February 4, 2015
Horgan: What do you make of the antipathy toward religion expressed by Richard Dawkins and other “New Atheists?”
Kauffman: … moral behavior requires no belief in God. Morality probably evolved in Paleolithic to some extent. But to dismiss those who do believe in God, in any sense, is arrogant and useless and divisive.
We need accelerating expansion of universe for free energy and “tuned constants” but those are necessary, not sufficient. The anti-entropic process may be, with others, sufficient. I am writing a new book about this.
My comment: The anti-entropic process is biophysically constrained. Biological energy from the sun fine-tunes the constants of all anti-entropic processes. Photosynthesis links the speed of light from contact with water to differences in spectral energy and receptor-mediated RNA-directed DNA methylation and the chemistry of RNA-mediated amino acid substitutions linked to protein folding.
For example, light-induced amino acid substitutions differentiate the cell types of plants, algae, and mollusks. Viral microRNAs cause changes in the microRNA/messenger RNA balance. The changes link thermodynamic cycles of protein biosynthesis and degradation to quantitative trait loci (QTLs). The QTLs link changes in the microRNA/messenger RNA balance to anti-entropic amino acid substitutions. This links RNA-mediated protein folding to fixation of the amino acid substitutions that differentiate the cell types of all cells in all individuals of species from microbes to man via differences in their species-specific nutrient-dependent pheromone-controlled physiology of reproduction.
The physiology of nutrient-dependent reproduction links ecological variation to ecological adaptation manifested in the morphological and behavioral phenotypes of all genera. Nutient-dependent QTLs benefit the stability of DNA via alternative splicings and amino acid substitutions. If the QTLs provide increased stability over time, the fixation of amino acid substitutions that leads to biodiversity occurs in the context of species-specific nutrient-dependent reproduction, which is controlled by pheromones in all animals. The direct link from QTLs to cell type differentiation via amino acid substitutions appears to have led researchers to make claim s about “…a yet-unidentified cellular mechanism that regulates gene expression.” Their claim helps to make difference between mutations and amino acid substitutions clear. Simply put, accumulated mutations do not differentiate cell types. Amino acid substitutions differentiate cell types.
For example see: A universal trend of amino acid gain and loss in protein evolution.
“We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.”
The trend that links nutrient-dependent amino acid substitutions in proteins to cell type differentiation in individuals of different species before there was a last universal common ancestor links the sun’s biological energy to light-induced RNA-mediated amino acid substitutions in plants and animals, like algae and sea slugs. See: FISH Labeling Reveals a Horizontally Transferred Algal (Vaucheria litorea) Nuclear Gene on a Sea Slug (Elysia chlorotica) Chromosome.
In 1996, it became clear that cell type differentiation in animals was RNA-mediated and controlled by pheromones. Our model was extended to insects and to the life history transitions of the honeybee, which made the role of nutrient uptake and pheromone-controlled fixation of all cell type differentiation perfectly clear. See also: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees. Facts about the RNA-mediated de novo creation of olfactory receptor genes now link them from nutrient uptake to fixation of amino acid substitutions that differentiate cell types in all individuals of all species. There is only one model for that. Nutrient-dependent/pheromone-controlled adaptive evolution: a model. That model links the sun’s biological energy to the anti-entropic process of cell type differentiation manifested in the increasing organismal complexity of species from microbes to man.
Science seekers can now ask theorists for experimental evidence to support Kauffman’s claims. Where did the anti-entropic process come from? One approach to finding its origins was suggested by Lewis Thomas (1980):
“I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries (p. 732).”
Others seem to not recognize which mysteries about the origin of the anti-entropic process have been solved. Food odors are linked via the natural selection of nutritious foods to the odor-induced de novo creation of olfactory receptor genes. The RNA-mediated creation of these receptors links nutrient uptake to cell type differentiation in all cells of all individuals of all animal species via the metabolism of nutrients to species-specific pheromones.
That claim can be placed into the context of neo-Darwinian theory. See for example: Odor representations in the olfactory bulb evolve after the first breath and persist as an odor afterimage.
Reported as: “The findings combine to implicate the brain, rather than the nose, as being responsible for the afterimages.” See also: Sense of Smell: The Nose and Brain Make Quite a Team, in Disconnection
My comment: Everything published by serious scientists during the past decade attests to the fact that Darwin’s nutrient-dependent ‘conditions of life’ must come first.
For example, Conclusion: “In summary, the neuroscientists were able to show that the representation of an odor changes after the first breath, and that an olfactory retentivity persists at the central level, a phenomenon comparable to what occurs in other sensory systems, such as vision and hearing. These movements undoubtedly enable the identification of new odors in complex environments or participate in the process of odor memorization.”
Also, “The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012). — cited in Kohl, 2013.
All experimental evidence of biologically-based cause and effect links biological energy from the sun to nutrient-dependent pheromone-controlled anti-entropic processes and cell type differentiation during life history transitions in honeybees and to cell type differentiation during life history transitions in species from microbes to humans.
Excerpt: “So ancient a love affair exists between humans and saffron, that it can no longer reproduce without our help. Could its antidepressant and health-promoting properties be an example of saffron ‘returning the favor’?”
My comment: It is impossible for me to ignore the link from the anti-entropic process in honeybees to humans. Minimally, others should begin to think about it, since the most obvious link has been predicted across 35 years of published works. I reiterate, in 1980 Lewis Thomas wrote:
“I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries (p. 732).” — cited in Kohl and Francoeur (1995 / 2002).
“The act of smelling is remarkably like the act of thinking itself (p. 732).”
Stuart Kauffman has consistently make tractable scientific progress that led to his claims about the anti-entropic process. His claims can be compared to those made by Theodosius Dobzhansky. Dobzhansky tried to get others to consider the fact that “…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.” — Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973).
At the time of Dobzahsky’s death in 1975, no one seems to have noticed that amino acid substitutions are anti-entropic. If Dobzhansky was not still dead, I think he might clarify the reasons he claimed to be both a creationist and an evolutionist. Recently, however, others have begun to look at Dobzhansky’s claims in the light of what is known about the conserved molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA in species from microbes to man. See for instance: Combating Evolution to Fight Disease
Conclusion: “…but perhaps, too, “nothing in evolution makes sense except in the light of biology.” Although the latter might be an exaggeration, an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve.”
See also: ‘Oming in on RNA–protein interactions
Excerpt: “…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6].”
My comment: As it turns out, nothing in molecular biology makes sense except in the light of what is known about how the sun’s biological energy is linked to the anti-entropic process that links cell type differentiation across all species via their nutrient-dependent pheromone-controlled physiology of reproduction. The sun’s biological energy is linked to cell type differentiation by “…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities.”
In our 1996 Hormones and Behavior review, we (TB) wrote: “Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…”
Our focus was on the link from alternative splicing techniques of pre-mRNA to sex differences in cell types, but most serious scientists could be expected to understand that the link from sex differences in cell types would extend to all cell type differentiation in species that sexually reproduce. That understanding should lead other serious scientists to examine the conserved molecular mechanisms of cell type differentiation that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of all species, or stop making claims that mutations can somehow be linked the evolution of biodiversity.
We can take the systems complexity of physics, chemistry, and molecular biology down a few levels by starting with top-down causation. I start by removing de Vries definition of “mutation.” The definition of mutation made the energy jumps appear to be what Schoedinger referred to in the context of quantum biology. Luca Turin’s works continue to link top-down causation to quantum biology via olfaction. See my review of this book about Luca Turin:The Emperor of Scent: A Story of Perfume, Obsession and the Last Mystery of the Senses by Chandler Burr New York: Random House (2003). I had hoped more progress would have been made during the past decade. His 1996 published work linked our review to hormone-organized and hormone-activated behaviors via my model of nutrient-dependent pheromone-controlled pulses of gonadotropin releasing hormone.