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Our future, our universe, and other weighty topics


Monday, May 8, 2023

Don't Be Impressed by Equation Spraying That Does Not Really Calculate

 Recently we got from a Harvard professor of evolutionary biology (Lloyd  A. Demetrius) a pair of papers announcing what the author apparently considers some grand new insight. He announces something he calls Directionality Theory, which claims there is an "Entropic Principle of Self-Organization." The claims Demetrius makes about this principle are not at all cautious. Hinting his principle is something that explains one or more of the biggest mysteries of nature, Demetrius makes this boast in his paper "Self–Organization, Evolutionary Entropy and Directionality Theory": 

"This principle is a universal rule, applicable to the self–assembly of structures ranging from the folding of proteins, to branching morphogenesis, and the emergence of social organization. The principle also elucidates the origin of cellular life: the transition from inorganic matter to the emergence of cells, capable of replication and metabolism."

Like the term "emergence," the term "self-organization" has always been a "last resort" term of desperation pulled out by scientists when they have no credible tale to tell of how some amount of organization arose. On page 5 of the paper, Demetrius gives this rather vacuous definition of "self-organization":  "Self–organization is a process of assembly in which the formation of macroscopic patterns spontaneously emerge from the collective behavior of the individual components." Demetrius gives two examples of what he calls "static self-assembly": the formation of crystals and "the folding of small proteins." We do not know why proteins form into three-dimensional shapes that are necessary for their function. Claims that such events occur because of "energy minimization" are not credible. Calling protein folding "self-assembly" or "self-organization" does nothing to explain why protein folding occurs. We have no understanding of anything within a polypeptide chain (a sequence of amino acids) that would cause it to form into some functional shape that would be incredibly improbable to arise from chance conformations.  Protein folding is not a known example of "self-assembly." 

We later read this: 

"The central concept in this study of self–organization is evolutionary entropy, Demetrius (1974), (2013). This concept is a statistical measure of cooperativity, which we define as the extent to which the individual components of the network are held together by the interacting forces. These forces may be intermolecular, modulated by molecular recognition; intercellular, encoded in terms of morphology or physiology; or organismic, cooperation driven by individual behavior."

We can start to suspect here that Demetrius is attempting some kind of mashup between physics and biology. We can understand why he might want to do such a thing. Physics has always been a hard science, based on equations and mathematics. Evolutionary theory was born in the nineteenth century as an utterly unmathematical ideology. Darwin had little interest or ability in mathematics, and his work The Origin of Species shows not the slightest interest in physics or mathematics. Totally shunning mathematics was one of Darwin's ways of avoiding probability calculations that would have been fatal to his explanatory boasts. Many Darwinists have  had a kind of "physics envy," and many of them hoped to one day make Darwinism sound like some kind of "hard science," which it definitely is not. So many a Darwinist has tried to mix some physics or math in with Darwinian theory, to make it sound more scientific-sounding. 

The phase "evolutionary entropy" as used by Demetrius sounds very clumsy indeed. Below are the first two definitions of "entropy" I get when doing a Google search for "entropy definition":

"(1) PHYSICS: a thermodynamic quantity representing the unavailability of a system's thermal energy for conversion into mechanical work, often interpreted as the degree of disorder or randomness in the system.

(2) lack of order or predictability; gradual decline into disorder."

But in one of his many definitions of the term, which don't agree with each other, Demetrius has defined "evolutionary entropy" as a  "statistical measure of cooperativity, which we define as the extent to which the individual components of the network are held together by the interacting forces." That sounds like rather the opposite of how a physicist would define entropy.  I guess this is what we might expect from an evolutionary biologist. From the group that keeps talking about the selection that isn't really selection, we now have talk about the entropy that is kind of the opposite of entropy. So whenever we read Demetrius talk about "evolutionary entropy" perhaps we should regard it as kind of an Orwellian Newspeak term, like referring to the government torture center as the Ministry of Love. 

And also we should not take too seriously a principle Demetrius defines like this: "The Entropic Principle of Self–Organization: The equilibrium states of a self–assembly process is contingent on the external resource constraints, and characterized by the maximization of evolutionary entropy." Entropy isn't self-organization, but something like the opposite, so the term "Entropic Principle of Self–Organization" sounds like someone talking about "the peaceful use of city detonations by hydrogen bomb explosions." 

In a paper Demetrius gives varying different definitions of "evolutionary entropy," definitions which seem to conflict with each other, and all definitions never  matching the physics idea of entropy.  Here are the paper's definitions of "evolutionary entropy" (I have added boldface to some of the text):

  •  "Evolutionary entropy describes the rate at which a network of interacting metabolic units convert an external energy source into mechanical energy and work" (page 2).
  • "A statistical measure of cooperativity, which we define as the extent to which the individual components of the network are held together by the interacting forces" (page 8).
  • "Evolutionary entropy, a statistical measure of the cooperativity of the individuals of a given genotype" (page 9).
  •  "Evolutionary entropy describes the rate at which a population converts the external resources into metabolic energy and biomass" (page 9).
  • "Evolutionary entropy, in the context of this class of models, depicts the variability in the age at which individuals in a population reproduce and die" (page 10).
  • "Evolutionary entropy is a statistical measure of Darwinian fitness" (page 21).
  • "Evolutionary entropy, a fundamental parameter of the extent to which the component share and distribute the internal energy of macroscopic aggregate, describes the rate at which the components transform the external energy into mechanical energy and biological work." (page 21). 
  • "The statistical parameter, evolutionary entropy, is a measure of the geometry of convection patterns" (page 35). 
  • "Evolutionary entropy, a measure of cooperativity — the extent to which the internal energy of the system is shared and distributed between the interacting components" (page 36).
  • In another paper  "Evolutionary Entropy and the Second Law of Thermodynamics," the same author defined "evolutionary entropy" like this:

    • "Evolutionary entropy, a statistical measure which describes the number and diversity of metabolic cycles in a population of replicating organisms" (page 2). 
    • "Evolutionary entropy describes the multiplicity of cyclic pathways of energy flow between the different metabolic states in a population of replicating organisms" (page 3).
    • "Evolutionary entropy can be considered a measure of temporal order, and organized state of energy" (page 4) -- a statement that oddly contrasts with the statement on page 3 that "thermodynamic entropy can be considered a measure of positional disorder."
    • "Evolutionary entropy, i.e., the number of replicating cycles generated by the interaction between the individuals" (page 25).
    • "Evolutionary entropy describes the rate at which the population appropriates chemical energy from the external environment and converts this energy into biological work" (page 33). 
    In another paper  "Evolutionary Entropy: A Predictor of Body Size, Metabolic Rate and Maximal Life Span" the same author defined "evolutionary entropy" like this: "Evolutionary entropy is a function of the age-specific fecundity and mortality variables and has an information-theoretic interpretation: the uncertainty in the age of the mother of a randomly chosen newborn." It rather seems that Demetrius loves very much using the term "evolutionary entropy," but that he keeps changing around his definition of the term, wandering "all over the map," as if he can't make up his mind about what evolutionary entropy is. Unfortunately, since he has written several papers all centered upon this inconsistently-defined phrase "evolutionary entropy," it rather seems that such papers fall short. 

    What we seem to get in these papers (and another I will discuss) is lots of what I may call equation sprayingI may define equation spraying as the abundant use of arcane equations to create some superficial impression of deep thought and intelligent analysis, particularly when such mystifying symbolism is not necessary, or when it obfuscates or distracts you from realizing the author is speculating or hand waving or engaging in dubious logic. The biggest equation sprayers are theoretical cosmologists and theoretical physicists. They love to use equation spraying to fill up their papers with so many arcane symbols that you might be impressed unless you realize that they're just speculating like crazy. Biologists may engage in equation spraying when they are trying to fool you into thinking that their hazy unbelievable speculations are some kind of rigorous thought like that used to calculate the gravitational influences on spacecraft or the energy that would be released by an asteroid striking Earth at a particular speed. 

    Some symptoms suggesting the possibility of equation spraying are below:

    (1) We get equations that are not well documented, in which there are obscure symbols in strange fonts, without any decent explanation of what some or most of the symbols mean. If an explanation is given, it may be merely some imprecise phrase with no clear meaning. An example would be when Demetrius says on page 9 of this paper this: "The function Φ represents the resource production rate; γ denote the temporal correlation in resource production." Another example would be on page 13 of the same paper where he says, "The quantity W denote the total number of microstates of a system consistent with a given macrostate." Another example would be on page where we get something ("ϕ") very vaguely defined as "a potential function on Ω which describes the interaction between the individual components."  Equally obscure examples could be quoted from papers of the same author. When you see the parts of equations described so imprecisely, or not described at all, you may get the impression an author never actually intended to calculate using such equations, and you may get the suspicion the equations are largely decorations intended to impress us. 

    (2) Some obscure concept that does not correspond to a quantifiable reality known to exist in nature (such as "cooperativity" or "the inflaton field") is represented by some symbol, often a letter of the Greek alphabet. There may be multiple occurrences of such a thing in the same paper. 

    (3) There are very few or no worked examples that show a case of how the equations would specifically work in the real world to produce a particular calculated number. Basically no concrete use is made of the equations to produce some particular calculated number or numerical output.

    (4) Key terms may be inconsistently defined in different ways that do not agree with each other.  

    Looking at the four papers Demetrius has on the Cornell science paper preprint server, the ones here, here, here and here, I find very many equations (more than 200?), but I seem to find only one case in which such equations are used to calculate anything: on page 10 of the paper here, there is a specific calculation which produces the not-very-grand calculation that a particular plant (dipsacus sylvestris, the wild teasel) has a generation time of 2.91 years. 


    The wild teasel

    Another recent paper by Demetrius is entitled "Directionality Theory and the Origin of Life." In this paper he announces, "The main tenet of Directionality Theory is the Entropic Principle of Collective Behavior: The collective behavior of aggregates of organic matter is contingent on the population size and the external energy source, and characterized by extremal states of evolutionary entropy." 

    The first sentence in the section entitled "Introduction" is this very bad misstatement: "Cellular life, the fundamental unit of living organisms, consists of an elaborate set of self– reproducing chemical reactions." No cellular life consists of something vastly more: various states of enormously high organization, such as the existence of hundreds of different types of protein molecules that each have an average of hundreds of well-arranged parts. Saying that cellular life consists of chemical reactions is as bad an error as saying that jet aircraft consist of energy use. Just as jet aircraft are something vastly more than just energy use, cellular life is something vastly more than just chemical reactions. 

    Later in the paper, Demetrius tries to make use of one of the shadiest rhetorical devices of origin-of-life theorists: appealing to the concept of "protocells." The sleazy trick works like this: you get some description of a disorganized bubble, and try to call that a "protocell." A similar trick might be to find a little metal junk in a junkyard, and call that a "proto-jetliner." The difference in organization between the little bubbles labeled as "protocells" and self-reproducing cells is like the difference between a handful of junk parts and a modern 747 aircraft capable of carrying more than 100 passengers across the Atlantic ocean. The membranes of cells are actually extremely complex things requiring many different types of specialized protein molecules (each consisting of thousands of well-arranged atoms) in order for such membranes to act the way they do (rather like some intelligent gatekeeper). 

    goofy research

    Demetrius tells us this: "Protocells are compartmented systems composed of two types of RNA polymers, namely the information units, the precursors to DNA, and the catalytic units, the precursors to proteins." The precursors to DNA are nucleosides (combinations of ribose sugar and pyrimidines or purines) and nucleotides (a nucleoside plus a phosphate).  The precursors to protein molecules are amino acids. No experiments realistically simulating the early Earth have produced either nucleosides or any of the twenty amino acids used by living things, so there is no reason to believe that protocells (as described by Demetrius) ever would have existed. Like so many other other origin-of-life theorists, Demetrius appeals to the Miller-Urey experiments, but such appeals are fallacious. The Miller-Urey experiment never realistically simulated early Earth conditions. That experiment used "every other day" continuous electrical bombardment within a glass sphere, unlike anything that would have occurred on the early Earth. The mixture of gases it used to try to simulate the early Earth did not match the early Earth's atmosphere as scientists now understand it, and the specially constructed glass apparatus used by the Miller-Urey experiment did not correspond to anything that ever would have existed before humans existed.   

    What would you have if you had some so-called "protocell" consisting of "the precursors of DNA" and "the precursors of proteins"?  That would be like a balloon filled with some Scrabble letters. But that would do nothing to explain the origin of life, which requires tens of thousands of very well-arranged amino acids (to make hundreds of different types of proteins), and tens of thousands of very well-arranged nucleosides (to make a DNA molecule specifying the amino acid contents of such proteins). Claiming that some so-called "protocell" consisting of "the precursors of DNA" and "the precursors of proteins"  explains the origin of cells is like claiming that well-written books can accidentally arise merely because you have some  Scrabble sets or some boxes of Alpha Bits consisting of disordered letters not arranged into sentences.   

    Figure 3 of the paper by Demetrius ("Directionality Theory and the Origin of Life") is a misleading diagram that has as its bottom something that is the equivalent of this:

    Protocells --> Darwinian evolution -->  Cellular life

    This is nonsensical. As very many Darwinists have admitted, Darwinian evolution requires life to first exist, so it cannot possibly explain a transition from nonliving protocells to living reproducing cells.  The predecessors of a self-reproducing cell would not be disorganized protocells but enormously organized things such as protein molecules and organelles. 

    1 comment:

    1. Élan vital is a much better hypothesized principle than is the speculative ideas of Lloyd Demetirus. IMO, Élan vital is a valid metaphysical hypothesis which was supposedly discredited by physicalism, but which is now re-emerging thanks to various scientists, such as biochemist Michael Behe. It also helps toward explaining why the universe itself is so improbably conducive to life, and more than that, to civilization and technology.

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