Shape up scientists: quit defending theory

December 2, 2013 | James Kohl

Taking Shape

The causes of a cell’s three-dimensional structure remain a fundamental mystery of cell biology.

By | December 1, 2013

Excerpt 1: “Biologists often refer to the genome as the internal blueprint of a cell or organism, but it is not a blueprint in the conventional sense: it does not specify the location of each part. Rather, the genome can only specify what parts to make and when to make them, but not where they go or how they fit together.

So what dictates a cell’s geometric shape?”

My comment: The laws of physics dictate and constrain the geometric shapes of cells. The thermodynamics of intercellular signaling and stochastic gene expression result in organism-level thermoregulation in different species. In my model, the laws of physics appear to apply in the context of different geometric shapes in different cell types. When viewed from any perspective on adaptations in unicellular organisms such as bacteria, we see different shapes that are biophysically constrained. Many different types of bacteria also are classified via differences in their cell walls. For example, we have gram-positive and gram negative rods and cocci.

However, even the antigenic properties of the human influenza virus appear to be biophysically constrained via the same molecular mechanisms of thermodynamically controlled protein folding that is required to produce a functional cell wall in a functional cell. See for example, my comment on Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution.

Excerpt 2: “Given the fact that cell shape involves not only biochemistry and genetics, but also physics and mathematics, progress in this field is going to require a highly interdisciplinary approach, which should serve as a paradigm for combining the physical and biological sciences with applied mathematics.” 

No one plans a paradigm shift, which is why many academics do not realize it has occurred. Besides,  a plan without a schedule is just a dream. Unless someone proposes a schedule of events, which is required to predict when the paradigm shift is likely to occur, the suggested paradigm will remain a “dream.” And unless someone who has climbed high up the ladder of the current academic hierarchy attests to the likelihood that the paradigm will change soon, other academics will suppress any information that might otherwise precipitate a more rapid shift.

Besides, evolutionary theorists are not going to let the dreams of any biologists come true. Indeed, some of the theorists already realize that the laws of physics do not allow organismal complexity to result from mutation-initiated natural selection. Others realize that their mathematical models of population genetics do not fit within existing biophysical constraints. Adaptations across species occur much too quickly and no experimental evidence has ever suggested that mutations are fixed in the DNA of the organized genome in any species.

We have reached a point where theorists are attempting to remove physics from the chemistry of protein folding and the conserved molecular mechanisms of adaptions that link microbes to man. Carl Zimmer addressed this succinctly when he wrote:  “Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.

He may have been referring to “No entailing laws, but enablement in the evolution of the biosphere” while also predicting a theme issue summary that stated: Each of these papers, in one way or another, consolidates the idea that there will probably be no fixed law, like gravity, to explain at the molecular level how endless forms most beautiful and most wonderful have been, and are being evolved.

The laws of physics are fixed, like gravity. That’s why I question the idea that there will be no fixed law that explains the diversity of adaptations. I also believe that extant diversity was correctly attributed to single amino acid substitutions by Dobzhansky in Nothing in Biology Makes Any Sense Except in the Light of Evolution. In 1973, he wrote  “…alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.”

In the context of Darwin’s ‘conditions of life,” that makes sense, especially if the substitutions are nutrient-dependent and pheromone-controlled.  What does not make sense is that the substitutions would be caused by random mutations or even non-random mutations that were associated with something like radiation exposure. No experimental evidence from any organism suggests that mutations cause beneficial adaptations. That fact attests to the power of mathematical models to convince theorists that the theory of mutation-driven evolution is an acceptable alternative to acceptance of biological facts. Dobzhansky, the Creationist, tentatively revealed those facts.

Unfortunately, at the same time he inferred that the amino acid substitutions could be caused by mutations. However, some researchers have since accepted the fact that the substitutions are caused by changes in single base pairs that either result from 1) a beneficial epigenetic effect on organism-level thermoregulation; 2) have no  immediate effect;  or 3) contribute to mutations, diseases, and disorders of protein folding that limit the physiology of reproduction, which is nutrient-dependent.

Reproduction is not controlled by predation. It is controlled by the metabolism of nutrients to species-specific pheromones in the context of morphogenesis and differences in the cell types of unicellular and multicellular organisms.  However, that fact is like a nightmare for evolutionary theorists. Some of them may think it will not be a recurring nightmare. Dobzhansky predicted it always will be, since nothing about evolutionary theory makes sense except in the light of biology. Theorists should probably stop trying to make sense of biology outside the constraints of physics and chemistry, simply because they thought they could make sense of biology via mathematical models of population genetics.

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James Vaughn Kohl

James Vaughn Kohl

James Vaughn Kohl was the first to accurately conceptualize human pheromones, and began presenting his findings to the scientific community in 1992. He continues to present to, and publish for, diverse scientific and lay audiences, while constantly monitoring the scientific presses for new information that is relevant to the development of his initial and ongoing conceptualization of human pheromones.