short book The World of Many Worlds (Vilenkin, 2007), but the works of Steven Weinberg (Weinberg, 1994), Alan Guth (Guth, 1998a), Leonard Suskind (Susskind, 2006b), Sean Carroll (Carroll, 2010), and Lee Smolin (in a controversial book on "cosmic natural selection"; Smolin, 2010). These books are much more than great popularizations: each of them attempts to present a coherent, general view of both the fundamental nature of the world and the state of the science that investigates it. Each of these pictures of the world is unique, but in many ways they go side by side and complement each other. Each of them is based on rigorous science, but contains elements of extrapolation and conjecture, broad generalizations and, of course, contradictions. The more I read these books and thought about the implications of the emerging new world view, the more I wanted to do something similar in my own field, molecular biology. At some point, while reading Vilenkin's book, I realized that perhaps there is a direct and fundamentally important relationship between the new views on probability and chance, dictated by modern cosmology, and the origin of life - or rather, the origin of biological evolution. The great role of chance in the origin of life on Earth, which is present in this line of thought, is certainly extraordinary and will certainly confuse many, but I felt that it could not be ignored if we were to take seriously the problem of the origin of life.

This book is my own approach to describing the current state of evolutionary biology in terms of comparative genomics and systems biology; therefore, it inevitably includes not only established facts and confirmed theoretical models, but also conjectures and assumptions. In this book, I try to draw the line between fact and conjecture as clearly as possible. I wanted to write a book in the style of the aforementioned excellent popular science books on physics, but the presentation became stubborn and refused to be written that way. The result is a text that is much more scientific than originally intended, although it is for the most part not very specialized and describes very few methods, and in a very simplistic manner. One important caveat: although the book is devoted to various aspects of evolution, it remains a collection of chapters on selected topics and in no way claims to be a comprehensive work. Many important and popular topics, such as the origin of multicellular organisms or the evolution of animal development, are quite consciously left untouched. As far as possible, I have tried to stick to the theme of the book: the interaction between chance and orderly processes. Another delicate moment is related to references to the literature: if I tried to include, if not all, but at least the main sources, the bibliography would amount to many thousands of references. I have given up trying to do this from the outset, and thus the bibliography at the end of the book is only a small selection of relevant works, and their selection is partly subjective. I offer my sincere apologies to colleagues whose important work has been left unmentioned.

Despite all these warnings, I hope that the generalizations and ideas presented here will be of interest to many of my fellow scientists and students - not only biologists, but also physicists, chemists, geologists, and anyone interested in evolution and the origin of life.

I read it again. Some time ago the author kindly sent me the then unpublished English version. And now in Yekaterinburg I bought a Russian edition (organized by I-P) in a bookstore and re-read it with great pleasure. By the way. eugene_koonin in the preface he expresses cautious doubts: why do we need a Russian edition at all, if the language of science is English? Well, for example, it is much easier for me to read such texts in Russian, that's why.

Reservations that I am not a specialist, etc., are inappropriate - naturally, this is my journal, and I express my personal opinion, and what and what I understand / do not understand, readers (at least, regular readers) have long formed their own opinion.

The book is undeniably outstanding. It is rare to read a popular book (of course, "popular" it is very conditional) with such pleasure and with such benefit. Two things were postponed as philosophically important.

1. Understanding complexity as slightly modulated chaos. It turned out to be so constructive that I had already discussed with an employee very specific calculations that need to be made for some purely physical reason. But not only. In general, this is all about neutral evolution, about a meaningless, basically, genome, about evolution as a workman who spins the wheels in the existing mechanism, and does not create everything new and ideal - a very, very important thought for me. Even at a very early age, he noted Lem's casual remarks (especially in The Voice of the Lord) about the role of chance in evolution, and even then they made a deep impression. But there is a whole book, arguments, explanations, everything.

2. The meaninglessness of the concept of biological progress, anti correlation of complexity (organismic) and fitness. The most evolutionarily successful critters are simple, optimal, in their genome they have all at least two, as in the Manual on Shooting, some kind of directly effective managers. And we are freaks, not culled by selection solely because of our small number. Yes, yes, this is also about the social structure (in which associations the author, of course, is not to blame, this is to the extent of my depravity).

Thoroughly cleared the brains about Darwin, Lamarck, STE and other things that Rabinovich (in a bad sense) used to sing.

Now... Oh. Yes, yes, yes, about the last chapters, about the anthropic principle, the Multiverse and inflation. I read these chapters and quietly rejoiced that I was not a biologist. That I have, in the words of the great Larkin, not "scenarios", but calculations and results (as well as explanations and predictions of very specific experiments). Suddenly I realized that molecular biology (and evolutionary biology, although, as I understand it, non-evolutionary biology, according to the author, simply does not exist) is very similar to our "fundamental physics". Now, quantum field theory, gravity, cosmology, that's all. And my condensed state, with a direct ambition to understand the world around us, is an analogue of classical field biology, all this zoology-botany. And this is a completely different psychology of scientific creativity, different motivation. If I were a biologist, I would study some kind of fish behavior (there was such a group in Leiden, they seem to have been dispersed for poor formal performance compared to molbiologists). And it is quite natural that in physics "global" biologists are attracted not by the physics of the condensed state, which seems to be closer to them in the nature of the objects under study, as Schrödinger said there - an aperiodic crystal? - then it's for us, and quantum cosmology. How is Mayakovsky? "The state is interested in big things - all sorts of Fordisms, this and that ... a time machine."

And how happy we, physicists, are that the condensed state is more than half of all physics, that the stringers did not drive us under the plinth, like field molecular biologists, that the husband was maimed in battles, that the court caresses us for that ... Ugh, where - it didn't go there.

Well, it is clear that nuclear physics was far more important than anything else. Until it turned out that transistors and lasers invented without noise and pump are much more important than the atomic bomb, not to mention colliders. It was, everything was. And passed. This too shall pass.