Category Archives: Evolutionary Theory

Origin of Animal Body Plans

Whether you can observe a thing or not depends on the theory which you use. It is the theory which decides what can be observed.

— Albert Einstein, 1926

[Gold reminds us we must not forget] … the striking reformation of evolutionary theory implied by the well-documented genetic and developmental homologies alone. De Robertis expresses this key argument in the final line of his 1997 article on the ancestry of segmentation: “The realization that all Bilateria are derived from a complex ancestor represents a major change in evolutionary thinking, suggesting that the constraints imposed by the previous history of species played a greater role in the outcome of animal evolution than anyone would have predicted until recently.” (Gould 2002: 1152) [De Robertis, E.M. 1997. The ancestory of segmentation. Nature 387: 25-26. See also, De Robertis, E.M., G. Oliver, and C.V.E. Wright. 1990. Homeobox genes and the vertebrate body plan. Scientific American, July, pp. 46-52; De Robertis, E.M., and Y. Sasai. 1996. A common plan for dorsoventral patterning in Bilateria. Nature 380: 37-40.]

(….) Hughes (2000, p. 65) has expressed this cardinal discovery of evo-devo in phyletic and paleontological terms: “It is hard to escape the suspicion that what we witness in the Cambrian is mainly tinkering with developmental systems already firmly established by the time these Cambrian beasts showed up.” (Gould 2002: 1155) [Hughes, N.C. 2000. The rocky road to Mendel’s play. Evol. and Develop. 2: 63-66.]

Gould, Stephen J. The Structure of Evolutionary Theory. Cambridge: Harvard University Press; 2002; p. 1152; 1155.

As it turns out, the miracle of complex life is more amazing, yet ironically simpler, than anyone ever expected. Researchers now know that life’s building materials are few, and they were “invented” near the dawn of animals. More specifically, a surprisingly small number of genes—”tool kit genes”—are the primary components for building all animals, and these genes emerged at a time before the Cambrian Explosion, some 600 million years ago. Thus the amazing diversity of the animal kingdom is the result of the flexibility of a small number of building blocks that have existed for eons.

This means, for example, that the gene that controls the formation of an arm on a human is the same gene that controls the formation of a wing on a bird, a fin on a fish, and a leg on a centipede, and that this gene has been around since the first animals grew the first appendage of any kind. Some prominent scientists have argued that if we could rewind the tape of life and start over again, the result would be a totally different world from that which exists today. They are wrong. Tool kit genes conserve the essence of animals, and they react to ecological cues in very consistent ways [emphasis added].

Carroll, Sean B. Endless Forms Most Beautiful: The New Science of Evo Devo. New York: Norton; 2005: Inside Dustjacket.

We now need to confront the question of whether the biological community or at least the large proportion of it has come to accept a theory of evolution that is based on a broadly parallel error. Our case studies on the action of natural selection all involve microevolutionary changes occurring within particular lineages hundreds of millions of years after the origin of the major body plans of which the species concerned represent variations. Many of these case-studies are well known, especially the evolution of industrial melanism in Biston (Bishop and Cook 1980), the evolution of pigmentation patterns in Cepaea (Jones, Leith and Rawlings 1977) and the evolution of Batesian mimicry in several lepidopterans (Turner 1977). Many paleontological case studies are also restricted to particular lineages, with studies on the horse (Simpson 1951; MacFadden 1992) and the mollusks of Lake Turkana (Williamson 1981) being among the best known. While such studies are usually transspecific, and therefore in the realm of ‘macroevolution’, they are only a very short distance in that direction from an origin-of-body-plans perspective. (Simpson (1944) used the term ‘mega-evolution’ for the biggest-scale evolutionary events such as body plan origins, but this term has not become widely adopted.)

So, this book is starting with an exhortation to the reader to believe that current evolutionary theory, based on natural selection and adaptation in present-day lineages is, at the very least, incomplete; and this exhortation is based on the drawing of a parallel between the processes of development and evolution. (Arthur 1997: 2-3)

(….) Regardless of timing of early [Cambrian] divergences, it appears that no phylum-level body plans have arisen in the animal kingdom in the last 500 my. This contrasts with the situation in plants, where teh angiosperm body plan arose relatively recently (probably about 130 my ago: see Hickey and Doyle 1977; Crane, Friis and Pederson 1995). Perhaps this difference relates to a difference in developmental-genetic control mechanisms in the two kingdoms, with some genes controlling the determination of animal body axes and other key processes of early ontogeny being more ‘generatively entrenched’ (Wimsatt 1986) than their nearest equivalents in plants. (Arthur 1997: 7)

(….) [O]ur current (neo-Darwinian) theory of evolution is incomplete…. In fact, neo-Darwinian theory is incomplete even when assessed against its own criteria. The essence of the neo-Darwinian view is that the evolutionary process is of a two-fold nature, involving the production of organismic novelties (of whatever sort) ultimately by mutation and the sieving of these by natural selection. (Arthur 1997: 9)

(….) The main problem with neo-Darwinism in its current form is that its theoretical structure is extremely lopsided. There has been sustained development of quantitative models of the action of selection, from the pioneering work of Fisher (1930), Haldane (1932) and Wright (1931) up to recent work such as that of Charlesworth (1994); while the mutational and developmental production of the variants being sieved by selection has continued to be treated by too many evolutionists as a ‘black box’, despite the numerous advances that have been made in developmental genetics in recent years. Essentially, the individual and population levels have been treated as quasi-independent. The fitness of mutant genotypes have been considered to be crucially important in models of selection, while the ways in which fitness effects are produced … have been largely disregarded. (Arthur 1997: 9-10)

This situation should of course be considered undesirable by all evolutionary biologists, including the strictest of neo-Darwinians, but how serious a problem the lack of a mutational/developmental component of evolutionary theory is perceived to be depends on the extent to which the ‘perceiver’ is a gradualist. If, despite the views put forward herein, all evolution proceeds through the accumulation of very minor variations — an extreme view popularized by Dawkins (1986) — then it may not be too much of a deficiency in the theory to simply assume that mutation perpetually generates morphologies that are slight variants on the existing form. But to anyone proposing the existence of one or more radical morphogenetic phases in evolution, the need for an adequate picture of the genetic architecture of development and of the ways in which this is altered by mutation becomes compelling. Hence the feelings of dissatisfaction that many evolutionary developmental biologists have with neo-Darwinism. There is nothing wrong with elaborate models of selection, but a detailed quantitative statement of how existing types are sorted and selectively eliminated (or held in a state of stable equilibrium) cannot pretend to be a complete theory. (Arthur 1997: 10)

Ironically, most of the alternative approaches to evolution that have proliferated in the last few decades have allowed the focus on destructive rather than creative forces to persist. The neutral theory of molecular evolution (Kimura 1983) — arguably within a broad neo-Darwinian world view — concentrates on the stochastic loss of neutral and nearly neutral alleles produced in an unspecified way by mutation. Punctuated equilibrium (Eldredge and Gould 1972) is a pattern, not a process, and may simply be a geological reflection of the standard neo-Darwinian mechanism of allopatric speciation, although some authors (e.g. Williamson 1981) have suggested otherwise…. (Arthur 1997: 10)

(….) The only approach [as of 1997, at the time of this writing] to evolution that has attempted to focus on creative forces has been that of Evolutionary Developmental Biology. I use this label (… Hall 1992) to cover the work of a heterogeneous group of biologists including, among others, von Baer (1828), Thompson (1917), de Beer (1930), Goldschmidt (1940), Waddington (1957), Gould (1977b [2002]), Raff and Kaufman (1983), Buss (1987), Arthur (1988), Thomson (1988) and Raff (1996). (Arthur 1997: 11)

A Work in Progress

[E]volutionary economics is a work in progress…. The term “evolutionary economics” has been used to denote a wide range of economic research and writing…. [T]he authors, believe that the value of a broad theoretical perspective, such as that of evolutionary economics, should be judged in terms of the strength and quality of the understanding of empirical phenomena and the illumination of policy questions provided by research oriented by that perspective. We believe that the research done over the last thirty years oriented by evolutionary economic theory has amply demonstrated the value of that theory, and we want to increase the number of scholars who appreciate that. (Nelson et. al. 2018)

(….) At the root of the difference between evolutionary economics and economics of the sort presented in today’s standard textbooks is the conviction of evolutionary economists that continuing change, largely driven by innovation, is a central characteristic of modern capitalist economies, and that this fact ought to be built into the core of basic economic theory. Economies are always changing, new elements are always being introduced and old ones disappearing. Of course economic activities and economic sectors differ in the pace and character of change. In many parts of the economy innovation is rapid and continuing, and the context for economic action taking is almost always shifting and providing new opportunities and challenges. And while in some activities and sectors the rate of innovation is more limited, attempts at doing something new are going on almost everywhere in the economy, and so too change that can make obsolete old ways of doing things. Neoclassical theory, which is a significant influence on how most professionally trained economists think, represses this. (Nelson et. al. 2018)

[To be continued … dd]

Greedy Reductionism and Statistical Shadows

Biological evolution is, as has often been noted, both fact and theory. It is a fact that all extant organisms came to exist in their current forms through a process of descent with modification from ancestral forms. The overwhelming evidence for this empirical claim was recognized relatively soon after Darwin published On the Origin of Species in 1859, and support for it has grown to the point where it is as well established as any historical claim might be. In this sense, biological evolution is no more a theory than it is a “theory” that Napoleon Bonaparte commanded the French army in the late eighteenth century. Of course, the details of how extant and extinct organisms are related to one another, and of what descended from what and when, are still being worked out, and will probably never be known in their entirety. The same is true of the details of Napoleon’s life and military campaigns. However, this lack of complete knowledge certainly does not alter the fundamental nature of the claims made, either by historians or by evolutionary biologists. (Pigliucci et al. 2006: 1)

On the other hand, evolutionary biology is also a rich patchwork of theories seeking to explain the patterns observed in the changes in populations of organisms over time. These theories range in scope form “natural selection,” which is evoked extensively at many different levels, to finer-grained explanations involving particular mechanisms (e.g., reproductive isolation induced by geographic barriers leading to speciation events). (Pigliucci et al. 2006: 1)

(….) There are a number of different ways in which these questions have been addressed, and a number of different accounts of these areas of evolutionary biology. These different accounts, we will maintain, are not always compatible, either with one another or with other accepted practices in evolutionary biology. (Pigliucci et al. 2006: 1)

(….) Because we will be making some potentially controversial claims throughout this volume, it is crucial for the reader to understand two basic ideas underlying most of what we say, as well as exactly what we think are some implications of our views for the general theory of evolutionary quantitative genetics, which we discuss repeatedly in critical fashion. (Pigliucci et al. 2006: 2)

(….) The first central idea we wish to put forth as part of the framework of this book will be readily familiar to biologists, although some of its consequences may not be. The idea can be expressed by the use of a metaphor proposed by Bill Shipley (2000) …. the shadow theater popular in Southeast Asia. In one form, the wayang golek of Bali and other parts of Indonesia, three-dimensional wooden puppets are used to project two-dimensional shadows on a screen, where the action is presented to the spectator. Shipley’s idea is that quantitative biologists find themselves very much in the position of wayang golek’s spectators: we have access to only the “statistical shadows” projected by a set of underlying causal factors. Unlike the wayang golek’s patrons, however, biologists want to peek around the screen and infer the position of the light source as well as the actual three-dimensional shapes of the puppets. This, of course, is the familiar problem of the relationship between causation and correlation, and, as any undergraduate science major soon learns, correlation is not causation (although a popular joke among scientists is that the two are nevertheless often correlated). (Pigliucci et al. 2006: 2)

The loose relationship between causation and correlation has two consequences that are crucial…. On the one hand, there is the problem that, strictly speaking, it makes no sense to attempt to infer mechanisms directly from patterns…. On the other hand, as Shipley elegantly show in his book, there is an alternative route that gets (most of) the job done, albeit in a more circuitous route and painful way. What one can do is to produce a series of alternative hypotheses about the causal pathways underlying a given set of observations; these hypotheses can then be used to “project” the expected statistical shadows, which can be compared with the observed one. If the projected and actual shadows do not match, one can discard the corresponding causal hypothesis and move on to the next one; if the two shadows do match (within statistical margins of error, of course), then one had identified at least one causal explanation compatible with the observations. As any philosopher or scientist worth her salt knows, of course, this cannot be the end of the process, for more than one causal model may be compatible with the observations, which means that one needs additional observations or refinements of the causal models to be able to discard more wrong explanations and continue to narrow the field. A crucial point here is that the causal models to be tested against the observed statistical shadow can be suggested by the observations themselves, especially if coupled with further knowledge about the system under study (such as details of the ecology, developmental biology, genetics, or past evolutionary history of the populations in question). But the statistical shadows cannot be used as direct supporting evidence for any particular causal model. (Pigliucci et al. 2006: 4)

The second central idea … has been best articulated by John Dupré (1993), and it deals with the proper way to think about reductionism. The term “reductionism” has a complex history, and it evokes strong feelings in both scientists and philosophers (often, though not always, with scientists hailing reductionism as fundamental to the success of science and some philosophers dismissing it as a hopeless epistemic dream). Dupré introduces a useful distinction that acknowledges the power of reductionism in science while at the same time sharply curtailing its scope. His idea is summarized … as two possible scenarios: In one case, reductionism allows one to explain and predict higher-level phenomena (say, development in living organisms) entirely in terms of lower-level processes (say, genetic switches throughout development). In the most extreme case, one can also infer the details of the lower-level processes from the higher-level patterns produced (something we have just seen is highly unlikely in the case of any complex biological phenomenon because of Shipley’s “statistical shadow” effect). This form of “greedy” reductionism … is bound to fail in most (though not all) cases for two reasons. The first is that the relationships between levels of manifestation of reality (e.g., genetic machinery vs. development, or population genetics vs. evolutionary pathways) are many-to-many (again, as pointed out above in our discussion of the shadow theater). The second is the genuine existence of “emergent properties” (i.e., properties of higher-level phenomena that arise from the nonadditive interaction among lower-level processes). It is, for example, currently impossible to predict the physicochemical properties of water from the simple properties of individual atoms of hydrogen and oxygen, or, for that matter, from the properties of H20 molecules and the smattering of necessary impurities. (Pigliucci et al. 2006: 4-5)

Biological Emergence and Pan-selection Hand-Waving

Epigenetic Algorithms

Mechanical metaphors have appealed to many philosophers who sought materialist explanations of life. The definitive work on this subject is T. S. Hall’s Ideas of Life and Matter (1969). Descartes, though a dualist, thought of animal bodies as automata that obeyed mechanical rules. Julien de la Mettrie applied stricter mechanistic principles to humans in L’Homme machine (1748). Clockwork and heat engine models were popular during the Industrial Revolution. Lamarck proposed hydraulic processes as causes of variation. In the late nineteenth century, the embryologists Wilhelm His and Wilhelm Roux theorized about developmental mechanics. However, as biochemical and then molecular biological information expanded, popular machine models were refuted, but it is not surprising that computers should have filled the gap. Algorithms that systematically provide instructions for a progressive sequence of events seem to be suitable analogues for epigenetic procedures. (Reid 2007: 263)

A common error in applying this analogy is the belief that the genetic code, or at least the total complement of an organism’s DNA contains the program for its own differential expression. In the computer age it is easy to fall into that metaphysical trap. However, in the computer age we should also know that algorithms are the creations of programmers. As Charles Babbage (1838) and Robert Chambers (1844) tried to tell us, the analogy is more relevant to creationism than evolutionism. At the risk of offending the sophisticates who have indulged me so far, I want to state the problems in the most simple terms. To me, that is a major goal of theoretical biology, rather than the conversion of life to mathematics. (Reid 2007: 263)

Robert G.B. Reid (2007, 263) Biological Emergences: Evolution by Natural Experiment. The Vienna Series in Theoretical Biology.

If the emergentist-materialist ontology underlying biology (and, as a matter of fact, all the factual sciences) is correct, the bios constitutes a distinct ontic level the entities in which are characterized by emergent properties. The properties of biotic systems are then not (ontologically) reducible to the properties of their components, although we may be able to partially explain and predict them from the properties of their components… The belief that one has reduced a system by exhibiting [for instance] its components, which is indeed nothing but physical and chemical, is insufficient: physics and chemistry do not account for the structure, in particular the organization, of biosystems and their emergent properties (Mahner and Bunge 1997: 197) (Robert 2004: 132)

Jason Scott Robert (2004, 132) Embryology, Epigenesis, and Evolution: Taking Development Seriously

The science of biology enters the twenty-first century in turmoil, in a state of conceptual disarray, although at first glance this is far from apparent. When has biology ever been in a more powerful position to study living systems? The sequencing juggernaut has still to reach full steam, and it is constantly spewing forth all manner of powerful new approaches to biological systems, many of which were previously unimaginable: a revolutionized medicine that reaches beyond diagnosis and cure of disease into defining states of the organism in general; revolutionary agricultural technology built on genomic understanding and manipulation of animals and plants; the age-old foundation of biology, taxonomy, made rock solid, greatly extended, and become far more useful in its new genomic setting; a microbial ecology that is finally able to contribute to our understanding of the biosphere; and the list goes on. (Woese 2005: 99)

All this is an expression of the power inherent in the methodology of molecular biology, especially the sequencing of genomes. Methodology is one thing, however, and understanding and direction another. The fact is that the understanding of biology emerging from the mass of data that flows from the genome sequencing machines brings into question the classical concepts of organism, lineage, and evolution as the same time it gainsays the molecular perspective that spawned the enterprise. The fact is that the molecular perspective, which so successfully guided and shaped twentieth-century biology, has effectively run its course (as all paradigms do) and no longer provides a focus, a vision of the biology of the future, with the result that biology is wandering will-nilly into that future. This is a prescription for revolution–conceptual revolution. One can be confident that the new paradigm will soon emerge to guide biology in this new century…. Molecular biology has ceased to be a genuine paradigm, and it is now only a body of (very powerful) technique…. The time has come to shift biology’s focus from trying to understand organisms solely by dissecting them into their parts to trying to understand the fundamental nature of biological organization, of biological form. (Woese 2005: 99-100)

Conceptualizing Cells

We should all take seriously an assessment of biology made by the physicist David Bohm over 30 years ago (and universally ignored):

“It does seem odd … that just when physics is … moving away from mechanism, biology and psychology are moving closer to it. If the trend continues … scientists will be regarding living and intelligent beings as mechanical, while they suppose that inanimate matter is to complex and subtle to fit into the limited categories of mechanism.” [D. Bohm, “Some Remarks on the Notion of Order,” in C. H. Waddington, ed., Towards a Theoretical Biology: 2 Sketches. (Edinburgh: Edinburgh Press 1969), p. 18-40.]

The organism is not a machine! Machines are not made of parts that continually turn over and renew; the cell is. A machine is stable because its parts are strongly built and function reliably. The cell is stable for an entirely different reason: It is homeostatic. Perturbed, the cell automatically seeks to reconstitute its inherent pattern. Homeostasis and homeorhesis are basic to all living things, but not machines.

If not a machine, then what is the cell?

Carl R. Woese (2005, 100) on Evolving Biological Organization

(….) When one has worked one’s entire career within the framework of a powerful paradigm, it is almost impossible to look at that paradigm as anything but the proper, if not the only possible, perspective one can have on (in this case) biology. Yet despite its great accomplishments, molecular biology is far from the “perfect paradigm” most biologists take it to be. This child of reductionist materialism has nearly driven the biology out of biology. Molecular biology’s reductionism is fundamentalist, unwavering, and procrustean. It strips the organism from its environment, shears it of its history (evolution), and shreds it into parts. A sense of the whole, of the whole cell, of the whole multicellular organism, of the biosphere, of the emergent quality of biological organization, all have been lost or sidelined. (Woese 2005: 101)

Our thinking is fettered by classical evolutionary notions as well. The deepest and most subtle of these is the concept of variation and selection. How we view the evolution of cellular design or organization is heavily colored by how we view variation and selection. From Darwin’s day onward, evolutionists have debated the nature of the concept, and particularly whether evolutionary change is gradual, salutatory, or of some other nature. However, another aspect of the concept concerns us here more. In the terms I prefer, it is the nature of the phase (or propensity) space in which evolution operates. Looked at one way, variation and selection are all there is to evolution: The evolutionary phase space is wide open, and all manner of things are possible. From this “anything goes” perspective, a given biological form (pattern) has no meaning outside of itself, and the route by which it arises is one out of an enormous number of possible paths, which makes the evolution completely idiosyncratic and, thus, uninteresting (molecular biology holds this position: the molecular biologist sees evolution as merely a series of meaningless historical accidents). (Woese 2005: 101)

The alternative viewpoint is that the evolutionary propensity space is highly constrained, being more like a mountainous terrain than a wide open prairie: Only certain paths are possible, and they lead to particular (a relatively small set of) outcomes. Generic biological form preexists in the same sense that form in the inanimate world does. It is not the case that “anything goes” in the world of biological evolution. In other words, biological form (pattern) is important: It has meaning beyond itself; a deeper, more general significance. Understanding of biology lies, then, in understanding the evolution and nature of biological form (pattern). Explaining biological form by variation and selection hand-waving argumentation is far from sufficient: The motor does not explain where the car goes. (Woese 2005: 101-102)

The Regulatory Genome

THE SYSTEM OF HEREDITY AS A CONTROL SYSTEM

In a world dominated by thermodynamical forces of disorder and disintegration, all living systems, sooner or later, fall in disarray and succumb to those forces. However, living systems on Earth have survived and evolved for ~3 billion years. They succeeded in surviving because a. during their lifetime they are able to maintain the normal structure by compensating for the lost or disintegrated elements of that structure, and b. they produce offspring. The ability to maintain the normal structure, despite its continual erosion, indicates that living systems have information for their normal structure, can detect deviations from the “normalcy” and restore the normal structure. This implies the presence and functioning of a control system in living organisms. In unicellulars the control system, represented by the genome, the apparatus for gene expression and cell metabolism, functions as a system of heredity during reproduction. Homeostasis and other facts on the development of some organs and phenotypic characters in metazoans prove that a hierarchical control system, involving the CNS [Central Nervous System] and the neuroendocrine system, is also operational in this group. It is hypothesized that, in analogy with unicellulars, the control system in metazoans, in the process of their reproduction, serves as an epigenetic system of heredity.

Nelson R. Cabej (2004, 11) Neural Control of Development: The Epigenetic Theory of Heredity

A general character of genomic programs for development is that they progressively regulate their own readout, in contrast, for example, to the way architects’ programs (blueprints) are used in constructing buildings. All of the structural characters of an edifice, from its overall form to local aspects such as placement of wiring and windows, are prespecified in an architectural blueprint. At first glance the blueprints for a complex building might seem to provide a good metaphoric image for the developmental regulatory program that is encoded in the DNA. Just as in considering organismal diversity, it can be said that all the specificity is in the blueprints: A railway station and a cathedral can be built of the same stone, and what makes the difference in form is the architectural plan. Furthermore, in bilaterian development, as in an architectural blueprint, the outcome is hardwired, as each kind of organism generates only its own exactly predictable, species-specific body plan. But the metaphor is basically misleading, in the way the regulatory program is used in development, compared to how the blueprint is used in construction. In development it is as if the wall, once erected, must turn around and talk to the ceiling in order to place the windows in the right positions, and the ceiling must use the joint with the wall to decide where its wires will go, etc. The acts of development cannot all be prespecified at once, because animals are multicellular, and different cells do different things with the same encoded program, that is, the DNA regulatory genome. In development, it is only the potentialities for cis-regulatory information processing that are hardwired in the DNA sequence. These are utilized, conditionally, to respond in different ways to the diverse regulatory states encountered (in our metaphor that is actually the role of the human contractor, who uses something outside of the blueprint, his brain, to select the relevant subprogram at each step). The key, very unusual feature of the genomic regulatory program for development is that the inputs it specifies in the cis-regulatory sequences of its own regulatory and signaling genes suffice to determine the creation of new regulatory states. Throughout, the process of development is animated by internally generated inputs. “Internal” here means not only nonenvironmental — i.e., from within the animal rather than external to it but also, that the input must operate in the intranuclear compartments as a component of regulatory state, or else it will be irrelevant to the process of development. (Davidson 2006: 16-17)

(….) The link between the informational transactions that underlie development and the observed phenomena of development is “specification.” Developmental specification is defined phenomenologically as the process by which cells acquire the identities or fates that they and their progeny will adopt. But in terms of mechanism, specification is neither more nor less than that which results in the institution of new transcriptional regulatory states. Thereby specification results from differential expression of genes, the readout of particular genetic subprograms. For specification to occur, genes have to make decisions, depending on the new inputs they receive, and this brings us back to the information processing capacities of the cis-regulatory modules of the gene regulatory networks that make regulatory state. The point cannot be overemphasized that were it not for the ability of cis-regulatory elements to integrate spatial signaling inputs together with multiple inputs of intracellular origin, then specification, and thus development, could not occur. (Davidson 2006: 17)

Evolution by Natural Experiment

This is the age of the evolution of Evolution. All thoughts that the Evolutionist works with, all theories and generalizations, have themselves evolved and are now being evolved. Even were his theory perfected, its first lesson would be that it was itself but a phase of the Evolution of other opinion, no more fixed than a species, no more final than the theory which it displaced.

— Henry Drummond, 1883

Charles Darwin described The Origin of Species as “one long argument” for evolution by natural selection. Subsequently Ernst Mayr applied the expression to the continuing debate over Darwin’s ideas. My explanation of why the debate lingers is that although Darwin was right about the reality of evolution, his causal theory was fundamentally wrong, and its errors have been compounded by neo-Darwinism. In 1985 my book Evolutionary Theory: The Unfinished Synthesis was published. In it I discussed Darwinian problems that have never been solved, and the difficulties suffered historically by holistic approaches to evolutionary theory. The most important of these holistic treatments was “emergent evolution,” which enjoyed a brief moment of popularity about 80 years ago before being eclipsed when natural selection was mathematically formalized by theoretical population geneticists. I saw that the concept of biological emergence could provide a matrix for a reconstructed evolutionary theory that might displace selectionism. At that time, I naively thought that there was a momentum in favor of such a revision, and that there were enough open-minded, structuralistic evolutionists to displace the selectionist paradigm within a decade or so. Faint hope! (Robert G. B. Reid. Biological Emergences: Evolution by Natural Experiment (Vienna Series in Theoretical Biology) (Kindle Locations 31-37). Kindle Edition.)

Instead, the conventional “Modern Synthesis” produced extremer forms of selectionism. Although some theoreticians were dealing effectively with parts of the problem, I decided I should try again, from a more general biological perspective. This book is the result. (Reid 2007, Preface)

The main thrust of the book is an exploration of evolutionary innovation, after a critique of selectionism as a mechanistic explanation of evolution. Yet it is impossible to ignore the fact that the major periods of biological history were dominated by dynamic equilibria where selection theory does apply. But emergentism and selectionism cannot be synthesized within an evolutionary theory. A “biological synthesis” is necessary to contain the history of life. I hope that selectionists who feel that I have defiled their discipline might find some comfort in knowing that their calculations and predictions are relevant for most of the 3.5 billion years that living organisms have inhabited the Earth, and that they forgive me for arguing that those calculations and predictions have little to do with evolution. (Reid 2007, Preface)

Evolution is about change, especially complexifying change, not stasis. There are ways in which novel organisms can emerge with properties that are not only self-sufficient but more than enough to ensure their status as the founders of kingdoms, phyla, or orders. And they have enough generative potential to allow them to diversify into a multiplicity of new families, genera, and species. Some of these innovations are all-or-none saltations. Some of them emerge at thresholds in lines of gradual and continuous evolutionary change. Some of them are largely autonomous, coming from within the organism; some are largely imposed by the environment. Their adaptiveness comes with their generation, and their adaptability may guarantee success regardless of circumstances. Thus, the filtering, sorting, or eliminating functions of natural selection are theoretically redundant. (Reid 2007, Preface)

Therefore, evolutionary theory should focus on the natural, experimental generation of evolutionary changes, and should ask how they lead to greater complexity of living organisms. Such progressive innovations are often sudden, and have new properties arising from new internal and external relationships. They are emergent. In this book I place such evolutionary changes in causal arenas that I liken to a three-ring circus. For the sake of bringing order to many causes, I deal with the rings one at a time, while noting that the performances in each ring interact with each other in crucial ways. One ring contains symbioses and other kinds of biological association. In another, physiology and behavior perform. The third ring contains of developmental or epigenetic evolution. (Reid 2007, Preface)

After exploring the generative causes of evolution, I devote several chapters to subtheories that might arise from them, and consider how they might be integrated into a thesis of emergent evolution. In the last chapter I propose a biological synthesis. (Reid 2007, Preface)

~ ~ ~

Introduction Re-Invention of Natural Selection

I regard it as unfortunate that the theory of natural selection was first developed as an explanation for evolutionary change. It is much more important as an explanation for the maintenance of adaptation.
George Williams, 1966

Natural selection cannot explain the origin of new variants and adaptations, only their spread.
John Endler, 1986

We could, if we wished, simply replace the term natural selection with dynamic stabilization….
Brian Goodwin, 1994

Nobody is going to re-invent natural selection….
Nigel Hawkes, 1997

Ever since Charles Darwin published The Origin of Species, it has been widely believed that natural selection is the primary cause of evolution. However, while George Williams and John Endler take the trouble to distinguish between the causes of variation and what natural selection does with them; the latter is what matters to them. In contrast, Brian Goodwin does not regard natural selection as a major evolutionary force, but as a process that results in stable organisms, populations, and ecosystems. He would prefer to understand how evolutionary novelties are generated, a question that frustrated Darwin for all of his career. (Reid 2007)

During the twentieth century, Darwin’s followers eventually learned how chromosomal recombination and gene mutation could provide variation as fuel for natural selection. They also re-invented Darwinian evolutionary theory as neo-Darwinism by formalizing natural selection mathematically. Then they redefined it as differential survival and reproduction, which entrenched it as the universal cause of evolution. Nigel Hawkes’s remark that natural selection cannot be re-invented demonstrates its continued perception as an incorruptible principle. But is it even a minor cause of evolution? (Reid 2007)

Natural selection supposedly builds order from purely random accidents of nature by preserving the fit and discarding the unfit. On the face of it, that makes more than enough sense to justify its importance. Additionally, it avoids any suggestion that a supernatural creative hand has ever been at work. But it need not be the only mechanistic option. And the current concept of natural selection, which already has a history of re-invention, is not immune to further change. Indeed, if its present interpretation as the fundamental mechanism of evolution were successfully challenged, some of the controversies now swirling around the modern paradigm might be resolved. (Reid 2007)

A Paradigm in Crisis?

Just what is the evolutionary paradigm that might be in crisis? It is sometimes called “the Modern Synthesis.” Fundamentally it comes down to a body of knowledge, interpretation, supposition, and extrapolation, integrated with the belief that natural selection is the all-sufficient cause of evolutionif it is assumed that variation is caused by gene mutations. The paradigm has built a strong relationship between ecology and evolution, and has stimulated a huge amount of research into population biology. It has also been the perennial survivor of crises that have ebbed and flowed in the tide of evolutionary ideas. Yet signs of discord are visible in the strong polarization of those who see the whole organism as a necessary component of evolution and those who want to reduce all of biology to the genes. Since neo-Darwinists are also hypersensitive to creationism, they treat any criticism of the current paradigm as a breach of the scientific worldview that will admit the fundamentalist hordes. Consequently, questions about how selection theory can claim to be the all-sufficient explanation of evolution go unanswered or ignored. Could most gene mutations be neutral, essentially invisible to natural selection, their distribution simply adrift? Did evolution follow a pattern of punctuated equilibrium, with sudden changes separated by long periods of stasis? Were all evolutionary innovations gene-determined? Are they all adaptive? Is complexity built by the accumulation of minor, selectively advantageous mutations? Are variations completely random, or can they be directed in some way? Is the generation of novelty not more important than its subsequent selection? (Reid 2007)

Long before Darwin, hunters, farmers, and naturalists were familiar with the process that he came to call “natural selection.” And they had not always associated it with evolution. It is recognized in the Bible, a Special Creation text. Lamarck had thought that evolution resulted from a universal progressive force of nature, not from natural selection. Organisms responded to adaptational needs demanded by their environments. The concept of adaptation led Lamarck’s rival, Georges Cuvier, to argue the opposite. If existing organisms were already perfectly adapted, change would be detrimental, and evolution impossible. Nevertheless, Cuvier knew that biogeography and the fossil record had been radically altered by natural catastrophes. These Darwin treated as minor aberrations during the long history of Earth. He wanted biological and geographical change to be gradual, so that natural selection would have time to make appropriate improvements. The process of re-inventing the events themselves to fit the putative mechanism of change was now under way. (Reid 2007)

Gradualism had already been brought to the fore when geologists realized that what was first interpreted as the effects of the sudden Biblical flood was instead the result of prolonged glaciation. Therefore, Darwin readily fell in with Charles Lyell’s belief that geological change had been uniformly slow. Now, more than a century later, catastrophism has been resurrected by confirmation of the K-T (Cretaceous-Tertiary) bolide impact that ended the Cretaceous and the dinosaurs. Such disasters are also linked to such putative events as the Cambrian “Big Bang of Biology,” when all of the major animal phyla seem to have appeared almost simultaneously.’ The luck of the draw has returned to evolutionary theory. Being in the right place at the right time during a cataclysm might have been the most important condition of survival and subsequent evolution. (Reid 2007)

Beyond the fringe of Darwinism, there are heretics who believe the neo-Lamarckist tenet that the environment directly shapes the organism in a way that can be passed on from one generation to the next. They argue that changes imposed by the environment, and by the behavior of the organism, are causally prior to natural selection. Nor is neo-Lamarckism the only alternative. Some evolutionary biologists, for example, think that the establishment of unique symbioses between different organisms constituted major evolutionary novelties. Developmental evolutionists are reviewing the concept that evolution was not gradual but saltatory (i.e., advancing in leaps to greater complexity). However, while they emphasize the generation of evolutionary novelty, they accommodate natural selection as the complementary and essential causal mechanism. (Reid 2007)

Notes on isms

Before proceeding further, I want to explain how I arbitrarily, but I hope consistently, use the names that refer to evolutionary movements and their originators. “Darwinian” and “Lamarckian” refer to any idea or interpretation that Darwin and Lamarck originated or strongly adhered to. Darwinism is the paradigm that rose from Darwinian concepts, and Lamarckism is the movement that followed Lamarck. They therefore include ideas that Darwin and Lamarck may not have thought of nor emphasized, but which were inspired by them and consistent with their thinking. Lamarck published La philosophie zoologique in 1809, and Lamarckism lasted for about 80 years until neo-Lamarckism developed. Darwinism occupied the time frame between the publication of The Origin of Species (1859) and the development of neo-Darwinism. The latter came in two waves. The first was led by August Weismann, who was out to purify evolutionary theory of Darwinian vacillation. The second wave, which arose in theoretical population genetics in the 1920s, quantified and redefined the basic tenets of Darwinism. Selectionism is the belief that natural selection is the primary cause of evolution. Its influence permeates the Modern Synthesis, which was originally intended to bring together all aspects of biology that bear upon evolution by natural selection. Niles Eldredge (1995) uses the expression “ultra-Darwinian” to signify an extremist position that makes natural selection an active causal evolutionary force. For grammatical consistency, I prefer “ultra-Darwinist,” which was used in the same sense by Pierre-Paul Grasse in 1973. (Reid 2007)

The Need for a More Comprehensive Theory

I have already hinted that the selectionist paradigm is either insufficient to explain evolution or simply dead wrong. Obviously, I want to find something better. Neo-Darwinists themselves concede that while directional selection can cause adaptational change, most natural selection is not innovative. Instead, it establishes equilibrium by removing extreme forms and preserving the status quo. John Endler, the neo-Darwinist quoted in one of this chapter’s epigraphs, is in good company when he says that novelty has to appear before natural selection can operate on it. But he is silent on how novelty comes into being, and how it affects the internal organization of the organismquestions much closer to the fundamental process of evolution. He is not being evasive; the issue is just irrelevant to the neo-Darwinist thesis. (Reid 2007)

Darwin knew that nature had to produce variations before natural selection could act, so he eventually co-opted Lamarckian mechanisms to make his theory more comprehensive. The problem had been caught by other evolutionists almost as soon as The Origin of Species was first published. Sir Charles Lyell saw it clearly in 1860, before he even became an evolutionist:

If we take the three attributes of the deity of the Hindoo Triad, the Creator, Brahmah, the preserver or sustainer, Vishnu, & the destroyer, Siva, Natural Selection will be a combination of the two last but without the first, or the creative power, we cannot conceive the others having any function.

Consider also the titles of two books: St. George Jackson Mivart’s On the Genesis of Species (1872) and Edward Cope’s Origin of the Fittest (1887). Their play on Darwin’s title emphasized the need for a complementary theory of how new biological phenomena came into being. Soon, William Bateson’s Materials for the Study of Variation Treated with Especial Regard to Discontinuity in the Origin of Species (1894) was to distinguish between the emergent origin of novel variations and the action of natural selection. (Reid 2007)

The present work resumes the perennial quest for explanations of evolutionary genesis and will demonstrate that the stock answerpoint mutations and recombinations of the genes, acted upon by natural selectiondoes not suffice. There are many circumstances under which novelties emerge, and I allocate them to arenas of evolutionary causation that include association (symbiotic, cellular, sexual, and social), functional biology (physiology and behavior), and development and epigenetics. Think of them as three linked circus rings of evolutionary performance, under the “big top” of the environment. Natural selection is the conservative ringmaster who ensures that tried-and-true traditional acts come on time and again. It is the underlying syndrome that imposes dynamic stabilityits hypostasis (a word that has the additional and appropriate meaning of “significant constancy”). (Reid 2007)

Selection as Hypostasis

The stasis that natural selection enforces is not unchanging inertia. Rather, it is a state of adaptational and neutral flux that involves alterations in the numerical proportions of particular alleles and types of organism, and even minor extinctions. It does not produce major progressive changes in organismal complexity. Instead, it tends to lead to adaptational specialization. Natural selection may not only thwart progress toward greater complexity, it may result in what Darwin called retrogression, whereby complex and adaptable organisms revert to simplified conditions of specialization. This is common among parasites, but not unique to them. For example, our need for ascorbic acid-vitamin C-results from the regression of a synthesis pathway that was functional in our mammalian ancestors. (Reid 2007)

On the positive side, it may be argued that dynamic stability, at any level of organization, ensures that the foundations from which novelties emerge are solid enough to support them on the rare occasions when they escape its hypostasis. A world devoid of the agents of natural selection might be populated with kludges-gimcrack organisms of the kind that might have been designed by Heath Robinson, Rube Goldberg, or Tim Burton. The enigmatic “bizarre and dream-like” Hallucigenia of the Burgess Shale springs to mind.’ Even so, if physical and embryonic factors constrain some of the extremest forms before they mature and reproduce, the benefits of natural selection are redundant. Novelty that is first and foremost integrative (i.e., allows the organism to operate better as a whole) has a quality that is resistant to the slings and arrows of selective fortune. (Reid 2007)

Natural selection has to do with relative differences in survival and reproduction and the numerical distribution of existent variations that have already evolved. In this form it requires no serious re-invention. But selectionism goes on to infer that natural selection creates complex novelty by saving adaptive features that can be further built upon. Such qualities need no saving by metaphorical forces. Having the fundamental property of persistence that characterizes life, they can look after themselves. As Ludwig von Bertalanffy remarked in 1967, “favored survival of `better’ precursors of life presupposes self-maintaining, complex, open systems which may compete; therefore natural selection cannot account for the origin of those symptoms.” These qualities were in the nature of the organisms that first emerged from non-living origins, and they are prior to any action of natural selection. Compared to them, ecological competitiveness is a trivial consequence. (Reid 2007)

But to many neo-Darwinists the only “real” evolution is just that: adaptationthe selection of random genetic changes that better fit the present environment. Adaptation is appealingly simple, and many good little examples crop up all the time. However, adaptation only reinforces the prevailing circumstances, and represents but a fragment of the big picture of evolution. Too often, genetically fixed adaptation is confused with adaptabilitythe self-modification of an individual organism that allows responsiveness to internal and external change. The logical burden of selectionism is compounded by the universally popular metaphor of selection pressure, which under some conditions of existence is supposed to force appropriate organismic responses to pop out spontaneously. How can a metaphor, however heuristic, be a biological cause? As a metaphor, it is at best is an inductive guide that must be used with caution. (Reid 2007)

Even although metaphors cannot be causes, their persuasive powers have given natural selection and selection pressure perennial dominance of evolutionary theory. It is hard enough to sideline them, so as to get to generative causes, far less to convince anyone that they are obstructive. Darwin went so far as to make this admission:

In the literal sense of the word, no doubt, natural selection is a false term…. It has been said that I speak of natural selection as an active power or Deity…. Everyone knows what is meant and is implied by such metaphorical expressions; and they are almost necessary for brevity…. With a little familiarity such superficial objections will be forgotten. [Darwin 1872, p. 60.]

Alas, in every subsequent generation of evolutionists, familiarity has bred contempt as well as forgetfulness for such “superficial” objections. (Reid 2007)

Are All Changes Adaptive?

Here is one of my not-so-superficial objections. The persuasiveness of the selection metaphor gets extra clout from its link with the vague but pervasive concept of adaptiveness, which can supposedly be both created and preserved by natural selection. For example, a book review insists that a particular piece of pedagogy be “required reading for non-Darwinist `evolutionists’ who are trying to make sense of the world without the relentless imperatives of natural selection and the adaptive trends it produces.” (Reid 2007)

Adaptiveness, as a quality of life that is “useful,” or competitively advantageous, can always be applied in ways that seem to make sense. Even where adaptiveness seems absent, there is confidence that adequate research will discover it. If equated with integrativeness, adaptiveness is even a necessity of existence. The other day, one of my students said to me: “If it exists, it must have been selected.” This has a pleasing parsimony and finality, just like “If it exists it must have been created.” But it infers that anything that exists must not only be adaptive but also must owe its existence to natural selection. I responded: “It doesn’t follow that selection caused its existence, and it might be truer to say ‘to be selected it must first exist.”‘ A more complete answer would have addressed the meaning of existence, but I avoid ontology during my physiology course office hours. (Reid 2007)

“Adaptive,” unassuming and uncontroversial as it seems, has become a “power word” that resists analysis while enforcing acceptance. Some selectionists compound their logical burden by defining adaptiveness in terms of allelic fitness. But there are sexually attractive features that expose their possessors to predation, and there are “Trojan genes” that increase reproductive success but reduce physiological adaptability. They may be the fittest in terms of their temporarily dominant numbers, but detrimental in terms of ultimate persistence. (Reid 2007)

It is more logical to start with the qualities of evolutionary changes. They may be detrimental or neutral. They may be generally advantageous (because they confer adaptability), or they may be locally advantageous, depending on ecological circumstances. Natural selection is a consequence of advantageous or “adaptive” qualities. Therefore, examination of the origin and nature of adaptive novelty comes closer to the fundamental evolutionary problem. It is, however, legitimate to add that once the novel adaptive feature comes into being, any variant that is more advantageous than other variants survives differentiallyif under competition. Most biologists are Darwinists to that extent, but evolutionary novelty is still missing from the causal equation. Thus, with the reservation that some neutral or redundant qualities often persist in Darwin’s “struggle for existence,” selection theory seems to offer a reasonable way to look at what occurs after novelty has been generatedthat is, after evolution has happened. (Reid 2007)

“Oh,” cry my student inquisitors, “but the novelty to which you refer would be meaningless if it were not for correlated and necessary novelties that natural selection had already preserved and maintained.” So again I reiterate first principles: Self-sustaining integrity, an ability to reproduce biologically, and hence evolvability were inherent qualities of the first living organisms, and were prior to differential survival and reproduction. They were not, even by the lights of extreme neo-Darwinists, created by natural selection. And their persistence is fundamental to their nature. To call such features adaptive, for the purpose of implying they were caused by natural selection, is sophistry as well as circumlocution. Sadly, many biologists find it persuasive. Ludwig von Bertalanffy (1952) lamented:

Like a Tibetan prayer wheel, Selection Theory murmurs untiringly: ‘everything is useful,’ but as to what actually happened and which lines evolution has actually followed, selection theory says nothing, for the evolution is the product of ‘chance,’ and therein obeys no ‘law. [Bertalanffy 1952, p. 92.]

In The Variation of Animals in Nature (1936), G. C. Robson and O. W. Richards examined all the major known examples of evolution by natural selection, concluding that none were sufficient to account for any significant taxonomic characters. Despite the subsequent political success of ecological genetics, some adherents to the Modern Synthesis are still puzzled by the fact that the defining characteristics of higher taxa seem to be adaptively neutral. For example, adult echinoderms such as sea urchins are radially symmetrical, i.e., they are round-bodied like sea anemones and jellyfish, and lack a head that might point them in a particular direction. This shape would seem to be less adaptive than the bilateral symmetry of most active marine animals, which are elongated and have heads at the front that seem to know where they want to go. Another puzzler: How is the six-leg body plan of insects, which existed before the acquisition of wings, more or less adaptive than that of eight-legged spiders or ten-legged legged lobsters? The distinguished neo-Darwinists Dobzhansky, Ayala, Stebbins, and Valentine (1977) write:

This view is a radical deviation from the theory that evolutionary changes are governed by natural selection. What is involved here is nothing less than one of the major unresolved problems of evolutionary biology. []

The problem exists only for selectionists, and so they happily settle for the first plausible selection pressure that occurs to them. But it could very well be that insect and echinoderm and jellyfish body plans were simply novel complexities that were consistent with organismal integritythey worked. There is no logical need for an arbiter to judge them adaptive after the fact.

Some innovations result from coincidental interactions between formerly independent systems. Natural selection can take no credit for their origin, their co-existence, or their interaction. And some emergent novelties often involve redundant features that persisted despite the culling hand of nature. Indeed, life depends on redundancy to make evolutionary experiments. Initially selectionism strenuously denies the existence of such events. When faced with the inevitable, it downplays their importance in favor of selective adjustments necessary to make them more viable. Behavior is yet another function that emphasizes the importance of the whole organism, in contrast to whole populations. Consistent changes in behavior alter the impact of the environment on the organism, and affect physiology and development. In other words, the actions of plants or animals determine what are useful adaptations and what are not. This cannot even be conceived from the abstract population gene pools that neo-Darwinists emphasize.

If some evolutionists find it easier to understand the fate of evolutionary novelty through the circumlocution of metaphorical forces, so be it. But when they invent such creative forces to explain the origin of evolutionary change, they do no better than Special Creationists or the proponents of Intelligent Design. Thus, the latter find selectionists an easy target. Neo-Darwinist explanations, being predictive in demographic terms, are certainly “more scientific” than those of the creationists. But if those explanations are irrelevant to the fundamentals of evolution, their scientific predictiveness is of no account.

What we really need to discover is how novelties are generated, how they integrate with what already exists, and how new, more complex whole organisms can be greater than the sums of their parts. Evolutionists who might agree that these are desirable goals are only hindered by cant about the “relentless imperatives of natural selection and the adaptive trends it produces.”

(….) Reductionism

Reduction is a good, logical tool for solving organismal problems by going down to their molecular structure, or to physical properties. But reductionism is a philosophical stance that embraces the belief that physical or chemical explanations are somehow superior to biological ones. Molecular biologists are inclined to reduce the complexity of life to its simplest structures, and there abandon the quest. “Selfish genes” in their “gene pools” are taken to be more important than organisms. To compound the confusion, higher emergent functions such as intelligence and conscious altruism are simplistically defined in such a way as to make them apply to the lower levels. This is reminiscent of William Livant’s (1998) “cure for baldness”: You simply shrink the head to the degree necessary for the remaining hair to cover the entire patethe brain has to be shrunk as well, of course. This “semantic reductionism” is rife in today’s ultra-Darwinism, a shrunken mindset that regards evolution as no more than the differential reproduction of genes.

Although reducing wholes to their parts can make them more understandable, fascination with the parts makes it too easy to forget that they are only subunits with no functional independence, whether in or out of the organism. It is their interactions with higher levels of organization that are important. Nevertheless, populations of individuals are commonly reduced to gene pools, meaning the totality of genes of the interbreeding organisms. Originating as a mathematical convenience, the gene pool acquired a life of its own, imbued with a higher reality than the organism. Because genes mutated to form different alleles that could be subjected to natural selection, it was the gene pool of the whole population that evolved. This argument was protected by polemic that decried any reference to the whole organism as essentialistic. Then came the notion that genes have a selfish nature. Even later, advances in molecular biology, and propaganda for the human genome project, have allowed the mistaken belief that there must be a gene for everything, and once the genes and their protein products have been identified that’s all we need to know. Instead, the completion of the genome project has clearly informed us that knowing the genes in their entirety tells us little about evolution. Yet biology still inhabits a genocentric universe, and most of its intellectual energy and material resources are sucked in by the black hole of reductionism at its center.

(….) Epigenetic Algorithms

Mechanical metaphors have appealed to many philosophers who sought materialist explanations of life. The definitive work on this subject is T. S. Hall’s Ideas of Life and Matter (1969). Descartes, though a dualist, thought of animal bodies as automata that obeyed mechanical rules. Julien de la Mettrie applied stricter mechanistic principles to humans in LʼHomme machine (1748). Clockwork and heat engine models were popular during the Industrial Revolution. Lamarck proposed hydraulic processes as causes of variation. In the late nineteenth century, the embryologists Wilhelm His and Wilhelm Roux theorized about developmental mechanics. However, as biochemical and then molecular biological information expanded, popular machine models were refuted, but it is not surprising that computers should have filled the gap. Algorithms that systematically provide instructions for a progressive sequence of events seem to be suitable analogues for epigenetic procedures.

A common error in applying this analogy is the belief that the genetic code, or at least the total complement of an organism’s DNA contains the program for its own differential expression. In the computer age it is easy to fall into that metaphysical trap. However, in the computer age we should also know that algorithms are the creations of programmers. As Charles Babbage (1838) and Robert Chambers (1844) tried to tell us, the analogy is more relevant to creationism than evolutionism. At the risk of offending the sophisticates who have indulged me so far, I want to state the problems in the most simple terms. To me, that is a major goal of theoretical biology, rather than the conversion of life to mathematics. (Robert G. B. Reid. Biological Emergences: Evolution by Natural Experiment (Vienna Series in Theoretical Biology) (p. 263). Kindle Edition.)

Natural selection of algorithms?

If we suppose that the action of the human brain, conscious or otherwise, is merely the acting out of some very complicated algorithm, then we must ask how such an extraordinary effective algorithm actually came about. The standard answer, of course, would be ‘natural selection’. as creatures with brains evolved, those with more effective algorithms would have a better tendency to survive and therefore, on the whole, had more progeny. These progeny also tended to carry more effective algorithms than their cousins, since they inherited the ingredients of these better algorithms from their parents; so gradually the algorithms improved not necessarily steadily, since there could have been considerable fits and starts in their evolution until they reached the remarkable status that we (would apparently) find in the human brain. (Compare Dawkins 1986). (Penrose 1990: 414)

Even according to my own viewpoint, there would have to be some truth in this picture, since I envisage that much of the brain’s action is indeed algorithmic, and as the reader will have inferred from the above discussion I am a strong believer in the power of natural selection. But I do not see how natural selection, in itself, can evolve algorithms which could have the kind of conscious judgements of the validity of other algorithms that we seem to have. (Penrose 1990: 414)

Imagine an ordinary computer program. How would it have come into being? Clearly not (directly) by natural selection! Some human computer programmer would have conceived of it and would have ascertained that it correctly carries out the actions that it is supposed to. (Actually, most complicated computer programs contain errors usually minor, but often subtle ones that do not come to light except under unusual circumstances. The presence of such errors does not substantially affect my argument.) Sometimes a computer program might itself have been ‘written’ by another, say a ‘master’ computer program, but then the master program itself would have been the product of human ingenuity and insight; or the program itself might well be pieced together from ingredients some of which were the products of other computer programs. But in all cases the validity and the very conception of the program would have ultimately been the responsibility of (at least) one human consciousness. (Penrose 1990: 414)

One can imagine, of course, that this need not have been the case, and that, given enough time, the computer programs might somehow have evolved spontaneously by some process of natural selection. If one believes that the actions of the computer programmers’ consciousness are themselves simply algorithms, then one must, in effect, believe algorithms have evolved in just this way. However, what worries me about this is that the decision as to the validity of an algorithm is not itself an algorithmic process! … (The question of whether or not a Turing machine will actually stop is not something that can be decided algorithmically.) In order to decide whether or not an algorithm will actually work, one needs insights, not just another algorithm. (Penrose 414-415)

Nevertheless, one still might imagine some kind of natural selection process being effective for producing approximately valid algorithms. Personally, I find this very difficult to believe, however. Any selection process of this kind could act only on the output of the algorithms and not directly on the ideas underlying the actions of the algorithms. This is not simply extremely inefficient; I believe that it would be totally unworkable. In the first place, it is not easy to ascertain what an algorithm actually is, simply by examining its output. (It would be an easy matter to construct two quite different simple Turing machine actions for which the output tapes did not differ until, say, the 2^65536th place — and this difference could never be spotted in the entire history of the universe!) Moreover, the slightest ‘mutation’ of an algorithm (say a slight change in a Turing machine specification, or in its input tape) would tend to render it totally useless, and it is hard to see how actual improvements in algorithms could ever arise in this random way. (Even deliberate improvements are difficult without ‘meanings’ being available. This inadequately documented and complicated computer program needs to be altered or corrected; and the original programmer has departed or perhaps died. Rather than try to disentangle all the various meanings and intentions that the program implicitly depended upon, it is probably easier just to scrap it and start all over again!) (Penrose 1990: 415)

Perhaps some much more ‘robust’ way of specifying algorithms could be devised, which would not be subject to the above criticisms. In a way, this is what I am saying myself. The ‘robust’ specifications are the ideas that underlie the algorithms. But ideas are things that, as far as we know, need conscious minds for their manifestation. We are back with the problem of what consciousness actually is, and what it can actually do that unconscious objects are incapable of — and how on earth natural selection has been clever enough to evolve that most remarkable of qualities. (Penrose 1990: 415)

(….) To my way of thinking, there is still something mysterious about evolution, with its apparent ‘groping’ towards some future purpose. Things at least seem to organize themselves somewhat better than they ‘ought’ to, just on the basis of blind-chance evolution and natural selection…. There seems to be something about the way that the laws of physics work, which allows natural selection to be much more effective process than it would be with just arbitrary laws. The resulting apparently ‘intelligent groping’ is an interesting issue. (Penrose 1990: 416)

The non-algorithmic nature of mathematical insight

… [A] good part of the reason for believing that consciousness is able to influence truth-judgements in a non-algorithmic way stems from consideration of Gödel’s theorem. If we can see that the role of consciousness is non-algorithmic when forming mathematical judgements, where calculation and rigorous proof constitute such an important factor, then surely we may be persuaded that such a non-algorithmic ingredient could be crucial also for the role of consciousness in more general (non-mathematical) circumstances. (Penrose 1990: 416)

… Gödel’s theorem and its relation to computability … [has] shown that whatever (sufficiently extensive) algorithm a mathematician might use to establish mathematical truth — or, what amounts to the same thing, whatever formal system he might adopt as providing his criterion of truth — there will always be mathematical propositions, such as the explicit Gödel proposition P(K) of the system …, that his algorithm cannot provide an answer for. If the workings of the mathematician’s mind are entirely algorithmic, then the algorithm (or formal system) that he actually uses to form his judgements is not capable of dealing with the proposition P(K) constructed from his personal algorithm. Nevertheless, we can (in principle) see that P(K) is actually true! This would seem to provide him with a contradiction, since he ought to be able to see that also. Perhaps this indicates that the mathematician was not using an algorithm at all! (Penrose 1990: 416-417)

(….) The message should be clear. Mathematical truth is not something that we ascertain merely by use of an algorithm. I believe, also, that our consciousness is a crucial ingredient in our comprehension of mathematical truth. We must ‘see’ the truth of a mathematical argument to be convinced of its validity. This ‘seeing’ is the very essence of consciousness. It must be present whenever we directly perceive mathematical truth. When we conceive ourselves of the validity of Gödel’s theorem we not only ‘see’ it, but by so doing we reveal the very non-algorithmic nature of the ‘seeing’ process itself. (Penrose 1990: 418)