This chapter describes a mathematical model of epigenesis, and starts by translating the traditional but vague definitions of that concept into expressions that are increasingly more precise. The first step consists in defining epigenesis as a convergent increase of complexity. The second states that this process is equivalent to a reconstruction from incomplete information, and in the third step this becomes a reconstruction from incomplete projections. In this way, we can model epigenesis as a special case of the problem of reconstructing structures from projections, a problem that arises in many fields (for example in computerised tomography) and whose mathematics is well known. What is less well known is that a reconstruction can be achieved even when the starting information is incomplete, provided that appropriate memories and codes are employed. This is illustrated with a few practical examples, and the logic of that unusual kind of reconstruction is described first in words and then in formulae. At that stage we can go back to biological epigenesis and conclude that a convergent increase of complexity in organic life necessarily requires organic codes and organic memories. And this gives us the two critical concepts that will be used in the rest of the book for an entirely new approach to the problem of biological complexity.

The logic of embryonic development

The discovery of genes that control embryonic development has started a true revolution in biology, both from an experimental and from a theoretical point of view.

Semantic biology has been developed in stages since the 1970s. The mathematical papers appeared in 1974 and 1987 (Barbieri, 1974a, 1974b, 1987). The first biological paper was “The ribotype theory on the origin of life” (Barbieri, 1981) and the first general theory (the concept of evolution by natural conventions) was proposed in The Semantic Theory of Evolution (Barbieri, 1985). The idea that splicing and signal transduction are based on organic codes was introduced much later (Barbieri, 1998), and so was the term semantic biology (Barbieri, 2001). There are at least five new concepts in this biology (ribotype, organic codes, organic memories, reconstruction from incomplete information and evolution by natural conventions), and they have all gone unnoticed for a long time. Something similar happened to the ideas of Edward Trifonov, who has been calling attention to sequence codes since 1988, and perhaps that was not a coincidence. Things however seem to be changing. The discoveries of the sugar code (Gabius, 2000) and of the histone code (Strahl and Allis, 2000; Turner, 2000) have made some impact, and there is a growing awareness that real organic codes do exist in nature. A parallel development has also taken place in philosophy and in linguistics. In 1963, Thomas Sebeok proposed that semiotics must have a biological basis, and has campaigned ever since for a more general approach which today is known as biosemiotics (Sebeok, 2001).

There is a strange paradox in modern biology. On the one hand, new discoveries are made at such a high rate that our science of life appears full of surprises and in a constant state of flux. On the other hand, all new findings are apparently accommodated within a theoretical framework that remains remarkably stable. Present-day biology, in other words, seems to be in that phase of development that Thomas Kuhn referred to as “normal science”, a phase in which an endless stream of novelties is smoothly accounted for by an unchanging paradigm. And this is definitely not for want of alternatives. No efforts have been spared to provide different explanations of life, but none has withstood the test of time. What makes us feel good about our present paradigm (which many call universal Darwinism) is that only the truth – or something very near the truth – can resist so many assaults and outlive generations of critics. In such a situation, I find it almost embarrassing to suggest that our beloved paradigm is not as perfect as we like to think. But this is the message that is coming from nature, and I had better tell you straight away the reasons that lead to this conclusion. The main points are three: the existence of organic codes, a mathematical model of epigenesis and a new theory of the cell.

The organic codes

From time immemorial it has been thought that codes, or conventions, exist only in the mutable world of culture, while nature is governed by immutable laws.

The cell theory and the theory of evolution are the two pillars of modern biology, but only the latter seems to be the object of ongoing research and debates. The cell theory is generally regarded as a closed chapter, a glorious but settled issue in the history of science. The emphasis today is on cell experiments, not on cell theory, and there is no doubt that one of our greatest challenges is the experimental unravelling of the extraordinary complexity that has turned out to exist in the cellular world. At various stages of this book, however, we will see that the experimental results suggest new ideas, and at the end of the book it will be possible to combine them in a new model of the cell. This is because cells are not only what we see in a biological specimen through the lenses of a microscope, but also what we see through the lenses of a theory. The cell, after all, is a system, and understanding the logic of a system requires some theorising about it. And since this theorising has a long history behind it, let us begin by retracing the main steps of that intellectual journey. This chapter shows that the concept of the cell had to be imposed on us by the microscope because it was unthinkable in the world-view of classic philosophy. And after that intrusion, the concept has gradually changed and in so doing it has changed our entire approach to the problems of generation and embryonic development.

After the origin of life, our planet has been inhabited only by single cells for some 3000 million years, i.e. for more than 85% of the entire history of life on Earth. Multicellular creatures appeared only at the end of that unimaginably long period, but when they did they quickly diversified into all known kingdoms. This chapter presents a brief account of what we can reconstruct about the age of the cell, and its conclusions are not always in line with present thinking. It is shown, for example, that the bacteria-first view is unlikely to be correct, despite it persistent popularity. Another minor unorthodox conclusion is that the kingdoms of life are probably seven, and not five or six as reported in most textbooks. The major divergence from orthodoxy, however, comes from the fact that cellular evolution is reconstructed by taking organic codes into account. The emergence of the cell nucleus, for example, is related to the full development of the splicing codes, because it is these codes that allow a physical separation, in space and time, between transcription and translation. There are also good arguments for the existence of cytoskeleton codes and compartment codes, thus suggesting that these were instrumental to the evolution of other major eukaryotic structures. The idea that organic codes have something to do with the great events of macroevolution, in brief, does not seem unreasonable, and gives substance to the concept of evolution by natural conventions.

Genetics was born in the first years of the twentieth century with the discovery that hereditary characters are carried by molecules that are physically present in chromosomes. These molecules of heredity – the genes – are responsible for the visible structures of the organisms but do not enter into those structures, which means that in every cell there are molecules which determine the characteristics of other molecules. In 1909, Wilhelm Johannsen concluded that this distinction is similar to the difference which exists between a project and its physical implementation, and represents therefore a dichotomy of the living world which is as deep as the Cartesian dichotomy between mind and body.

In order to distinguish the two types of molecules Johannsen called them genotype and phenotype, but such a dualism was almost universally rejected. At that time it was thought that proteins were responsible for both the visible structures and the hereditary characters, and all biological features seemed reducible to a single type of molecule. The reality of the genotype–phenotype distinction was proved only in the 1940s and 1950s, when molecular biology discovered that genes are chemically different from proteins, and, above all, when it became clear that genes carry linear information whereas proteins function through their three–dimensional structure.

The genotype–phenotype duality is therefore a dichotomy which divides not only two different biological functions (heredity and metabolism), but also two different physical quantities (information and energy).

The existence of organic codes and organic memories is essentially an experimental problem, but experiments are planned and interpreted with criteria that are expressed in words. This inevitably requires some agreement about the terminology, and so this chapter starts with a few definitions. A code is defined as a correspondence between two independent worlds, and this definition immediately suggests a useful operative criterion. It means that the existence of a real organic code is based on (and can be inferred from) the existence of organic molecules – called adaptors – that perform two independent recognition processes. In the genetic code the adaptors are the transfer RNAs, but it will be shown that adaptors also exist in splicing and in signal transduction, which means that there are at least other two organic codes in real life. An organic memory is defined as a deposit of organic information, and this immediately qualifies the genome as an organic memory. It will be shown however that the determination state of embryonic cells is also a deposit of information, and so there are at least two different kinds of organic memory in real life. We conclude that codes and memories, as predicted by the mathematical model of epigenesis, do exist in the organic world. A conclusion that sets the stage for the problem of the next chapters, i.e. for the role that organic codes played in the history of life.

(From Noam Lahav's Biogenesis, 1999; from Martino Rizzotti's Defining Life, 1996; and from personal communications by David Abel, Pietro Ramellini and Edward Trifonov, with permission).

Jean Baptiste LAMARCK (1802)

Life is an order or a state of things in the component parts of a body that makes organic movement possible and that effectively succeeds, as long as it persists, in opposing death.

Ludwig BÜCHNER (1855)

Spontaneous generation exists, and higher forms have gradually and slowly developed from previously existing lower forms, always determined by the state of the earth, but without immediate influence of a higher power.

Rudolf VIRCHOW (1855)

Life will always remain something apart, even if we should find out that it is mechanically aroused and propagated down to the minutest detail.

Ernst HAECKEL (1866)

Any detailed hypothesis concerning the origin of life must, as yet, be considered worthless, because up till now we have no satisfactory information concerning the extremely peculiar conditions which prevailed on the earth at the time when the first organisms developed.

Thomas Henry HUXLEY (1868)

The vital forces are molecular forces.

Justus von LIEBIG (1868)

We may only assume that life is just as old and just as eternal as matter itself … Why should not organic life be thought of as present from the very beginning just as carbon and its compounds, or as the whole of uncreatable and indestructible matter in general?

The appearance of all animal phyla in a narrow geological stratum at the base of the Cambrian has been one of the greatest discoveries of all times, but has also been, and still is, one of the greatest unsolved problems of biology. What has to be explained is primarily the origin of all animal phyla in a geologically brief period of time, but there are other two closely related problems which are also waiting for an answer. One is the fact that the animal body plans have been strongly conserved after the Cambrian explosion, but not before. The other problem comes from embryology. The body plan is built during development and becomes visible at the phylotypic stage, the brief period in which the embryos of all the species of a phylum have the greatest degree of similarity. Before and after that stage, the embryos of different species become increasingly diverse, but in a very puzzling way. Before the phylotypic stage the differences are decreasing, whereas after that stage they are steadily increasing. The Cambrian explosion, in short, gives us three major problems: the origin of the animal phyla, the conservation of the body plan and the conservation of the phylotypic stage. In this chapter it is shown that if animals are described as idealised multicellular structures which are reconstructed from incomplete information, all three problems can be solved. Needless to say, it is a solution of an idealised Cambrian explosion obtained with idealised organisms, but the principles involved should not be dismissed lightly.

New theories on the origin of life appear at almost regular intervals in the scientific literature, thus creating the impression that there are virtually endless solutions to the problem. In reality most theories are but variations on two basic themes: the metabolism-first paradigm proposed by Oparin and the replication-first paradigm of J.B.S. Haldane. This is because every organism is conceived as a duality of genotype and phenotype (software and hardware), and since a sudden appearance of such a system would be little short of a miracle, there seemed to be no choice but to start either from primordial genes or from primordial proteins. In 1981, however, I proposed that an alternative does exist, because the cell is not a duality but a trinity of genotype, phenotype and ribotype. And the ribotype has a logical and a historical priority over genotype and phenotype. At the end of the chapter this proposal is illustrated with a metaphor that compares the cell to a city, where proteins are the houses and genes are their blueprints. The traditional paradigms would ask “Which came first, the houses or the blueprints?” while the ribotype theory amounts to saying that “It was the inhabitants who came first. It was they who made houses and blueprints.” The aim of this chapter, in short, is to present an overview of all paradigms on the origin of life: the gene-first, the protein-first and the ribotype-first approach.

Our view of evolution has gone through various building stages in the last two centuries, and this chapter presents a bird's-eye view of those steps. It starts by emphasising that for the two founding fathers – Lamarck and Darwin – evolution was necessary not to explain the past but to understand the present. More precisely, it was the only way to account for the experimental fact that organisms are admirably adapted to their niches and lifestyles. In the end, it was Darwin's idea of natural selection that solved the problem, and today this is virtually a closed chapter: adaptation is always the result of natural selection. Adaptation, however, is not everything in life, and the existence of other mechanisms has been repeatedly debated. The best example is genetic drift, whose reality is now beyond doubt and which clearly is a second mechanism of evolution at the molecular level, even if the relative contribution of natural selection and neutral drift at this level remains an open problem. A third mechanism of molecular evolution has been inspired by Barbara McClintock's work and can be referred to as evolution by genomic flux, or, in Gabriel Dover's terminology, by molecular drive, but in this case the consensus is not yet widespread. Another topical issue in evolutionary biology has been the unification of all life sciences under the principle of natural selection, a project that up until recently was called the Modern Synthesis, or panselectionism, while today it is generally referred to as universal Darwinism.