Light Energy

Creating nothing but a theory (3)

Life is physics and chemistry and communication Any model of biologically-based cause and effect must link atoms to ecosystems via the levels of organization in the diagram. That fact has been known to me since the early 1990s, when I was told that my model must start with sensory input linked to gene activation based on articles like this: Understanding the bases of sex differences Excerpt: “The articles in this issue summarize the factors surrounding sex differences with respect to…

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Creating nothing but a theory

De novo design of a transmembrane Zn2+-transporting four-helix bundle Excerpt 1) The de novo design of proteins is an important endeavor that critically tests our understanding of the principles underlying protein folding and function, while also laying the foundation for the design of proteins and molecular assemblies with desired properties. Much progress has been recently demonstrated… but no designed membrane protein has been experimentally shown to adopt the desired fold at atomic resolution. Excerpt 2) Nevertheless, these findings… provide support…

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2 genes in 2 species (too expensive and too insignificant)

Characterisation of two Neurogenin genes from the brook lamprey Lampetra planeri and their expression in the lamprey nervous system by Ricardo Lara Ramirez et al. Abstract excerpt: “Here we report the isolation of two Neurogenin genes, LpNgnA and LpNgnB, from the lamprey Lampetra planeri. Phylogenetic analyses show both genes have orthologues in other lamprey species and in a hagfish.” My comment: “…the identity of a single functional GPH [glycoprotein hormone] of the hagfish, hagfish GTH, provides critical evidence for the…

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Epigenetic effects of soil bacteria on plants

Soil Bacteria Live on Wine Grapes The earthiness of Merlot may have to do with grapevine-dwelling microbiota. By Kerry Grens | March 25, 2015 Excerpt: “…our next step is to figure out how those bacteria are affecting the chemistry of the plant.” My comment: Progress may then lead others to learn how the balance of viral microRNAs and nutrient-dependent microRNAs is linked to cell type differentiation in plants and animals via RNA-directed DNA methylation and RNA-mediated amino acid substitutions linked…

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Quantum correlations/pseudoscience

A quantum advantage for inferring causal structure Preprint excerpt: “The causal inference schemes described here promise extensive applications in experiments exhibiting quantum eff ects. For instance, they can provide a test of whether the dynamics of a given open quantum system is Markovian or not [17{24]. This is because in a non-Markovian evolution, the environment acts as a common cause between the dynamical system at one time and the same system at a later time. Our inference schemes may also help…

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Anti-entropic solar energy

“We have a group trying to model the mitochondrion” — Ulla Mattfolk Trash pickup problem Excerpt: “The PGAM5 protein would be regulated by an allosteric mechanism, in which its biological function would switch from activation of the PINK1/PARKIN pathway for removal of damaged mitochondria to the FUNDC1 pathway for removal of damaged mitochondria,” according to Hannink. “Peptides behave like drug molecules; any time you can identify a biological process that is regulated by a peptide, that peptide becomes a leading…

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Correctly modeling life on this planet

We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms. — Jordan et al., (2005) The increase in the number of…

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Correctly modeling biological energy

The light-activated “origins of life” issue (see: Correctly modeling ecological adaptation) forces others to come out of the woodwork and try to overwhelm the biologically underinformed masses with the complexities of their existence after decades of attributing what is currently known about viruses, viral microRNAs, entropic elasticity, anti-entropic biological energy from the sun, and nutrient-dependent microRNAs, to mutations and evolution. Theorists have denied the obvious facts about light-induced amino acid substitutions and cell type differentiation controlled by the physiology of…

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UV-light mutations and gene loss (not gain)

The Neanderthals live on in us March 13, 2015 Excerpt: “He opted instead for a medical degree and then a PhD at the University of Uppsala, where he was supposed to be probing the DNA secrets of a virus.” My comment: If he had done what he was supposed to be doing, he might have learned how viral microRNAs and nutrient-dependent microRNAs contribute to cell type differentiation in all cells of all individuals of all species. If he had done…

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Virus-driven origin of life

On the Origins of Life A new experimental system demonstrates that precursors of ribonucleotides, amino acids, and lipids may have simultaneously arisen from the same prebiotic chemistry. By Jef Akst | March 17, 2015 “This is a very important paper,” Jack Szostak, a molecular biologist and origin-of-life researcher… See also: Luis P. Villarreal: We Need a Nonlinear Language for Life Nobelist Jack Szostak has told me this about autocatalytic sets: the people who came up with the original idea, like…

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