Ecological adaptation: The third way

July 3, 2014 | James Kohl

The Third Way

The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon supernatural intervention by a divine Creator. The other way is Neo-Darwinism, which has elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems. Both views are inconsistent with significant bodies of empirical evidence and have evolved into hard-line ideologies. There is a need for a more open “third way” of discussing evolutionary change based on empirical observations.

Contact:

Excerpt: “Please do get in touch if you would like to recommend a scientist or their work to add to the list. We would also like to hear if you have any relevant books or news items that you would like us to include on the website.”

My request for consideration:

A series of published works on cell type differentiation began with From Fertilization to Adult Sexual Behavior in 1996.

Excerpt: “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 (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.” (p. 337)

Sex differences in cell types that are responsible for sex differences in morphology and behavior arise in the context of ecological variation and the conserved molecular mechanisms that have since been detailed in my other published works on adaptive evolution.

Kohl, J.V. (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology, 3: 20553.

Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338.

I would like these works to be considered for inclusion at The Third Way of Evolution.com

Thank you for your consideration in this regard,

James V. Kohl
Medical laboratory scientist (ASCP)
Independent researcher
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Biological evolution: a direct contradiction

June 28, 2014 | James Kohl

Biological evolution: Some genetic considerations

It will probably not be long until at least one prominent evolutionary theorist acknowledges this fact, “The concept of biological evolution… stands in direct contradiction with our current knowledge regarding the behavior as well as the structural and functional characteristics of the human genome and human proteome.”

When that fact is acknowledged, all of evolutionary theory will be exposed for what it has been since the invention of neo-Darwinism, which placed mutations and natural selection before ‘conditions of life’ that are obviously nutrient-dependent and pheromone-controlled.

Others may then ask evolutionary theorists why they thought mutations were the source of biodiversity, which is obviously nutrient-dependent and what they thought controlled the physiology of reproduction in species from microbes to man. The metabolism of nutrients to species-specific pheromones controls the physiology of reproduction. Ask a theorist how they could not know that fact.

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Nutrient-dependent chromatin organization?

June 24, 2014 | James Kohl

Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation open access

Conclusion: “…delineating the epigenetic regulation of neuronal development is crucial to our understanding of intellectual-disability disorders caused by mutations in epigenetic modifying enzymes. As a whole, our findings highlight the complexity and functional diversity of Snf2h-containing CRCs during brain development, and their roles in controlling chromatin organization as cells modulate their chromatin environment from a ‘largely open’ progenitor state to the ‘highly restricted’ state of a fully differentiated neuron during cerebellar morphogenesis and neural maturation (Fig. 9i)60.

Reported as:

Team finds gene critical for development of brain motor center

Excerpt: “ATP-dependent chromatin remodelling proteins that assemble, reposition and space nucleosomes, and are robustly expressed in the brain.”

My comment: ATP-dependent chromatin remodelling  seems likely to be nutrient-dependent.

If so, it might link ecological variation in nutrient availability to ecological, social, neurogenic, and socio-cognitive niche construction via the conserved molecular mechanisms of nutrient-dependent pheromone-controlled amino acid substitutions that differentiate the cell types of species from microbes to man.

Cell type differentiation appears to enable the ecological adaptations in morphological and behavioral phenotypes that are perturbed when nutrient stress or social stress alter protein folding, which leads to mutations.

It does not seem likely that mutations and natural selection somehow lead to the manifestation of biodiversity that theorists claim has evolved. If there is no model for that, this experimental evidence appears to refute neo-Darwinian theory (again).

As always, I would be grateful if anyone could tell me about any experimental evidence of biologically-based cause and effect that appears to support the invention of neo-Darwinian theory and definitions that were used to make it seem that mutations and natural selection are responsible for the evolution of biodiversity, which this report — and all others that I have read — suggest results from ecological variations that lead to ecological adaptations in species from microbes to man via nutrient-dependent chromatin organization, which appears to be pheromone-controlled.

See for instance our 1996 review for information on sex difference in cell type differentiation that are probably nutrient-dependent and pheromone-controlled in species from yeasts to mammals.

Excerpt: Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). 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 (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

My comment: The link from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from yeasts to Drosophila, mice, and humans was made clear by our co-author, Teresa Binstock, in the context of molecular epigenetics and epigenetic imprinting more than 17 years ago. Nothing but confirmations of cause and effect have been published since then and yet neo-Darwinian theory has continued to be touted in the absence of any experimental evidence to support ridiculous claims.

MBD2 and MeCP2 regulate distinct transitions in the stage-specific differentiation of olfactory receptor neurons is but one of many articles published during the past 1.5 decades that should have called attention to the fact that our model of epigenetic cause and effect had replaced evolutionary theory with evidence of how ecological adaptations occur. It will be interesting to see how much longer it takes for evolutionary theorists to admit that they never really knew anything about biologically-based cause and effect, but believed in a ridiculous theory rather than learn anything about molecular biology.

 

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Drunks and monkeys (2): Seeing the light

June 24, 2014 | James Kohl

Drunks and Monkeys

Understanding our primate ancestors’ relationship with alcohol can inform its use by modern humans.

By Robert Dudley | June 1, 2014

Excerpt:  “…the next time you enjoy a drink or two, think about primates enjoying the pleasure of ripe, squishy fruit in tropical rainforests. Realize that you are consuming the products of yeast metabolism.”

My comment: Drunks, monkeys, and evolutionary theorists are not capable of seeing the light of biologically-based cause and effect. Drunks and monkeys may not care. Evolutionary theorists seem to care enough to invent more theories. However,  nutrient-dependent pheromone-controlled protein biosynthesis and degradation in brewer’s yeast is linked to alcohol addiction and other addictions via conserved molecular mechanisms of cell type differentiation in species from microbes to man. The story that yeast tell us is one of how organisms respond to ecological variation with ecological adaptations.

Yeasts produce alcohol that kills bacteria. The molecular mechanisms of survival in yeasts also include cell type differentiation at the advent of sexual differentiation of cell types in a unicellular organism. Some evolutionary theorists seem to understand the importance of sexual behavior to species survival in species that sexually reproduce. However, I have never met an evolutionary theorist who could tell me how sex differences in morphological phenotypes, or in behavioral phenotypes “evolved.”  If yeasts could talk, they could probably carry on a more intelligent conversation about sexual reproduction compared to evolutionary theorists.

What’s known about yeasts already tells everyone that gene duplication is nutrient-dependent and pheromone-controlled, which means that sex differences in cell types arose from nutrient-dependent differences in alleles. For example,  “…yeast cells have developed multiple signaling pathways that respond to the availability of sugars, nitrogen, amino acids, and other nutrients.” Schmidt (2013) also noted that “The mechanism by which one signaling pathway regulates a second provides insight into how cells integrate multiple stimuli to produce a coordinated response.” That insight was included in his article “Signaling Crosstalk: Integrating Nutrient Availability and Sex.”

It should not be difficult, except for evolutionary theorists, to move forward from signaling crosstalk to an understanding of how Secreting and Sensing the Same Molecule Allows Cells to Achieve Versatile Social Behaviors.  Indeed, nearly all serious scientists realize that Feedback loops link odor and pheromone signaling with reproduction via changes in social behaviors and the nutrient-dependent pheromone-controlled physiology of reproduction. Social scientists, however, seem willing to continue telling us that mutations and natural selection somehow led to the evolution of biodiversity that is manifested in the morphological and behavioral phenotypes of all species. Seeing the light of  nutrient-dependent pheromone-controlled ecological adaptations may not be possible for them.

Instead, evolutionary psychologists and other social scientists are more likely to cite Dobzhansky (1973) and claim “Nothing in Biology Makes Any Sense Except in the Light of Evolution”. Unfortunately, citing that famous work may have kept them and others from learning about the conserved molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA in all organized genomes of all species. Without learning about molecular biology, social scientists are doomed. They may never realize that nothing about evolution makes sense except in the light of Creation. In fact, they probably don’t realize that Dobzhansky was a Creationist. As did other Creationists of his time, he thought that mutations might be the cause of natural selection and evolution. But today’s Creationists have either learned that ecological variation causes ecological adaptations, or simply refuse to believe the pseudoscientific nonsense of population geneticists, which is how serious scientists continue to make scientific progress.

 

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Symbiosis and ecological adaptation

June 22, 2014 | James Kohl

One Plus One Equals One

John Archibald
224 pages | 216x135mm
978-0-19-966059-9 | Hardback | 26 June 2014

Excerpt from the book description: “All living organisms use the same molecular processes to replicate their genetic material and the same basic code to ‘read’ their genes. The similarities can be seen in their DNA. Here, John Archibald shows how evolution has been ‘plugging-and-playing’ with the subcellular components of life from the very beginning and continues to do so today. For evidence, we need look no further than the inner workings of our own cells. Molecular biology has allowed us to gaze back more than three billion years, revealing the microbial mergers and acquisitions that underpin the development of complex life. One Plus One Equals One tells the story of how we have come to this realization and its implications.

Readership: Popular science readership interested in biology and molecular biology, as well as students of these courses.”

My comment: Symbiosis exemplifies how ecological variation results in ecological adaptations, not how organismal complexity evolved. The problem with this book appears to be common to all books written for a “popular science readership.” The theory of evolution is popular, and most of the science readership does not realize that the theory was invented by population geneticists in an attempt to support Darwin’s claims.

To do that, they started with what he observed and began to suggest what caused the manifestations of morphological and behavioral phenotypes while focusing only on the morphological phenotypes. They ignored the physiology of reproduction that links nutrient-dependent morphological phenotypes to the pheromone-controlled behavior of reproduction via conserved molecular mechanisms in species from microbes to man.

If John Archibald does anything more that tell the same story of natural selection and the evolution of biodiversity, he may teach others what they need to learn about ecological adaptations under the guise of telling them about the evolution of complex life. However, until someone who is academically responsible puts some distance between evolutionary theory by teaching others about the biological facts, which link the epigenetic landscape to the physical landscape of DNA in organized genomes, we can expect nothing more than more pseudoscientific nonsense.

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