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Friday, 9 July 2021

Maths vs. Darwin.

 Marcel-Paul Schützenberger

Introduction

Until his death, the mathematician and doctor of medicine Marcel-Paul Schützenberger (1920-1996) was Professor of the Faculty of Sciences at the University of Paris and a member of the Academy of Sciences. [See "From the Editors" for additional biographical information.] In 1966, Schützenberger participated in the Wistar Symposium on mathematical objections to neo-Darwinism. His arguments were subtle and often misunderstood by biologists. Darwin's theory, he observed, and the interpretation of biological systems as formal objects, were at odds insofar as randomness is known to degrade meaning in formal contexts. But Schützenberger also argued that Darwin's theory logically required some active principle of coordination between the typographic space of the informational macromolecules (DNA and RNA) and the organic space of living creatures themselves -- which Darwin's theory does not provide. In this January 1996 interview with the French science monthly La Recherche, here published in English for the first time, he pursued these themes anew, finding inspiration for his ideas both in the mathematical ideas that he had pioneered and in the speculative tradition of French biological thought that stretched from Georges Cuvier to Lucien Cuenot. M.P. Schützenberger was a man of universal curiosity and great wit; throughout his life, he was both joyful and unafraid. The culture that he so brilliantly represented disappears with him, of course. It was his finest invention and it now belongs to the inventory of remembered things.


Q: What is your definition of Darwinism?

S: The most current, of course, a position generically embodied, for example, by Richard Dawkins. The essential idea is well-known. Evolution, Darwinists argue, is explained by the double action of chance mutations and natural selection. The general doctrine embodies two mutually contradictory schools -- gradualists, on the one hand, saltationists, on the other. Gradualists insist that evolution proceeds by means of small successive changes; saltationists that it proceeds by jumps. Richard Dawkins has come to champion radical gradualism; Stephen Jay Gould, a no less radical version of saltationism.

Q: You are known as a mathematician rather than a specialist in evolutionary biology...

S: Biology is, of course, not my specialty. The participation of mathemeticians in the overall assessment of evolutionary thought has been encouraged by the biologists themselves, if only because they presented such an irresistible target. Richard Dawkins, for example, has been fatally attracted to arguments that would appear to hinge on concepts drawn from mathematics and from the computer sciences, the technical stuff imposed on innocent readers with all of his comic authority. Mathematicians are, in any case, epistemological zealots. It is normal for them to bring their critical scruples to the foundations of other disciplines. And finally, it is worth observing that the great turbid wave of cybernetics has carried mathematicians from their normal mid-ocean haunts to the far shores of evolutionary biology. There up ahead, Rene Thom and Ilya Prigogine may be observed paddling sedately toward dry land, members of the Santa Fe Institute thrashing in their wake. Stuart Kauffman is among them. An interesting case, a physician half in love with mathematical logic, burdened now and forever by having received a Papal Kiss from Murray Gell-Mann. This ecumenical movement has endeavored to apply the concepts of mathematics to the fundamental problems of evolution -- the interpretation of functional complexity, for example.

Q: What do you mean by functional complexity?

S: It is impossible to grasp the phenomenon of life without that concept, the two words each expressing a crucial and essential idea. The laboratory biologists' normal and unforced vernacular is almost always couched in functional terms: the function of an eye, the function of an enzyme, or a ribosome, or the fruit fly's antennae -- their function; the concept by which such language is animated is one perfectly adapted to reality. Physiologists see this better than anyone else. Within their world, everything is a matter of function, the various systems that they study -- circulatory, digestive, excretory, and the like -- all characterized in simple, ineliminable functional terms. At the level of molecular biology, functionality may seem to pose certain conceptual problems, perhaps because the very notion of an organ has disappeared when biological relationships are specified in biochemical terms; but appearances are misleading, certain functions remaining even in the absence of an organ or organ systems. Complexity is also a crucial concept. Even among unicellular organisms, the mechanisms involved in the separation and fusion of chromosomes during mitosis and meiosis are processes of unbelieveable complexity and subtlety. Organisms present themselves to us as a complex ensemble of functional interrelationships. If one is going to explain their evolution, one must at the same time explain their functionality and their complexity.

Q: What is it that makes functional complexity so difficult to comprehend?

S: The evolution of living creatures appears to require an essential ingredient, a specific form of organization. Whatever it is, it lies beyond anything that our present knowledge of physics or chemistry might suggest; it is a property upon which formal logic sheds absolutely no light. Whether gradualists or saltationists, Darwinians have too simple a conception of biology, rather like a locksmith improbably convinced that his handful of keys will open any lock. Darwinians, for example, tend to think of the gene rather as if it were the expression of a simple command: do this, get that done, drop that side chain. Walter Gehring's work on the regulatory genes controlling the development of the insect eye reflects this conception. The relevant genes may well function this way, but the story on this level is surely incomplete, and Darwinian theory is not apt to fill in the pieces.

Q: You claim that biologists think of a gene as a command. Could you be more specific?

S: Schematically, a gene is like a unit of information. It has simple binary properties. When active, it is an elementary information-theoretic unit, the cascade of gene instructions resembling the cascade involved in specifying a recipe. Now let us return to the example of the eye. Darwinists imagine that it requires what? A thousand or two thousand genes to assemble an eye, the specification of the organ thus requiring one or two thousand units of information? This is absurd! Suppose that a European firm proposes to manufacture an entirely new household appliance in a Southeast Asian factory. And suppose that for commercial reasons, the firm does not wish to communicate to the factory any details of the appliance's function -- how it works, what purposes it will serve. With only a few thousand bits of information, the factory is not going to proceed very far or very fast. A few thousand bits of information, after all, yields only a single paragraph of text. The appliance in question is bound to be vastly simpler than the eye; charged with its manufacture, the factory will yet need to know the significance of the operations to which they have committed themselves in engaging their machinery. This can be achieved only if they already have some sense of the object's nature before they undertake to manufacture it. A considerable body of knowledge, held in common between the European firm and its Asian factory, is necessary before manufacturing instructions may be executed.

Q: Would you argue that the genome does not contain the requisite information for explaining organisms?

S:Not according to the understanding of the genome we now possess. The biological properties invoked by biologists are in this respect quite insufficient; while biologists may understand that a gene triggers the production of a particular protein, that knowledge -- that kind of knowledge -- does not allow them to comprehend how one or two thousand genes suffice to direct the course of embryonic development.

Q: You are going to be accused of preformationism...

S: And of many other crimes. My position is nevertheless strictly a rational one. I've formulated a problem that appears significant to me: how is it that with so few elementary instructions, the materials of life can fabricate objects that are so marvelously complicated and efficient? This property with which they are endowed -- just what is its nature? Nothing within our actual knowledge of physics and chemistry allows us intellectually to grasp it. If one starts from an evolutionary point of view, it must be acknowledged that in one manner or another, the earliest fish contained the capacity, and the appropriate neural wiring, to bring into existence organs which they did not possess or even need, but which would be the common property of their successors when they left the water for the firm ground, or for the air.

Q: You assert that, in fact, Darwinism doesn't explain much.

S: It seems to me that the union of chance mutation and selection has a certain descriptive value; in no case does the description count as an explanation. Darwinism relates ecological data to the relative abundance of species and environments. In any case, the descriptive value of Darwinian models is pretty limited. Besides, as saltationists have indicated, the gradualist thesis seems completely demented in light of the growth of paleontological knowledge. The miracles of saltationism, on the other hand, cannot discharge the mystery I have described.

Q: Let's return to natural selection. Isn't it the case that despite everything the idea has a certain explanatory value?

S: No one could possibly deny the general thesis that stability is a necessary condition for existence -- the real content of the doctrine of natural selection. The outstanding application of this general principle is Berthollet's laws in elementary chemistry. In a desert, the species that die rapidly are those that require water the most; yet that does not explain the appearance among the survivors of those structures whose particular features permits them to resist aridity. The thesis of natural selection is not very powerful. Except for certain artificial cases, we are yet unable to predict whether this or that species or this or that variety will be favored or not as the result of changes in the environment. What we can do is establish after the fact the effects of natural selection -- to show, for, example that certain birds are disposed to eat this species of snails less often than other species, perhaps because their shell is not as visible. That's ecology: very interesting. To put it another way, natural selection is a weak instrument of proof because the phenomena subsumed by natural selection are obvious and yet they establish nothing from the point of view of the theory.

Q: Isn't the significant explanatory feature of Darwinian theory the connection established between chance mutations and natural selection?

S:With the discovery of coding, we have come to understand that a gene is like a word composed in the DNA alphabet; such words form the genomic text. It is that word that tells the cell to make this or that protein. Either a given protein is structural, or a protein itself works in combination with other signals given by the genome to fabricate yet another protein. All the experimental results we know fall within this scheme. The following scenario then becomes standard. A gene undergoes a mutation, one that may facilitate the reproduction of those individuals carrying it; over time, and with respect to a specific environment, mutants come to be statistically favored, replacing individuals lacking the requisite mutation. Evolution could not be an accumulation of such typographical errors. Population geneticists can study the speed with which a favorable mutation propagates itself under these circumstances. They do this with a lot of skill, but these are academic exercises if only because none of the parameters that they use can be empirically determined. In addition, there are the obstacles I have already mentioned. We know the number of genes in an organism. There are about one hundred thousand for a higher vertebrate. This we know fairly well. But this seems grossly insufficient to explain the incredible quantity of information needed to accomplish evolution within a given line of species.

Q: A concrete example?

S: Darwinists say that horses, which were once mammals as large as rabbits, increased their size to escape more quickly from predators. Within the gradualist model, one might isolate a specific trait -- increase in body size -- and consider it to be the result of a series of typographic changes. The explanatory effect achieved is rhetorical, imposed entirely by trick of insisting that what counts for a herbivore is the speed of its flight when faced by a predator. Now this may even be partially true, but there are no biological grounds that permit us to determine that this is in fact the decisive consideration. After all, increase in body size may well have a negative effect. Darwinists seem to me to have preserved a mechanic vision of evolution, one that prompts them to observe merely a linear succession of causes and effects. The idea that causes may interact with one another is now standard in mathematical physics; it is a point that has had difficulty in penetrating the carapace of biological thought. In fact, within the quasi-totality of observable phenomena, local changes interact in a dramatic fashion; after all, there is hardly an issue of La Recherche that does not contain an allusion to the Butterfly Effect. Information theory is precisely the domain that sharpens our intuitions about these phenomena. A typographical change in a computer program does not change it just a little. It wipes the program out, purely and simply. It is the same with a telephone number. If I intend to call a correspondent by telephone, it doesn't much matter if I am fooled by one, two, three or eight figures in his number.

Q: You accept the idea that biological mutations genuinely have the character of typographical errors?

S: Yes, in the sense that one base is a template for another, one codon for another, but at the level of biochemical activity, one is no longer able properly to speak of typography. There is an entire grammar for the formation of proteins in three dimensions, one that we understand poorly. We do not have at our disposal physical or chemical rules permitting us to construct a mapping from typographical mutations or modifications to biologically effective structures. To return to the example of the eye: a few thousand genes are needed for its fabrication, but each in isolation signifies nothing. What is significant is the combination of their interactions. These cascading interactions, with their feedback loops, express an organization whose complexity we do not know how to analyze (See Figure 1). It is possible we may be able to do so in the future, but there is no doubt that we are unable to do so now. Gehring has recently discovered a segment of DNA which is both involved in the development of the vertebrate eye and which can induce the development of an eye in the wing of a butterfly. His work comprises a demonstration of something utterly astonishing, but not an explanation.

Q:But Dawkins, for example, believes in the possibility of a cumulative process.

S: Dawkins believes in an effect that he calls "the cumulative selection of beneficial mutations." To support his thesis, he resorts to a metaphor introduced by the mathematician Emile Borel -- that of a monkey typing by chance and in the end producing a work of literature. It is a metaphor, I regret to say, embraced by Francis Crick, the co-discoverer of the double helix. Dawkins has his computer write a series of thirty letters, these corresponding to the number of letters in a verse by Shakespeare. He then proceeds to simulate the Darwinian mechanism of chance mutations and selection. His imaginary monkey types and retypes the same letters, the computer successively choosing the phrase that most resembles the target verse. By means of cumulative selection, the monkey reaches its target in forty or sixty generations.

Q: But you don't believe that a monkey typing on a typewriter, even aided by a computer...

S:This demonstration is a trompe-l'oeil, and what is more, Dawkins doesn't describe precisely how it proceeds. At the beginning of the exercise, randomly generated phrases appear rapidly to approach the target; the closer the approach, the more the process begins to slow. It is the action of mutations in the wrong direction that pulls things backward. In fact, a simple argument shows that unless the numerical parameters are chosen deliberately, the progression begins to bog down completely.

Q:You would say that the model of cumulative selection, imagined by Dawkins, is out of touch with palpable biological realities?

S: Exactly. Dawkins's model lays entirely to the side the triple problems of complexity, functionality, and their interaction.

Q: You are a mathematician. Suppose that you try, despite your reservations, to formalize the concept of functional complexity...

S: I would appeal to a notion banned by the scientific community, but one understood perfectly by everyone else -- that of a goal. As a computer scientist, I could express this in the following way. One constructs a space within which one of the coordinates serves in effect as the thread of Ariane, guiding the trajectory toward the goal. Once the space is constructed, the system evolves in a mechanical way toward its goal. But look, the construction of the relevant space cannot proceed until a preliminary analysis has been carried out, one in which the set of all possible trajectories is assessed, this together with an estimation of their average distance from the specified goal. The preliminary analysis is beyond the reach of empirical study. It presupposes -- the same word that seems to recur in theoretical biology -- that the biologist (or computer scientist) know the totality of the situation, the properties of the ensemble of trajectories. In terms of mathematical logic, the nature of this space is entirely enigmatic. Nonetheless, it is important to remember that the conceptual problems we face, life has entirely solved; the systems embodied in living creatures are entirely successful in reaching their goals. The trick involved in Dawkin's somewhat sheepish example proceeds via the surreptitious introduction of a relevant space. His computer program calculates from a random phrase to a target, a calculation corresponding to nothing in biological reality. The function that he employs flatters the imagination, however, because it has that property of apparent simplicity that elicits naïve approval. In biological reality, the space of even the simplest function has a complexity that defies understanding, and indeed, defies any and all calculations.

Q: Even when they dissent from Darwin, the saltationists are more moderate: they don't pretend to hold the key that would permit them to explain evolution...

S: Before we discuss the saltationists, however, I must say a word about the Japanese biologist Mooto Kimura. He has shown that the majority of mutations are neutral, without any selective effect. For Darwinians upholding the central Darwinian thesis, this is embarrassing... The saltationist view, revived by Stephen Jay Gould, in the end represents an idea due to Richard Goldschmidt. In 1940 or so, he postulated the existence of very intense mutations, no doubt involving hundreds of genes, and taking place rapidly, in less than one thousand generations, thus below the threshold of resolution of paleontology. Curiously enough, Gould does not seem concerned to preserve the union of chance mutations and selection. The saltationists run afoul of two types of criticism. On the one hand, the functionality of their supposed macromutations is inexplicable within the framework of molecular biology. On the other hand, Gould ignores in silence the great trends in biology, such as the increasing complexity of the nervous system. He imagines that the success of new, more sophisticated species, such as the mammals, is a contingent phenomenon. He is not in a position to offer an account of the essential movement of evolution, or at the least, an account of its main trajectories. The saltationists are thus reduced to invoking two types of miracles: macromutations, and the great trajectories of evolution.

Q: In what sense are you employing the word 'miracle'?

S:A miracle is an event that should appear impossible to a Darwinian in view of its ultra-cosmological improbability within the framework of his own theory. Now speaking of macromutations, let me observe that to generate a proper elephant, it will not suffice suddenly to endow it with a full-grown trunk. As the trunk is being organized, a different but complementary system -- the cerebellum -- must be modified in order to establish a place for the ensemble of wiring that the elephant will require to use his trunk. These macromutations must be coordinated by a system of genes in embryogenesis. If one considers the history of evolution, we must postulate thousands of miracles; miracles, in fact, without end. No more than the gradualists, the saltationists are unable to provide an account of those miracles. The second category of miracles are directional, offering instruction to the great evolutionary progressions and trends -- the elaboration of the nervous system, of course, but the internalization of the reproductive process as well, and the appearance of bone, the emergence of ears, the enrichment of various functional relationships, and so on. Each is a series of miracles, whose accumulation has the effect of increasing the complexity and efficiency of various organisms. From this point of view, the notion of bricolage [tinkering], introduced by Francois Jacob, involves a fine turn of phrase, but one concealing an utter absence of explanation.

Q: The appearance of human beings -- is that a miracle, in the sense you mean?

S: Naturally. And here it does seem that there are voices among contemporary biologists -- I mean voices other than mine -- who might cast doubt on the Darwinian paradigm that has dominated discussion for the past twenty years. Gradualists and saltationists alike are completely incapable of giving a convincing explanation of the quasi-simultaneous emergence of a number of biological systems that distinguish human beings from the higher primates: bipedalism, with the concomitant modification of the pelvis, and, without a doubt, the cerebellum, a much more dexterous hand, with fingerprints conferring an especially fine tactile sense; the modifications of the pharynx which permits phonation; the modification of the central nervous system, notably at the level of the temporal lobes, permitting the specific recognition of speech. From the point of view of embryogenesis, these anatomical systems are completely different from one another. Each modification constitutes a gift, a bequest from a primate family to its descendants. It is astonishing that these gifts should have developed simultaneously. Some biologists speak of a predisposition of the genome. Can anyone actually recover the predisposition, supposing that it actually existed? Was it present in the first of the fish? The reality is that we are confronted with total conceptual bankruptcy.

Q:You mentioned the Santa Fe school earlier in our discussion. Do appeals to such notions as chaos...

S:I should have alluded to a succession of highly competent people who have discovered a number of poetic but essentially hollow forms of expression. I am referring here to the noisy crowd collected under the rubric of cybernetics; and beyond, there lie the dissipative structures of Prigogine, or the systems of Varela, or, moving to the present, Stuart Kauffman's edge of chaos -- an organized form of inanity that is certain soon to make its way to France. The Santa Fe school takes complexity to apply to absolutely everything. They draw their representative examples from certain chemical reactions, the pattern of the sea coast, atmosphere turbulence, or the structure of a chain of mountains. The complexity of these structures is certainly considerable, but in comparison with the living world, they exhibit in every case an impoverished form of organization, one that is strictly non-functional. No algorithm allows us to understand the complexity of living creatures, this despite these examples, which owe their initial plausibility to the assumption that the physico-chemical world exhibits functional properties that in reality it does not possess.

Q: Should one take your position as a statement of resignation, an appeal to have greater modesty, or something else altogether?

S: Speaking ironically, I might say that all we can hear at the present time is the great anthropic hymnal, with even a number of mathematically sophisticated scholars keeping time as the great hymn is intoned by tapping their feet. The rest of us should, of course, practice a certain suspension of judgment.

Epicureanism:an overview.

 Epicureanism is a system of philosophy founded around 307 BC based upon the teachings of the ancient Greek philosopher Epicurus. Epicureanism was originally a challenge to Platonism. Later its main opponent became Stoicism.


Few writings by Epicurus have survived. However, there are independent attestations of his ideas from his later disciples. Some scholars consider the epic poem De rerum natura (Latin for On the Nature of Things) by Lucretius to present in one unified work the core arguments and theories of Epicureanism. Many of the scrolls unearthed at the Villa of the Papyri at Herculaneum are Epicurean texts. At least some are thought to have belonged to the Epicurean philosopher Philodemus. Epicurus also had a wealthy 2nd c. AD disciple, Diogenes of Oenoanda, who had a portico wall inscribed with tenets of the philosophy erected in Oenoanda, Lycia (present day Turkey).

Epicurus was an atomic materialist, following in the steps of Democritus. His materialism led him to a general attack on superstition and divine intervention. Following the Cyrenaic philosopher Aristippus, Epicurus believed that the greatest good was to seek modest, sustainable pleasure in the form of a state of ataraxia (tranquility and freedom from fear) and aponia (the absence of bodily pain) through knowledge of the workings of the world and limiting desires. Correspondingly, Epicurus and his followers generally withdrew from politics because it could lead to frustrations and ambitions which can directly conflict with the Epicurean pursuit for peace of mind and virtues.

Although Epicureanism is a form of hedonism insofar as it declares pleasure to be its sole intrinsic goal, the concept that the absence of pain and fear constitutes the greatest pleasure, and its advocacy of a simple life, make it very different from "hedonism" as colloquially understood.

Epicureanism flourished in the Late Hellenistic era and during the Roman era, and many Epicurean communities were established, such as those in AntiochiaAlexandriaRhodes, and Herculaneum. By the late 3rd century CE Epicureanism all but died out, being opposed by other philosophies (mainly Neoplatonism) that were now in the ascendant. Interest in Epicureanism was resurrected in the Age of Enlightenment and continues in the modern era.

Conditional immortality :a recent history.

 During the Reformation, Luther, "Tyndale", and Wycliffe supported the view of conditional immortality. In 1520 in response to Bull of Pope Leo X Luther rejected the doctrine of natural immortality.


The British Evangelical Alliance ACUTE report states the doctrine is a "significant minority evangelical view" that has "grown within evangelicalism in recent years". In the 20th century, conditional immortality was considered by certain theologians in the Eastern Orthodox Church.

Proponents of conditional immortality ("conditionalists") point to Genesis 2 and Revelation 22, where the Tree of Life is mentioned. It is argued that these passages, along with Genesis 3:22–24 teach that human beings will naturally die without continued access to God's life-giving power.

As a general rule, conditionalism goes hand in hand with annihilationism; that is, the belief that the souls of the wicked will be destroyed in Gehenna (often translated "hell", especially by non-conditionalists and non-universalists) fire rather than suffering eternal torment. The two ideas are not exactly equivalent, however, because in principle God may annihilate a soul which was previously created immortal. While annihilationism places emphasis on the active destruction of a person, conditionalism places emphasis on a person's dependence upon God for life; the extinction of the person is thus a passive consequence of separation from God, much like natural death is a consequence of prolonged separation from food, water, and air.

In secular historical analysis, the doctrine of conditional immortality reconciles the ancient Hebrew view that humans are mortal with the Christian view that the saved will live forever.

Belief in forms of conditionalism became a current in Protestantism beginning with the Reformation, but it was only adopted as a formal doctrinal tenet by denominations such as early Unitarians, the churches of the English Dissenting Academies, then Seventh-day AdventistsChristadelphians, the Bible Students and Jehovah's Witnesses.

Mortalist writers, such as Thomas Hobbes in Leviathan, have often argued that the doctrine of natural (or innate) immortality stems not from Hebrew thought as presented in the Bible, but rather from pagan influence, particularly Greek philosophy and the teachings of Plato, or Christian tradition. Bishop of Durham N.T. Wright noted that 1 Timothy 6:15–16 teaches "God… alone is immortal," while in 2 Timothy 1:10 it says that immortality only comes to human beings as a gift through the gospel. Immortality is something to be sought after (Romans 2:7) therefore it is not inherent to all humanity.

These groups may claim that the doctrine of conditional immortality reconciles two seemingly conflicting traditions in the Bible: the ancient Hebrew concept that the human being is mortal with no meaningful existence after death (see שאול, Sheol and the Book of Ecclesiastes), and the later Jewish and Christian belief in the resurrection of the dead and personal immortality after Judgment Day.

Wednesday, 7 July 2021

And still yet more primeval tech vs. Darwin.

 





New Paper Investigates Engineering Design Constraints on the Bacterial Flagellum

Casey Luskin


A new peer-reviewed paper in the journal BIO-Complexity, “An Engineering Perspective on the Bacterial Flagellum: Part 1 — Constructive View,” comes out of the Engineering Research Group and Conference on Engineering in Living Systems that Steve Laufmann recently wrote about. The author, Waldean Schulz, holds a PhD in computer science from Colorado State University, and is a signer of the Scientific Dissent from Darwinism list. What could a computer scientist say about the bacterial flagellum? Well, Schulz explains that his study “examines the bacterial flagellum from an engineering viewpoint,” which aims to concentrate on the “the structure, proteins, control, and assembly of a typical flagellum, which is the organelle imparting motility to common bacteria.” 

This technique of examining biology through the eyes of engineering is not necessarily new — systems biologists have been doing it for years. However, since engineering is a field that tries to determine how to better design technology, the field of intelligent design promises to yield new engineering-based insights into biology. Schulz’s paper is a prime example of such a contribution. It produces what is arguably the most rigorous logical demonstration of the irreducible complexity of the flagellum produced to date. 

A Goal-Directed Approach

Intelligent design is fundamentally a goal-directed approach to studying natural systems, where the various parts and components biological organisms are coordinated to work together in the top-down manner of engineering. Schulz’s paper thus takes a “constructive approach” which requires a “top-down specification.” Here’s how this approach works:

It starts with specifying the purpose of a bacterial motility organelle, the environment of a bacterium, its existing resources, its existing constitution, and its physical limits, all within the relevant aspects of physics and molecular chemistry. From that, the constructive approach derives the logically necessary functional requirements, the constraints, the assembly needs, and the hierarchical relationships within the functionality. The functionality must include a control subsystem, which needs to properly direct the operation of a propulsion subsystem. Those functional requirements and constraints then suggest a few — and only a few — viable implementation schemata for a bacterial propulsion system. The entailed details of one configuration schema are then set forth.

This approach is very similar to Paul Nelson’s ideas about “design triangulation”: you identify some function that is needed, and if the system was intelligently designed then you can back-engineer other components and parts that will be needed for that function to be fulfilled. After all, “engineers regularly specify and design systems top-down, but they construct those systems bottom-up.” Thus an engineering analysis of the flagellum seems the best way to understand it. 

Schulz introduces engineering methodologies to study the flagellum, which flow naturally from of an ID paradigm. He writes:

A common engineering methodology, called the Waterfall Model, first produces a formal Functional Requirements Specification document. Then a design is proposed in a System Design Specification, which must comport with the Requirements Spec. Typically this methodology is often accompanied by a Testing Specification, which measures how well the subsequently constructed system satisfies the requirements. This methodology was and is successfully applied at Intel, Image Guided Technologies, and Stryker. A similar specification method can be used by a patent agent or attorney in helping inventors clarify in detail what they have invented for a patent application.

When applying this method, one examines “overall purpose for the proposed system, the usage environment, necessary functionality, available materials, tools needed for construction, and various parameters and constraints (dimensions, form, cost, materials, energy needs, timing, costs, and other conditions).”  After doing this, “a design is proposed that logically comports with those requirements.”

What Are the Requirements for Bacterial Motility?

Schulz then applies this method to the flagellum, asking What are the requirements for bacterial motility? “In doing this,” he notes, “the constructive approach becomes — in effect — the engineering documentation that must be written as if a clever bioengineer were tasked to devise a motility system for a bacterium lacking a motive organelle.” He answers various questions outlined by the “Waterfall Model”:

  • What is the overall needed function? Answer: “First, the system should enable a bacterium to sense and move toward nutrients needed for metabolic energy, self-repair, and reproduction. Second, the system should enable its bacterium to sense and escape hostile locales, such as toxic or noxious material.”
  • What is the environment of the flagellum? Answer: “The environment of a typical bacterium generally may include both nutrients and deleterious substances. Further, the bacterium typically is suspended within a liquid or semi-fluid medium.”

Thinking Like an Engineer 

Schulz thus determines that the system requires “a propulsion subsystem to accomplish motion.” It also requires “some form of primitive redirection subsystem, working in concert with or integrated with the propulsion subsystem” to help the bacterium find nutrients. There must also be a “collateral control subsystem” which can “sense favorable or unfavorable substances.” He outlines logic controls of this system — including signals that indicate the bacterium should proceed “full speed ahead” or “flee and redirect.” 

The response time for these signals and the motility speeds they induce must also be appropriate to fulfill the needed functions. However, the speeds should be appropriate. For example, “A substantially faster speed would be wasteful of energy,” and “The energy cost to operate the propulsion subsystem must be less than the energy obtained by navigating to and consuming nutrients.” And there are also assembly constraints — including that “The material resources and energy requirements to build a propulsion system must be low enough to justify its construction — that is, to justify the benefit of motion to find new nutrients for metabolism.” 

An Irreducibly Complex System

He notes that all of these resulting requirements present us with an irreducibly complex system: 

[T]he goal is to specify only a minimal set of requirements, assuring that all the requirements of the subsystem are essential. That would imply that the specified sensory-propulsion-redirection system is effectively irreducible. That is, if some part is missing or defective, then, at best, there would be noticeably diminished motility, if any.

Schulz then proposes a design for the bacterial flagellum to fulfill these requirements of flagellar motility. Some of the following requirements must be met:

  • “the propulsion subsystem needs a source of power to operate”
  • “there must be a power-to-motion transducer”
  • “there must be sensors to detect whether the propulsion system should move the bacterium forward … there must be some external member physically interacting with the environmental medium containing the bacterium.”

There must also be various assembly requirements. Construction materials could include a variety of potential biomolecules, including sugars, RNA, DNA, nucleotide bases, or proteins. The answer is clear: “an obvious generic requirement of using available fabrication tools, templates, and control effectively rules out the use of other materials, such as sugars or non-protein polymers.” 

There are a variety of potential basic designs for propulsion. One is a jet-like nozzle (which would require a bladder and many more parts). Another is a rhythmic flexing (which would require a long, flexible body and much more). Still another is a leg-like appendage (which would require appendages), or a snake-like caterpillar crawl (again requiring a long flexible body), or a helical propeller. Schulz explores what would be necessary for a helical propeller — the actual design of bacterial flagella. He discusses various needed parts — including “an armature or mounting structure, a motor rotor, a drive shaft of appropriate length, a helical propeller, and possibly adaptors to bind those components together.” Further, he notes, “there need to be bearings and seals between the rotary components and static components.” Here’s a larger description of the needs:

The static subassembly requires the following components: the semi-rigid cell membrane(s) for rigid mounting, a motor stator, multiple sealed bearings where the rotary subassembly penetrates cell membranes, and an energy conduction pathway.

The stator together with the motor rotor produces torque. The stator must be rigidly attached to some or all of the bacterium’s inner and outer membranes and the peptidoglycan layer. The rigid attachment transfers necessary counter-torque to the cell body as well as providing stability for the rotary subassembly. For each membrane or layer the drive shaft penetrates, there must be a bearing. Each bearing must (a) stabilize the drive shaft, (b) provide a low-friction contact with the drive shaft, and (c) provide a seal to prevent movement of molecules past where the shaft penetrates its host membrane or layer.

A Dependency Network 

Schulz finally develops a dependency network for these requirement showing their “interdependency relationships” which addresses all of the above constraints, including the “purpose, environment, required functions, constraints, and the logically implied static, structural requirements.” It’s quite a detailed diagram — here it is — it’s a bit large so click here for a full-resolution version:

In an impressive table, Schulz lists all of the different components and properties of the flagellum and the rationale for their inclusion. He notes that although there are a couple of different ways to build the system, “In either case, the specified bacterial motility system would be irreducibly complex” and that the “intricate coherence” of all of the parts, systems, and design requirements of the flagellum “is essentially irreducible.” He concludes:

Current evolutionary biology proposes that the flagellum could have been “engineered” naturalistically by cumulative mutations, by horizontal gene transfer, by gene duplication, by co-option of existing organelles, by self-organization, or by some combination thereof. See the summary and references by Finn Pond. Yet to date, no scenario in substantive detail exists for how such an intricate propulsion system could have evolved naturalistically piece by piece. Can any partial implementation of a motility system be even slightly advantageous to a bacterium? Examples of a partial system might lack sensors, lack decision logic, lack control messages, lack a rotor or stator, lack sealed bearings, lack a rod, lack a propeller, or lack redirection means. Would such partial systems be preserved long enough for additional cooperating components to evolve?

That is the key question — which will be explored in future papers that Schulz aims to publish. Based upon the “intricate coherence” and “irreducible complexity” of the numerous parts and properties of the flagellum, the answers to these questions would seem to be no

Tuesday, 6 July 2021

It's Darwinism all the way down?

 Many remember the joke about the best way to open a can: “Assume a can opener.” Or the joke about what holds up the Earth, if the Earth is supported by a turtle: “It’s turtles all the way down.” We laugh at these vacuous explanations, but is not Darwinism like that? It’s a catch-all explanation for everything. Just assume it, and it will explain any data. Darwin may have defined it in terms of the origin of species, but today, natural selection is the Swiss Army knife applied in widely divergent fields. It can be used as a can opener, corkscrew, scraper, screwdriver, and even a dagger for defending itself against critics. Simply assume this can opener and the explanatory work is done. If not, there are more Swiss Army knives all the way down.

Serious papers have used natural selection to explain bacterial antibiotic resistance, human politics, and the multiverse. Any phenomenon that undergoes change but survives seems fair game for bringing out Darwin’s all-purpose explanatory pocket tool. Put another way, it’s like a demon. Maxwell’s demon was a thought experiment about a possible way to violate a natural law; even today, physicists argue about ways to test it. Natural selection is another occult force, complete with mystical “selection pressures” that can create eyes and wings by chance. This demon, too, makes possible violations of a natural law: the law of cause and effect. Natural selection could be called “Darwin’s demon” or, as the demon likes to portray itself, Darwin’s genie. It will fulfill its master’s every wish.

Historical Blunders

Critics of the Origin of Species immediately pounced on Darwin’s fallacious analogy of selective breeding with his new notion of natural selection. The former is done by people with minds acting with foresight toward a goal, they pointed out; the latter is supposed to be blind and unguided. Nevertheless, Darwin’s disciples ever since have played fast and loose with natural selection, applying it in situations where it doesn’t belong, without regard to any human intelligence involved. A recent example appeared a PNAS special issue about economics. In their introductory article to the series, Simon A. Levin and Andrew W. Lo praise Darwin as they repeat his blunder of flawed analogical reasoning.

We motivate this ambitious initiative with an analogyThe brilliant evolutionary insights of Darwin and others have revolutionized our understanding of the world. Darwin was impressed by the “tangled bank” of elaborate forms that emerged from the undirected processes of evolution to produce the complexity of the biological world. Through continuous innovation coupled with the deceptively simple filter known as natural selection, the characteristics of species and their interactions change in response to changing environments. However, evolution is not limited only to the biological world. Wherever the evolutionary forces of reproduction, variation, and selection exist — as they do in financial markets — evolutionary consequences will follow.[Emphasis added.]

Under the Bus

Never mind the traders, innovators, and theorists in the science of economics. They have been thrown under the bus. It’s natural selection all the way down. Intelligent choice by skilled people with free will responding as wisely as possible to rapidly changing market conditions is old hat. Entrepreneurship is gone. Economic theory by tenured professors like Thomas Sowell is gone. Everything now is Darwin’s demon at work, bringing enlightenment about the true nature of economics. People are just pawns of selection pressures. Economics is now like rafts in rapids without pilots. The luckiest will survive, and the genie will smile at an explanatory job well done.

Evolution is about short-term, relative optimality with respect to other participants in the system. In the biosphere, natural selection acts to improve reproductive success relative to the benchmark of other genomes, within and across species. Evolutionary change can thus be thought of in terms of differential fitness: that is, small differences in reproductive rates between individuals over time leading to large differences in populations.Even the very mechanisms of evolution — including those that generate new variation — are subject to constant modification. In the financial world, the evolutionary forces of mutation, recombination, reproduction, and selection often work on financial institutions and market participants through direct competition, finance “red in tooth and claw.” Financial concepts and strategies thus reproduce themselves through cultural transmission and adoption based on their success in the marketplace. These strategies undergo variation through financial innovation, analogous to mutation or genetic recombination in a biological system, but take place at the level of information and abstract thought in financial contexts. It is “survival of the richest.”

If evolution itself evolves, one doesn’t need people in this picture. One only needs “evolutionary forces” pushing objects around, be they molecules, cells, organisms, men or universes.

No Intelligence Allowed

The other papers in the series repeat the error. Their authors conjure up Darwin’s genie to create the appearance of scientific explanation for human endeavors.

In “Sunsetting as an adaptive strategy,” Roberta Romano and Simon Levin liken corporate decisions to discontinue products to apoptosis (programmed cell death). “Apoptosis, death, and extinction are part of a spectrum of responses but are essential features of the evolutionary play,” they explain gleefully as they discuss boardroom banter.

In “The landscape of innovation in bacteria, battleships, and beyond,” Burnham and Travisano compare Lenski’s Long-Term Evolution Experiment (LTEE) with naval warfare. “The message from naval warfare and the LTEE is that competition fosters innovation,” they say with liberal applications of “selection” from the genie. No admirals allowed.

No Authors Allowed

In “How quantifying the shape of stories predicts their success,” Toubia, Berger, and Eliashberg justify that Darwinian bad habit, just-so storytelling. “Why are some narratives (e.g., movies) or other texts (e.g., academic papers) more successful than others?” they begin. Once again, it’s due to a “selection mechanism” acting silently behind the scenes. They fail to see what this does to their own hypothesis.

In “Social finance as cultural evolution, transmission bias, and market dynamics,” Akçay and Hirshleifer continue the game with Darwin’s genie. “In this paradigm, social transmission biases determine the evolution of financial traits in the investor population,” they say. “It considers an enriched set of cultural traits, both selection on traits and mutation pressure, and market equilibrium at different frequencies.”

In “Moonshots, investment booms, and selection bias in the transmission of cultural traits,” Hirshleifer joins Plotkin to apply natural selection to risk-taking in business. For once, they introduce cognitive reasoning into the mix:

We view adoption or rejection of the risky project as a cultural trait transmitted between firms. We employ the Price Equation to decompose this trait’s evolution into a component due to natural selection and a component due to mutation. Surprisingly, despite the central role of selection bias in the evolution of project choice in the model, the predominant source of cultural change in our context is not natural selection, but, rather, mutation pressure. The importance of mutation during transmission differs sharply from cultural evolutionary models with biased imitation, in which there is only natural selection. This feature of our analysis highlights the role of cognitive reasoning in the cultural evolution of risk-taking behaviors.

Cognitive reasoning cannot overcome the power of Darwin’s genie, however. “The Price Equation decomposes evolutionary change into selection and nonselection effects,” they explain. “The nonselection component is often called mutation pressure — the degree to which traits shift through the inheritance process instead of fitness-biased biased replication.” Thus, cognitive reasoning degenerates into a form of mutation pressure. Does that happen in the process of writing scientific papers, too?

In “Evolved attitudes to risk and the demand for equity,” Robson and Orr continue the use of terms natural selection, fitness, and survival to financial planning. Risk-taking and choice by real people with minds and values is the same kind of thing as the foraging strategies of cattle.

Design Advocates Beware

A theory this plastic makes any debate about Darwinism all but impossible to win. Tackle the genie here, and he will reappear over there. He can always outsmart the debater by shape-shifting into another form. Natural selection is a meaningless concept if the professors over in the Economics building are like evolving bacteria in a long-term evolution experiment. 

These papers give an appearance of erudition through an illusion of mathematical rigor (e.g., Robson and Orr speak of “Convex–Concave Ψ in Biology and Economics”) but what does natural selection really do to scientific explanation? If all human choice and action reduce to selection pressures acting on mindless objects, the intellectual world implodes. Even the writing of scientific papers about “evolutionary models of financial markets” becomes nothing more than a survival strategy.

The Last Laugh 

In his essay The Abolition of Man, C. S. Lewis warned that scientism is dehumanizing to science itself. The Darwinists are today’s Conditioners teaching the populace about the true nature of things. They view themselves as victors in the conquest of Nature, “explaining away” and “seeing through” human values, which are now “mere natural phenomena” like natural selection. 

This is not a victory, Lewis says, but a defeat. It is not conquering medieval magic, but embracing it. Lewis does not suppose that the Conditioners are bad men; “They are, rather, not men (in the old sense) at all. They are, if you like, men who have sacrificed their own share in traditional humanity in order to devote themselves to the task of deciding what ‘Humanity’ shall henceforth mean.” 

The last laugh is for Darwin’s demon. He tricked them. He manifested himself as a genie of explanation. He promised to bring them enlightenment, the ability to see through the outward appearance of things to their true natures. He promised to explain away human values in natural terms.

But you cannot go on ‘explaining away’ forever: you will find that you have explained explanation itself away. You cannot go on ‘seeing through’ things for ever. The whole point of seeing through something is to see something through it. It is good that the window should be transparent, because the street or garden beyond it is opaque. How if you saw through the garden too? It is no use trying to ‘see through’ first principles. If you see through everything, then everything is transparent. But a wholly transparent world is an invisible world. To ‘see through’ all things is the same as not to see.

Sunday, 4 July 2021

On origins and loaded dice.

 

Bernoulli, Keynes, and the Big Bang

Robert J. Marks II

Jacob Bernoulli made a now obvious observation about probability over three-and-a-half centuries ago: If nothing is known about the outcome of a random event, all outcomes can be assumed to be equally probable. Bernoulli’s Principle of Insufficient Reason (PrOIR) is commonly used. Throw a fair die. There are six outcomes, one for each face of the cube. The chance of getting five pips showing on the roll of a die is therefore one sixth. If a million lottery tickets are sold and you buy one ticket, the chances of winning are one in a million. This reasoning is intuitively obvious. 

If the Die Is Loaded

The assumption about the die is wrong if the die is loaded. But you don’t know that. You know nothing. So Bernoulli’s PrOIR provides the best model based on the known. If the lottery is fixed and you’re not in on the fix, your chances of winning will be less that one in a million. Maybe zero. But you don’t know the game is fixed. You know and assume nothing. Under the circumstances, equal probability is the best assumption you can make.

In analysis of fine-tuning, No Free Lunch Theorems, and conservation of information, Bernoulli’s PrOIR is foundational. In thermodynamics, uniform distributions correspond to maximum entropy. In the absence of air currents or thermal gradients, the temperature is the same in the middle of the room as it is in the corners.  

Those who disagree with Bernoulli’s PrOIR consistently misapply the principle. They don’t appreciate the definition of “knowing nothing.” The concept of “knowing nothing” can be tricky. The sentences “knowing nothing means knowing something” and “knowing nothing means knowing nothing” are both curious puns.

Strange Ideas in Economics

The most visible opposition of Bernoulli’s PrIOR comes from the economist John Maynard Keynes who is most famous for some strange ideas in Keynesian economics. Keynes’ problems with Bernoulli’s assumption are discussed in his book A Treatise on ProbabilityTwo of his objections, Bertand’s Paradox and the distribution of reciprocals, are soundly debunked in Introduction to Evolutionary Informatics by Ewert, Dembski and me.

A third argument made by Keynes stems from the sort of data economists would deal with. Here is the example: Consider presenting a man who is either from Great Britain or France. You know nothing about the selection process. Bernoulli then says the chances of the man being French is one half. Consider a second situation where locations are finer grained. You are told the visitor is either from Scotland, Wales, or France. Is the chance the man is French now one third? Since both Scotland and Wales are part of Great Britain, what does this say about the first answer where the chance of being French is one half? Is this a case where Bernoulli’s PrOIR breaks down?

No. In reaching this contradiction, Keynes knew something. He did not know nothing” as required by Bernoulli’s PrOIR.

Read the rest at Mind Matters News, published by Discovery Institute’s Walter Bradley Center for Natural and Artificial Intelligence.