NORAD: air defense and defense against genomic entropy
- North American Aerospace Defense Command… that provides aerospace… defense for North America
- Norwegian Agency for Development Cooperation
- Noradrenaline, a hormone and a neurotransmitter with multiple biological roles
My comment: The modern use of radar includes air-defense systems and ocean surveillance systems. High tech radar systems are designed to use the systems complexity of signaling and sensing to extract useful information from levels of very high noise. In the context of protection from virus-driven genomic entropy use of the acronym NORAD in biology links air defense to the reportedly heretofore unknown purpose of signaling, sensing, and extracting information in the context of everything known about physics, chemistry, and molecular epigenetics.
NORAD now may refer to: Noncoding RNA Activated by DNA Damage (NORAD)
See also: Scientists discover a new role for RNA in safeguarding human chromosome number
…identified a gene called NORAD that helps maintain the proper number of chromosomes in cells, and that when inactivated, causes the number of chromosomes in a cell to become unstable, a key feature of cancer cells.
“In the absence of the NORAD RNA, the number of chromosomes in cells becomes highly abnormal,” explained Dr. Joshua Mendell, Professor of Molecular Biology at UT Southwestern and a Howard Hughes Medical Institute Investigator. “This is an entirely new function for a noncoding RNA and may have implications in cancer biology since genomic instability is a hallmark of tumor cells.”
My comment: NORAD appears to be essential to the strategic defense system that protects organized genomes from virus-driven entropy. The strategic defense system is referred to by all serious scientists as the innate immune system. The conserved molecular mechanisms of immune system function link this long non-coding RNA (lncRNA)-dependent mechanism to a post-transcriptional regulatory axis that must help to maintain genomic stability in the all the cell types of all individuals in all living genera. For example, direct effects of the epigenetic landscape that begin with hydrogen-atom transfer in DNA base pairs must be linked via nutrient-dependent RNA-mediated DNA repair. That fact recently introduced serious scientists to a new level of systems complexity in the context of links from atoms to ecosystems.
Serious scientists know that there is no defined link between atoms and ecosystems because the link from epigenetics to genetics has not been defined. Previously, pseudoscientists have used de Vries definition of mutation to link epigenetics to genetics via theories about how long it might take for accumulated mutations to cause one species to evolve into another.
For example, see:
Beyond neo-Darwinism—an epigenetic approach to evolution
Contrary to the neo-Darwinian view, we point out that the variations of the phenotype, on which natural selection could act, do not arise at random; they are produced by interactions between the organism and the environment during development.
My comment: Interactions between the organism and the environment during development link ecological variation to ecological adaptation via NORAD, not via evolution.
No Genetics without Epigenetics? No Biology without Systems Biology?
…a unified understanding of life requires: (1) a view on its component parts, the cells, (2) a view on the life cycles of all cells—their formation, growth, development, and reproduction—as based in chemical reactions among similar sorts of molecules, (3) a view on the way in which amino acids are put together to form proteins, as specified by DNA and RNA according to a nearly universal and precise scheme.1
My comment: Pseudoscientists cannot seem to grasp the fact that the amino acids that are put together to form proteins are nutrient-dependent amino acids.
Mae-Wan Ho: No Boundary Really Between Genetic and Epigenetic
…when we eat food nucleic acids can get into our cells. Also, there is a theory that our cells in the body keep sending out nucleic acids and one theory has it that it seems to correct the mistakes that other cells have suffered from mutations. . . .
My comment: There is a model for that. This is not just a theory.
See: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors
Among different bacterial species existing in similar environments, DNA uptake (Palchevskiy & Finkel, 2009) appears to have epigenetically ‘fed’ interspecies methylation and speciation via conjugation (Fall et al., 2007; Finkel & Kolter, 2001; Friso & Choi, 2002). This indicates that reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms (Margulis, 1998)
…it is very unlikely that DNA is simplistic, given that RNA is so diverse. Hence, we hypothesize that many such ‘apegenetic’ (from Greek apeftheias, meaning direct) modifications exist. In the future, this ‘apegenome’ and its functions remain to be discovered and further investigated.
My comment: No matter what you call it, something must link the epigenetic landscape to the physical landscape of supercoiled DNA in species from microbes to primates. Thus, the term apegenome may be appropriate for use to describe in one term all the links from nutrient-dependent microRNAs to adhesion proteins and supercoiled DNA in primate species that vary by as little as a single base pair substitution linked to a single amino acid substitution in the light of ecological variation and what is known about ecological adaptation.
For example, 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. (p. 127)
My comment: Since 1973, and possibly even before, that fact has been repeatedly reported in the context of spectacular news, like this:
The studying of histones that bind to DNA has the primary focus of epigenetic modification research. These histones can be modified, which can result in genes being read or not. There are basically 5 different types of Histone proteins called H2A,H2B, H3 and H4 which form a bead on which the DNA is wrapped (with two molecules each, so a total 8 protein molecules in the bead and one called H1 between two beads). Within the histones, it is actually the amino acids that are modified.
My comment: The link from atoms to ecosystems must include the link from base pairs to RNA-mediated amino acid substitutions that are fixed in the organized genomes of all living genera in the context of their physiology of nutrient-dependent reproduction. Did you know that amino acid substitutions are fixed in the histones?
That fact was also reported in the context of this news release about the diversity of epigenetic links from metabolic networks to genetic networks:
A theory is presented which shows how the metabolism of individual organisms controls the flow of carbon through ecosystems. The theory synthesizes top-down, ecosystem-level and bottom-up, organism-level approaches to ecological energetics and material cycles. The theory predicts a very simple straight-line relationship between residence time of carbon molecules and the ratio of whole-ecosystem biomass to primary productivity. This and additional predictions for total throughfow and recycling are supported by numerical models and data from real ecosystems.
There’s a model for that: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Highly conserved ligand–receptor signaling mechanisms are the biochemical mechanisms of ecological epigenetics. They enable nutrient-dependent pheromone-controlled reproduction in all organisms. These molecular mechanisms allow life to recognize the difference between self and non-self chemical cues and to respond to novelty. The behavioral responses to novelty appear to be the basis for diversified life (Monahan & Lomvardas, 2012).
My comment on Monahan & Lomvardas, (2012)
Is what’s being elucidated the bottom-up epigenetic effects on stochastic gene expression via chromatin remodeling, which is controlled by the top-down epigenetic effects of pheromones on reproduction in species from microbes to man?
Lomvardas answered yes, albeit with extreme prejudice and obfuscation.
See also: Role of olfaction in Octopus vulgaris reproduction
Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). — p. 61
My comment: Perhaps the most important thing to remember is that gene activation must start with the de novo creation of genes, not the definition of mutation. De Vries “jump-like” changes in energy cannot be linked to the evolution of biodiversity via constraint-breaking mutations, unless the mutations are biophysically constrained. In my model, they are constrained by nutrient-dependent DNA repair in the context of metabolic networks and genetic networks in all living genera.
For comparison to everything known to serious scientists about biologically-based cause and effect, this claim should be examined:
Bacteria use these systems to sense and respond to their environment, which include stresses and nutrient conditions, but also include other bacteria and their antagonistic enzymes and specialized metabolites.
To identify the active molecule, we analyzed the HPLC-purified sample by UV absorbance and ESI-mass spectrometry. The molecule showed strong UV absorbances at 319, 333, and 351 nm, indicative of a conjugated pentaene moiety .
My comment: All organisms appear to use nutrient uptake to support their innate immune system function, which enables NORAD to link the sun’s anti-entropic virucidal energy from UV light to absorbances in bacteria and the response of bacteria to stresses and nutrient conditions that enable their ecological adaptation instead of virus-induced genomic entropy. Unfortunately, the stability of molecules stabilized by intramolecular hydrogen bonds on one side, and a conjugated pentaene moiety on the other side is beyond my depth. Perhaps that is because others have not yet detailed the interactions at the level of atomic resolution that is required to link atoms to ecosystems in all living genera. If a neo-Darwinian theorist or theoretical physicist knows how to link atoms to ecosystems via mutations, I will try to find more information about thermodynamic cycles of protein biosynthesis and degradation for comparison to their model of biologically-based cause and effect.
Until then, I’ll stick with the thermodynamics and let others bring kinetics into the picture.
See: Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network
Each time I’ve asked about the “fifth force” in the past, I’ve been led to information of a highly theoretical nature. Apparently, others are going to put their theories into the context of what is known about models that link atoms to ecosystems, but it won’t make much difference until all theorists start to look at experimental evidence of biologically-based cause and effect. It is no longer enough to claim that “the force is out there” or ask that the force be with you. If you can’t link atoms to ecosystems, the force of your argument is not going to convince any serious scientist.