An evolutionary theory killer

How to create biologically uninformed theorists

Summary: On March 2, 2018, Philip C. Ball and Nick Lane started making claims about proton gradients. Their claims are based on my model of quantized energy as information. This post includes added support for what is known to all serious scientists about the light-activated endogenous substrates that link molecular epigenetics to RNA-mediated autophagy.
See first: Energy as information and constrained endogenous RNA interference (audio/visual aid 2017)

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy.

The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes.

For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

Added support for the light-activated molecular epigenetics of autophagy:
Light-powering Escherichia coli with proteorhodopsin (2007)

…we quantify the coupling between light-driven and respiratory proton currents… and show that light-driven pumping by PR can fully replace respiration as a cellular energy source in some environmental conditions.

Structure of the Deactive State of Mammalian Respiratory Complex I (2018)

…the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles.

Global collective motions in the mammalian and bacterial respiratory complex I (2018)

…we identify here transitions between experimentally resolved structures of the mammalian complex I as low-frequency collective motions of the enzyme, highlighting similarities and differences between the bacterial and mammalian enzymes. Despite the reduced complexity of the smaller bacterial enzyme, our results suggest that the global dynamics of complex I is overall conserved.

The conservation of light-powered functional structures and energy-dependent proton gradients link the deactive state in critical structures to the active state via the creation of enzymes in species from bacteria to mammals. The energy-dependent creation of the enzymes links metabolism of the energy (e.g., food energy) from pheromones to biophysically constrained viral latency in the context of the physiology of reproduction.
The pheromone-controlled physiology of reproduction in species from microbes to humans links our visual perception of energy and mass in the context of how ecological variation must be linked to energy-dependent ecological adaptations in all living genera.
See: Olfaction Warps Visual Time Perception

Our perception of the world builds upon dynamic inputs from multiple senses with different temporal resolutions, and is threaded with the passing of subjective time. How time is extracted from multisensory inputs is scantly known. Utilizing psychophysical testing and electroencephalography, we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

See also: Odors Alter Subjective Time Experience Author: Dr. ZHOU Wen’s Research Group Update time: 2017/05/15

The brain is not a timepiece. Whereas it is equipped with senses like vision, audition, touch, smell, and taste, it has no direct access to or measure of the physical time (unless you read from a clock). Rather, it constructs the subjective “time” of an event from the dynamic multisensory inputs associated with that event. Yet different senses come with different temporal precisions. For instance, when standing near an apple tree, you can detect the falling of an apple much better with your eyes or ears than the nose. How does the brain coordinate multisensory signals entering different brain regions with different temporal resolutions, and come up with the subjective time?

A team at the Institute of Psychology at Chinese Academy of Sciences tackled this issue using odors and images. Specifically, Dr. Bin Zhou, the study’s lead author, and his colleagues examined whether odors could modulate one’s temporal sampling and subjective duration of visual objects. In their study, participants viewed two series of flickering isoluminant images in red and green (Figure 1A). One of the series contained opposite images of an apple or bananas; the other contained only images of red and green fields. When the images alternated at a frequency beyond 20 Hz, the participants started to have difficulty reporting which series contained an object. Indeed, for most people, chromatic flicker fusion frequency (CFF), the limit at which alternating colors become perceived as a stable fused color, falls somewhere between 20 and 25 Hz. Interestingly, the participants’ object detection accuracies around CFF were improved under the exposure of a congruent, as opposed to an incongruent, odor. In other words, the participants detected a rapidly flickering apple better when they smelled an apple odor rather than a banana odor, and vice versa (Figure 1B, left panel). In effect, the presence of a congruent odor facilitated the brain’s temporal sampling of a visual object and elevated its CFF (Figure 1B, right panel). Based on electrical activities recorded from the participants’ scalp, the researchers found that the integration between smell and vision strengthened the signals of the corresponding object in a brain region heavily implicated in object representations called the right temporal cortex, about 150-300 ms after object onset. They further showed that such integration lengthened one’s subjective duration of the corresponding object in a duration comparison task. The researchers concluded that subjective time is warped by the neural energy involved in representing multisensory inputs at subsecond scales.

Until Philip C. Ball mentioned that Nick Lane believed proton gradients came before the energy-dependent creation of RNA, I did not realize how little they knew about this link from differences in the energy of photons to consciousness.
See: What Affective Neuroscience Means for Science Of Consciousness (2013)

The coupling of the two circuits promotes an endogenous feedback that supports conscious processes. Within this framework, we present the defence that detailed study of both affective and cognitive processes, their interactions, as well of their respective brain networks, is necessary for a science of consciousness.

The coupling of the two circuits links differences in the energy of photons from the proton motive force to the light-activated endogenous feedback loops and Feedback loops link odor and pheromone signaling with reproduction.
It is extremely difficult for intelligent people to not link this experimental evidence to biophysically constrained viral latency in the context of reports that claim “Creatures’ Adaptability Begins with Their Sensors.”
But, see for comparison: David Attenborough on creationsim May, 2015

My comment on his nonsense: First steps to neutralizing Zika: How highly potent antibody neutralizes Zika infection discovered

This is framed within the context of energy-dependent changes in pH, which facilitate receptor-mediated entry of nutrients or viruses into specific cell types of species-specific tissues via stress-linked changes in hydrogen-atom transfer in DNA base pairs.

Virus-driven energy theft has been linked to all pathology in all living genera via the conserved molecular mechanisms of RNA-mediated polycombic protein folding chemistry compared to the hecatombic evolution of pathology manifested first in the differences between archaea and bacteria. Admitting that Carl Woese was wrong about the different domains of life is the first step towards understanding the difference between healthy longevity and the evolution of all virus-driven pathology.

Carl Woese was wrong

God did not create the viruses. He created the anti-entropic virucidal energy of sunlight, which protects all organized genomes from virus-driven entropy. Only the choices of our ancestors could have led to the increasing amout of virus-driven pathology during the past ~6000 years that pseudoscientists place into the context of millions of years of evolution. Then, they blame God, like these two pseudoscientists do. Darwin knew they would do that, which is why he insisted that others put conditions of life before natural selection. But they bastardized his theory anyway and taught their revision to anyone who was foolish enough to believe in it. It’s called the “Modern Synthesis” and was based on de Vries 1902 definition of “mutation.”

Celebrate Your Inner Virus

It is important that we understand the design present in viruses because God made them.

It is no wonder that Sir David Attenborough and many others like Philip C. Ball and Nick Lane are confused about the energy-dependent creation of healthy longevity and consciousness. Even some young earth creationists have failed to link the creation of the sun’s anti-entropic virucidal energy from changes in electrons to ecosystems via the proton motive force. That leaves every aspect of creation to be placed back into the context of ridiculous theories. The theories start with the virus-driven theft of quantized energy as information. The energy theft links mutations to all virus-driven pathology. The theft of quantized energy as information cannot be linked by serious scientists from beneficial mutations to the evolution of one species from another.
For comparison, pseudoscientists have no problem touting this confusing nonsense:
Sign of selection on mutation rate modifiers depends on population size (
1)  Genetic variation—the raw material for evolution—is ultimately generated by mutation.
2). …beneficial alleles never become deleterious and deleterious alleles never become beneficial.

Whether these phenomena can be united in a single theoretical framework remains an open question that we are actively exploring. In any case, our results add to a growing appreciation of nonclassical population size dependence in evolution by natural selection (41, 42).

Funding for research that attempts to link natural selection to evolution via mutation-driven genetic variation should be used to link food odors and pheromones from the physiology of reproduction to biophysically constrained viral latency and ecological adaptations. It is time to stop creating more biologically uninformed theorists.


Science journalists or paid propagandists? (3)

See: Science journalists or paid propagandists? (2)
See also from the first blog post in this series: Science journalists or paid propagandists?
Differential Expression of Putative Pheromone-detecting Cells and Receptors in the Olfactory Epithelium of an African Cichlid Fish
The link from sunlight and chirality to nutrient energy-dependent reproduction is not addressed in the presentationss from SICB 2017
There is nothing in a search for chirality
At the 2016 meeting, Epigenetic regulation of Toll-like Receptor 4 expression as a facilitator of invasiveness in Kenyan house sparrows (Passer domesticus) seemed to suggest that epigenetic regulation automagically occurred.
There is one abstract fron 2017 that links sunlight to chirality without reporting on chirality, but at least they report on autophagy.
Disease Resistant Corals Activate Autophagy over Apoptosis after an Immune Challenge 

…disease resistant corals upregulated pathways involved in autophagy, indicating attempts at adapting to changing conditions. These data show how cell survival pathways contribute to the immune response and subsequent patterns of disease resistance on coral reefs. Understanding these mechanisms will help inform trajectories of reefs under continuous climate and disease pressure.

There is one 2017 abstract that links chirality and autophagy to energy-dependent RNA-mediated amino acid substitutions.
ATP Production Increases with Addition of Varying Concentrations of Vespa Amino Acid Mixture (VAAM)

…our previous work suggests VAAM affects the electron transport chain and ATP synthase activity. While increased exercise capacity shortly after VAAM exposure has been observed in multiple species, the relationship between VAAM and ATP production has been assumed without supporting data, until now.

They haven’t decided whether or not RNA-mediated DNA repair is a good thing.
See also: Molecular organization of Octopus brains: Insight into unique memory center signaling

We identified 16,194 transcripts in the VL and found ~25.5% appear to be cephalopod-specific. Next we used targeted and unbiased computational predictions and manual annotation to identify putative signaling molecules form the VL transcriptomes. We have cloned and localized 11 neuropeptides (NP) to components of the VL circuit. NPX3 is abundantly expressed in the cell bodies of the SFL, where the VL circuit originates and NPX1 & 2 localize to the AM cell bodies of each VL gyrus. Among the 7 NPs that localize to the VL LE neurons, 2 unique cephalopod NPs, NPX4 & 5, are abundant in Octopus, but absent in the ancestrally branching Nautilus (which lacks a VL). This expansion of signaling molecules in the VL circuit may be a key feature of unique memory systems of cephalopods, implying extensive parallel evolution of cephalopod brains and memory circuits.

The expansion of the signaling molecules is nutrient energy-dependent and the increasing organismal complexity is pheromone-controlled via the physiology of reproduction in species from microbes to humans.
Conservation, convergence, and novelty in Octopus bimaculoides embryogenesis

To shed light on the gene networks important in this highly derived developmental program, we sequenced and analyzed transcriptomes from five stages spanning embryogenesis in the California two-spot octopus, Octopus bimaculoides. Genome analysis has shown that the core developmental gene repertoire of the octopus is broadly similar to that found in typical invertebrate bilaterians (Albertin et al. 2015). We detect transcripts for these developmental transcription factors and signaling ligands primarily during the middle stages that coincide with the emergence of the body plan, but not before. Bioinformatics-based differential expression analysis identified suites of genes that show dynamic changes, including stage-specific expression profiles. Notably, many of the differentially expressed genes in the early transcriptomes are not found in the genomes of other sequenced animals. These results indicate that the fish-like early stages of cephalopod development deploy cephalopod-specific genes, and suggest a major role for taxonomically restricted genes in the evolution of cephalopod developmental mechanisms.

They fail to link the sun’s anti-entropic virucidal energy to the light they try to shed on gene networks that automagically “…coincide with the emergence of the body plan, but not before.” The coincidental emergence fails to link Dobzhansky’s (1973) “light of evolution” to deferentially expressed genes that are not found in the early transcriptomes or organized genomes of other sequenced animals.
Behavioral Dynamics of Niche Partitioning between Two Octopus Species in a Shallow Coastal Environment

O. vulgaris uses parachute attack and spends more time foraging on rock and rubble, mostly nocturnally. This study identifies ecological and behavioral components that facilitate coexistence of sympatric species, provides insight into cephalopod ecology and baseline conservation requirements for unique sand-dwelling organisms.

They link nutrient energy-dependent changes in niche construction from ecological variation to ecological adaptation and the coexistence of sympatric species via foraging behaviors, foraging times and diet, but fail to link the foraging and diet to the pheromone-controlled physiology of reproduction and transgenerational epigenetic inheritance of morphological and behavioral phenotypes in all living genera via conserved molecular mechanisms of biologically-based cause and effect..
Feeding on the Unseen: Ingestion and Assimilation of Bacteriophages by Brachionus plicatilis (Rotifera)

… bacteriophages (< 0.05 μm) are abundant in seawater (to 108/mL) and represent a potential food source for rotifers and other planktonic invertebrates.

They linked the ingestion of viruses from metabolic networks to genetic networks via dichlorotriazinylamino fluorescein (DTAF)-labeled bacteriophages and found that the fluorescence of rotifers was greater in the DTAF-bacteriophage treatments, which led to the hypothesis that viuses in seawater may be a food source for planktonic invertebrates and their larvae.
See for comparison: Viral and cellular messenger RNA targets of viral microRNAs appear to link the nutrient energy-dependent physiology of pheromone-controlled reproduction to protection from virus-driven energy theft and genomic entropy via virally encoded microRNAs. The virus-driven energy theft benefits the viruses. Nutrient energy-dependent metabolic and genetic networks link hydrogen-atom transfer in DNA base pairs in solution form energy-dependent microRNA flanking sequences to viral latency (prevention of viral replication cycles) in the context of energy-dependent autophagy.
Abstract excerpt:

Emerging data suggest that viral miRNAs may be particularly important for regulating the transition from latent to lytic replication and for attenuating potentially inhibitory host antiviral immune responses.

It is time to link the emerging data to energy-dependent healthy longevity and virus-driven energy theft to all pathology, instead of playing word games. See for example: Epigenetics and Genetics of Viral Latency

… viral latency is responsible for life-long pathogenesis and mortality risk…

See also: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

They insult the intelligence of any serious scientist who has ever linked energy-dependent changes from angstroms to ecosystems and all healthy longevity and all serious scientists who have linked virus-driven energy theft to all pathology via the transgenerational epigenetic inhertance that links the virus-mediated archaeal hecatomb to Zika virus-damaged DNA in human infants.
See also from the 2017 SICB annual meeting
Pheromone-mediated Communication in a Bird Ectoparasite

Pheromone-mediated communication governs many aspects of insect behavior, population dynamics, and community ecology.

We are currently working to determine the structures of volatile compounds produced by lice and to identify their use in pheromonal communication.

Someone is paying them to do that.
Evolutionary Mechanisms that Inhibit Interspecies Mating in Drosophila

Given that the sensory pathway for inhibiting inter-species mating is conserved, we are using modern genetic tools to understand how the neural circuits underlying mate choice have evolved in disparate fly species. We generated novel transgenic lines in D. melanogaster and other fly species to determine whether Gr32a functions in an analogous manner across species. These studies involve examining the control of Gr32a expression and its function in different species. Taken together, my studies will lead to a better understanding of how behavioral reproductive isolation has evolved.

Reproductive isolation did not evolve. Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for his works on chromosomal inheritance and Schrodinger/Dirac won the Prize
Flight Stability and Olfactory Navigation is Supported by Multisensory Antennal Inputs in the Moth Manduca sexta 

To characterize the effects of different environments on plume tracking, we challenged males with only one odor-detecting antenna to track a plume in an either turbulent or laminar air flow.

Be ready to compare the reports from science journalists to what was known about moth pheromones in 1959 and energy-dependent RNA synthesis in 1964.
Pheromones: a new term for a class of biologically active substances
Then, prepare to die from virus-driven energy theft if you allow theorists to continue touting their pseudoscientific nonsense or allow science journalist to continue reporting it.
Obama Advisers Urge Action Against CRISPR Bioterror Threat

For the past two decades, the government has focused its biodefense efforts on a list of known pathogens—such as anthrax, smallpox, and Ebola—declared by the Department of Health and Human Services and Department of Agriculture to have the “potential to pose a severe threat to public health and safety.” Government-funded research on these pathogens receives special scrutiny, and the National Institutes of Health limits researchers from conducting experiments that could make certain germs, like influenza, more dangerous.

See also: CRYPTOCHROME mediates behavioral executive choice in response to UV light

Opsin-based light sensing is clearly critical for behavioral light responses… CRY is a major modulator of a wide range of fly behavioral responses to UV light.

This may be your last chance.

1) Admit that the de novo creation of G protein-coupled receptors links the anti-entropic virucidal effects of UV light to the innate immune system and supercoiled DNA.
2) Admit that supercoiled DNA links chemotaxis and phototaxis to the pheromone-controlled weekend resurrection of the bacterial flagellum.
3) Admit that the weekend resurrection of the bacterial flagellum attests to what is known to all serious scientists about biophysically constrained RNA-mediated protein folding chemistry.
Alternatively, wait for serious scientists to demand that you and all other theorists be ousted from your positions in academia if you do not stop touting pseudoscientific nonsense about beneficial mutations and evolution. Energy is information and virus-driven energy theft links mutations to all pathology. If you do not agree, try to invent another theory on your way out the door of your ivory tower.