Masters of Physics in Nature

Excerpt:

This interaction raises the possibility that particle velocity information and electrical information, and interactions between them, can be encoded by a single hair.” It also raises the possibility that “electroreception is widespread in arthropods, fulfilling functions beyond the detection of floral electric fields.

My comment: Energy-dependent microRNA flanking sequences linked all invertebrates to all vertebrates in the context of what was published as:  The phylogenetic utility and functional constraint of microRNA flanking sequences and reported in advance (with my comment) as All in the (bigger) family and later as ‘Junk DNA’ Used To Sort Species

The Creation Evolution editor removed my comment about the “Epigenetics and Genetics of Viral Latency.” I tried to focus attention on this. On May 11, 2016, Paul M. Lieberman claimed that “…viral latency is responsible for life-long pathogenesis and mortality risk…” But the Creation Evolution editor didn’t ask me what I thought the widespread conservation of electroreception in arthropods had to do with physics in nature. The editor’s claim was that:

jvkohl, your comment had nothing to do with the article….

That ended my attempt to discuss what Jeffrey Tomkins reported about the epigenetics and genetics of viral latency in: “Viral Genome Junk Is Bunk.” Tomkins included an important quote: “As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.” 6 Other molecular biologists understand the importance of providing quotes and citations. Journalists and editors may not.

See for example: “Quantum mechanical DNA. The weird world of quantum mechanics operates in DNA, the molecule of life.” That statement was not linked to this report Sound-like bubbles whizzing around in DNA are essential to life.

I added this comment on the Creation Evolution site:

Thanks. The article failed to provide a link to this information.

Sound-like bubbles whizzing around in DNA are essential to life http://phys.org/news/2016-06-sound-like-whizzing-dna-essential-life.html

Excerpt: “It is believed that DNA has regions where a specific sequence of bases modifies the stiffness of the double helix favouring the formation of bubbles. This causes a break of the weak bonds between the strands showing the transcription and replication enzymes where to start their task.”

That’s what I tried to address in my comment. Why introduce the topic of Quantum mechanical DNA if you would rather it not be discussed in the context of “Masters of Physics in Nature?”

My comment about a new book by George Ellis was simply removed, and I suspect my second comment will also be removed. The problem for anyone touting Intelligent Design for comparison to Creation is that the book How Can Physics Underlie the Mind?: Top-Down Causation in the Human Context fails to link virus-driven energy theft to all pathology. Instead, it places all biophysically constrained protein folding chemistry and constraint-breaking mutations into the context of evolution.

See also:

…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).” Mutation-Driven Evolution (published June 14, 2013)

See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (published June 14, 2013)

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

The conclusions from 3 years ago vary significantly. One eliminates consideration of teleological elements (e.g., biologically-based cause and effect), and the model demands consideration of everything known to serious scientists about energy-dependent RNA-mediated amino acid substitutions and cell type differentiation in the context of the physiology of reproduction, which links olfaction from the innate immune system to supercoiled DNA. Supercoiled DNA links everything known to serious scientists about energy-dependent cell type differentiation and virus-driven energy theft, which links mutations to all pathology. In that model of how ecological variation must be linked to ecological adaptation by the physiology of energy-dependent reproduction, the facts speak for themselves.  They link the incredibly complexity of metabolic networks to genetic networks via the innate immune system, and link all pathology to the effect of virus-driven energy theft.

Creationists who don’t think it is important to learn what other creationists are claiming in the context of facts that link nutritional epigenetics to healthy longevity — as in Biblical Genesis are more likely to be among those who will discuss Intelligent Design, but deny the existence of a Creator. They are also more likely to miss the misrepresentations that other creationists, like George Ellis, use to support their claims of theistic evolution.

Advance praise for the book I co-authored in 1995 included this: “This is science at its best, with adventure, ideas, and lots of facts”. — Helen Fisher (biological anthropologist)

I was happy when George Ellis responded to my comment about food odors and pheromones with this claim from 2012:

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: http://rsfs.royalsocietypublishing.org/content/2/1.toc

and then this:

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 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540967/ – See more at: http://community.frontiersin.org/people/GeorgeEllis_1/51729#sthash.RcztWMUN.dpuf

I thought that by now, 2 decades after book publication and nearly 2 decades after publication of our 1996 review of molecular epigenetics, that George Ellis and I might share the same perspective.

I was wrong, as anyone can see if only they read the Advance Praise for his book

Excerpt: 1)

A stark lacuna lies at the heart of science: half the causal narrative has been omitted! — Paul Davies, Beyond Center, Arizona State University

My comment: The half that’s missing is virus-driven energy theft, which is linked to all pathology.

Excerpt 2)

The sweep of the book is enormous as it details the evidence and the impact in each area of science. It forms a major landmark, and it does so at an exciting time, when the purely gene-centric views of biology are being seriously challenged. — Denis Noble, CBE FRS, University of Oxford

My comment: Gene-centric views of biology have not been considered by serious scientists who began to learn about molecular epigenetics in the mid-1990’s.

Excerpt 3)

…this defense of “strong emergence” sets a high, perhaps unreachable bar for scientific reductionists. –Philip Clayton, author of Mind and Emergence

My comment: Claims about “strong emergence” are meaningless when placed into the context of evolution. Angstroms and ecosystems have been linked via the de novo creation of genes — the “holy grail” of biology.  The genes are olfactory receptor genes that link food odors and pheromones to energy-dependent RNA-mediated cell type differentiation in species from microbes to humans.

Excerpt 4)

…other modes of explanation, including those based on emergence and top-down causation, are vital for a fully orbed account of the natural world. — Ard Louis, Rudolph Peierls Centre for Theoretical Physics University of Oxford

My comment: Claims about “emergence and top-down causation” do not account for energy theft.  Supercoiled DNA prevents it. Viruses cause it. Nothing evolves! Every species must adapt to the threat viruses pose to nutrient energy-dependent survival via the physiology of reproduction.

Excerpt 5)

George Ellis argues with admirable charity of thought that much of the world we live in is governed not by the blind dance of atoms, but by high-level causes and purposes. — Giulio Tononi, University of Wisconsin-Madison

My comment: Is he claiming that George Ellis is arguing for  non-random creation and a purpose-driven life?

Excerpt 6)

A carefully crafted argument, steeped in the scholarly literature, yet accessible to the ordinary reader. — Alister E. McGrath, University of Oxford

My comment: What carefully crafted argument is he claiming that George Ellis developed in the context of the scholarly literature? What scholarly literature still touts emergence and evolution in attempts to craft arguments that all serious scientists dismiss because they fail to include experimental evidence of facts that link energy-dependent changes from angstroms to ecosystems?

Summary. If those who offered their advance praise had been more specific about what they were praising, their comments would not appear to me to be coming from a “good old boy’s club” of those who agree with each other because that is what they agreed to do — sometime before the turn of this century.  I suspect that they agreed to ignore what is known about energy-dependent biophysically constrained cell type differentiation and virus-driven energy theft, which links mutations to all pathology.

What’s left is emergence and natural selection with or without mutations, which means the evolutionary theorists and big bang cosmologists can have it both ways. Both ways are theoretical.  I don’t think that serious scientists will accept any more claims from either group of theorists.

Energy-dependent RNA methylation has emerged from the ranks of serious scientists as the obvious link from ecological variation to nutrient-dependent biophysically constrained ecological adaptations. Virus-driven energy theft has emerged as the obvious link from mutations to all pathology. If the facts about energy-dependent cell type differentiation cannot be placed into a model that links physics and chemistry to what is already known about molecular epigenetics, theorists must agree to stay at least 20 years behind the experimental evidence of biologically-based cause and effect. Will you join their club, or join the serious scientists who are Combating Evolution to Fight Disease?

My comment:

“An alternative theory proposes environmentally induced change in an organism’s behavior as the starting point (1), and “phenotypic plasticity” that is inherited across generations through an unspecified process of “genetic assimilation” (2).” http://www.sciencemag.org/content/332/6034/1161.short

This is now more than merely an alternative theory of genetic assimilation. It links transgenerational epigenetic effects from nutrient uptake and RNA-mediated events to amino acid substitutions that differentiate the cell types of all cells in all individuals of all organisms. See, for example: Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans http://www.cell.com/cell/abstract/S0092-8674(14)00806-X

The nutrient stress-induced RNA-mediated events, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, also link morphological and behavioral diversity via conserved molecular mechanisms exemplified in the context of biologically plausible ecological speciation in nematodes.

See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes http://linkinghub.elsevier.com/retrieve/pii/S0092867412015000

A difference in their feeding behavior and in the anatomy of their mouth parts is linked from nutrient-dependent pheromone-controlled feedback loops to ecological, social, and neurogenic niche construction. The change in focus from mutations, natural selection, and the evolution of biodiversity via unknown evolutionary events to nutrient-dependent pheromone-controlled RNA-mediated events that differentiate cell types may be required for others to realize the difference between evolutionary theories and biologically-based facts about RNA-mediated events.

RNA-mediated events are biophysically constrained, which means they are a biologically plausible way to link the physics and chemistry of protein folding to increasing organismal complexity via molecular biology. RNA-mediated events can also be compared to any unknown evolutionary events that might arise in the context of an alternative theory about constraint-breaking mutations, or other theories that do not mention RNA-mediated events.

Summary: Theories are like stories that tell people about only half of what must be epigenetically linked from energy-dependent changes in angstroms to ecosystems.  For example, George Ellis now includes information on energy-dependent emergence and evolution.

But he seems unwilling to tell people anything about the virus-driven energy theft that others have linked to all pathology in all living genera. The pathology exemplifies the fact that some species have not adapted via their nutrient-energy dependent innate immune system. There are missing links between metabolic networks and genetic networks, which fail to support the physiology of reproduction and the functional structure of supercoiled DNA.

It is time for Ellis and his cronies to admit that they know nothing about how energy-dependent RNA methylation is linked to behavior and successful reproduction by RNA-mediated amino acid substitutions. The substitutions link hydrogen-atom transfer in DNA base pairs in solution to energy-dependent ecological adaptation via DNA repair in the context of quantized energy from the sun on contact with water.  From the time others learned about the de novo creation of nucleic acid precursors, which was detailed in Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism to the time that the information on the origins of RNA was linked to healthy longevity can now be compared to how quickly others have learned that virus-driven energy theft links viral nucleic acids to all pathology.

When the link from olfaction and the innate immune system to RNA methylation and behavior establishes an even clearer path from the epigenetic landscape to the physical landscape of supercoiled DNA, those who have told only half the story will be exposed by those who tell others the truth and the consequences of ignorance.

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