Building the Most Complex Structure on Earth: An Epigenetic Narrative of Development and Evolution of Animals

Nikoleta

Preface

In this book, I intent to succinctly present my theory of the epigenetic mechanisms of evolution and development. By making its presentation accessible to a wide range of readership, I hope not to have sacrificed scientific rigor.

An earlier extensive substantiation of this theory and its biological ramifications in Epigenetic Principles of Evolution (2008, 2012) allows me to focus on the principal ideas—and present only the most representative empirical evidence in support of the theory—in this work. I have also expanded my epigenetic view of development and evolution to the world of unicellulars and marginally to the plant kingdom.

Herein, epigenetics is dealt with as a biological discipline on its own rather than as a branch, or frontier area, of genetics or any other discipline. I extend the epigenetics’ object beyond the classical areas of the DNA methylation, histone acetylation, and chromatin remodeling, which in this book are considered downstream elements of signal cascades at the systemic level.

I include in epigenetics the vast areas of the nongenetic mechanisms of reproduction, growth, cell differentiation, development, and evolution. It is in this broader context that epigenetics promises to be the genetics of the twenty-first century.

As it occurs often in the study of biological phenomena, an overlap of epigenetics with the objects of the study of other disciplines is unavoidable. So, for example in studying epigenetic mechanisms of homeostasis, its object overlaps with that of physiology, and in studying mechanisms of reproduction and development, it overlaps with the disciplines of genetics and endocrinology.

At the core of my comprehensive vision of epigenetics is the concept of the epigenetic control and regulation of gene expression to include changes in the developmental mechanisms that produce evolutionary novelties without changes in genes. In this vision, epigenetics is functions of the integrated control system, which, I think, represents the core of the epigenetics as the new northstar of the biological research.

The predominant genetic approach to the study of inheritance has naturally led to the use of the adjective genetic synonymously to inherited. By expanding the field of study of the phenomenon of inheritance to nongenetic mechanisms, epigenetics imposes a reconsideration of the synonymous use of these words. In our time, biological inheritance is a shared object of study where epigenetics and genetics come into a complex, but clear relationship, characterized by epigenetic control and regulation of genetic functions and structures.

My son’s, Redon, help in preparing the manuscript of this book can hardly be overestimated.

1

Control Systems in the Living World

The Nature of Living Systems

Although biologists are still arguing about the nature and definition of life, humans have always been able to distinguish intuitively between living and nonliving things. It is obvious that the Matterhorn mountain is inanimate, while the tree alongside it is alive (Figure 1.1).

Figure 1.1 The Matterhorn in the Swiss Alps and a tree.

We viscerally distinguish between a mountain as a nonliving entity and a tree as a living thing. The key difference is the biological pattern of the tree, which is repeated regularly. Matterhorn is unique, naturally unrepeatable, and there is no Matterhorn pattern. This unmistakable biopattern is unique to living things.

But, ill defined as it is, the biopattern may not always be a reliable indication of life, and most will agree that the pictures below may defy our perception of biopattern and animal pattern. At first glance, one may not notice the difference between a stick insect and a dead twig (Figure 1.2) or a living one (Figure 1.3), but our doubts disappear as soon as we see them move or react to our touch. Our gut instinct, again, is that only living things are irritable and display motile avoidance behavior. Besides, humans also always knew that living things grow and reproduce.

Figure 1.2 A stick insect on a dead branch.

Figure 1.3 A stick insect on a living twig.

λης, 384–322 BC) used a similar empirical approach 23 centuries ago to develop his classification of the living world, which was based on visual perceptions of living things and phenomena. He believed both living and nonliving things exist and are distinguished by the soul, which is found only in living organisms. Aristotle characterized the plants as living entities with souls, which enables them to grow and reproduce; in addition, an evolved type of soul allows animals to perceive the external world, move, and react to it instinctively, while the human soul enables us to do everything animals do, plus use logic and think.

Since Aristotle, biology has made considerable progress in attempting to know the structure and function of living systems and understand their essential properties behind the visual perception. Two centuries after the discovery of the cell by the English scientist Robert Hooke (1635–1703), zoologist Theodor Schwann (1810–1882) and biologist Matthias Jakob Schleiden (1804–1881) suggested that cells were the basic units of all living beings, unicellulars and multicellulars, animals and plants. This great generalization had a profound heuristic effect on biological studies and represents a landmark in the development of biology and in its gradual transformation from a descriptive into a causal science.

The progress in the study of the cell and living systems in general has created a detailed picture of high organization and functional complexity. Life is a process that biological systems have to perform in order to maintain and to perpetuate, via reproduction, their highly improbable structures. Life is an inseparable manifestation of the existence of living systems, and all living systems, from a unicellular prokaryote to a human being, have in common several essential properties.

Living Systems Have Clear-Cut Boundaries

Living systems build clear boundaries that separate them from the environment, thus determining the range of action or territoriality of the organism’s homeostatic mechanisms. On the inner side of the boundary is the system; on the outer is its surrounding. In unicellulars, this boundary is represented by the cell membrane. In multicellulars, it is represented by skin/integument (animals) or bark (plants). Living cells build boundaries to control the flow of matter and energy rather than isolate themselves from the environment. The cell membrane is an integral part of the living system. It is designed to allow for the controlled intake of nutrients and the excretion of waste and nonusable energy (heat), while preventing the free diffusion of solutes that is necessary to maintain differences in concentration between the cell and its environment. It represents the front line for the antientropic drama of the living system, to vanquish thermodynamic forces of disorder and to build, maintain, and perpetuate its physically improbable structure.

Metabolism

In performing their vital functions, living systems obtain energy by breaking down nutrients, depleting their reserves of matter and free energy (catabolism). In order to maintain their structure and function, living systems have to compensate for the loss by synthesizing the lost components through the nutrients they take in with food (anabolism). The equilibrium between the catabolism and anabolism in living systems represents their normal metabolism, which enables them to maintain a state of dynamic material and energetic equilibrium.

Since the seventeenth century, metabolism has been considered a defining property of living systems (viruses are metabolic parasites, and it is the host cell that goes astray to produce its own killers). The maintenance of the structure and functions of the cell require spatiotemporal coordination of a multitude of anabolic and catabolic reactions occurring in the living cell. But the maintenance of the naturally eroding cell structure requires that the cell somehow knows or has information on the structure to be maintained and does the species-specific work at the right places and at the right times within the cell’s nanospace.

How does the cell accomplish this? If metabolism is understood to be the work that the cell does to retain its structural identity, then how does the cell get the information on the changes occurring in the system, how does it detect the deviations from the norm, and, finally, how does it generate instructions to restore the normal structure and send them to the changed structures? But if the living cell is not controlled by external forces, as is clearly the case, metabolism implies the presence of a built-in control system.

Control Systems Are Prerequisites of Living Systems

A cell is a supercomplex microscopic structure that performs thousands of reactions coordinated perfectly in space and time every moment, and from the perspective of physics, it is clearly an improbable construction. Nevertheless, it survives and perpetuates its structure via reproduction. Theoretically, there are two alternative ways that the living cell might accomplish this marvel of nature’s biotechnology; all these reactions are spontaneously coordinated, or, alternatively, the cell has evolved a control system to coordinate that myriad of chemical reactions within the cell.

The first possibility, that thousands of spatiotemporally precisely coordinated biochemical reactions within the cell can spontaneously occur, seems next to impossible. Emergence is a descriptive term that does not explain or help us explain anything. The same can be said of self-regulation. Loose as they are, these terms only avoid the questions on how cell structures arise and are maintained.

The alternative explanation of the phenomenon is that the wonderful spatiotemporal coordination of many thousands of chemical reactions occurring in a cell, and many more in a multicellular organism, are controlled by a specialized system. Human experience shows that even the simplest artificial devices or machines cannot function without control systems involving continued human supervision and regulation of material and energetic supply or built-in control systems.

An example of a simple, one-variable control system with a built-in controller is a thermostat used for regulating a room’s temperature. The control system consists of a thermostat and a furnace. The thermostat is the controller of the system; it receives information on the temperature of the room via a sensor (thermometer) and compares it to the desired temperature, a selected set point. When the temperature is lower than the set point, the thermostat switches on the circuit, which causes the furnace to produce heat. When the temperature exceeds the set point, the circuit opens, and the furnace switches off until the temperature falls below the set point again, and the cycle repeats. But if regulation of a single variable, room temperature, cannot be achieved without a control system, what should one think of incomparably complex systems such as living cells or multicellular organisms, which have to both control and regulate thousands of different variables, in differential patterns in tens or hundreds of different cell types? The control system is a sine qua non of the existence of all living organisms. The emergence and evolution of living systems are inseparable from the evolution of the control system; the evolution of complex animal structures and functions is associated by a parallel increase in the complexity of the control systems.

If a control system with a controller is necessary for regulation of a single variable such as the temperature of a room, it is absolutely necessary to regulate hundreds and thousands of variables coordinated in time and the nanospaces of a cell. In multicellular animals, the development and maintenance of normal structure are a function of an integrated control system (Figure 1.4). It is a hierarchical system of controls on several levels of organization, in which higher levels of control impose restrictions on lower levels to minimize the noise in the transmission of information downward to the cell level, where gene expression is regulated and patterns of gene expression are determined.

Figure 1.4 A generalized and simplified diagram of the integrated control system in metazoans, with a central nervous system (CNS) acting as controller of the system. Metazoan structure degrades continually due to intrinsic, thermodynamically determined causes, as well as a result of adverse influences of the environment. Changes in the structure and function of the organism and environmental changes are monitored by a pervasive network of interoceptors and exteroceptors and communicated to the CNS. In the CNS, the afferent input is compared to the neurally determined set points (1). Deviations from the norm are identified (2), and pathways for restoring the norm are determined (3). Instructions, or commands for restoring the norm (4), are sent to effectors (pituitary, target endocrine glands, or cells in target tissues) through signal cascades. Via the molecular and afferent feedback input, the controller receives continual information on the restored/degraded state of the system (Cabej, 2012).

The continued evolution of control systems increased the independence of living systems from their environment, and as a rule, the degree of complexity of a living system parallels the degree of the complexity and sophistication of the control system. More complex systems require more complex and sophisticated control systems.

Recognition of the presence of a control system that is capable of maintaining the normal structure of the organism implies that it knows what the normal structure is. But if it has information about its own structure, there is no reason to doubt that it is capable of transmitting it to its offspring.

Biological Reproduction

However successful they are in maintaining their normal structure, living systems have to succumb to the thermodynamic forces of disintegration and decomposition sooner or later; their life expectancy is temporally limited, varying from minutes in unicellulars to thousands of years in trees such as olives. Yet life on Earth has been prospering and evolving for more than 3 billion years because living systems invented a special trick of circumventing the second law of thermodynamics. In order to avoid their unavoidable demise, they live or subsist long enough to reproduce themselves before dying. The progeny will also be engaged in the same struggle against the hostile thermodynamic forces, but ultimately it will give in to these forces after producing progeny and so forth, in recurring cycles of reproduction that enable the species to survive at the expense of the individual. Thus, a species’ existence is perpetuated by sacrifices of individual lives, or the species owes its existence to the reproduction of mortal individuals.

Given the exceptionally high degree of the functional and structural complexity of living systems, unrivaled by anything existing in nature or ever created by humans, their capability to reproduce is far from self-explanatory. The genome or genetic information, as an answer, is out of the question for obvious qualitative and quantitative reasons (see later in Chapter 2, section Is there any program in the genome?). Erecting animal structure requires more than the production of proteins, which are the only products genes are known to account for. An animal organism is more complex than a bag of proteins. Cells, not proteins, are the basic unit of life. Under no circumstances can a protein, gene, or genome, or any combination of them, function as a living system; only a cell can (or at least a cell of a unicellular organism can).

As pointed out earlier, the ability of the control system of an organism to monitor the structure, to identify deviations from the norm and send instructions for restoring the norm, clearly shows that it has information on the structure and is capable of transmitting that information to the offspring.

Unicellulars reproduce via binary fission or sexual reproduction. In strict terms, their reproduction does not fit well into the conventional mother-to-daughter reproduction scheme. Cell division does not produce two daughter cells; the result of the division is only two cells, rather than three. It would not be correct to say that it produces one daughter cell, because the semiconservative mechanism of cell duplication, from both the genetic and epigenetic viewpoint, makes it impossible to determine which of the cells resulting from cell division is the mother or daughter. Hence, each of the resulting cells is the twin of the other. Cell division, thus, leads to production of two twin cells. Each of the twin cells is equally ancestral to, and descendant of, the other. The distinction can be clear only at the generational level, where we can speak of successive generations or ancestral and descendant generations.

From this viewpoint, unicellular forms also defy our traditional dichotomic concept of death and life—unicellular forms of life virtually are potentially immortal—the dividing cell does not die, but half-lives in the structure and functions of the two cells of the next generation. This semantic aspect aside, what is essential is the fact that in unicellulars, the two sister cells after division are fully capable of independent life and reproduction, which is in marked contrast with what is observed in multicellular organisms.

The epigenesis-preformation dichotomy also seems hardly applicable in the case of the reproduction of unicellular organisms. Transformation of an original organism into two implies quantitative change; that is, duplication of existing cell mass, including duplication of the genetic information and epigenetic information contained in epigenetic structures of the unicellular organism.

At the multicellular level of organization, biological systems shifted from the reproduction mode of unicellulars. They do not reproduce semiconservatively, producing a twin of themselves within the existing system and sharing its original structure with it, as unicellular organisms do. The basic mode of reproduction in multicelllulars—sexually and nonsexually reproducing multicellulars alike—is via gametes. Theirs is an epigenetic mode of reproduction that comprises both qualitative (biological development) and quantitative (growth) changes via the sequential steps of cell differentiation, organogenesis, and morphogenesis of the egg/zygote into an adult organism.

The idea that multicellulars produce copies of themselves is also controversial. What we actually observe are gametes, eggs, and sperm cells (eggs only in parthenogenetic organisms), or newborns that follow an independent complex development until they become copies of their parents. Parents provide gametes with the epigenetic information necessary to develop to an early embryonic stage, the phylotypic stage, when only one organ system, the nervous system, is operational. At this early embryonic stage, when the maternal epigenetic information provided to the embryo via gametes is exhausted, the CNS is already capable of stepwise computation of the epigenetic information necessary for the development of the adult metazoan supracellular structures.

The capability of living systems to reproduce their kind leads to two other properties of the living systems: evolvability and growth.

Evolvability

This is a relatively new biological concept, and its definition depends on the question addressed (Pigliucci, 2008). In this context, evolvability is the ability of living organisms to adapt their phenotype by changes in developmental pathways. Since evolutionary changes occur in the process of development, the evolution and evolvability of living systems is related to, and is enabled by, the phenomenon of biological reproduction. Evolvability is thought to evolve (Kirschner and Gerhart, 1998), as is clearly indicated by evidence of the acceleration of the rate of evolution.

Genetic changes are too rare and overwhelmingly deleterious to account for the huge diversity of forms in the living world. The prevailing idea that changes in genes are necessary for the evolution of living systems is challenged by numerous biological phenomena. The concept of the phenotype as a result of the interaction of genes with the environment fails to explain how, in concrete terms, a change in a gene or DNA can produce an adaptive morphological change. I emphasize the word adaptive because it is well known that mutations in genes can lead to phenotypic changes at the molecular level; that is, deleterious changes sensu Archibald Garrod’s (1857–1936) inborn errors of metabolism. Genome sequencing of various species of unicellular and multicellular organisms, conservation of the genetic toolkit, biological phenomena such as developmental plasticity (intragenerational developmental plasticity and especially transgenerational plasticity), reversion of ancestral morphological characters, metamorphosis in invertebrates and vertebrates, cell differentiation, loss of morphological characters, etc., suggest that it is not changes in genes or DNA, but epigenetically determined changes in patterns of gene expression in the process of individual development that may be responsible for evolution of structure and morphology.

Growth

In unicellular organisms, growth is a stage in the process of their reproduction. It consists of a stepwise and ordered increase in the size of the cytoplasm, including the increase in the number (e.g., ribosomes mitochondria) or duplication of organelles, (chromosomes, centrosomes, cell nuclei, etc.). In multicellular organisms, as the founders of the cell theory determined almost two centuries ago, growth consists of the growth of the number of cells in the process of development, comprising prephylotypic development, histogenesis, and organogenesis.

Homeostasis and Adaptability

Both these properties of living systems are regulated by the control system. In order to function normally, unicellular and multicellular organisms must maintain a relatively constant internal environment under considerably varying conditions in the external environment.

Homeostasis and mechanisms of its regulation are better known in mammals, especially in humans. These organisms maintain the level of many physicochemical parameters in their fluids constant (see later section Homeostasis - The maintenance of Constant Internal Environment is Prerequisite of Living Systems, in this chapter). Among the most important homeostatic parameters they regulate are body temperature, pH, levels of electrolytes, hormones, growth factors, secreted proteins, etc. So, for example, in winter when the external temperature falls, in warm-blooded animals, a specialized part of the controller of their control system, the hypothalamus, activates neuroendocrine mechanisms to increase heat generation. On the other hand, in the summer when the environmental temperature rises above the normal body temperature, it activates mechanisms that reduce heat production and increase heat loss. Living organisms can respond adaptively to changes in the environment with changes in their structure, function, behavior, and life history that tend to neutralize the harmful effects of environmental changes or agents and maintain homeostasis. Numerous described cases of developmental plasticity, both intragenerational and transgenerational (see Chapter 4), illustrate the high capability of living systems to adapt and survive even under unfavorable environmental conditions. The adaptability increased the independence of living systems from their environment.

The above properties are unique to living systems, and the control system is fundamental to all of them: reproduction, growth, evolution, adaptability, and evolution. An organism can live without reproducing, evolving, or growing for considerable spans of time, from a few minutes for a bacterium, to one century for a human being, to thousands of years for some trees. But any human being would almost instantly perish in the absence of the control system. From this view, all the essential properties and functions of living systems are subordinate to the control system.

The Principle of Entropy and Erosion of Material Structures

From experience, anyone knows that inanimate objects always tend to reach stabler states. We consider quite natural to see a book fall from a shelf, a brick from a wall, or a shingle to the ground, but we do not expect the fallen book, brick, or shingle to go back to their original positions on the shelf, wall, or roof, respectively. Such miracles could happen in the world of myth and fiction but not in the real world ruled by the rigorous laws of nature. We consider the above objects to have found their stabler or more probable, although less-ordered, states.

All the above-mentioned examples are unidirectional and less-ordered states, and the spontaneous return to the original ordered state is impossible. But exceptions exist. Nests of birds and beaver dams are ordered structures, artifacts that cannot arise naturally. Termites build mounds, which clearly are structures that cannot occur spontaneously (Figure 1.5). They build their mounds above their subterranean multichambered nests, and the mounds may be of different sizes, shapes, and heights, with complex mazes of tunnels and shafts used for ventilation. But whether a bird’s nest, a beaver dam, or a termite mound, left under natural conditions, sooner or later all of them are doomed to lose their order and break down.

Figure 1.5 A complex termite mound in Cape York, Australia.

Over centuries, human civilizations around the globe have added order and created naturally highly ordered structures by investing work and information. Yet observe what remains of Athens’s ancient Acropolis, or of thousands of remnants of ancient and prehistoric works of art, inhabited centers, fortifications, and castles. No one could expect that under natural conditions, the heads of the US presidents carved in granite on Mount Rushmore will remain as originally sculpted by Gutzon and Lincoln Borglum (Figure 1.6) 60 years ago. In fact, fractures in the granite have already occurred. No spontaneous process or event can improve the structure or function of a Porsche; only the opposite is possible. Since the probability of occurrence of less-ordered states is infinitely greater than the ordered state, less-ordered states are more probable, and hence statistically more stable. This explains the observation that all objects in nature tend to reach stabler states: stabler states are statistically more likely to occur.

Figure 1.6 Mount Rushmore National Memorial.

Such observations of the natural trend of the loss of order in nature, which goes as far back as the origins of humanity, found a theoretical explanation only around the second half of the nineteenth century with the discovery of the second law of thermodynamics, which, in the opinion of many scientists, may be the most universal law governing the universe. Central to the second law of thermodynamics is the principle of entropy. For the purpose of this discussion, a simple and classical definition of the law is:

In an isolated system, only processes that are associated with increase of entropy can occur.

The movement of molecules of a gas under moderate temperatures may be described as disordered, but molecules of water are less so, while nitrogen bases in DNA are highly ordered. Working on a mechanical theory of gases, Rudolf Clausius (1822–1888) coined the term transformation content (Verwandlungsinhalt) or entropy (from the Greek en+trope—toward+turn) for describing the direction of the flow of heat from a hotter compartment of a gas system to a colder one. This leads to a state of equilibrium in the system where the temperature (the average speed of gas molecules in the whole system) equalizes. Reversion to the original state (i.e., segregation of high-speed gas molecules from low-speed ones in the system) cannot occur. Extrapolating this to the universe, Clausius concluded that the entropy of the universe tends to be at a maximum. Later, Ludwig Boltzmann (1844–1906) popularized the idea of entropy as a measure of disorder in a system. He tried to explain why material systems tend to increase their entropy or states of disorder; this is because the number of disordered states in a gas system is infinitely larger than the ordered state. Accordingly, the stabler state is the one that the system has the highest probability to reach.

Boltzmann tried to explain why the entropy increases in one direction only: past→present→future. To account for this time asymmetry of entropy, he suggested that in the endless universe, isolated spaces still exist, which have not reached the equilibrium state (maximal entropy) and are still increasing their entropy. Boltzmann reasoned that since the probability of disordered states in these isolated spaces is incomparably higher than the ordered one, it follows that these spaces will continue to increase their entropy as time progresses. He argued that the direction of the increase in entropy in the part of the universe we live in might determine our perception of the movement of time from the present to the future, not the present back to the past. Accordingly, in regions of the universe where the entropy is maximal, time may be symmetrical, or there should be no time direction.

First, let us elucidate the meaning of entropy from Boltzmann’s physical view as a measure of atomic disorder. Under moderate temperatures, water molecules are more disordered than in lower temperatures when they transform into ice, where atoms are arranged in highly determined spatial patterns in three-dimensional crystal lattices. But if conditions change (e.g., if the temperature rises above the melting point or if the ice crystal plunges into water), the crystalline structures vanish; atoms dissociate from the lattice and begin moving randomly. In the liquid state, the order of the crystalline structure is lost, and thus, the system increased its molecular disorder or entropy. In both cases, the temperature rise increases the entropy or the disorder of the system. The opposite will occur when the water temperature falls, and it can be imagined that by lowering the temperature to absolute zero (i.e., −273.15°C (−459.67°F or 0 K)), the entropy of the system will decline to zero (when virtually no atomic movements occur) and order will be maximal.

The second law of thermodynamics concerns isolated systems that exchange neither matter nor energy with the external world. Since such systems exist in human imagination rather than in nature, it follows that the second law does not forbid the increase of order or decrease of entropy in open systems. Living systems, by definition, are open systems (i.e., out of the realm (range of action) of the second law), and they do not mind if open systems find ways to decrease their entropy. This is what living systems actually do, although not very honorably (fairly)—they do it by stealing the neighborhood’s existing