Cryo-EM: Linking spatial and conformational constraints

By: James V. Kohl | Published on: February 13, 2018

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On Darwin Day (2018) Carl Zimmer suggested use of the twitter hashtag #Istudyevolution to report whatever aspect of biology people were studying. For example, Richard Lenski reported that he studied adaptation in E. coli. When I told others that ecological adaptation is nutrient-dependent and pheromone-controlled in species from microbes to humans, he blocked me from seeing his comments. Evidently he did not want people to know that he had been studying ecological adaptation for more than 2 decades but reporting the adaptations in the context of neo-Darwinian theories about mutations and evolution. For further clarification of that fact see:
Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility

…the mechanisms responsible for increased transport activity are not well understood, largely owing to limited structural information. We used cryo-electron tomography (cryo-ET) to visualize the 3D structure of the MT-bound dynein–dynactin complex from Mus musculus and show that the dynactin–cargo adaptor complex binds two dimeric dyneins. This configuration imposes spatial and conformational constraints on both dynein dimers.

This spatial and conformational constraints were reported as: Microscopic chariots deliver molecules within our cells

This discovery was totally unexpected, and will change how this motor complex is represented in cell biology and biochemistry text books,” says Saikat Chowdhury, PhD, a TSRI research associate and co-first author of the study.

“There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule,” Lander adds.

Assuming there was just one dynein molecule is something that only a biologically uninformed theorist would do. An energy-dependent difference in two molecules is required for movement and for biophysical constraints on movement. For comparison, all discoveries that link energy-dependent changes from electrons to ecosystems were anticipated by Richard P. Feynman in his claims about Plenty of Room at the Bottom.He linked his claims about the size of letters in a code from atoms to ecosystems in the context of Food Energy and denigrated the works of all theorists in The key to science (Cornell, 1964)
See also McEwen et al., (1964) Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
Everything known to serious scientists links cryo-ET and cryo-EM technology from ecological niche construction to socio-cognitive niche construction via food energy-dependent amino acid substitutions in the microtubules, which link differences in animal behavior to human consciousness.
See: Untangling Neurodegenerative Diseases using Cryo-Electron Microscopy
Everything known about prevention of all pathology starts with the creation of sunlight.
See: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

In conclusion, we have shown for the first time that very low doses of far-UVC light efficiently inactivate airborne viruses carried by aerosols. For example, a very low dose of 2 mJ/cm² of 222-nm light inactivates >95% of airborne H1N1 virus. Our results indicate that far-UVC light is a powerful and inexpensive approach for prevention and reduction of airborne viral infections without the human health hazards inherent with conventional germicidal UVC lamps. If these results are confirmed in other scenarios, it follows that the use of overhead very low level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases. Public locations such as hospitals, doctors’ offices, schools, airports and airplanes might be considered here. This approach may help limit seasonal influenza epidemics, transmission of tuberculosis, as well as major pandemics.

Reported as: Special UV light safely kills airborne flu virus, finds study

In the study, aerosolized H1N1 virus—a common strain of flu virus—was released into a test chamber and exposed to very low doses of 222 nm far-UVC light. A control group of aerosolized virus was not exposed to the UVC light. The far-UVC light efficiently inactivated the flu viruses, with about the same efficiency as conventional germicidal UV light.

They confirmed the fact that UV light biophysically constrains the degradation of messenger RNA that links mutations to all pathology.
See also: Photon-Mediated Quantum Gate between Two Neutral Atoms in an Optical Cavity

Quantum logic gates are fundamental building blocks of quantum computers. Their integration into quantum networks requires strong qubit coupling to network channels, as can be realized with neutral atoms and optical photons in cavity quantum electrodynamics. Here we demonstrate that the long-range interaction mediated by a flying photon performs a gate between two stationary atoms inside an optical cavity from which the photon is reflected. This single step executes the gate in $2 μ s$ . We show an entangling operation between the two atoms by generating a Bell state with 76(2)% fidelity. The gate also operates as a cnot. We demonstrate 74.1(1.6)% overlap between the observed and the ideal gate output, limited by the state preparation fidelity of 80.2(0.8)%. As the atoms are efficiently connected to a photonic channel, our gate paves the way towards quantum networking with multiqubit nodes and the distribution of entanglement in repeater-based long-distance quantum networks.

Reported as: Light controls two-atom quantum computation

This interaction is the basis for performing characteristic gate operations between the atoms, for example the operation as a CNOT gate or the generation of entanglement. The new method offers a variety of advantages: for example, the gate operations take place within microseconds which is an asset for quantum information processing.

Quantized energy is the information that must be biophysically constrained and transferred from hydrogen-atoms in DNA base pairs in solution. That fact seems to have escaped the attention of biologically uninformed pseudoscientists and most so-called science journalists. The pseudoscientists and other theorists linked the emergence of the energy to the evolution of all biodiversity outside the context of the physiology of reproduction and autophagy, which biophysically constrains viral latency.
See for comparison to what serious scientist have done:Experimental Evidence of Radiation Reaction in the Collision of a High-Intensity Laser Pulse with a Laser-Wakefield Accelerated Electron Beam

The dynamics of energetic particles in strong electromagnetic fields can be heavily influenced by the energy loss arising from the emission of radiation during acceleration, known as radiation reaction. When interacting with a high-energy electron beam, today’s lasers are sufficiently intense to explore the transition between the classical and quantum radiation reaction regimes. We present evidence of radiation reaction in the collision of an ultrarelativistic electron beam generated by laser-wakefield acceleration ( $ϵ > 500 MeV$ ) with an intense laser pulse ( $a_{0} > 10$ ). We measure an energy loss in the postcollision electron spectrum that is correlated with the detected signal of hard photons ( $γ$ rays), consistent with a quantum description of radiation reaction. The generated $γ$ rays have the highest energies yet reported from an all-optical inverse Compton scattering scheme, with critical energy $ϵ_{crit} > 30 MeV$ .

Reported as: Intense laser experiments provide first evidence that light can stop electrons

“One thing I always find so fascinating about this is that the electrons are stopped as effectively by this sheet of light, a fraction of a hair’s breadth thick, as by something like a millimetre of lead. That is extraordinary.”

The data from the experiment also agrees better with a theoretical model based on the principles of quantum electrodynamics, rather than Maxwell’s equations, potentially providing some of the first evidence of previously untested quantum models.

Effects of quantized energy as information cannot be defined in the context of equations, which is why physicists have traditionally been ridiculed for any attempt to explain energy-dependent top-down causation in the context of biophysically constrained healthy longevity.

All species on Earth exhibit an undefined, incalculable, innate ability to biophysically constrain energy-dependent viral latency. That ability is food energy-dependent and controlled by the physiology of reproduction. Food energy comes from sunlight, either directly or indirectly via plant grown and the creation of microRNAs in plants. Serious scientists know how to light the sun’s anti-entropic virucidal energy to DNA repair.
See: Watson–Crick Base Pairing Controls Excited-State Decay in Natural DNA (2014)
Reported as: Base-pairing protects DNA from UV damage

…the Watson-Crick base-pairing mechanism itself controls the dissipation of the absorbed UV energy. This contradicts the conventional wisdom, which holds that the base sequence within the same strand is responsible for the deactivation of excited states,” says Wolfgang Zinth.

Ultrafast deactivation pathways bestow photostability on nucleobases and hence preserve the structural integrity of DNA following absorption of ultraviolet (UV) radiation. One controversial recovery mechanism proposed to account for this photostability involves electron-driven proton transfer (EDPT) in Watson–Crick base pairs. The first direct observation is reported of the EDPT process after UV excitation of individual guanine–cytosine (G⋅C) Watson–Crick base pairs by ultrafast time-resolved UV/visible and mid-infrared spectroscopy. The formation of an intermediate biradical species (G[−H]⋅C[+H]) with a lifetime of 2.9 ps was tracked. The majority of these biradicals return to the original G⋅C Watson–Crick pairs, but up to 10 % of the initially excited molecules instead form a stable photoproduct G*⋅C* that has undergone double hydrogen-atom transfer. The observation of these sequential EDPT mechanisms across intermolecular hydrogen bonds confirms an important and long debated pathway for the deactivation of photoexcited base pairs, with possible implications for the UV photochemistry of DNA.

There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.

The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the reprint edition:

“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (Roger Penrose 8 August 1991)

See also: From Fertilization to Adult Sexual Behavior In our section on molecular epigenetics, we wrote:

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.

It links the virus-driven theft of quantized energy from the degradation of messenger RNA to mutations and all pathology, and physicists cannot explain that fact with math and definitions. They tried with de Vries 1902 definition of mutations, and they have failed miserably ever since.

See: Amino acid–base interactions: a three-dimensional analysis of protein–DNA interactions at an atomic level (2001)

To assess whether there are universal rules that govern amino acid–base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein–DNA complex structures. DNA–backbone interactions are the most numerous, providing stability rather than specificity. For base interactions, there are significant base–amino acid type correlations, which can be rationalised by considering the stereochemistry of protein side chains and the base edges exposed in the DNA structure.

See also: Systematic prediction of DNA shape changes due to CpG methylation explains [quantized energy-dependent] epigenetic effects… (2018)
The effects of sunlight and quantum chemistry link energy-dependent fixation of RNA-mediated amino acid substitutions to the differentiation of all cell types in all living genera via the physiology of reproduction, which is controlled by pheromones in species from microbes to humans. Pheromones biophysically constrain viral latency in all animals that need to eat for their species to survive.

Cryo-EM technology predicts RNA-mediated DNA shape, which means the technology can be used to link the virus-driven degradation of messenger RNA from mutations to all pathology in the context of the games “Cytosis” and “Subatomic.”
When “Subatomic” is available, players will link what is known to all serious scientists who present during “Schrodinger at 75” to the overwhemling amount of pseudoscientific nonsense touted by theorists during the past 75 years.

Schrodinger linked the anti-entropic virucidal energy of sunlight to all biophysically constrained biodiversity via the physiology of reproduction in all plants and animals. Pseudoscientists decided to use mutations and natural selection instead of Darwin’s “conditions of life.” That is why pseudoscientists can — and soon may be — blamed for all extant pathology.

Subatomic: An Atom Building Board Game (Update #2)

Theorists failed to link subatomic particles to biophysically constrained viral latency via the “Virus Expansion” from “Cytosis.” That fact led to this admission of ignorance:

Microscopic chariots deliver molecules within our cells https://phys.org/news/2018-02-microscopic-chariots-molecules-cells.html

Excerpt: This discovery was totally unexpected, and will change how this motor complex is represented in cell biology and biochemistry text books,” says Saikat Chowdhury, PhD, a TSRI research associate and co-first author of the study.

“There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule,” Lander adds.

My comment: All the discoveries that have since linked energy-dependent changes from electrons to ecosystems were anticipated by Richard P. Feynman in his claims about “Plenty of Room at the Bottom.” Everything known to serious scientists links cryo-EM technology from ecological niche construction to socio-cognitive niche construction via food energy-dependent amino acid substitutions in the microtubules that link differences in animal behavior to human consciousness.

It will good to see “Subatomic” placed into the context of the admission that there are two dynein molecules. Others may begin to see the levels of complexity that must be represented in game play to prevent further assumptions based on ignorance of particle physics and energy transfer that biophysically constrains viral latency.

The fact that many people can readily learn more than most theoretical physicists have learned about subatomic particles and cell biology by playing games for fun is an exciting development for scientists and laypersons.

Magnus S. Magnusson wrote: James Kohl it [the Neil deGrasse Tyson meme] was not aimed at you, of course, understand that it is about the genera educational situation. BTW Einstein mostly missed biology and Hawking says the 21. century will be that of biology, which I also believe.”
The Icelandic atheist and hate monger, blocked me before I could comment further on Neil deGrasse Tyson’s overwhelming display of ignorance.
George FR Ellis, who co-authored with Stephen Hawking in the 60’s has already validated my model. See: Understanding and accounting for relational context is critical for social neuroscience

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics.

The Genius Games series from John Coveyou is the way forward. The games successfully link the creation of the sun’s anti-entropic virucidal energy from top-down causation to all biophysically constrained biodiversity via a model that links electrons to ecosystems.

See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems