Category Archives: Evolutionary Theory

Illusionary Progress

We live in an age of great technological success, in an atmosphere of materialistic philosophy tempered with misgivings and regrets, in a turmoil of social change and of conflicting political ideologies. We are uneasy with forebodings, for civilization may well die in the next war if it comes. We are little consoled by the prospect of dying amid new luxuries. Brilliant progress in the technological application of science stands in sharpest contrast with the social chaos of our generation. Will the critical historian of 3000 A.D. remember us chiefly for our success in one area or for our failure in the other? Can the echelons of science be diverted in part from the sector where they have won us an overwhelming victory to that where the battle turns against us? When and how? In the present article I shall suggest for the physical sciences a diversion of much effort from gadgetry to an extensive study of man himself, and for the biological sciences a keener, more integrative appraisal of evolutionary history as the basis for extrapolating from the past the course of man’s inevitable social destiny? (Williams 1948, 116)

It is scarcely necessary to belabor the point that within the past two centuries man has made unprecedented progress in the natural sciences. Basing action on this newly acquired knowledge he has harnessed steam, electricity, chemical reaction, and, presently, atomic fission to do his bidding. He has tapped field, forest, and subterranean depths for fuel, food, and materials of construction. He has erected towering cities, spanned the continents with rail and roadway, and girdled the globe with wires, radio beams, and swift flights of air armadas. Mechanical power and assembly lines have multiplied a hundred or a thousand fold the yield of goods from his hand and brain and eye. An economy of abundance is at length possible, but:— (Williams 1948, 116)

As ever increasing fraction of the fruits of human toil and ingenuity goes to feed the holocaust of war. The greatest drain on the exchequer of every government is the cost of present and past wars. The waste of ruined cities and scarred countrysides spreads over three continents where rose the most ancient of historic civilizations. More utter devastation looms on the horizon through the latest and most momentous of man’s scientific discoveries. Social progress since Roman times seems almost negligible. If legalized slavery has been well nigh abolished, chivalry has also waned. Conflicting political concepts of earliest history still persist in unresolved modern controversies. Democracy has just disarmed three major tyrannies at great cost but faces still another. The remaining one [i.e., Russian revolution] professes a prophetic vision for all mankind when its aegis shall have spread around the globe. (Williams 1948, 116)

The Russian people do not want war. Most probably the Russian government does not want it. Certainly neither the people nor the government of the United States desire World War III. Yet some inexorable force seems to impel both governments (and peoples) in that direction. Neither the leaders whom the Russians have chosen or accepted nor the leaders whom Americans follow are able to lead in the direction which everbody wants to go. Why? Because Russian thought and American thought are as far apart as the poles with reference to the basic political means which will achieve the universally desired end. There are no universally accepted political principles. Nothing indisputable has been learned in 5000 years of racial history. There is no scientific knowledge about politics. (Williams 1948, 116-117)

In economics the condition is essentially the same. There are almost as many schools of thought as there are thinkers. None will deny the tremendous impact of scientific technology upon our present economy, but beyond that few economic principles are universally accepted. The most elemental matters are in dispute: private property versus communal ownership; personal rights versus governmental sovereignty; economic versus political boundaries. Free trade versus protective tariff is, for example, still merely a matter of opinion. Our social systems are extremely diverse, and class strife of various sorts has rarely been more conspicuous. At best society is static; at worst, and more prevailingly, society moves off in all directions at one and gets nowhere. Fundamentally this is because social science is not science; its foundations are utterly insecure. It has no basis for proceeding from the known to the unknown, for virtually no principles are established beyond dispute. (Williams 1948, 117)

Scientists, however, have no occasion to be supercilious or sacrosanct. The failure of political, social, and economic theory to make progress is an old story. We are doing no worse than in Roman times, merely no better. The prime reason for the contrast lies in this, that for the most part in natural sciences we enjoy the benefits of the experimental method. We guess what should happen by a priori reasoning and then design a careful experiment whereby we verify or confound our prior reasoning. In social science the practice is to reason a priori and then assert the conclusion to be true. The experimental method is not practically available in social matters [except via historical perspective]. We may enact a measure, say the Smoot-Hawley act, but long before the experiment is complete a war, a new technology, a change of administration, or some other country’s countermeasure intervenes to invalidate any conclusion. All our so-called social experiments in domestic economy are fraught with similar hazards. (Williams 1948, 117)

One of the difficulties of the social sciences is that their problems are always problems of immediate concern to large numbers of people. Vox populi raises a distraction to disturb any objective contemplation. Public opinion focuses its attention about some controversial problem, and those who become the political leaders are those whose views are acceptable to the majority. All other contenders are disqualified for the moment though a decade later they may have proved themselves wiser than their opponents. The successful political leader is one who correctly senses the trend of public opinion. As Disraeli once quizzically remarked, “I must follow the people. Am I not their leader?” (Williams 1948, 117-118)

(….) In social problems there is no appeal to natural science, and natural science as such seeks no opportunity to be heard. Yet I beg to submit that human affairs are by no means unrelated to the kind of universe in which we dwell and with which science is so much concerned. The difficulty is that science is prevailingly either preoccupied with isolated phenomena in Nature or with the gadgetry of technology. The direction of human affairs is by common consent relegated to a position outside the field of scientific enquiry. We have already referred to the sad fact that the experimental method is inapplicable to social science. Otherwise we might be more sure footed in our social progress. (Williams 1948, 118)

Physics and chemistry are supreme examples of experimental science. Together with mathematics they account for most of the technical progress man has made. However, there is a large field of true science which is essentially observational rather than experimental. Astronomy and geology furnish us with many significant examples. We cannot turn the stars in their courses to ascertain experimentally the result, so it is necessary to infer indirectly much of what has been learned about their motions, masses, and composition, as well as their past history and future destiny. Similarly, in geology we cannot experimentally raise mountains, divert the course of great streams, or reproduce the conditions of ancient lakes. Yet few would deny that astronomy and geology are true sciences or that their conclusions are broadly trustworthy. (Williams 1948, 118)

Biology as a field lies between those of purely experimental and purely observational science. Many of its problems can be and have been attacked experimentally and successfully. Some of the great problems of biology are set on a time scale so vast that short-lived man cannot deal with them experimentally. Otherwise we might perhaps prove the descent of man from lower creatures by producing him on the sport for evidential purposes. However, the evolutionary process can be observed in the laboratory by the use of short-lived lower organisms and it can be turned to immediate practical account in breeding plants and animals of specifically desired characteristics. In spite of its many debatable regions, biology ranks as a sound science. (Williams 1948, 119-119)

According to my view each of these types of method has a potential application in human affairs. (….) In a thousand ways each person differs form his fellows. What we call personality is an integration of ten thousand traits each determined in part by heredity, in part by training and in part by current habits and ways of life [e.g., culture]. Some of these traits doubtless have a physiological basis if it could be traced. Some are psychological yet have an underlying physical basis, and many fall in the class of spiritual qualities. (Williams 1948, 119)

Personality is a fact of vital importance in our human relations. Yet one could assemble a very imposing array of physiologists, biochemists, psychologists, and physicians only discover that the whole battery of talent could not account for [the nature of personality]. These personality factors are of tremendous importance in many of our social problems. (Williams 1948, 119)

(….) So much for the potential of experimental natural sciences which would be much more significant for future human welfare at this stage than a new plastic, a more efficient freezing unit, a faster airplane, or a flossier automobile. We could get along with what technology already offers in those lines, but we keenly need means of preventing frustrated, futile lives and of raising the whole level of human happiness. These things must be recognized as within the potential field of science. We must get out of our ruts of thinking in terms of a single discipline and in terms of the physical things used for food, shelter, raiment, transportation, or amusement. We ourselves are more important than our environment. (Williams 1948, 120)

There is, however, a whole category of human problems of which the crux lines in the massing of humanity, rather than in the individual. A large group of humans bond together by some real or fancied community of need or circumstances acts differently at times than each of them the component individuals would be disposed to do if acting independently. People divide into groups by race, by language, by flags, by economic level, form of employment, or special intellectual interest or aptitude. Once so divided we are prone to forget our common humanity and place all emphasis upon our national or class interest. It is by the operation of this form of mass psychology that the problems of international antagonisms, political animosities, class and racial hatreds arise. In the present era, war, industrial strife between employer and employee, and racial hatred appear as the most outstanding destructive forces. There are, however, numerous lesser rivalries exemplified, for example, by pressure groups of farmers, manufacturers, dairymen, or what not. The study of individuals will not meet these problems. (Williams 1948, 120)

The most significant contribution which science might make to this category of problems is an emphasis on our common human heritage and the oneness of human life with all the life which preceded it in the evolutionary process. That is the route by which we came to be human and that is the road by which man may grow to greater stature. Biological evolution arrays hundreds of millions of years before us. May not science discern its trends and consider their validity for man today? (Williams 1948, 120)

(….) However, our social trends need to be undergirded by some broad philosophy which, endeavors to estimate results at least a generation hence. No social course which veers abruptly first in one direction then in another can possibly lead us happily forward. Yet that is precisely what we do in civic, political, and national life. (….) We proceed by impulse, not according to a reasoned course which becomes ingrained in the fiber of the people. Imagine a business enterprise succeeding with such a fluctuating policy. (Williams 1948, 121)

A popular philosophy cannot become second nature to a people within a few weeks or months or years. Its culture must pervade our educational processes for decades before the philosophy can ripen and bear fruit. It is, however, high time that such a social philosophy be born and that it have the endorsement of a large element of our most thoughtful people. How better can it be born than out of the womb of science and how will it gather more commanding support than if it comes from scientists. Science today enjoys an unprecedented popular respect, and no voice speaks with as much authority as does the scientist who is backed by the general opinion of his fellows. (Williams 1948, 121)

We had such a philosophy at the time of the birth of our republic, and, in spite of some dissent, we believed in it as a people. In the words of the Declaration of Independence “We hold these truths to be self evident: That all men are created equal; that they are endowed by their Creator with certain inalienable rights; that among these are life, liberty, and the pursuit of happiness. That to secure these rights governments are instituted among men, deriving their just powers from the consent of the governed;—” There are other philosophies abroad today. Not long since Hitler thundered “The state is everything, the individual nothing.” Today Russia’s Politburo justifies the dictatorship of a minority by defending its beneficent intentions. (Williams 1948, 121)

The divergent philosophies cannot all be true yet they were or are supported by the mass of scientists, as well as other people, resident in each of the respective countries. This could not possibly be true if science had generally recognized that humanity is a part of Nature and an outgrowth of her works. (Williams 1948, 121)

Some will object that evolution has had no consistent trends; that it has changed direction with climatic alterations as in the successive periods of glaciation. Its fundamental trends and causative factors have, however, in my opinion, maintained a high degree of constancy. The continuity of the evolutionary process has received amazing and unexpected support in the field of biochemistry during the past decade or two. The enzymes and other chemical mechanisms that operate in our tissues are present and operative also in the tissues of lower animals and even in plants and microorganisms for more primitive and far more ancient in their evolutionary origin. If life development has been so continuous that the oxidative mechanisms, for example, of its earliest forms of organisms are still operative in its latest and higher forms, it is scarcely reasonable to think its past trends are not still meaningful for man’s future. (Williams 1948, 121-122)

Evolution of Evolution

Atavism: The reappearance of an ancestral trait after many generations of absence. Dollo’s Law claims that “reverse evolution” never occurs for complex traits, but in fact there are exceptions. Atavisms can arise suddenly by mutation, but only rarely do they spread to fixation in a species. Sporadic throwbacks include hen’s teeth, horse’s toes, dew claws (extra digits) in dogs, premolars in mice, hindlimb flippers in dolphins and whales [148], and tails or extra nipples in humans. Possible reversions at the species level include frog teeth, lizard digits, reptile scales (= revived fish scales?), and dorsal fins in ichthyosaurs (= revamped fish fins?). One confirmed species-level atavism is sex-comb rotation in flies. One putative species-level atavism that was disproven involves wings in stick insects [2231].” (Held 2017, 264, How the Snake Lost its Legs: Curious Tales from the Frontier of Evo-Devo)

Held, Lewis I. Jr. (2017) How the Snake Lost its Legs: Curious Tales from the Frontier of Evo-Devo

How the vampire bat reinvented running

Bats are adept fliers, but most are clumsy on the ground. One exception is the vampire bat, Desmodus rotundus. When tested on a treadmill these bats run amazingly well. An analysis of their gait, published in 2005, showed that they “bound” into midair like mice, with their forefeet and hindfeet touching the ground at different times [1862]. The study’s authors argue that (1) the founders of the bat order had no need to run after they specialized as aerial insectivores, so (2) the neural circuits for running atrophied over millions of years (use it or lose it), but (3) vampire bats adapted to a new (blood-drinking) niche by reacquiring a running capability [1863]. Whether this talent is an atavism (old circuits revived) or a novelty (new circuits created) is unclear.

— Held, Lewis I. Jr. (2017) How the Snake Lost its Legs: Curious Tales from the Frontier of Evo-Devo

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.

Carroll, Sean B. (2005) Endless Forms Most Beautiful: The New Science of Evo Devo

Introduction: Birth of a Scientific Field

Every scientific field, no matter how broad its reach, has one or more basic goals that define its shape and direction. The central aim of evolutionary developmental biology is to delineate the precise mechanisms, processes, and events that have been responsible for generating the astonishing diversity of animal and plant forms that characterize our planet. If this exploration is productive, we should eventually come to comprehend the evolutionary routes by which, for example, mice came to differ from men, spiders from butterflies, and dandelions from sequoias. Despite all that has been learned about the general nature of evolution since the publication of Charles Darwin’s The Origin of Species in 1859, we are only just beginning to fathom such divergent evolutionary trajectories at the level of the actual genetic, developmental, and historical details. (Wilkins 2002, 3)

Evolutionary Developmental Biology

By 1959, the year of the centenary of the publication of The Origin, the atmosphere within evolutionary biology circles was quietly but profoundly celebratory.18 The puzzle of evolution was considered essentially solved; what remained was the good, steady work of filling in the details. Indeed, one would have had to search diligently to find suggestions that there were any major gaps or omissions in evolutionary theory. With Schmalhausen silent and in retirement, and Goldschmidt dead, Waddington (1959) remained a rather isolated dissenting voice, calling out to the field that something important, the evolution of developmental processes, had been badly neglected. (Wilkins 2002: 31)

And then, starting in the early 1970s, the consensus about the sufficiency of the evolutionary synthesis began to melt and break up like an iceberg that has drifted into warmer waters. Disputes began to arise about the best ways to reconstruct evolutionary history (a detailed and provocative history of this debate is given in Hull, 1988) and about the significant modes of genetic mechanisms of evolutionary change (Eldredge and Gould, 1972; Stanley, 1979; Dover, 1982). One contributory factor, certainly, was the advent of new methodologies. If, to change the metaphor, the evolutionary pot was beginning to simmer again, one important source of heat was the new science of molecular biology. (Wilkins 2002: 31)

(….) Many years ago, from a detailed phylogenetic survey of the distribution of eye structures within the Metazoa, Salvini-Plawen and Mayr (1977) argued that eyes had evolved independently, perhaps as often as 20 times, in different metazoan phyla. Thus, in their reconstruction, there was no single ancestral eye form in the Metazoa. Furthermore, in their scheme, continuity of appearance of structures was a cardinal test of homology. In cephalopods, for instance, it seems certain that ancestral molluscan forms did not possess eyes. Therefore, the eyes of cephalopods must have originated in lineages derived from forms lacking eye development (Salvini-Plawen and Mayr, 1977). In addition, there might not even have been a common ancestral metazoan photoreceptive field. The phylogenetic analysis of Salvini-Plawen and Mayr indicates that photoreceptor cells themselves may have evolved independently between 40 and 65 times during metazoan evolution. (Wilkins 2002: 166)

The only, or at least the simplest, way to reconcile this pattern with the equally unambiguous general role of Pax6 and its associated genes in eye development throughout the Bilateria is to posit shared genetic potential for development of eyes, even when the potential is not expressed. From this perspective, both the multiple independent occurrence of certain traits in different related lineages (cases of “parallelism”) and the reacquisition of a particular trait in a lineage that had seemingly lost it (a “reversal”) can, in principle, be accommodated. The key is the retention of genes and genetic architectures within those lineages and their suppression or revocation through certain genetic changes (Simpson, 1983; Wake, 1991; Butler and Saidel, 2000). Loss-of-function mutations that abrogate the operation of networks are easy to imagine. Similarly, suppression of the effects of such mutations, leading to a restoration of the network’ functions, can also be readily envisaged. In this conceptual framework, the widespread usage of Pax6 and its associated network of genes is a significant fact, while the polyphyletic pattern of eye development drawn by Salvini-Plawen and Mayr is not dismissed, but can be interpreted as reflecting losses and gains of the use of this network. (Wilkins 2002: 167)

Altogether, these considerations require some changes in the ways in which we view, and use, the term “homology.” The basic concept of shared possession of a trait through common descent remains intact, but the idea that the “same” trait in two different organisms may actually exhibit more points of visible difference than of discernible identity seems counterintuitive, to put it mildly. Nevertheless, the idea that homologous morphological traits and genes need not share tight, invariant relationships had been anticipated long ago by de Beer (1938, 1958, 1971) …. In effect, a set of decoupled relationships would involve the sharing of part of the same regulatory circuitry, but without visible (morphological) homology being involved. As Fernald (2000) has expressed it:

Recently, the discovery of conservation of many of the genes used during ontogeny of the eye, particularly Pax6, has led to the proposal that all eyes are monophyletic that is, they arose from an “Ur” eye. However, our current level of understanding of the genetic control of eye development does not support this conclusion. Instead, there appears to be a continuity of genetic information that regulates the development of similar but nonhomologous eyes.

Perhaps, however, it is the traditional framework that needs reevaluation. In cladistic terms, a homologous trait is a synapomorphy. If morphological similarity is not a reliable guide to homologous relationships, what precisely would such a snyapomorphy consist of? In light of the material presented here, one can suggest that it would be a combination of shared key genes (one or more) plus a shared biological or developmental function for which those genes are crucial. This is a rather radical revision of the concept of homology, which for 150 years has been tied to visible similarity, and which has specifically disavowed shared function as a criterion of homology. The formulation put forward here, however, allows one to incorporate the observations on conserved key regulatory genes without invoking convergent evolution, and it preserves the basic idea of homology as “continuity of [genetic] information.” Davidson (2001, p. 201) has reached a similar position. In his words, when it comes to assessing homologous relationships, “seeing is not [necessarily] believing.” (Wilkins 2002: 167)

From this perspective, the eyes of insects and vertebrates are homologous, even though they look different from each other, develop differently, and may have arisen independently in separate lineages from ancestors lacking eyes. What they share is the inherited regulatory machinery and the ancestral use (function) of that machinery dating to early in metazoan evolutionary history for light sensing or some rudimentary form of vision. (Wilkins 2002: 16)

~ ~ ~

18 Writing a few years afterward, Ernst Mayr captured the mood on the century of The Origin: “Symposia and conferences were held all over the world in 1959 in honor of the Darwin centennial, and were attended by all the leading students of evolution. If we read the volumes resulting from these meetings at Cold Spring Harbor, Chicago, Philadelphia, London, Gottingen, Singapore, and Melbourne, we are almost startled at the complete unanimity in the interpretation of evolution presented by the participants. Nothing could show more clearly how internally consistent and firmly established the synthetic theory is.” (Mayr, 1963, p.8)

Machine Dreams

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)

Sarkar (1998; Gilbert and Sarkar 2000) makes a helpful distinction between two kinds of reductionism — genetic reductionism and physical reductionism. Physical reductionism sees physics as the most basic of the sciences and holds that all scientific explanations may (and should) eventually be recast in the terms of physics; genetic reductionism holds that ‘genes can explain all phenotypic features of an organism’ (Sarkar 1998: 174). These types of reductionism are not coextensive, though both champions and critics of reductionism tend to conflate these two varieties; but whereas physical reductionism is a thesis about relations between the sciences, genetic reductionism is a thesis about the role of genes in organismal development. Both varieties of reductionism may be problematic, though for different reasons. (Robert 2004, 136)

Robert, Jason Scott (2004) Embryology, Epigenesis, and Evolution: Taking Development Seriously. Cambridge Studies in Philosophy and Biology.

If one starts from the axiom-premise organisms are complex machines (which within certain limits I have no problem with) and the economy is merely a network of automata functioning like an “revealed preference” calculating machines one can rather easily develop mathematically tractable models. But these models hide the real world political and social dimensions of business and economics. Economies are more like organisms than machines. And more importantly one organism in particular, the human organism, including our ability to create other machines, systems, institutions, political and social structures, norms, and practices which allow us to modify physical, social, and even intellectual reality. Through our intelligent use of our minds and bodies we create other mechanisms, physical and social (living) relationships. These have their own levels of appropriate analysis. Social science, like biology, cannot be reduced to chemistry and physics. Neither can it be reduced to genetic algorithms or computational rules. Social science cannot be reduced to a natural science via some yet-to-be-discovered social mathematics. Human beings are not just more complex social insects. These are machine dreams or more to the point machine delusions rooted in a form of scientism.

THE GENE MYTH is not just a myth about genes. It is a story about the nature of the organism and the character of biological explanation. Inspired by our experience with machines, the story (in one of its versions) is narrated in a language of causal analysis, where some things make other things happen, and our investigation of a collection of parts, one by one, enables us to piece together a knowledge of the integrated whole. The continual elucidation of explanatory “mechanisms” has seemed to vindicate the story, supported further by promises of a better life for humans and a steady stream of stunning technical achievements in data gathering and manipulation of organisms. It is no wonder that the Human Genome Project aroused such high expectations.

But this story has now come to the end of its useful life. The loss of the gene at the head of a chain of causal mechanisms explaining the organism represents more than the loss of the master link in the chain. It exemplifies the failure of every link considered as machinelike. The seeming chaos of causal arrows now being documented under the heading of “gene regulation” repeats itself in every aspect of the cell. Researchers dutifully trying to follow arrows of causation end up chasing hares running in all directions. Is there any subdiscipline of molecular biology today where research has been reducing cellular processes to a more clearly defined set of causal relations instead of rendering them more ambiguous, more plastic and context dependent, and less mechanical? Consider a few examples. (Talbot 2013, 51) [And here the interesting part begins …]

Stephen L. Talbott (2013) The Myth of the Machine-Organism: From Genetic Mechanisms to Living Beings. In Genetic Explanations: Sense and Nonsense.

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)

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

More attention to the history of Science is needed, as much by scientists as by historians, and especially by biologists, and this means a deliberate attempt to understand the thoughts of the great masters of the past, to see in what circumstances or intellectual milieu their ideas were formed, where they took the wrong turning or stopped short on the right track. (R. A. Fisher, 1959)

Wilkins, Adam S. (2002) The Evolution of Developmental Pathways

Because the great controversies of the past often reach into modern science, many current arguments cannot be fully understood unless one understands their history. ERNST MAYR 1982, 1

McCloskey, Deirdre Nansen; Ziliak, Steve. The Cult of Statistical Significance (Economics, Cognition, And Society) (Kindle Locations 2036-2038). University of Michigan Press.

As the relations between development and evolution were explored in the last decades of the twentieth century, mutations in those genes that regulate development also assumed great significance. Regulatory (homeobox) genes were reported that affected whole sets of genes, and some paleontologists [and developmental geneticists, etc.] have emphasized that mutations in such regulatory genes result in large discontinuous evolutionary changes (a reshuffling of parts) and may be a macromechanism of evolution. But symbiosis–the inheritance of acquired genomes, wholes or parts–was trivialized or ignored by paleontologists. Gould himself regarded the symbiotic origin of mitochondria and chloroplasts as “entering the quirky and incidental side” of evolution. (Sapp 2003: 250-251)

Most of the great controversies and conceptual oppositions of the nineteenth century are still present at the beginning of the twenty-first century: religion and vitalism versus evolution and materialism, structuralism versus functionalism, reductionism versus holism, gradualism versus saltationism, selectionism versus nonadaptationism, the inheritance of acquired characteristics, and nurture versus nature. What has changed is not so much the nature of the ideas but the evidence supporting them and the intensity of the debates. (Sapp 2003: 267)

Jan Sapp (2003) Genesis: The Evolution of Biology

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

DECONSTRUCTING MARGINALIST MICROECONOMICS

What is the essence of homo economicus? Homo economicus is a man in search of pleasure. He is man who knows what he wants and how to get it. There are fixed limits on what homo economicus can obtain, but he is a master of getting the best that he can from within those limits. The term was first coined as a criticism. It would seem that when certain people in the nineteenth century read the famous economist and philosopher John Stuart Mill, they did not like what they found. They accused Mill of reducing the human being to nothing but a calculator of his immediate pleasures. They said that Mill had removed anything properly human from Man and replaced him instead with some sort of amoral robot [e.g., automaton]; this robot they called homo economicus (Persky 1995). (Pilkington 2016, 71)

Mill himself was quite explicit about what he was doing. He claimed that economics—which was then called ‘political economy’—was concerned only with certain specific facets of Man’s existence. It did not poach on the preserves of other moral disciplines but rather abstracted from them and reasoned as if they did not exist. Mill wrote:

[Political economy] does not treat of the whole of man’s nature as modified by the social state, nor of the whole conduct of man in society. It is concerned with him solely as a being who desires to possess wealth, and who is capable of judging of the comparative efficacy of means for obtaining that end. It predicts only such phenomena of the social state as take place in consequence of the pursuit of wealth. It makes entire abstraction of every other human passion or motive; except those which may be regarded as perpetually antagonizing principles to the desire of wealth, namely, aversion to labor, and desire of the present enjoyment of costly indulgences … Political economy considers mankind as occupied solely in acquiring and consuming wealth; and aims at showing what is the course of action into which mankind, living in a state of society, would be impelled, if that motive, except in the degree in which it is checked by the two perpetual counter-motives above adverted to, were absolute ruler of all their actions. (Mill 1844) (Pilkington 2016, 71-72)

What concerned those who criticised Mill’s homo economicus was that it highlighted some of what they considered to be the less seemly aspects of Man’s existence. This was the age of high morality, and Mill’s construction seemed to many to be against the morality of the day. This was also an age of mass wealth accumulation, and Mill’s construction probably showed up a certain truth that some were less than pleased to deal with as it ran contrary to what they considered good behavior. (Pilkington 2016, 72)

By the mid- to late twentieth century, mass consumption had become a way of life and contemporary morality was more accommodative to the homo economicus. Indeed, today he seems like a rather natural construction in an age where people constitute their lives through accumulation and consumption. He has also been given more precision. Today, following on from the work of the early marginalists, he is modelled using indifference curves and differential calculus. To a critic of the theory, it is less the morality that stands out as it is the image of Man that is put forward. Man is seen as a sort of automaton with fixed, ordered preferences [or “if-then” rules as envisioned by genetic algorithms], a vast capacity for information that would be the envy of even the most powerful of computers. Whereas yesteryear homo economicus seemed offensively amoral, today he seems offensively unrealistic. (Pilkington 2016, 72, bold added)

The fact of this matter cannot be overstated enough If we turn, for example, to the main macroeconomic model used by the European Central Bank at the time of writing, we find it populated with a plethora of homo economicus. In their key forecasting model which is supposed to represent the Eurozone economy, they write:

Each household h maximises its lifetime utility in a given period t by choosing purchases of the consumption good, Ch,t, purchases of the investment good, Ih,t. (Christoffel et. al. 2008, p. 11)

Thus they turn every household into a homo economicus and then lump these homo economicus together and spell out their exact behaviour in a series of equations. If the assumption that each household acts like a homo economicus can be shown to be nonsense, then the findings of the model will also be nonsense. This cannot be stressed enough: this assumption is at the absolute core of many ‘very serious’ theories; without it they literally cannot function. Yet if the construction can be shown to be false, and by that I mean if it can be shown not to be a reasonable approximation of the real object of study (economic agents), then the theories themselves must also be false and central banks can be shown to be wasting an awful lot of time and resources employing people to build such theories. (Pilkington 2016, 73)

Concepts and Controversies

Granted that, as de Duve says, we are compelled by our calling to insist at all times on strictly naturalistic explanations; life must, therefore, have emerged from chemistry. Granted also that simple organic molecules were present at the beginning, in uncertain locations, diversity and abundance. Leave room for contingency, some rare chemical fluctuation that may have played a seminal role in the inception of living systems; and remember that you may be mistaken. With all that, I still cannot bring myself to believe that rudimentary organisms of any kind came about by the association of prefabricated organic molecules, born of purely chemical processes in their environment. Did life begin as a molecular collage? To my taste, that idea smacks of the reconstitution of life as we know it rather than its genesis ab initio. It overestimates what Harold Morowitz called the munificence of nature, her generosity in providing building blocks for free. It makes cellular organization an afterthought to molecular structure, and offers no foothold to autopoiesis. And it largely omits what I believe to be the ultimate wellspring of life, the thermodynamic drive of energy dissipation, creating mounting levels of structural order for natural selection to winnow. If it is true that life resides in organization rather than in substance, than what is left out of account is the heart of the mystery: the origin of biological order. (Harold 2001: 250)

(….) It would be agreeable to conclude this book with a cheery fanfare about science closing in, slowly but surely, on the ultimate mystery; but the time for rosy rhetoric is not yet at hand. The origin of life appears to me as incomprehensible as ever, a matter for wonder but not for explication. Even the principles of biopoiesis still elude us, for reasons that are as much conceptual as technical. The physical sciences have been exceedingly successful in formulating universal laws on the basis of reproducible experiments, accurate measurements, and theories explicitly designed to be falsifiable. These commendable practices cannot be fully extrapolated to any historical subject, in which general laws constrain what is possible but do not determine the outcome. Here knowledge must be drawn from observation of what actually happened, and seldom can theory be directly confronted with reality. The origin of life is where these two ways of knowing collide. The approach from hard science starts with the supposition that physical laws exercise strong constraints on what was historically possible; therefore, even though one can never exclude the intervention of some unlikely but crucial happenstance, one should be able to arrive at a plausible account of how it could have happened. This, however, is not how matters have turned out. The range of permissible options is to broad, the constraints so loose, that few scenarios can be firmly rejected; and when neither theory nor experiment set effective boundaries, hard science is stymied. The tools of “soft,” historical science unfortunately offer no recourse: the trail is too cold, the traces too faint. (Harold 2001: 251-252)

The tell a story of Max Delbrück, one of the pioneers of molecular genetics and the ironic inventor of DNA, whom I was privileged to meet during his later years at the California Institute of Technology. He had stopped reading papers on the origin of life, Max once observed; he would wait for someone to produce a recipe for the fabrication of life. So are we all waiting, not necessarily for a recipe but for new techniques of apprehending the utterly remote past. Without such a breakthrough, we can continue to reason, speculate and argue, but we cannot know. Unless we acquire novel and powerful methods of historical inquiry, science will effectively have reached a limit. (Harold 2001: 252)

Franklin M. Harold (2001) The Way of the Cell: Molecules, Organisms and the Order of Life. Oxford University Press.

[T]he origin of life is not what Darwin’s mechanism for evolutionary biology is about, as he himself wrote in the Origin of Species. Complaining that Darwinian evolution can’t explain life’s origin is like complaining that your Mercedes can’t fly. It wasn’t supposed to do that in the first place…. In the case of Darwin’s theory of evolutionary biology, this is providing a causal mechanism by which organisms like newts, monkeys, tuna, spiders, and ostriches attained their current diversity…. [I]t is very important to realize that studies of abiogenesis comprise a distinct field of science, one that does not draw on the same mechanisms relevant to Darwinian evolutionary biology. (Asher 2012: 184)

Robert J. Asher (2012) Evolution and Belief: Confessions of a Religious Paleontologist. Cambridge University Press.

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?

Woese, Carl R. (2005) Evolving Biological Organization. In Microbial Phylogeny and Evolution: Concepts and Controversies (Jan Sapp, ed.). Oxford: Oxford University Press, p. 100.

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 revolutionconceptual 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)

(….) 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)

(….) Evolutionary limitations imposed by a primitive translation mechanism. One cannot look at the cellular translation apparatus without being overwhelmed by its complexity, by the number of parts and their possible interactions. It is even more daunting to contemplate the evolution of such a mechanism. In a very real sense the evolution of translation is the evolution of the cell: Translation is the heart of the evolving cell design. Cellular evolution requires entire suites of novel proteins never before seen on Earth, and it is the performance characteristics of the primitive apparatus that determine what general types of proteins can and cannot evolve. (Woese 2005: 107)

A translation apparatus today must do two main things: accurately match codons with corresponding amino acids across an entire message RNA (perhaps thousands of nucleotides in length) and maintain the correct reading frame throughout the process. It seems impossible that a simple primitive translation mechanism could perform with the requisite precision to accurately produce a large (modern) protein. (The point here is not only common sense but can be inferred from the fact that the structure of the genetic code appears to have been optimized to reduce the phenotypic consequences of codon recognition error.) Primitive cells, then, would comprise only small proteins, which, of course, has broad implications as to the nature of the evolving cells. In almost cases the primitive version of a particular function would be less sophisticated and precise than its modern counterpart…. A name has been given to cells that have primitive translation capacities. The name, “progenote,” signifies that the genotype-phenotype link has yet to complete its evolution. (Woese 2005: 107)

(….) How translation might have began. If we know how modern translation worked, we would be on far safer grounds in conjecturing how it began. (….) The progenote model sees organisms as genetically communal and the community as evolving as a whole, not the individual cell lines therein…. The real mystery, however, is how this incredibly simple, unsophisticated, imprecise communal progenote—cells with only ephemeral genealogical traces—evolved to become complex, precise, integrated, individualized modern cells, which have stable organismal genealogical records. This shift from a primitive genetic free-for-all to modern organisms must by all accounts have been one of the most profound happenings in the whole of evolutionary history. Although we do not yet understand it, the transition needs to be appropriately marked and named. “Darwinian threshold” (or “Darwinian Transition”) seems appropriate: crossing the threshold means entering a new stage, where organismal lineages and genealogies have meaning, where evolutionary descent is largely vertical, and where the evolutionary course can begin to be described by tree representation. (Woese 2005: 109)

The most important, if not the only, thing that can be said right now about the progression from pre-Darwinian progenote to cells typical of the Darwin era (i.e., modern cells), is that in the process the cell design becomes more integrated. Connectivity, coupling (among componentry) is key to the nature of that transition. The cell is a complex dynamic system. Complex dynamic systems characteristically undergo saltations at “critical points.” Drastic changes in the system result. An increase in the connectivity of a system is one factor that can bring it to such a critical point. Does the Darwinian Threshold, then, denote a critical point in the evolutionary process? I say it does. We can be confident in any case that in the full evolutionary course, from an abiotic earth to modern cells and organisms, evolutionary saltations must have occurred. The transition from the nondescript, horizontally [non-Darwinian] intermeshed, and simple progenote to the complex individual cell lineages (with stable genealogical traces and vertical descent) that we know surely has the feel of a saltation. (Woese 2005: 109)

Gosse’s Dilemma and Adam’s Navel

‘Tis a dangerous thing to ingage the authority of Scripture in disputes about the Natural World, in opposition to Reason, lest Time, which brings all things to light, should discover that to be false which we had made Scripture to assert.

Thomas Burnet, Archaelogiae Philosophicae, 1692

In the late nineteenth century intellectuals assumed that truth had spiritual, moral, and cognitive dimensions. By 1930, however, intellectuals had abandoned this broad conception of truth. They embraced, instead, a view of knowledge that drew a sharp distinction between “facts” and “values.” They associated cognitive truth with empirically verified knowledge and maintained that by this standard, moral values could not be validated as “true.” In the nomenclature of the twentieth century, only “science” constituted true knowledge. Moral and spiritual values could be “true” in an emotional or nonliteral sense, but not in terms of cognitively verifiable knowledge. The term truth no longer comfortably encompassed factual knowledge and moral values.

Julie A. A. Reuben (1996) The Making of the Modern University: Intellectual Transformation and the Marginalization of Morality

Truth

Certain people have different standards for recognizing “truth.” Given access to the same facts, two individuals can look at an issued and reach utterly different conclusions, to the point where they believe those with a different opinion belong somewhere on a spectrum from stupid to perverse…. (Asher 2012: xiv)

(….) The creationist has something at stake, some worldview or allegiance, that makes a fair, honest view of the data behind Darwinian evolutionary biology impossible. Why?

(….) [T]here is an obvious explanation for antipathy toward Charles Darwin among various anti-evolutionist groups of the last 150 years, groups that are often connected to one kind of intense religious creed or another: they think Darwin threatens their worldview. Contributing to this conviction are those biologists who portray evolution as tied to atheism, who help convince the devout that a natural connection of humanity with other organisms is incompatible with their religion. Compounding things further is the fact that adherence to many religious worldviews is not flexible, and any scientific theory or philosophy that seems to threaten certain beliefs must be wrong, whatever some scientist may say about evidence. (Asher 2012: xvi)

Coyne says there is one way to be rational, and any of this stuff about alternative “truth” is relativist nonsense not worth the flatscreen monitor on which it is written:

What, then, is the nature of “religious truth” that supposedly complements “scientific truth”?… Anything touted as a “truth” must come with a method for being disproved—a method that does not depend on personal revelation. … It would appear, then, that one cannot be coherently religious and scientific at the same time. That alleged synthesis requires that with one part of your brain you accept only those things that are tested and supported by agreed-upon evidence, logic, and reason, while with the other part of your brain you accept things that are unsupportable or even falsified.

I disagree, and would argue that there are many things in life that deserve the descriptor “truth” but are not amenable to rational disproof. Coyne is absolutely correct to say that coddling the irrational—those for whom “religious truth” means stoning adulterers or drinking poisoned Kool-Aid—is incompatible with science and, more generally, civil society. However, while science is a-religious, it is not anti-religious, at least in the important sense that it does not (indeed, cannot) concern itself with phenomena beyond what we rationally perceive. It is not only possible to portray science as lacking fatal consequences for those religious tenets that concern things we cannot empirically observe (such as purpose or agency in life), but it is precisely what scientists have got to do to make a compelling case to the public. Coyne tosses “religion” into the same dumpster as any passing superstition, and actively encourages the perception that science is corrosive to any religious sentiment. Yes, there are religious claims that are demonstrably wrong in an empirical sense. … However, such specific claims do not do justice to the religion integrally tied into the identity of many lay-people and scientists alike, an identity that by any meaningful definition is worthy of the name “truth.” (Asher 2012: xvii-xviii)

Asher, Robert J. Evolution and Belief [Confessions of a Religious Paleontologist]. Cambridge: Cambridge University Press; 2012; p. xiv.

When we reflect on scienceits aims, its values, its limitswe are doing philosophy, not science. This may be bad news for the high priests of scientism, who reject philosophy, but there is no escaping it.

(….) There is a general agreement that science concentrates on aspects of the world that can be studied through theories that can be tested by doing experiments. Those aspects relate to spatiotemporal patterns in nature, for this is what makes experiments possible. If other dimensions of reality exist, they simply cannot be studied using the methods of the empirical sciences.

(….) Modern science is an enormously wonderful and powerful achievement of our species, a culturally transcendent, universal method for studying the natural world. It should never be used as an ideological weapon. Scientific progress demands a respect for truth, rigor, and objectivity, three ethical values implied in the ethos of science. We can nevertheless draw different conclusions from our analyses of science, but we should always present them carefully, distinguishing what can be said in the name of science from personal interpretations that must be supported by independent reasons, or acknowledged simply as personal opinions. Our analysis shows that the Oracles differ in important points and are not consistently fighting for a common cause. When they go beyond their science, they use different arguments and arrive at different conclusions.

We conclude with one final insight. Science is compatible with a broad cross section of very different views on the deepest human problems. Weinberg, an agnostic Jew from New York, shared his Nobel Prize with Abdus Salam, a devout Muslim from Pakistan. They spoke different languages and had very different views on many important topics. But these differences were of no consequence when they came together to do science. Modern science can be embraced by any religion, any culture, any tribe, and brought to bear on whatever problems are considered most urgent, whether it be tracing their origins, curing their diseases, or cleaning up their water. Science should never be fashioned into a weapon for the promotion of an ideological agenda. Nevertheless, as history has shown, science is all too frequently enlisted in the service of propaganda; and, as we have argued in this book, we must be on guard against intellectual nonsense masquerading as science.

Karl Giberson and Mariano Artigas (2007) in Oracles of Science: Celebrity Scientists versus God and Religion.

Darwinism as an ideology

One of the most interesting developments of the twentieth century has been the growing trend to regard Darwinian theory as transcending the category of provisional scientific theories, and constituting a “world- view.” Darwinism is here regarded as establishing a coherent worldview through its evolutionary narrative, which embraces such issues as the fundamental nature of reality, the physical universe, human origins, human nature, society, psychology, values, and destinies. While being welcomed by some, others have expressed alarm at this apparent failure to distinguish between good, sober, and restrained science on the one hand, and non-empirical metaphysics, fantasy, myth and ideology on the other. In the view of some, this transition has led to Darwinism becoming a religion or atheist faith tradition in its own right.

Denis R. Alexander and Ronald L. Numbers (2010) in Biology and Ideology: From Descartes to Dawkins.

It is difficult to overestimate the importance of Darwinian thinking to American economic reform in the Gilded Age and Progressive Era. Evolutionary thought was American economic reform’s scientific touchstone and a vital source of ideas and conceptual support. The Wharton School’s Simon Nelson Patten, writing in 1894, observed that the century was closing with a bias for biological reasoning and analogy, just as the prior century had closed with a bias for the methods of physics and astronomy. The great scientific victories of the nineteenth century, Patten believed, were “in the field of biology.”

SOMETHING IN DARWIN FOR EVERYONE

To understand the influence of evolutionary thought on American economic reform, we must first appreciate that evolutionary thought in the Gilded Age and Progressive Era in no way dictated a conservative, pessimistic, Social Darwinist politics. On the contrary, evolutionary thought was protean, plural, and contested.

It could license, of course, arguments that explained and justified the economic status quo as survival of the fittest, so-called Social Darwinism. But evolutionary thought was no less useful to economic reformers, who found in it justification for optimism rather than pessimism, for intervention rather than fatalism, for vigorous rather than weak government, and for progress rather than drift. Evolution, as Irving Fisher insisted in National Vitality, did not teach a “fatalistic creed.” Evolution, rather, awakened the world to “the fact of its own improvability.”

In the thirty years bracketing 1900, there seems to have been something in Darwin for everyone. Karl Pearson, English eugenicist and founding father of modern statistical theory, found a case for socialism in Darwin, as did the co-discoverer of the theory of evolution by natural selection, Alfred Russel Wallace. Herbert Spencer, in contrast, famously used natural selection, which he called “survival of the fittest,” to defend limited government.

Warmongers borrowed the notion of survival of the fittest to justify imperial conquest, as when Josiah Strong asserted that the Anglo-Saxon race was “divinely commissioned” to conquer the backward races abroad. Opponents of war also found sustenance in evolutionary thought. Pyotr Kropotkin argued that the struggle for existence need not involve conflict, much less violence. Cooperation could well be the fittest strategy. David Starr Jordan, president of Stanford from 1891 to 1913 and a leader of the American Peace Movement during World War I, opposed war because it selected for the unfit. The fittest men died in battle, while the weaklings stayed home to reproduce.

Darwin seems to have been pro-natalist, on the grounds that more births increased the variation available for natural selection. Margaret Sanger argued that restricting births was the best way to select the fittest. Darwin’s self-appointed “bulldog,” T. H. Huxley, thought natural selection justified agnosticism, whereas devout American interpreters, such as botanist Asa Gray, found room in Darwinism for a deity.

It is a tribute to the influence of Darwinism that Darwin inspired exegetes of nearly every ideology: capitalist and socialist, individualist and collectivist, pacifist and militarist, pro-natalist and birth-controlling, as well as agnostic and devout.

Darwinism was itself plural, and Progressive Era evolutionary thought was more plural still. The ideas of other prominent evolutionists (notably, Herbert Spencer and Alfred Russel Wallace) were also influential in the Progressive Era, both when they accorded with Darwin and when they didn’t.

— Thomas C. Leonard (2016) in Illiberal Reformers: Race, Eugenics, and American Economics in the Progressive Era.

[L]iberal theology reconceptualizes the meaning of Christianity in the light of modern knowledge and ethical values. It is reformist in spirit and substance, not revolutionary. Specifically it is defined by its openness to the verdicts of modern intellectual inquiry, especially historical criticism and the natural sciences; its commitment to the authority of individual reason and experience; its conception of Christianity as an ethical way of life; its advocacy of moral concepts of atonement or reconciliation; and its commitments to make Christianity credible and socially relevant to contemporary people. In the nineteenth century, liberal theologians denied that God created the world in six days, commanded the genocidal extermination of Israel’s ancient enemies, demanded the literal sacrifice of his Son as a substitutionary legal payment for sin [see Laughing Buddha], and verbally inspired the Bible. Most importantly, they denied that religious arguments should be settled by appeals to an infallible text or ecclesial authority. Putting it positively, nineteenth-century liberals accepted Darwinian evolution, biblical criticism, a moral influence view of the cross, an idea of God as the personal and eternal Spirit of love, and a view of Scripture as authoritative only within Christian experience. Nineteenth- teenth- and early-twentieth-century liberals expected these views to prevail in Christianity as a whole, but in the twenty-first century they remain contested beliefs.

Gary Dorrien. The Making of American Liberal Theology: Crisis, Irony, and Postmodernity: 1950-2005 (Kindle Locations 155-157). Kindle Edition.

Unless the moral insight and the spiritual attainment of mankind are proportionately augmented, the unlimited advancement of a purely materialistic culture may eventually become a menace to civilization. A purely materialistic science harbors within itself the potential seed of the destruction of all scientific striving, for this very attitude presages the ultimate collapse of a civilization which has abandoned its sense of moral values and has repudiated its spiritual goal of attainment.

The materialistic scientist and the extreme idealist are destined always to be at loggerheads. This is not true of those scientists and idealists who are in possession of a common standard of high moral values and spiritual test levels. In every age scientists and religionists must recognize that they are on trial before the bar of human need. They must eschew all warfare between themselves while they strive valiantly to justify their continued survival by enhanced devotion to the service of human progress. If the so-called science or religion of any age is false, then must it either purify its activities or pass away before the emergence of a material science or spiritual religion of a truer and more worthy order.

What both developing science and religion need is more searching and fearless self-criticism, a greater awareness of incompleteness in evolutionary status. The teachers of both science and religion are often altogether too self-confident and dogmatic. Science and religion can only be self-critical of their facts. The moment departure is made from the stage of facts, reason abdicates or else rapidly degenerates into a consort of false logic.

~ ~ ~

By the mid-nineteenth century, there were really only three ways in which natural theologians could deal with the growing evidence that the earth was very old, that it was recycling inexorably beneath their feet, and that life on earth had constantly changed over millions of years. They could ignore it, they could accommodate it to the biblical accounts of history by more or less denying the literal truth of Genesis, or they could explain it all away. The later natural theologians largely ignored it. The sacred theorists tried unsuccessfully to reconcile geology with the Bible. And one man above all others tried to explain it away. He was Philip Henry Gosse (1810-1888), a writer on natural history whose books caught the imagination of generations of Victorians and whose life became a tortured tale of religion contesting with science…. (Thomson 2007: 223)

Gosse’s dilemma was that of all natural theologians, especially after the publication in 1844 of an anonymously authored, thrillingly dangerous, and wildly successful book on evolution…. The book’s title, with an allusion to James Hutton that nobody could miss, was Vestiges of Creation. Chambers’ theory was largely derived from Lamarck’s which, like Erasmus Darwin’s, depended upon organisms being subject to change as a direct result of environmental pressures and exigencies [which today is know to be possible via epigentics]. Chambers probably set Charles Darwin back fifteen years — much to the benefit of all. In many ways he blazed the trail that Darwin could more cautiously follow with an even more convincing theory in hand. Darwin must have realized, with the example of Chambers in front of him (and approval of the political left and censure from both the religious and scientific right) that he would have to ensure his theory would have a better reception. (Thomson 2007: 224)

Gosse knew that various versions of what we now call evolution had been around for more than a hundred years. By the mid-1850s, most scientists in Britain knew which way the wind was blowing. Darwin had been hard at work in private since 1842, preparing the ground for his idea of natural selection, and knowing how popular a scientist Gosse was, he tried to enlist him to support his theory. Darwin’s self-designated ‘bull dogs’, including Thomas Huxley, were steadily persuading the sceptics Huxley had been lecturing formally on an evolutionary relationship between men and apes as early as 1858. This growing movement evolutionary movement offered a new way of explaining the evidence of organic changes, but only at the expense of much accepted religious belief. It threatened to change radically the whole frame of intellectual reference and to produce a new explanation of cause. For a huge number of theologians, clerics, philosophers and ordinary people, evolution was changing the metaphysical balance of power. Among those who felt this most keenly was Gosse. (Thomson 2007: 224)

One’s heart has to ache for Gosse, one of the most sympathetic characters of the evolutionary saga, a man weighed down by the burdens of fundamentalist Christianity and at the same time a brilliant naturalist…. He was the first to introduce to a popular audience the life of the seashore, the fragile world of exquisite beauty and strength that lies just a few inches beneath the surface of the sea and in the rocky pools of the coast. Before Gosse, all this was largely unseen. Gosse single-handedly created marine biology and home aquaria, and became one of the great chroniclers of the intricate worlds revealed by the microscope. (Thomson 2007: 225)

(….) Once Lamarck and Chambers had made it possible (even necessary) to take evolution seriously, and after his meeting with Charles Darwin had shown how powerful was the extent of the challenge to his fundamentalist beliefs, Gosse felt called to respond; as a Plymouth Brother and as a scientist, it was his responsibility, just as it had been Paley’s and before Paley John Ray’s or Thomas Burnet’s. Gosse’s dilemma was to try to find a way to reconcile his science and his faith. He chose to challenge the rapidly growing support for evolutionists from the geological record. (Thomson 2007: 226)

(….) Huxley had a favourite lecture a “Lay Sermon’ entitled Essay on a Piece of Chalk. He would stand before an eager crowd and take a piece of common chalk from his pocket, asking the audience what it could possibly tell them about the history of the cosmos and of life on earth. The answer is that chalk (in those days, before blackboard chalk was an artificial, hypo-allergenic substance) represents the accumulation on an ancient sea bottom of the skeletons of countless billions of microscopic planktonic organisms that once inhabited vast tropical oceans that extended across the earth, from Europe and the Middle East to Australia and North America. (Thomson 2007: 227)

(….) Philip Gosse knew only too well what a piece of chalk looked like under a microscope and that the earth’s crust consisted of thousands of feet of different rocks, some bearing fossils, others the remains of ancient lava flows, dust storms, water-borne sediments, and even ancient coral reefs just like those he had seen in Jamaica…. How could Gosse explain away this all-too-solid evidence of the ancient history of the earth and its denizens? What did it have to say about the biblical account of creation in six days? (Thomson 2007: 228)

(….) Gosse’s answer cost him dearly. The dilemma figuratively tore him scientist and fundamentalist Christian in half. In a classic example of ad hoc reasoning, he explained away all this appearance of change in a book entitled Omphalos, the Greek for ‘navel’, and in that one word is contained the core of Gosse’s argument. It is the old conundrum: did Adam have a navel? If God created Adam as the first man out of nothing, Adam would have no need for a navel, since he had never been connected by an umbilical cord to a mother. Nor indeed had Eve, of whose origin Genesis gives two accounts. Nor indeed (remembering that the Bible tells us that God made man in his own image) would God physiologically have needed navel. (Thomson 2007: 229)

Gosse simply asserted that at the moment of creation, just as God made Adam with a navel, he also made the earth with all its complex layers, its faults, every one of its fossils, volcanoes in mid-eruption and rivers in full spate carrying a load of sediment that had never been eroded from mountains that had never been uplifted. Similarly, at that instant, every tree that had never grown nevertheless had internal growth rings; every mammal already had partially worn teeth. He created rotting logs on the forest floor, the rain in mid-fall, the light from distant stars in mid-stream, the planets part-way around their orbits … the whole universe up and running at the moment of creation no further assembly required. (Thomson 2007: 229)

Such an argument, of course, can never be beaten. It says that God has created all the evidence that supports his existence and (shades of Hume) all the evidence that appears to cast doubt on it. Equally, of course, a theory that explains everything explains nothing. Omphalos is untestable and therefore one cannot concur rationally with its argument; you must simply close your eyes and believe. Or smile. (Thomson 2007: 229-230)

Over the years, Gosse’s argument has been bowdlerised to the slightly unworthy proposition that God set out the geological record, with all its evidence of change, in order to test man’s faith. It was, therefore, the ultimate celestial jest and cruel hoax. This was about as far from Gosse’s pious intention as Darwin’s impious theory. As for what Paley would have made of Omphalos I like to think he would have rejected it, but kindly, for he was a kind man. Victorian England not only rejected it, they laughed at it cruelly. Gosse became overnight a broken man, his reputation as a scientist in shatters. (Thomson 2007: 230)

But nothing is as simple as it ought to be. A community that mocked Omphalos and had no problem in coming to terms with the even more difficult issue of cosmology, still could not come to terms with geology. In fact, whether in Paley’s time or in Darwin’s, or indeed our own, one of the oddities in the history of interplay between science and religion is that cosmology never seems to have become as serious a threat to revealed religion as natural science. When pressed, people often revert to believing two things at once. The evidence that the universe is huge and ancient can be assimilated seemingly without shaking the conviction that the earth itself is 6,000 years old and that all living creatures were created over a two-day period. For example: ‘The school books of the present day, while they teach the child that the earth moves, yet assure him that that it is a little less than six thousand years old, and that it was made in six days. On the other hand, geologists of all religious creeds are agreed that the earth has existed for an immense series of years.’ These last words were written in 1860 and appear in a work that arguably presented a greater threat to the Established Church than the evolutionism of Erasmus Darwin, Lamarck, Robert Chambers or even Charles Darwin. Essays and Reviews was an example of the enemy within, a compilation of extremely liberal theological views by noted churchman and academics. Among their targets was the unnecessary and outmoded belief in miracles and the biblical account of the days of creation. The battle is still being fought. (Thomson 2007: 230-231)

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)

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 Panselection 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

THE EPIGENETICS OF EVOLUTIONARY CHANGE
Under the influence of external/internal stimuli, the CNS may induce adaptive changes in morphological and life history characters without any changes in genes. Commonly, these changes are not heritable, i.e. they do not reappear in the offspring if the offspring is not exposed to the same stimuli. This is the case for the overwhelming majority of described examples of predatory-induced defenses, polyphenisms, and adaptive camouflage. But reproducible cases of transgenerational changes, without changes in genes, changes that are transmitted to the offspring for one or more generations, occur and are described. All the cases of non-genetic, inherited changes are determined by underlying neural mechanisms. Such changes may represent the “primed”, ready-made material of evolution. The evidence on the neurally induced transgenerational nongenetic changes cannot be overestimated in respect to possible evolutionary implications of the epigentic system of heredity. (Cabej 2004: 201)

— Nelson R. Cabej (2004, 201) Neural Control of Development: The Epigenetic Theory of Heredity

Indeed, epigenetic modifications of phenotypic expression are sometimes considered to be “Lamarckian” because they can be transmitted to subsequent generations after being acquired. Not surprisingly, then, it has taken decades for these molecular effects to be accepted as a part of mainstream genetics. Contemporary awareness of molecular epigenetics has expanded the neo-Darwinian view of DNA sequence as the fundamental mode of inherited developmental information (Jablonka and Lamb 2002; Mattick 2012), placing even the initial phase of gene expression squarely in a dynamic cellular, organismic, and environmental context. (Sultan 2015, 11)

At the mechanistic level, epigenetic modification shape gene expression by altering protein-gene interactions that determine the accessibility of DNA to the biochemical machinery of gene transcription. (….) Epigenetic mechanisms may also be a heretofore unrecognized source of selectively important phenotypic variation in natural populations.

It has become clear that heredity is mediated at the molecular level not purely by discrete, stably transmitted DNA sequence variants but also by multiple information-altering mechanisms that lend the process an unlooked-for flexibility. Qualitatively new modes of cross-generational gene regulation are continuing to be found, including several that show gene silencing and other epigenetic roles for noncoding RNA (Bernstein and Allis 2005; Mattick and Mehler 2008: Lenhard et. al. 2012; Ha and Kim 2014). (Sultan 2015, 12)

Many genomic sequences that were previously considered “junk” are now known to code for small or “micro” RNAs (and possibly long RNAs as well) that play a role, for instance by altering enzymatic access to the chromatin by binding to DNA (Koziol and Rinn 2010). … Interestingly, noncoding RNAs may carry environmentally induced effects on the phenotype form one generation to the next, including the neurobehavioral effects of social environment. In one recent study, traumatic, unpredictable, separation of newborn mice from their mothers altered several aspects of microRNA activity in the pups, including their hippocampi and other brain structures involved in stress responses. These epigenetic changes were associated with different behavioral responses to aversive conditions such as brightly illuminated maze compartments. When sperm RNA from traumatized males was injected into fertilized wild-type egg cells, these phenotypic effects were reproduced in the F2 generation; this result indicates that RNA can contribute to the transmission of stress-induced traits in mammals (Gapp et. al. 2014) (Sultan 2015, 12-13)

Sonia E. Sultan (2015) Organism & Environment: Ecological Development, Niche Construction, and Adaptation

~ ~ ~

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

Darwin has often been depicted as a radical selectionist at heart who invoked other mechanisms only in retreat, and only as a result of his age’s own lamented ignorance about the mechanisms of heredity. This view is false. Although Darwin regarded selection as the most important of evolutionary mechanisms (as do we), no argument from opponents angered him more than the common attempt to caricature and trivialize his theory by stating that it relied exclusively upon natural selection. In the last edition of the Origin, he wrote (1872, p. 395):

As my conclusions have lately been much misrepresented, and it has been stated that I attribute the modification of species exclusively to natural selection, I may be permitted to remark that in the first edition of this work, and subsequently, I placed in a most conspicuous position—namely at the close of the introduction—the following words: “I am convinced that natural selection has been the main, but not the exclusive means of modification.” This has been of no avail. Great is the power of steady misinterpretation.

Charles Darwin, Origin of Species (1872, p. 395)

— Gould, Stephen J., & Lewontin, Richard C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON, SERIES B, VOL. 205, NO. 1161, PP. 581-598. [ See: Just So Stories and Hardened Adaptationism and Natural Selection as a Creative Force and The Evolution of the Genome ]

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.)