Autophagy is the antiphage defense strategy
The “Antiphage Defense Strategy” in Vibrio anguillarum is called autophagy by many serious scientists. It links nutrient energy-dependent pheromone-controlled quorum sensing to viral latency, healthy longevity, symbiosis, reproduction, and biodiversity from microbial species to humans.
For an evolutionary approach to energy-dependent autophagy that fails to address any aspect of how virus-driven energy theft causes all pathology see: (12/7/16) Part I: Living together: The symbiosis of host-microbial interactions (12/7/16)
See also: 12/7/16
….McFall-Ngai tells the story of a symbiosis between the Hawaiian bobtail squid and Vibrio fischeri (V. fischeri), a type of luminescent bacteria that enables the squid to hunt at night. McFall-Ngai and collaborators have identified the molecular mechanism by which nascent Hawaiian bobtail squid select V. fischeri from the thousands of other bacteria in their habitat. V. fischeri induces developmental changes in the squid that drive daily rhythms of gene expression, which are necessary to control bacterial growth, a crucial cycle in this symbiotic partnership.
Bobtail squid select bacteria that become luminescent. The squid do not not select archaea. That fact exemplifies how natural selection for energy-dependent codon optimality links top-down causation from the sun’s anti-entropic biological energy to ecological adaptation.
Whether or not you accept this fact, energy-dependent natural selection continues in the context of symbiosis among the most ecologically adapted species.
“The four stages of acceptance: ― J.B.S. Haldane
1. This is worthless nonsense.
2. This is an interesting, but perverse, point of view.
3. This is true, but quite unimportant.
4. I always said so.”
Natural selection cannot link mutations to evolution in the context of symbiosis because the interactions among species are far too complex.
…the pattern of microbial exchange is “likely circular in nature.” That means that captive dragons contribute microbes to their environment, and they reacquire these same microbes from their environment, repeating this exchange in an ongoing cycle without other external sources of microbial diversity.
Pattern recognition is essential to the understanding of how the microbiome of bobtail squid is linked to symbiosis via the microbiome in all other living genera via the anti-entropic virucidal energy of sunlight.
Beneficial microbes kill beneficial mutations
1/15/15 Excerpt: McFall-Ngai, Bonnie Bassler, Anna Di Cosmo and others, continue to show that Darwin’s ‘conditions of life’ are nutrient-dependent and pheromone-controlled by linking:
1) metabolic networks,
2) genetic networks,
3) reproduction in microbes,
4) reproduction in their model organisms.
Environment epigenetically shapes the immune system
1/15/15 Excerpt: 1) –with my emphasis Re: “There’s nothing here that is revolutionary or requires rethinking of our assumptions about how the immune system functions…”
Quantum physics, quantum biology, and quantum consciousness
2/15/15 Excerpt: One would think that the representations of McFall-Ngai that appear to link light-induced amino acid substitutions from the stability of DNA in luminescent microbes to the stability of DNA in squid would invite more attention to details than attempts to pirate ideas about epigenetic links from Turin’s links and my links from quantum physics to Gunther Witzany’s Life is physics and chemistry and communication.
8/25/15 Excerpt: See also my invited review of nutritional epigenetics. I submitted it by request for a special issue of “Nutrients” and posted the submission to Figshare.com on April 11, 2014, after the submission was returned without review.
6/25/16 Excerpt: Quorum sensing links the physiology of energy-dependent reproduction and virus-driven energy theft from the microRNAome of and light organ of bobtail squid to the bull sperm microbiome, which links microRNAs in breast milk to human brain development. The bacteria that populate the light organ have already been linked by Bonnie Bassler’s group and Margaret McFall-Ngai’s group to everything known about the physiology of energy-dependent reproduction in all living genera.
See also: Autophagy.pro vs Nature Publications Group December 11, 2017