Abstract excerpt: A key question in evolutionary developmental biology is how DNA sequence changes have directed the evolution of morphological diversity. The widely accepted view was that morphological changes resulted from differences in number and/or type of transcription factors, or even from small changes in the amino acid sequence of similar proteins.
My comment: This is the first time I have seen anyone claim that the “…small changes in the amino acid sequence of similar proteins…” is a widely accepted view of how the number and/or type of transcription factors lead to morphological changes. See for comparison: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.
In my model, RNA-mediated amino acid substitutions link atoms to ecosystems. Their claim is linked to an “…increasing amount of data, especially from the plant field…” They claim that data “…implies that changes in cis-regulatory sequences in fact played a major role in evolution.” I claim that the same data links the epigenetic landscape to the physical landscape of DNA in the organized genomes of all genera via conserved molecular mechanisms of cell type differentiation. In my model, the honeybee model organism links species from microbes to man via the conserved molecular mechanisms that link light-induced amino acid substitutions to cell type differentiation in plants and other animals. I intend to learn more about their claim. Perhaps it is based on confusion caused by definitions that appear to make mutations, which perturb protein folding, and amino acid substitutions, which stabilize protein folding, the same thing.
Abstract excerpt: Most studies of GRN evolution focus on changes to cis-regulatory DNA, and it was historically theorized that changes to the transcription factors that bind to these cis-regulatory modules (CRMs) contribute to this process only rarely. A growing body of evidence suggests that changes to the coding regions of transcription factors play a much larger role in the evolution of developmental gene regulatory networks than originally imagined.
My comment: Their claim is that documentation of mutation-driven evolution was based on the imaginations of evolutionary theorists.
Abstract except: Gene regulatory networks (GRNs) describe the progression of transcriptional states that take a single-celled zygote to a multicellular organism. It is well documented that GRNs can evolve extensively through mutations to cis-regulatory modules (CRMs).
My comment: Their claim is that mutation-driven evolution of gene regulatory networks has been well documented.
Three questions arise:
1) What data suggests that mutations played a major role in the evolution of plants?
2) What data links mutations in plants to mutations in cis-regulatory modules and gene regulatory networks during the development of a single-celled zygote to a multicellular organism?
3) Does experimental evidence that links light-induced amino acid substitutions in plants and animals to cis-regulatory modules and gene regulatory networks during the development of gene regulatory networks link the nutrient-dependent pheromone-controlled development of morphological and behavioral phenotypes in the honeybee model organism, link entropic plasticity to examples of anti-entropic epigenesis and epistasis via RNA-mediated amino acids substitutions in the DNA or organized genome of species from microbes to man?
The only thing that can be said with flowers about the evo-devo debate is that the honeybee model organism ends the debate. Morphological and behavioral development in animals is nutrient-dependent and pheromone-controlled. The morphological and behavioral phenotypes of birds are linked to the biodiversity of plants via the nutrient-dependent pheromone-controlled behavior of bees.
Excerpt: Selection began to operate not simply on genes for ascorbic acid synthesis but also across a distributed network of sensory biases, behavioural inclinations and digestive-metabolic mechanisms that increased the probability of obtaining ascorbic acid from the environment. In this way, within certain degrees of freedom, if there is degeneracy between environmental and genomic factors, then selection can result in an offloading of function from the genome to the environment, or a potential divergence of the environmental and genomic elements leading to the random exploration of adjacent function space.
My comment: Exploration that increases the probability of finding specific nutrients is based on the ability of food odors to cause the de novo creation of olfactory receptor genes via amino acid substitutions in the DNA of organized genomes of iinsects and other organisms. The physiology of nutrient-dependent reproduction is controlled by the metabolism of nutrients to species-specific pheromones that enable fixation of the amino acid substitutions that leads to nutrient-dependent biodiversity in all genera.
The link from entropic plasticity to anti-entropic epigenesis and epistasis can also be viewed from a creationist perspective in: Honey Bee Orphan Genes Sting Evolution.
“…orphan genes unique to social honey bees (Apis mellifera) play an important role in all the different glands and organs mentioned above where gene expression was specifically measured and quantified in each structure. Even the brain and midgut were found to contain significant levels of orphan-gene expression—which makes sense in light of the honey bees’ unique social behavior and diet. And not only are orphan genes uniquely expressed in specific organs, they were also found to play a major role in gene expression differences between forager and nurse workers. While bees initially grow and develop using the same genome, epigenetic changes (chemical tags in the chromosomes) allow them to diversify into two different specialized social roles in the colony.5″
My comment: I learned that this article had been published when I read Honey Bee Orphan Genes Sting Evolution. A subscription is required, which means you may need to take my word for this fact: There is no mention of “mutation” or “amino acids” in the text of the article. As is typical of current published works, their claims about natural selection and evolution are made in the absence of any experimental evidence that might otherwise link the claims to what is known about physics, chemistry, and the nutrient-dependent pheromone-controlled molecular biology of cell type differentiation. Perhaps that’s why their claims were cited in Honey Bee Orphan Genes Sting Evolution. There is no need to bring up the absence of experimental evidence of mutation-driven evolution. Creationists are typically aware of the lack of experimental evidence that might otherwise support theories about mutation-driven evolution.
Summary: The data that links light-induced amino acid substitutions in plants and animals to nutrient-dependent RNA-mediated amino acid substitutions and pheromone-controlled behavior in animals integrates what is currently known about physics, chemistry, and the conserved molecular mechanisms that enable biophysically constrained biodiversity. Alternatively, a recent textbook conclusion attributed biodiversity to Mutation-Driven Evolution. “In other words, genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements.” (p. 199)
Whether or not you are a creationist, it should be obvious that ideas about constraint-breaking mutations must be considered outside the context of quantum physics, the chemistry of protein folding, and the conserved molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA in the organized genome of species from microbes to man. Mutations are directly linked from perturbed protein folding to physiopathology, not to increasing organismal complexity. Amino acid substitutions are directly linked to increasing organismal complexity, not to physiopathology. Dobzhansky (1973) stated clearly 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.” See Combating Evolution to Fight Disease for an extension of Dobzhansky’s views to what is currently known about biologically-based cause and effect.
Biologists have now approached what theoretical physicists can only approach with mathematics. Quantum physics, for example, cannot address the reality of biologically 3D interactions. See: Inching toward the 3D genome
Excerpt: “…the nucleome structure changes as cells age, differentiate, and divide, and researchers want to understand how and why.”
My comment: The extension of what is currently known about the organization of the 3D genome to nucleome structure changes during life history transitions, is also addressed by placing what is now referred to in the context of 4 dimensions (4D). Life history transitions have been linked from the biology of life to physics and chemistry and communication. See for instance: Life is physics and chemistry and communication.
If the sun’s biological energy is the link from entropic plasticity to anti-entropic epigenesis and epistasis, questions about top-down causation can be answered: Top-down causation: an integrating theme within and across the sciences?
Moreover, the questions can be answered in the context of what already is known about biologically-based cause and effect. See: Understanding and accounting for relational context is critical for social neuroscience.
Again, the honeybee model organism is a model — this time of the relational context that epigenetically links nutrient-dependent pheromone-controlled life history transitions from microbes to humans. See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Excerpt: Nutrient-dependent pheromone-controlled reproduction underlies what is common (Locasale, 2012) to all models of natural selection, sexual selection, and species diversity (Frady, Palmer, & Kristan, 2012). Animal models are often used to model human physical and mental disorders. 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).
My comment: The honeybee model organism links light-induced amino acid substitutions in plants and animals to odor-induced amino acid substitutions to the receptor-mediated entry of nutrients into cells that metabolize the nutrients to species-specific pheromones that control the physiology of reproduction. The pheromone-controlled physiology of reproduction links fixation of the amino acid substitutions to 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.
Conclusion: 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).
See for comparison to links from the sun’s biological energy to entropic plasticity, to anti-entropic epigenesis, and to epistasis. Simply put, there is no historical support for evolutionary theory in the context of quantum physics. That suggests evolutionary theory (neo-Darwinism) is based on pseudoscience. Darwin’s theory was based on ‘conditions of life.’
Life does not exist on this planet without the biological energy from the sun.