17th Century Variola Virus Reveals the Recent History of Smallpox

…our data clearly show that the VARV lineages eradicated during the 20th century had only been in existence for ∼200 years…

Reported as: Smallpox, once thought an ancient disease, may have emerged in more recent times

… smallpox virus evolved into two circulating strains, variola major and minor, after English physician Edward Jenner famously developed a vaccine in 1796.

How does any virus-driven pathology evolve into two different strains and “emerge?”

Experimental evidence of biologically-based cause and effect provides clear indications in the extant literature that virus-driven theft of quantized energy is the link from viral latency to all pathology. Pathology emerges when the innate immune system is compromised by nutrient stress, social stress — and even physical stress.For example, excessive exposure to intense sunlight causes the physical stress of a “sunburn” and the immune system overload may cause the reactivation of a latent herpes virus infection.

Edward C. Holmes is a co-author of 17th Century Variola Virus Reveals the Recent History of Smallpox. Learn why young earth creationists think that accurate “calibration” of molecular clocks is essential to accurate representations of top-down energy-dependent biophysically constrained biologically-based cause and effect, which must be placed into the context of the physiology of reproduction in species from microbes to humans.

His 2003 monograph was cited in Viral Genome Junk Is Bunk

…secular scientists compared the gene sequences of viruses to their counterparts in animal genomes and found that, at most, the variation in these sequences indicates they can be no more than 50,000 years old.2 Molecular clocks and the puzzle of RNA virus origins

See also: The extent of codon usage bias in human RNA viruses and its evolutionary origin

…the strong correlation between base and dinucleotide composition and codon usage bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the codon bias observed. However, we also detected correlations between codon usage bias and some characteristics of viral genome structure and ecology, with increased bias in segmented and aerosol-transmitted viruses and decreased bias in vector-borne viruses. This suggests that translational selection may also have some influence in shaping codon usage bias.

Translational selection links codon usage bias from energy-dependent changes in base pairs to codon usage and RNA-mediated protein folding chemistry, which links the epigenetic landscape to the physical landscape of DNA in all living genera via the physiology of reproduction and fixation of amino acid substitutions.

Natural selection for energy-dependent codon optimality replaced neo-Darwinian theories that linked mutation pressure to natural (translational) selection.

See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes (Ikemura, 1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

See for comparison: A Feathered Dinosaur Tail with Primitive Plumage Trapped in Mid-Cretaceous Amber

The integration of developmental studies [5, 7, 33] and paleontology yields enriched models of morphological character evolution that help explain major evolutionary transitions in key clades such as theropods, including birds. With preservation in amber, the finest details of feathers are visible in three dimensions, providing concrete evidence for feather morphologies and arrangement upon the tail, as well as supporting an important role for barbs and barbules in feather evolution.

They falsely elevate the explanatory power of models that examine only morphological character evolution at the same time that calibration of molecular clocks has again been called into question in the context of the energy-dependent amino acid optimality code. They ignore the energy-dependent code and assume millions of years of evolution have occurred by examining morphology. This can only be done without comparing phenotypes in the context of experimental evidence that links virus-driven energy theft to all pathology in all living genera.

The energy-dependent amino acid optimality code links energy-dependent hydrogen-atom transfer in DNA base pairs to all biodiversity via the innate immune system, the physiology of reproduciton, and everything known about the structure and function of supercoiled DNA, including what happens in the context of virus-driven negative supercoiling.

Models of morphological character evolution fail to include any aspect of what serious scientists have learned about energy-dependent biophysically constrained cell type differentiation or what happens when viruses steal that energy. Simply put, models of morphological character ignore Darwin’s “conditions of life.” That is why models of morphological character have no explanatory power.

An anti-entropic virucidal force must be considered in any claim about evolution. Autophagy, for example, links the sun’s virucidal energy to DNA repair. Femotosecond blasts of UV light that have been linked to DNA repair show that all claims for comparison must also link ecological variation to ecological adaptation.

No experimental evidence of biologically-based cause and effect suggests that any species has evolved from any other species, except in the context of ridiculous theories that failed to consider Darwin’s “conditions of life.”

For comparison, experimental evidence of biologically-based cause and effect led to this claim.

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

See for comparison: First Dinosaur Tail Found Preserved in Amber

To scientists’ delight, the incredible appendage from 99 million years ago is covered in feathers.

Only pseudoscientists would be delighted by this finding because it is based on a report published in “Current Biology” on the same day that another work by Edward C. Holmes again called into question the calibration of the energy-dependent molecular clock. Molecular mechanisms and the computers used to model morphological character evolution do not auto-assemble or run themselves. Energy is required for assembly and for ongoing operations. Viruses steal that energy from computers and from all energy-dependent cell types.

But look, there’s a feathered dinosaur tail!

The morphological model suggests that dinosaurs evolved into birds, like the fruit dove. In that context a rainbow might suggest that the sun’s anti-entropic virucidal energy emerged before it slowed on contact with water, which led to the de novo creation of G protein-coupled receptors and the creation of all biodiversity via mutations and loss of those receptors.

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