Alternative splicings and amino acid substitutions (redux)

By: James V. Kohl | Published on: December 15, 2013

I apologize for the repetition. I’m trying to reduce the content here to something that can be readily “digested” by theorists, since I have been unable to make any intellectual dent in their inexplicable belief in evolutionary theory. Theorists continue to posit that mutations somehow cause adaptations without saying how that might be possible. However, it is extremely difficult for theorists to confront their belief in the impossible in the context of biological facts. Instead, they deny that the biological facts have been established in the context of experimental evidence that refutes theory. Therefore, I am trying to summarize the latest empirical facts (again).
Four concurrently published articles in the December 13, 2013 issue of Science Magazine collectively show that ecological variation; transcription; and nutrient-dependent pheromone-controlled gene expression enable alternative splicings and amino acid substitutions that differentiate cell types, individuals, observed morphology, and species-specific behaviors. Collectively, the following experimental evidence-based reports refute current beliefs about evolutionary theory. My comments to Science Magazine are linked here with regard to article 1) below and on article 2) below. Comments on the physorg news article about the Exonic Transcription study, just became interesting. Unfortunately, anonymous fools typically eliminate serious discussion of physorg representations, which is why I encourage participation here or on the Science Magazine site.
1) Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution. “Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.”
2) The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution. Amino acid substitutions delineate the lineage of aquatic species related to Mnemiopsis leidyi.
3) Cryptic Variation in Morphological Evolution: HSP90 as a Capacitor for Loss of Eyes in Cavefish Epigenetic effects of nutrients on amino acid substitutions are observed in eye regression in cavefish.
4) Fear Learning Enhances Neural Responses to Threat-Predictive Sensory Stimuli Primary olfactory input to the brain changes the neural representation of odor-associated learned fear.
Mutation-caused changes in gene expression cannot result in natural selection that allows ecological variation to result in adaptation, which is required for species diversification. That explains why no experimental evidence shows that mutations are fixed in the DNA of the organized genome in any species from microbes to man, and why there is no experimental evidence that indicates how mutations could result in adaptations via natural selection. Besides, if mutations were fixed so that they could somehow result in the creation of eyes, we would not observe eye regression in cavefish. Similarly, in the Mnemiopsis leidyi lineage, there is evidence that tissues and neural cell types do not linearly appear, and that they also come and go. Evidence that complex structures like eyes, tissues, and neural cell types come and go in one lineage requires evidence that this is not a general rule in the context of ecological, social, neurogenic, and socio-cognitive niche construction across species.
Until experimental evidence supports the idea of mutation-driven evolution, the idea of nutrient-dependent pheromone-controlled adaptations that occur due to ecological variation stands as the only accurate representation of experimentally established cause and effect. For example, conserved molecular mechanisms link the epigenetic landscape to the physical landscape of DNA via primary responses to odors in vertebrates and invertebrates. These responses are tractable to responses to olfactory/pheromonal input in species from microbes to man. The responses include what was known about the molecular epigenetics of sexual differentiation in microbes due to alternative splicings and the pheromone-controlled physiology of reproduction in yeasts. They now include what is known about amino acid substitutions in the olfactory receptor genes of humans that are linked to individual differences and species differences in responses to odors. See for example: The missense of smell: functional variability in the human odorant receptor repertoire
See also:
1) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
2) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors
3) Human pheromones: integrating neuroendocrinology and ethology
4) From Fertilization to Adult Sexual Behavior