Epigenetic Processes and Evolution of Life

Jana Švorcová, Anton Markoš

• Publisher: CRC Press
• Year: 2019
• ISBN:
  9781351009942
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Cell Biology
• Index: Biological Sciences

The book covers the possible story of emergence of life and its subsequent evolution, emphasizing the necessary evolutionary step negotiation of a common "language set" which kept all inhabitants in the biosphere together, ensuring a basic level of understanding among them. The book focuses on "protocols of communication" (both genetic and epigenetic) representing norms shared and understood across the whole biosphere, enabling a plethora of holobiotic relationships. Cooperative nature of organismal evolution and epigenetic processes as a major force in evolution are also covered. Topics discussed are illustrated in detail on selected casuistics.

1

Transgressing the Norms

One Ring to rule them all, One Ring to find them, One Ring to bring them all, and in the darkness bind them…

—J.R.R. Tolkien; The Lord of the rings

There were so many dialects spoken in England, in the Later Middle Ages, that people even from neighboring shires had difficulties understanding each other. In the Oxford history of Britain (Morgan 1999), we read: “Geoffrey Chaucer (1340–1400) had serious misgivings as to whether his writings would be understood across England—and he wrote for a limited, charmed circle.” Of course, such a situation is not exceptional for England; all modern nations arose from a pêle mêle of dialects, either by decree or by common consensus, only after a collective norm had been established and became respected by the community. Normative sets—grammar, spelling and phraseology became more or less binding—standing over all colloquial variants, and accompanied by a drastic reduction of vocabulary, grammatical forms, idioms, vocalization, etc. Similar trends towards normalization can be observed in other cultural endeavors, as law, religions, or political culture. What is obvious is the highly contingent and historical nature of such normative processes: no natural law, no strict necessity was at work here. No natural law at work, yet the spell of ‘rings’ of logic, tradition, scores, conventions, scripts, religious obedience, and more. The Norm constitutes the basic knowledge taught at the secondary school: not only in language courses, but also in, e.g., biochemistry, philosophy, or history.

No such historically established norm, however, is observed absolutely. Many colloquial variants from times past survive for quite long, e.g., within dialects, habits, or as pagan practices (even in areas with a long-lived Christian tradition; Ginzburg 1992a, b). By analogy, such ‘palimpsests’ found in the non-human life may point towards the origin of life. Soon after the establishment of the Norm, two important facts become obvious, be it in culture or life in general:

1.  All members of the community recognize it and take it as a given, even if no individual is able to abide strictly by all its rules; this applies not only in cases of everyday vernacular speech and behavior. For example, Rappaport (2010) states that for religious morals of societies: “The chaos of everyday life […] attains some stability to the degree that it is informed by ideas representing the social facts of a shared collective existence.” He introduces the concept of Ultimate Sacred Postulates that “not only stand beyond the reach of falsification by the rigorous procedures of logic of science, but are also impervious to disproof by the less formal but more compelling rigors of daily life. Their independence from ordinary experience, moreover, makes it possible for people of widely divergent experience to accept them” (Rappaport 2010). We invite the reader to treat textbook truths and norms as such presumed universals; it goes without saying, as we argue here, that this also applies to the whole of the biosphere.

2.  If, in the course of history, different ‘lineages’¹ have deviated from the norm, they never went so far that the ground would become indiscernible. Even uncommonly weird heritable modifications² display their grounding, either in universal postulates or in the norms of this or that life stage (as Tunicate larvae reveal their Chordate allegiance). The rings that bind the norm do not keep their grip absolutely, yet everybody feels their existence.

Once the rules are established for the game (whether ice hockey, opera, courtroom, or …), what is important is that the performance takes place within the framework of some such ring (chessboard, playground, or …). With this in mind, we invite the reader to compare two approaches. J. von Uexküll (2010) prods us to uncover—behind the tangled web of life—the scoring of the symphony of nature, which he sees as the very task of biology. In contrast, we argue that the ringing in the biosphere is not only the performing of symphony, but before all else, a genuine, endless jam session! Such jamming is the main topic of this present book. The statement does not suggest that the opposite does not exist—frozen communities do stick piously to the norm (sects, living fossils, etc.). They provide us a stable background for the jamming of others.

To return to our parable: The Norm becomes the acknowledged ground from which a plethora of creativity sprouts across various human activities; if we stay with the example of language, it becomes the fiction and poetry of different genres, the jargon and phraseology of the sciences, linguistics, philosophy, arts, law, diplomacy, and so on. An English laywoman may not understand a single sentence from an exposé of an English-speaking attorney, yet she recognizes that he speaks English; he may even be able to render his rumination into a form more comprehensible for her. Presumably, they will also be able to share the charm and entertainment of dinner party conversation.

For another parable pointing towards the difference between the norm and play, we take from E. Auerbach (1957) who compares classical theater with that of 16th century: “The dramatic occurrences of human life were seen by antiquity predominantly in the form of a change of fortune breaking in upon man from without and from above. In Elizabethan tragedy on the other hand—the first specifically modern form of tragedy—the hero’s individual character plays a much greater part in shaping his destiny. […] In the introduction to an edition of Shakespeare, which I have before me, I find it expressed in the following terms: ‘And here we come on the great difference between the Greek and Elizabethan drama: the tragedy in the Greek plays is an arranged one in which the characters have no decisive part. They but to do and die. But the tragedy in the Elizabethan plays come straight from the heart of the people themselves.’” Auerbach comments (1957): “In Shakespeare’s work the liberated forces show themselves as fully developed yet still permeated with the entire ethical wealth of the past. Not much later the restrictive countermovements gained the upper hand. Protestantism and the Counter Reformation, absolutistic ordering of society and intellectual life, academic and puristic imitation of antiquity, rationalism and scientific empiricism, all operated together to prevent Shakespeare’s freedom in the tragic from continuing to develop after him.” We are the heirs of those ‘countermovements’ that may obstruct our feelings towards ravings of the living.

Throughout this book, our intention is to apply many such parables of human experience to an understanding of biology in the hope that we succeed in highlighting some important aspects of the processes of living. Its topic is the origins of life and its subsequent evolution, the incessant labor that makes the world a home. The story begins at some point of prebiotic evolution when zillions of organic substances, volcanism, tides, ever-changing rocks, radiation, etc. supported and drove prebiotic ‘metabolic’ pathways. The control of such syntheses was gradually overtaken by telluric structures: the diversity of unnecessary compounds, chiral antipodes, etc. backed away in favor of controlled metabolic pathways established on mineral and organomineral surfaces with accumulation of much smaller sets of new compounds, opening further differentiation (even Darwinian selection) of self-propagating metabolites, catalyzers, etc. Bit-by-bit, such pathways became independent on mineral structures and turned into self-propagating entities. The first cells (LUCA biosphere; middle column in Fig. 1.1) turned up, representing closures from their environment, and equipped with a handful of pathways, compounds, and structures, and this repertoire has not changed much substantially in later evolution of newly established life. What has changed is vital manifestations, as reliable genetic memory, amount and efficiency of catalyzers and metabolic pathways, number and diversity of cell structures, and before all, the richness and capacity of symbolic communication. The latter has enabled the establishment of ecological networks comprising all inhabitants of the biosphere.

Back to the Norm that took grip with cells: it embrances, e.g., five nucleotides, twenty amino acids, a handful of phosphorylated sugars, etc., all with the proper molecular handedness (chirality). The first cells started building biospheres with such a humble set—essentially, with what we find in the basic biochemistry and cell biology textbooks. This is the underlying ‘logic of life’. As stated by the biochemist A. Lehninger (1975): “(1) There is an underlying simplicity in the molecular organization of the cell; (2) All living organisms have a common ancestor; (3) The identity of each species of organism is preserved by its possession of characteristic sets of nucleic acids and proteins; (4) There is an underlying principle of molecular economy in living organisms.” Such rules represent the set of rings binding all the inhabitants of the biosphere together, and ensuring some basic level of understanding among all.

Fig. 1.1: Before and after the appearance of life. Left: abiosphere, i.e., chemical evolution driven by telluric forces and supported by mineral structures. Middle: The Last Universal Common Ancestor (LUCA) and its presupposed properties (the Norm). Right: Biotic evolution—diversification of life’s functions and forms.

Upon the emergence of life, however, a completely new set of tools appeared, which complemented the original set to enable new forms and ways of living—derived from the Norm and rooted in it. Beside the ‘big bang’ of proteins and the establishment of basic functions and structures, this new set was founded in the development of sophisticated communication networks—of producing, transmitting, amplifying and decoding the many classes of signals, messages, signs. This enabled living forms (cells, multicellular organisms, communities), on one hand, to become informed of multifarious facets of their environment (consisting mainly of monitoring the presence and doings of others). On the other hand, it also allowed them to broadcast their own messages to others. Such basic ‘protocols of communication’—that is a norm of a different order and possible only in living beings—have become, and remain to this day, shared and understood (at least to some degree) across the whole biosphere. Thanks to such bindings, living beings can rely on some historically grounded basic level of understanding that backs the plethora of ecological and symbiotic interactions.

As in our metaphor of language, evolution (in the same sense as human history) proceeded through specialization in different ‘lineages’ and of different ways of living, but still retaining at least parts, or remnants, of the primeval potential of mutual understanding. For reasons explained later, we call such additional storeys of life’s potential epigenetic, to distinguish them from the genetic, or generic, norm.

Our speculations will stick to the scenario of earthly events, i.e., that organic compounds and life arose thanks to forces and structures of planetary origin. Moreover, it is obvious that we are not supporters of simple and non-explanatory statements such as: ‘Life is a chemical reaction (dissipative system, thermodynamic system, etc.).’ We maintain that life is a new quality that emerged upon a special, singular transition from non-living matter. Elsewhere, we have defined life as a semiotic category (Markoš et al. 2009, Markoš and Das 2016, Švorcová et al. 2018, Švorcová and Kleisner 2018); it means that all living beings are able to decipher meaning and react according to their memory (individual and/or inherited) and experience. Life is not a special brand of physics, but a fundamentally new quality. The idea is not new, and is traceable to one of Darwin’s key theories on the descent with modification.

The scope of the book is broad, and of the overall image, we can provide but a short outlook on some extremely interesting facets, or even leave them out completely. We bank on the idea that life emerged on our planet, and do not bother gathering evidence for panspermia, though such evidence may exist. We did not willfully withhold any evidence that would falsify our theses, neither have we deliberately twisted the conclusions of publication cited, though we do reserve the right to re-interpret the data. We mostly avoided explaining (and citing) basic elementary concepts and procedures such as protein, mRNA, transcription, etc. Instead, we focus on recent articles that may vindicate our approach. We perceive our model reader as working with the internet, and searching therein for explanations of what he does not know while extending what he does, filling in the gaps where we may not have paid sufficient attention, and building new connections with her/his knowledge.

Chapters 2, 3, 4 deal with the establishment of life on the planet, the process from non-living ‘abiosphere’ to biosphere, of establishing the norm. In the second chapter, we discuss planetogenesis and events favorable for the emergence of basic biochemical pathways, and the replication of successful solutions. The third chapter reconstructs life as it may have looked shortly after the singularity of its emergence. We argue that LUCA (Last Universal Common Ancestor) contained all the elements that we call the Norm, and we give a short survey of how it may have looked. The fourth chapter then provides a survey of novelties that have evolved after the basic life processes were established: we accentuate the communicative abilities of life, which are rooted in common memory as well as the experience of a particular lineage or community. Chapter 5 summarizes the concepts of heredity and theories of evolution from Lamarck to our days. It accentuates our lines of thinking, and sets the framework for understanding chapters that follow. In Chapters 6 and 7, we further develop the ‘post-Norm’ evolutionary achievements, especially ways and solutions leading to information networking, heredity, signal transmission, and signal interpretation. Such properties are further illustrated on three cases: Chapter 8 is focused on morphogenesis of multicellular forms of life; in Chapter 9, we deal with symbiotic interactions; and finally, Chapter 10 discusses holobiotic ways of living. The final Chapter (11) brings a theoretical summary of our investigations throughout the book, to justify our main thesis: “Life is a semiotic category”.

¹    We ask the reader to keep in mind that biological history, which is evolution, is reticular, i.e., no ‘pure lineages’ are available in the world of cultures, religions, holobionts, symbioses, and horizontal gene transfer. If, for simplicity, we use ‘lineage’ in such a context, we put it between commas.

²    Such as, e.g., the peculiar structure of mitochondrial genes in the protist group Kinetoplastida (Feagin et al. 1988).

2

The Manifold of Prebiotic Evolution

Present study throws light on past history and vice versa. Every existing organism is, in this sense, a fossil. It carries in it, by inference, all the evidence of its predecessors; and this remains the case even if we cannot read it clearly or at all. Naturally, the study of the past […] can give indications as to where to look in the present to find significant things.

—J.D. Bernal (1951)

As no direct fossils of prebiotic paths towards life have remained to our times in the geological record, and even most proxies are a matter of equivocal interpretation, we must work with conjectures—and with the ‘palimpsests’ retained in contemporary forms of life. This chapter brings a hypothetical scenario of events that preceded the establishment of life with its multiple closures. The enormous heterogeneity of prebiotic organic compounds, metabolic pathways and structures was, as we argue, gradually reduced to a small set of ‘standard’ substances that are well described in basic textbooks: five nucleotides; 20 amino acids; several phosphorylated sugars; membrane elements; metabolic pathways like fixation of CO₂, anaplerotic syntheses, etc.; and structures—capsids, proto-ribosomes, or RNA world. Effective coupling was required with both supplies of suitable forms of ...

Table of contents

• Cover
• Title Page
• Copyright Page
• Dedication
• Table of Contents
• Preface
• 1. Transgressing the Norms
• 2. The Manifold of Prebiotic Evolution
• 3. Life from Nonlife: Establishing Rules and Codes
• 4. Towards a New Manifold: The Biosphere
• 5. Concepts of Heredity and Theories of Evolution
• 6. New Dimensions of Diversity
• 7. Information Boom
• 8. Morphogenesis
• 9. Evolution by Cooperation: Communication between Different Lineages of Life
• 10. I, Holobiont
• 11. Life as Interpretation
• References
• Index