The Mind’s Eyes (revisited)

By: James V. Kohl | Published on: June 12, 2016

Author’s copy: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences (2007)

The across-species genetic conservation of intercellular and extracellular chemical communication enables unicellular and multicellular organisms to functionally distinguish between self and non-self.  Non-self olfactory/pheromonal input from the social environment elicits a vertebrate neuroendocrine response.  The organization and activation of this neuroendocrine response modulates the concurrent maturation of the mammalian neuroendocrine system, the reproductive system, and the central nervous system during the development of sexual preferences that may be expressed in sexual behavior.  Psychophysiological mechanisms for the development of these sexual preferences include focus on unconscious affects that are detailed in reciprocal cause and effect relationships.  Olfactory/pheromonal conditioning elicits neuroendocrine effects accompanied by unconscious affects on the development of sexual preferences.  Integrating these unconscious affects extends to humans a developmental model of behavior that includes the development of male sexual preferences for other males.

For comparison, see: How Can Physics Underlie the Mind? Top-Down Causation in the Human Context (2016)
by George Ellis

George Ellis, FRS, is one of the world’s leading researchers in general relativity theory and cosmology. He is Emeritus Distinguished Professor of Complex Systems in the Department of Mathematics and Applied Mathematics at the University of Cape Town in South Africa. He co-authored The Large Scale Structure of Space-Time with Cambridge physicist Stephen Hawking.

Book description:

  • Addresses one of science and philosophy’s biggest puzzles:  how complex structures that emerge from atoms and molecules can become causative agent
  • Argues that the human mind and resultant social agency has a special status among complex systems
  • Is fully consistent with present day physics, but also takes into account key features of biology and how the brain functions
  • Will appeal to general and academic readers alike

Available 6/12/16 from Amazon books

Physics underlies all complexity, including our own existence: how is this possible? How can our own lives emerge from interactions of electrons, protons, and neutrons? This book considers the interaction of physical and non-physical causation in complex systems such as living beings, and in particular in the human brain, relating this to the emergence of higher levels of complexity with real causal powers. In particular it explores the idea of top-down causation, which is the key effect allowing the emergence of true complexity and also enables the causal efficacy of non-physical entities, including the value of money, social conventions, and ethical choices.

On pages 3 and 4 from my online version, look for:

In the influential book What Is Life, written in 1945, Erwin Schrödinger wrote [80, p. 81]: From all we have learnt about the structure of living matter, we must be prepared to find it
working in a manner that cannot be reduced to the ordinary laws of physics. And that not on the ground that there is any ‘new force’ or what not, directing the behaviour of the single atoms within a living organism, but because the construction is different from anything we have yet tested in a laboratory.

See for comparison:

…the awkward expression ‘negative entropy’ can be he replaced by a better one: entropy, taken with the negative sign, is itself a measure of order. Thus the device by which an organism maintains itself stationary at a fairly high level of the orderliness ( = fairly low level of entropy) really consists continually sucking orderliness from its environment. This conclusion is less paradoxical than it appears at first sight. Rather could it be blamed for triviality. Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)

Look inside for information on the role of virus-driven energy theft. Search for viruses  on page 172 in my online version

Folding of Single-Stranded DNA Sequences Following Reverse Mutations. The selection of native nucleic acid folding (an irreducible higher level variable) is an epigenetic effect,with broad implications for the evolution of plants and their viruses. The folding structure (a higher level variable) corresponds to an equivalence class of lower level sequences, and is the biologically relevant variable determining the selection that occurs. How do we demonstrate this top-down causation? This has been shown in detail experimentally by Shepherd et al. [171].
Note: “…a three-nucleotide mutation adversely affected Rep nucleic acid folding…” and a “…single-nucleotide reversion [C(601)A] restored wild-type-like folding.”

My comment: This exemplifies the difference between virus-driven energy theft, which caused the mutation, and a nutrient energy-dependent change in a base pair, which was required to restore the energy-dependent biophysically constrained protein folding.
Look inside for information on the role of pheromones, on page 424 in my online version.

Hartwell et al. express the last point in the following way [104]:

Much of twentieth-century biology has been an attempt to reduce biological phenomena to the behaviour of molecules […] Despite the enormous success of this approach, a discrete biological function can only rarely be attributed to an individual molecule, in the sense that the main purpose of haemoglobin is to transport gas molecules in the bloodstream. In contrast, most biological functions arise from interactions among many components. For example, in the signal transduction system in yeast that converts the detection of a pheromone into the act of mating, there is no single protein responsible for amplifying the input signal.

My comment: Sensing and signalling of differences in cell types is energy-dependent. No one who knows that would expect to find a single protein that was involved in two different biophysically constrained functions, which must link metabolic networks to genetic networks in yeasts and humans via the innate immune system, the physiology of reproduction, RNA methylation, and learning and memory which must be linked to supercoiled DNA and all biodiversity.
But wait, Ellis cites Schrödinger, and ignores what Roger Penrose claimed in the forward of the reprint.

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?

It’s beginning to seem that George Ellis is going to tell only half of the story that he thinks explains how physics and the mind are connected, automagically. What about the energy source, George?

He is saved from ridicule only by the recognition that he may need to keep his faith in evolution despite the lack of experimental evidence of biologically-based cause and effect that could link neo-Darwinian theories to Darwin’s “conditions of life”. Clearly, he understands the need to establish the context in which his claims can be placed.

See page 141 Setting Values for Contextual Variables
Contextual variables set by the environment must lie in a suitable range. For example, the following are crucial to life as we know it:
• The environmental temperature must lie in a very narrow band.
• Oxygen and water must be available.
• A suitable energy source must be available (sunlight for a plant, food for an animal).
Without these contextual conditions being right,much life on Earth (animals, plants, and insects) would be in trouble. Other forms of life might have different sources of energy (e.g., thermal vents), but without some energy source, they will not survive.

My comment: Without a link from the contextual variables to the energy-dependent physiology of species-specific reproduction, the innate immune system could not be linked to all biodiversity. George Ellis knows that.

See also: Understanding and accounting for relational context is critical for social neuroscience
In the comments section, I wrote:
“New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.
Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”
— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012; 2: 17338 – DOI: 10.3402/snp.v2i0.17338
George Ellis replied: This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here:
George Ellis also responded: Great links, thanks. I’m intrigued by your work on pheromones. It is just possible it might relate to the issue of primordial emotional systems, see
See also:

I added: It’s interesting to look at how our works fit, which they must do if our findings correctly represent biophysically constrained ecological adaptations manifested in morphological and behavioral phenotypes. Others are quickly eliminating any perceived incongruities. For example, see: Maternal nutrition at conception modulates DNA methylation of human metastable epialleles This takes physics and chemistry to the one-carbon metabolism level of DNA methylation, which links ecological variation to ecological adaptations via micronutrients and macronutrients.

Since you are familiar with Panksepp’s works, I will note that my group won the seminal award in 2001 that his group won in 2002 . See Human pheromones: integrating neuroendocrinology and ethology and Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind Evolutionary theorists have since ignored or denied the role of nutrient-dependent species-specific pheromone production, which controls the physiology of reproduction, and continued to tout their ideas about mutations, natural selection and evolution.
Here we are more than a decade later and others are just now learning that the molecular mechanisms of signaling and sensing are conserved across species from yeasts to humans, which means the conserved molecular mechanisms must be the basis for emotional systems. At least one Nobel Laureate already has attested to that fact. See Feedback loops link odor and pheromone signaling with reproduction” “Indications that GnRH peptide plays an important role in the control of sexual behaviors suggest that pheromone effects on these behaviors might also involve GnRH neurons.” (p 683).
Start with yeasts: Signaling Crosstalk: Integrating Nutrient Availability and Sex;6/291/pe28 The nutrient-dependent production of the alpha mating pheromone exemplifies cell type differentiation at the advent of sexual reproduction, and when concentrated it elicits a luteinizing hormone (LH) response from the cultured pituitary cells of a mammal, the rat.
The mammalian GnRH-directed LH response has been the focus of my works for more than 2 decades since someone told me my mammalian model had to start with gene activation in hormone-secreting nerve cells of the brain. However, in 2010 , Richard Doty published a book an claimed that mammalian pheromones don’t exist. Simply put, they can’t — if you’re a social scientist. See: A Fear of Pheromones

When more experimental evidence became available, I added Timothy W. Bredy’s group has done it again. See: Long noncoding RNA-directed epigenetic regulation of gene expression is associated with anxiety-like behavior in mice.

Conclusion: Experience-dependent expression of lncRNAs plays an important role in the epigenetic regulation of adaptive behavior, and the perturbation of Gomafu may be related to anxiety and the development of neuropsychiatric disorders.

The most obvious correlation with what is now being discussed in the context of top-down causation and 4-D genome make-up that changes during life history transistions is: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults.
It shows the difference that a single amino acid substitution can make during experience-dependent RNA-mediated life history transitions that link metabolic networks to genetic networks.


George Ellis left our brief discussion, perhaps to work on the misrepresentations of biologically-based cause and effect he just included in his book. In the book, he links information on the energy-dependent pheromone-controlled physiology of reproduction to the energy-dependent pheromone-controlled physiology of reproduction in primates via Dobzhansky’s claims from Nothing in Biology Makes Any Sense Except in the Light of Evolution.


…the so-called 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 (p. 127).

My comment: Others have since shown that Feedback loops link odor and pheromone signaling with reproduction and that the energy-dependent changes linked from food odors to the pheromone-controlled physiology of reproduction are also linked to the Structural diversity of supercoiled DNA. 

Many serious scientists have joined the ranks of others who are Combating Evolution to Fight Disease by linking everything known about physics and chemistry to the molecular mechanisms of energy-dependent brain development from the origin of the nervous system in nematodes to the glorious representations that have been placed into the context of the energy-dependent de novo creation of nucleic acids, cell type differentiation, and biodiversity in the context of our 1996 Hormones and Behavior review, From Fertilization to Adult Sexual Behavior, my book chapter in The Handbook of the Evolution of Human Sexuality, and this 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

George Ellis has set the stage for others to accept, deny, or ignore everything Schrödinger probably long-ago expected to be linked from the anti-entropic energy of sunlight to all biodiversity.

See for instance: Epigenetics and Genetics of Viral Latency

…viral latency is responsible for life-long pathogenesis and mortality risk…

See also: Viral Nucleic Acids
Abstract excerpt:

…viral nucleic acids can be DNA or RNA, double-stranded or single-stranded, monopartite or multipartite, linear or circular, as short as 2 kb or up to 2500 kb long. The goal of a virus is to replicate itself. To do so, viruses have evolved various strategies to replicate their genomes…

See also: Applications of nucleic acid testing in diagnosis and therapy

1) Nucleic acid testing or nucleic acid amplification testing, often abbreviated as NAT or NAAT… has been associated with blood screening for some time. It was first introduced by the German Red Cross in 1997 for blood screening to reduce the risk of transfusion-transmitted viral infections due to the failure of serologic screening tests to detect recently infected donors in the pre-seroconversion “window” phase of infection.1

2) NAT is extensively used to detect and identify organisms for proper diagnosis, prognosis, and treatment of diseases.

3) Nucleic acid testing helps to identify genetic variations and predicts predisposition to cancer, alters diagnostic categories, enhances treatment strategies, enables early detection and prevention, and improves outcomes for cancer patients. Nucleic acid testing has led to the emergence of precision and personalized medicine—that is, the tailoring of treatment based on the individual’s genetic make-up.

The emergence of nucleic acid testing led to the emergence of precision and personalized medicine. Persoalized medicine has since led to the emergence of attempts that will link Cracking the Olfactory Code  from the National Microbiome Initiative to a series of  successful attempts that led others to report on Cracking the epitranscriptome.


…advances in recent years have dramatically expanded our toolkit for studying m6A and have begun to expose different levels at which RNA methylations are associated with phenotypic and molecular consequences.

George Ellis attempts to put everything known to physicists, chemists, and molecular biologists about the links from angstroms to ecosystems back into the context of the evolution of the human mind. But he waited to do that until after others cracked the epitranscriptome. That cracks me up. His sense of humor is as dry as Dobzhansky’s and hit wits are still sharp.

I’m almost certain the George Ellis is joking because he mentions Feynman’s works several times, but fails to put them into the context of Schrodinger’s anti-entropic force of sunlight; Dobzhansky’s “light of evolution;” or Roger Penrose’s question. “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?

For comparison, see:

Periodic Scarred States in Open Quantum Dots as Evidence of Quantum Darwinism

A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution.

If you’re not sure whether or not George Ellis is joking about the evidence of quantum Darwinism or the theory about docosahexanoic acid in energy-dependent cell type signaling that links the underlying physics from chemistry to the molecular epigenetics of brain development and the human mind, ask him a few questions. Does he know how my works on RNA-mediated amino acid substitutions linked the works of Luca Turin, Anna Di Cosmo, Eugene Daev, Bruce McEwen, the late Robert L. Moss, and Timothy W. Bredy to everything currently known about biophysically constrained energy-dependent RNA methylation and cell type differentiation in all living genera?

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