Category Archives: History of Biology

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)

Spotting the Spoof

According to this view, individuals within an economy follow simple rules of thumb to determine their course of action. However, they adapt to their environment by changing the rules they use when these prove to be less successful. They are not irrational in that they do not act against their own interests, but they have neither the information nor the calculating capacity to ‘optimise’. Indeed, they are assumed to have limited and largely local information, and they modify their behaviour to improve their situation. Individuals in complexity models are neither assumed to understand how the economy works nor to consciously look for the ‘best choice’. The main preoccupation is not whether aggregate outcomes are efficient or not but rather with how all of these different individuals interacting with each other come to coordinate their behaviour. Giving individuals in a model simple rules to follow and allowing them to change them as they interact with others means thinking of them much more like particles or social insects. Mainstream economists often object to this approach, arguing that humans have intentions and aims which cannot be found in either inanimate particles or lower forms of life.

Kirman et. al. (2018, 95) in Rethinking Economics: An Introduction to Pluralist Economics, Routledge.

Even such purely academic theories as interpretations of human nature have profound practical consequences if disseminated widely enough. If we impress upon people that science has discovered that human beings are motivated only by the desire for material advantage, they will tend to live up to this expectation, and we shall have undermined their readiness to moved by impersonal ideals. By propagating the opposite view we might succeed in producing a larger number of idealists, but also help cynical exploiters to find easy victims. This specific issue, incidentally, is of immense actual importance, because it seems that the moral disorientation and fanatic nihilism which afflict modern youth have been stimulated by the popular brands of sociology and psychology [and economics] with their bias for overlooking the more inspiring achievements and focusing on the dismal average or even the subnormal. When, fraudulently basking in the glory of the exact sciences, the psychologists [, theoretical economists, etc.,] refuse to study anything but the most mechanical forms of behavior—often so mechanical that even rats have no chance to show their higher faculties—and then present their mostly trivial findings as the true picture of the human mind, they prompt people to regard themselves and others as automata, devoid of responsibility or worth, which can hardly remain without effect upon the tenor of social life. (….) Abstrusiveness need not impair a doctrine’s aptness for inducing or fortifying certain attitudes, as it may in fact help to inspire awe and obedience by ‘blinding people with science’.

— Andreski (1973, 33-35) in Social Sciences as Sorcery. Emphasis added.

Complexity theory comes with its own problems of over-reach and tractability. Context counts; any theory taken to far stretches credulity. The art is in spotting the spoof. It is true irony to watch the pot calling the kettle black! To wit, mainstream economists questioning the validity of complexity theories use of greedy reductionism — often for the sole purpose of mathematical tractability — when applied to human beings; just because mainstream economists also have unrealistic assumptions (i.e., homo economicus) that overly simplify human behavior and capabilities doesn’t invalidate such a critique. Just because the pot calls the kettle black doesn’t mean the kettle and the pot are not black. Building models of human behavior solely on rational expectations and/or “social insects” qua fitness climbing ticks means we are either Gods or Idiots. Neither Gödel nor Turing reduced creatively thinking human beings to mere Turing machines.

~ ~ ~

The best dialogues take place when each interlocutor speaks from her best self, without pretending to be something she is not. In their recent book Phishing for Phools: The Economics of Manipulation and Deception, Nobel Prize–winning economists George Akerlof and Robert Shiller expand the standard definition of “phishing.” In their usage, it goes beyond committing fraud on the Internet to indicate something older and more general: “getting people to do things that are in the interest of the phisherman” rather than their own. In much the same spirit, we would like to expand the meaning of another recent computer term, “spoofing,” which normally means impersonating someone else’s email name and address to deceive the recipient—a friend or family member of the person whose name is stolen—into doing something no one would do at the behest of a stranger. Spoofing in our usage also means something more general: pretending to represent one discipline or school when actually acting according to the norms of another. Like phishing, spoofing is meant to deceive, and so it is always useful to spot the spoof.

Students who take an English course under the impression they will be taught literature, and wind up being given lessons in politics that a political scientist would scoff at or in sociology that would mystify a sociologist, are being spoofed. Other forms of the humanities—or dehumanities, as we prefer to call them—spoof various scientific disciplines, from computer science to evolutionary biology and neurology. The longer the spoof deceives, the more disillusioned the student will be with what she takes to be the “humanities.” (Morson, Gary Saul. Cents and Sensibility (pp. 1-2). Princeton University Press. Kindle Edition.)

By the same token, when economists pretend to solve problems in ethics, culture, and social values in purely economic terms, they are spoofing other disciplines, although in this case the people most readily deceived are the economists themselves. We will examine various ways in which this happens and how, understandably enough, it earns economists a bad name among those who spot the spoof.

But many do not spot it. Gary Becker won a Nobel Prize largely for extending economics to the furthest reaches of human behavior, and the best-selling Freakonomics series popularizes this approach. What seems to many an economist to be a sincere effort to reach out to other disciplines strikes many practitioners of those fields as nothing short of imperialism, since economists expropriate topics rather than treat existing literatures and methods with the respect they deserve. Too often the economic approach to interdisciplinary work is that other fields have the questions and economics has the answers. (Morson, Gary Saul. Cents and Sensibility (pp. 2-3). Princeton University Press. Kindle Edition.)

As with the dehumanities, these efforts are not valueless. There is, after all, an economic aspect to many activities, including those we don’t usually think of in economic terms. People make choices about many things, and the rational choice model presumed by economists can help us understand how they do so, at least when they behave rationally—and even the worst curmudgeon acknowledges that people are sometimes rational! We have never seen anyone deliberately get into a longer line at a bank. (Morson, Gary Saul. Cents and Sensibility (p. 3). Princeton University Press. Kindle Edition.)

Even regarding ethics, economic models can help in one way, by indicating what is the most efficient allocation of resources. To be sure, one can question the usual economic definition of efficiency—in terms of maximizing the “economic surplus”—and one can question the establishment of goals in purely economic terms, but regardless of which goals one chooses, it pays to choose an efficient way, one that expends the least resources, to reach them. Wasting resources is never a good thing to do, because the resources wasted could have been put to some ethical purpose. The problem is that efficiency does not exhaust ethical questions, and the economic aspect of many problems is not the most important one. By pretending to solve ethical questions, economists wind up spoofing philosophers, theologians, and other ethicists. Economic rationality is indeed part of human nature, but by no means all of it.

For the rest of human nature, we need the humanities (and the humanistic social sciences). In our view, numerous aspects of life are best understood in terms of a dialogue between economics and the humanities—not the spoofs, but real economics and real humanities. (Morson, Gary Saul. Cents and Sensibility (pp. 3-4). Princeton University Press. Kindle Edition.)

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 Pan-selection Hand-Waving

Epigenetic Algorithms

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

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

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

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

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

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

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

Conceptualizing Cells

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

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

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

If not a machine, then what is the cell?

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

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

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

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

The Regulatory Genome

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

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

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

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)