#80. The Restricted Weathering Theory of Abiogenesis

 CH   EV

Red, theory; black, fact

Last update: 08-21-2024

When the early Earth, which was initially molten, had cooled sufficiently to acquire a solid crust and allow liquid water to accumulate on the surface, the formation of the oceans presumably began.

Seawater forms from steam outgassing from volcanic vents, which simultaneously emit acid gasses such as hydrochloric acid. Therefore, the first rain would have been highly acidic. In the normal course of events, volcanic rain falls on surface rocks that contain sufficient alkalinity to completely neutralize the acid, contributing cations such as sodium in the process and producing salt water. However, I postulate that shortly after the formation of the Earth’s crust, the surface rocks were mostly encapsulated in carbonaceous pyrolysis residues, basically barbecue gunk, originating from carbon-bearing gasses in the atmosphere. How is the acid rain supposed to get to the rocks?

I postulate that sometimes it did, and sometimes it didn’t, leading to a scenario of nascent crust covered in interconnected puddles in which a broad range of pHs were simultaneously represented. At the connecting points, a pH gradient would have existed, which recalls the pH gradient across the mitochondrial membrane that powers ATP synthesis. 

More simply, a lump of lava coated in a capsule of pyrolysis residue and immersed in acid rainwater will have a proton gradient across the capsule with the correct direction to model the inner mitochondrial membrane with its enclosed matrix.

The carbon-bearing gasses in the atmosphere would have been methane and the result of methane combination with water (formaldehyde),  nitrogen (cyanide and cyanogen), and sulfur (DMSO, only plausible), all triggered by solar ultraviolet. This suggests that the pyrolysis residues will contain sulfur, oxygen, and nitrogen heteroatoms, as does coal. An imaginary pore through the capsule will be lined with such heteroatoms, which are candidates for playing the role of the arginine, lysine, aspartate, and glutamate residues in the ATP synthase catalytic site. Protonation-deprotonation reactions would be available for powering the formation of polyphosphate (a plausible ATP precursor) from orthophosphate. The conformational changes so important in the modern ATP synthase do not appear to be available in this primordial system, so we need to demonstrate the presence of an equivalent. Conceivably, the phosphorus-rich species diffuse up and down in the pore, producing proton transport as they do so that is linked to phosphate condensation reactions. Judging by the modern ATP synthase, coordination of phosphate to magnesium ions may also be part of the mechanism. Mafic rocks such as lava are rich in magnesium.

06-30-2024: The flux of acid through the pore will dissolve orthophosphate out of some minerals in the rock such as apatite. If we suppose that the pore is lined with carboxylic acid groups modelling glutamate and aspartate side chains, then at some depth in the pore the pH in the pH gradient will equal the pKa of the acid, and the acid groups will spend half their time protonated and half ionized, resulting in general acid-base catalysis in a narrow zone in the pore. Magnesium-complexed orthophosphate will be catalytically converted to an equilibrium mixture containing some pyrophosphate in this zone and then proceed to diffuse out the exterior opening of the pore before it can be converted back. As a result, the condensing agent pyrophosphate will be available in the early oceans for catalyzing the formation of organic macromolecules such as early proteins and nucleic acids, which are forerunners of important building blocks of modern life forms. 

The efficiency of the pyrophosphate synthesis would be enhanced by a high phosphate concentration, which would be due to the restricted, underfilm spaces in which the weathering processes were occurring.

08-21-2024: The gradual expansion of the underfilm weathered pockets eventually undermines the local pyrolysis film, causing a flake to detach. The remaining rock surface will be largely coated in the first organic polymers created by condensing agents at low temperature. The process then repeats, leading to successive generations of biofilm creation and detachment. At this point, an evolution-like biofilm selection process can be postulated.

#79. A Cosmological Setting for a General Relativity-Quantum Mechanics Unification

“The Sphere,” campus of the National Research Council, Ottawa 

PH

Red, theory; black, fact

Figure 1. The expanding 5-ball

Figure 2. A wave packet

Last update: 11-05-2024

The spacetime of general relativity (GM) is here considered to be an expanding 4D hyperball (4-ball) on the surface of an expanding 5D hyperball (5-ball). The latter is surrounded by subatomic-sized 5-balls ("paramorfs") that can fuse with the big, nearby 5-ball, which is the mechanism by which the latter enlarges. (Technically, a “sphere” is just a surface, with a dimensionality one less than the embedding space. I use “ball” here to refer to the embedding space dimensionality.)

Each fusion event sends out a ripple on the surface of the big 5-ball that travels at the speed of light in vacuum. A sequence of fusions happening in the correct order causes the ripples to add up to a shock wave at some point. At the maximum of the shock wave, the surface of the 5-ball is thrown out especially far into the surrounding emulsion of paramorfs, where it makes contact with yet another paramorf, resulting in yet another fusion event and another ripple, which has the correct phase to add to the shock wave. The result is a self-sustaining cycle that leads to persistence and thus observable particle-like phenomena. The crest of the shock wave may have to pass through a depletion zone to reach the nearest paramorf. This mechanism is based on Born's rule of quantum mechanics. <03-30-24: If wave curvature rather than displacement amplitude determines paramorf fusion probability, then we get something even closer to Born’s rule, which states that the square of the wave function is proportional to the probability of observing a particle. The curvature of a sine wave is not its square, but the resemblance is striking. Perhaps an experimental verification of Born’s rule with unprecedented accuracy is warranted to distinguish the two theories.> 

<07-27-2024: The big 5-ball may be filled with an emulsion of yin paramorfs in a continuous yang phase, as well as being surrounded by an emulsion of yang paramorfs in a continuous yin phase. Droplets of yin space could get injected into the interior as a side effect after each yang paramorf fusion event. This would explain why curvature alone dictates fusion probability: a concavity reaching interior yin paramorfs is as effective as a convexity reaching exterior yang paramorfs, and no depletion zone will develop over time. Yin and yang space are terms coined in a previous post, “The Checkered Universe.”>

Particle formation is entropically disfavored (requires a precise configuration unlikely to arise by chance) and thus only happens when paramorf fusions are frequent due causes other than the presence of particles. Postulating that spontaneous fusions are more frequent when the curvature of the 5-ball is greater, spontaneous fusions will be abundant when the growing 5-ball is still tiny and thus intensely curved. This would be seen in our 4-ball as the inflationary era of the Big Bang. (Problem: the paramorfs themselves are the most intensely curved elements in this system. Possibly, a binary paramorf fusion event releases so much energy in such a confined space that the fusion product immediately splits apart, resulting in no net effect overall.) The surface of our 4-ball would be formed by the stable particles radiating out of our local inflationary zone on the 5-ball into newly-created, blank 4-surface (see Figure 1). This radiation would define the post-inflationary era. Our time dimension would be one of the radii.

These particles propagate in time the given, as opposed to time the clock reading. The position of the particle along its track is the clock reading.

This theory evolved to a six-dimensional form at the paragraph beginning “Close inspection…”, below. Earlier paragraphs have not been adjusted to reflect this.

The illustrated mechanism of particle creation (see Figure 2) is periodic-deterministic and may account for photons and leptons. The corresponding chaotic mechanism may account for baryons, and the corresponding probabilistic mechanism may account for dark matter. The close relationship we see today between protons and electrons could have been due to their relationship during the inflationary era; the vicinity of one could have served as an incubator for the other. The multitude of expanding spacetime ripples predicted to be around any massive object would comprise the spacetime curvature referred to by the Einstein tensor of the relativistic field equations. 

The asymmetry of the wave packet that leads to the shock wave accounts for momentum. According to special relativity, mass-equivalent energy is just the spacetime component of the momentum along the time axis.

Fixing radius = 1, the 5-ball has the greatest volume of any ball dimensionality. (See the Wiki on “n-sphere”) Thus, this dimensionality could have been forced by some principle of minimizing the radius-to-volume ratio, call it a compaction principle (in a physical, not topological sense), the existence of which is already implied by the assumed ball shape. We cannot invoke gravity here to produce compaction because gravity emerges at a higher level of description than this. A surface tension-like effect related to the permittivity of free space may serve, which is already implied by invoking ripples on the surface. However, mention of ripples implies that the governing differential equation has oscillatory solutions, which seems to also require a medium with inertia, which may be related to the permeability of free space.

08-07-2024: If an overarching process of yin-yang separation existed, which would explain why all observations are ultimately observations of contrasts, this process would arguably have a smoothing effect on any resulting interfaces. Such smoothing would suggest surface tension when considered spatially and inertia when considered temporally.

A limitation of this theory is that it does not have explain the assumed presence of discrete, ancient inflationary zones on the surface of the 5-ball.

03-20-24: Close inspection of the volume versus dimensionality curve for n-balls of radius 1 suggests that maximum volume occurs at a fractional dimensionality somewhat above 5, which looks to be about five and a quarter. Under the compaction principle, this circumstance would lead to a squashed (oblate) 6-ball about one-quarter as thick as it is wide, with greatest curvature at the equator. (Here I am making an analogy with the Earth’s surface, which is an oblate spheroid.) This uneven distribution of curvature would result in the equatorial region losing its inflationary status later than at the poles, suggesting that the universal equatorial region spawned all the particles we can now see during the late inflationary era and that our familiar 3-space corresponds to a line of latitude on the oblate 6-ball travelling steadily toward a pole. This scenario allows the existence of ancient, dilute matter of non-equatorial origin coexisting with our 3-space. <04-11-24: This ancient dilute matter could account for cosmic rays and some of the diffuse cosmic gamma glow. Some of these ancient particles would by chance approach us in our future light cones and would therefore interact with our 3-space as antimatter. The resulting annihilation events would produce gamma rays and neutrinos. Those particles that escape annihilation could potentially re-emerge from our spacetime in our past light cones and at a different point, becoming matter cosmic rays. Cosmic particles following spacelike trajectories may not interact strongly with us, like two waves crossing at right angles, but Born's rule predicts some interaction.>

03-25-24: A second limitation of this theory is that relativity theory denies the existence of an absolute frame of reference, which I have just re-introduced in the form of the surface of a large ball. <04-27-2024, 09-07-2024: Perhaps this limitation can be addressed by showing that the concept of no absolute frame of reference can be replaced with the concept of space-tilted matter, in which the lengths of meter sticks change due to a tilt of the structure of Figure 2 so that propagation is no longer purely in time, but now has a component in space, and the length change must be to a degree necessary to guarantee the null result of the Michelson--Morley experiment.> 

<05-04-2024: The surface of a 6-ball is a 5-dimensional space. Particle propagation on this surface uses up one of these dimensions, turning it into time. However, the resulting spacetime has four dimensions of space and we see only three. What happened to the other one? Most likely it was largely suppressed by black hole formation shortly after the inflationary era. Black hole formation should be very facile in four spatial dimensions because gravitational orbits are unstable and radiative cooling is relatively efficient. This places us on the event horizon of one of these 4-D black holes and suggests that the event horizon actually is the membrane it seems to be in some theoretical studies. Considered geometrically, the event horizon is a surface and will therefore have a dimensionality one less than that of the bulk. Life on this surface will therefore be three dimensional.>

09-03-2024: String theory posits that a particle is a one-dimensional vibrating string embedded in three dimensions. However, my theory posits that a particle is a three dimensional system embedded in six dimensions. We are situated in a privileged location in 6-space in which three of these dimensions have an inward and outward direction. An analogous point in 3-space would be the corner of a cube. The wave component of particles would oscillate along a vector that can rotate in a wholly extradimensional plane, and with an axis of rotation perpendicular to all three dimensions of space, possibly coinciding with time. This would be the spin of the particle. In the cube analogy, one of the edges parallel to the time dimension is spiralling. If the vector rotates in a plane contained within 3-space, this would be the circular polarization of light. See Figure 3.

Future directions of this inquiry are 1) obtaining the details of the postulated length contraction in space-tilted matter, and 2) exploring the possibility of synchronization and anti-synchronization of fusion events between adjacent particles. (Such an effect could account for the narrowness of the time slice we seem to be living in.)

Etymology: "warped spacetime," Greek: paramorfoménos chorochrónos, thus: "paramorf."

Figure 3. A hyper-black hole progressing across the surface of the big 6-ball. The three spatial dimensions of relativity theory have been suppressed for clarity and are represented by points A. t is time. The instantaneous structure resembles one edge of a cube merging with a surface. The line between points A may function as a closed chamber for fusion ripples because of the right-angle relationships at each end, leading to intensified shock waves inside and intensified paramorf fusion. This, in turn, dynamically maintains the geometry shown.

I suggest that in general, spacetime structures tend to evolve to greater efficiency in paramorf capture, and deviations from these structures will appear to be opposed by forces. This can be cited as a general principle in exploring the present theory. 

09-24-2024: For example, two fermions could capture paramorfs cooperatively: capture by one triggers an expanding ripple that reaches the other and triggers its own capture. This second capture then sends a ripple back to the first fermion, where it triggers a third capture, and so on. This duetting action is formally like light bouncing back and forth between parallel mirrors, as in the Michelson—Morley interferometer. If duetting efficiency maintains the length of meter sticks, we have the beginnings of the long-sought explanation of the null result of the Michelson—Morley experiment in terms that allow the existence of a medium for the wave aspect of particles.

11-05-2024: Velocity in space relative to the medium upsets the spatial relationships necessary for efficient duetting, triggering a compensatory reorganization of the spacetime structure to re-optimize paramorf capture efficiency, by the general principle enunciated above. This leads to the Fitzgerald contraction, one of the two basic effects previously explained in terms of Special Relativity. The other is time dilation; if fermions are always literally travelling along a time dimension as postulated here in connection with the space-tilted matter concept, a greater velocity along any spatial direction must come at the expense of a lesser velocity along the time dimension, leading to time dilation.

Thus, the unification of QM and Relativity may be at hand. 

10-13-2024: Duetting could account for attractive forces between fermions and destructive interference could account for repulsive forces. A difficulty is that the simple ripple model is one-sided whereas destructive interference assumes sinusoidal disturbances, which are two-sided. This could be remedied by assuming that the ripples have profiles like wavelets or the Laplacian of the Gaussian.

Zen weeds in the Rideau canal

Snail universe beside the Rideau canal

#77. How the Cerebellum May Adjust the Gains of Reflexes [Neuroscience]

 

NE

Red, theory; black, fact

The cerebellum is a part of the brain involved in ensuring accuracy in the rate, range, and force of movements and is well known for its regular matrix-like structure and the many theories it has spawned. I myself spent years working on one such theory in a basement, without much to show for it. The present theory occurred to me decades later on the way home from a conference on brain-mind relationships at which many stimulating posters were presented.

Background about the cerebellum

The sensory inputs to the cerebellum are the mossy fibers, which drive the granule cells of the cerebellar cortex, whose axons are the parallel fibers. The spatial arrangement of the parallel fibers suggests a bundle of raw spaghetti or the bristles of a paint brush. These synapse on Purkinje cells at synapses that are probably plastic and thus capable of storing information. The Purkinje cells are the output cells of the cerebellar cortex. Thus, the synaptic inputs to these cells are a kind of watershed at which stimulus data becomes response data. The granule-cell axons are T-shaped: one arm of the T goes medial (toward the midplane of the body) and the other arm goes lateral (the opposite). Both arms are called parallel fibers. Parallel fibers are noteworthy for not being myelinated; the progress of nerve impulses through them is steady and not by jumps. The parallel fibers thus resemble a tapped delay line, and Desmond and Moore seem to have [paywall] proposed this in 1988.

The space-time graph of one granule-cell impulse entering the parallel-fiber array is thus V-shaped, and the omnibus graph is a lattice, or trellis, of intersecting Vs.

The cerebellar cortex is also innervated by climbing fibers, which are the axons of neurons in the inferior olive of the brainstem. These carry motion error signals and play a teacher role, teaching the Purkinje cells to avoid the error in future. Many error signals over time install specifications for physical performances in the cerebellar cortex. The inferior olivary neurons are all electrically connected by gap junctions, which allows rhythmic waves of excitation to roll through the entire structure. The climbing fibers only fire on the crests of these waves. Thus, the spacetime view of the cortical activity features climbing fiber impulses that cluster into diagonal bands. I am not sure what this adds up to, but what would be cute?

A space-time theory

Cute would be to have the climbing fiber diagonals parallel to half of the parallel-fiber diagonals and partly coinciding with the half with the same slope. Two distinct motor programs could therefore be stored in the same cortex depending on the direction of travel of the olivary waves. This makes sense, because each action you make has to be undone later, but not necessarily at the same speed or force. The same region of cortex might therefore store an action and it’s recovery.

The delay-line theory, revisited

As the parallel-fiber impulses roll along, they pass various Purkinje cells in order. If the response of a given Purkinje cell to the parallel-fiber action potential is either to fire or not fire one action potential, then the timing of delivery of inhibition to the deep cerebellar neurons could be controlled very precisely by the delay-line effect. (The Purkinje cells are inhibitory.) The output of the cerebellum comes from relatively small structures called the deep cerebellar nuclei, and there is a great convergence of Purkinje-cell axons on them, which are individually connected by powerful multiple synapses. If the inhibition serves to curtail a burst of action potentials triggered by a mossy-fiber collateral, then the number of action potentials in the burst could be accurately controlled. Therefore, the gain of a single-impulse reflex loop passing through the deep cerebellar nucleus could be accurately controlled. Accuracy in gains would plausibly be observed as accuracy in the rate, range, and force of movements, thus explaining how the cerebellum contributes to the control of movement. (Accuracy in the ranges of ballistic motions may depend on the accuracy of a ratio of gains in the reflexes ending in agonist vs. antagonist muscles.)

Control of the learning process

If a Purkinje cell fires too soon, the burst in the deep cerebellar nucleus neuron will be curtailed too soon, and the gain of the reflex loop will therefore be too low. The firing of the Purkinje cell will also disinhibit a spot in the inferior olive due to inhibitory feedback from the deep nucleus to the olive. I conjecture that if a movement error is subsequently detected somewhere in the brain, this results in a burst of synaptic release of some monoamine modulator into the inferior olive, which potentiates the firing of any recently-disinhibited olivary cell. On the next repetition of the faulty reflex, that olivary cell reliably fires, causing long-term depression of concurrently active parallel fiber synapses. Thus, the erroneous Purkinje cell firing is not repeated. However, if the firing of some other Purkinje cell hits the sweet spot, this success is detected somewhere in the brain and relayed via monoamine inputs to the cerebellar cortex where the signal potentiates the recently-active parallel-fiber synapse responsible, making the postsynaptic Purkinje cell more likely to fire in the same context in future. Purkinje cell firings that are too late are of lesser concern, because their effect on the deep nucleus neuron is censored by prior inhibition. Such post-optimum firings occurring early in learning will be mistaken for the optimum and thus consolidated, but these consolidations can be allowed to accumulate randomly until the optimum is hit.

Photo by Robina Weermeijer on Unsplash

#76. Role of personalities in the human swarm intelligence [population]

PO

Red, theory; black, fact.

Précis: each of the Big Five personality traits is a dimension along which people differ in some socially important behavioral threshold. These are, respectively: openness > uptake of innovations; conscientiousness > uptake of taboos; extraversion >  committing to collectivism*; agreeableness > becoming militant; neuroticism > engaging in/submitting to persecution. The personality trait is written on the left of the ">" and the putatively impacted social threshold is on the right.

These threshold spectra enable social shifts that are noise-resistant, sensitive to triggers, and rapid. Noise resistance and sensitivity together are called good “receiver operating characteristics,” a concept often used in the scientific literature.

A metaphor that suggests itself is lighting a camp fire. The spark is first applied to the tinder. Ignition of the tinder ignites the kindling. Ignition of the kindling ignites the small sticks. Ignition of the small sticks ignites the big sticks, and everything is consumed.

Orderly fire-starting appears to require a spectrum of thresholds for ignition in the fuel, as may orderly social shifts. To further extend the metaphor, note that the fuel must be dry (i.e., situational factors must be permissive).

11-07-2022: Social novelties spread upward to higher-threshold social strata by meme propagation reinforced by emotional contagion. The emotional energy necessary for emotional contagion would come from the individual’s interaction with the novelty, which would feature a positive feedback.

Our capacities for all of the enumerated social shifts were selected in evolution and most can be assumed to be still adaptive when correctly triggered. In today’s world, shifts to persecution are probably the least likely to still be adaptive, and could be a holdover from our Homo erectus stage. Persecution leads to refugee production, and refugee production could have been the reason that guy was such a great disperser.

As the geologists say, “The present is the key to the past.”

* 01-17-2023: A possible anti-invasion adaptation and predictable from geography.

#75. A Tripartite Genetic Code [Genetics]

GE

 Red, theory; black, fact

(Originally posted in the "Enhancers" post.) 

The filamentous alga Cladophora.

Last update: 08-19-2024

In this post, conceived while I was in a hospital, I propose that there are three genetic codes, not one. Conventional thinking says that there is just one code, which encodes the amino acid sequence of proteins into DNA. Here are the two new ones:

A morphology code for the multicellular level

08-01-2022: The interaction of semipermanent charges on chromatin, a possibility introduced in the "Enhancers" post, could structure the chromosomes into reproducible configurations within the nucleus. For instance, a chromatin segment with a net positive charge will tend to stick to a segment with a net negative charge, leading to their respective chromosomes being spot-welded at that point. An analogy from protein chemistry would be a disulfide bridge. This structuring may be followed by transmission of nuclear 3D information through the nuclear membrane to dictate the nuclear diameter along which the centrosomes separate to initiate mitosis. This, in turn, will dictate the orientation of the mitotic division plane. In the context of a growing embryo, such control of the orientation of mitosis is arguably at the origin of organ and body morphology. For example, all planes parallel will result in a filamentous organism like Cladophora. Planes free to vary in only one angle (azimuth or elevation) will produce a sheet of cells, a common element in vertebrate embryology. Programmed variation in both angles can produce a complex 3D morphology like the vertebrate skeleton. Thus we begin to see a genetic code for morphology, distinct from the classical genetic code that specifies amino acid sequences. 

<08-05-22: Possibly, each chromosome folds in a hairpin turn near the center of the nucleus and ends up occupying a specific conical solid angle. A cell generation counter or the developmental signals around the cell then activate a centrosome-maker gene in one specific chromosome and no other. This gene is then transcribed into a long noncoding RNA molecule that protrudes from a specific nuclear pore and triggers the assembly of a new centrosome just outside the nucleus at a specific azimuth and elevation. The nucleus is tethered by cytoskeletal elements such as lamin, nesprin, actin, and tubulin to focal adhesions on the the cell membrane, non-rotatably, so that all angle information can be referred to the previous mitotic orientation. The final step is dislodging the old centrosome and sweeping it into the antipodal position of the new one. This could be done by an array of microtubules growing radially out of the new centrosome but constrained to stay close to the nuclear membrane. 

Thus, there appear to be two tiers of control of mitotic orientation available: controlling which chromosome or chromosome arm produces the centrosome-maker RNA, and controlling the pattern of histone epigenetic marks in the nucleus and thus the chromatin charge pattern and thus the 3D structure into which the chromosomes assemble, and thus the mitotic angles assigned to a given chromosome.> <09-01-22: At the DNA level, the code for multicellular morphology would take the form of promoter-controlled segments that transcribe into long noncoding RNAs having a special two-domain structure: a domain that binds to a particular kind of histone-modifying enzyme and a domain that binds to a particular DNA sequence. These lncRNAs would specify, at the second tier of control, local charge changes in chromatin in a context-dependent manner.><09-14-2022: In organisms that are morphologically complex but have few chromosomes in their karyotype, such as fruit flies, the mitotic angles could be assigned to reproducible chromatin loops as well as to whole chromosomes, suggesting a 3-tiered control system.><19-08-2024: The nucleus is usually spherical or ovoid and is about ten times more rigid than the surrounding cytoplasm, features which may be related to the demands of the morphology read-out process. Consistent with this, blood is a tissue without a morphology, and the nucleated cells of the blood have nuclei that are mostly irregular and lobate. The lymphocytes found in the blood have round nuclei, however, but these cells commonly form aggregates that can be considered to possess a simple morphology.>

A morphology code for the single-cell level in cells with nuclei

<08-20-22: I further propose a third genetic code: a code for single-cell morphology, and cell morphology can be very elaborate, especially in neurons. This will probably involve storing information about cytoskeleton morphology in DNA. Neurons express especially many long noncoding RNAs, so I suggest that these transcripts can carry morphological information about cytoskeletal elements. This information could be read out by using the lncRNA as a template on which to assemble the cytoskeletal element, then removing the template by enzymic hydrolysis or by some spirane-like enzyme. Greater efficiencies could be achieved by introducing some analog of transfer RNAs. LncRNAs are already implicated in transcriptional regulation, and this might be done indirectly by an action on the protein scaffolding of the chromatin. Moreover, as you would predict from this theory, lncRNAs are abundant in cytoplasm as well as in the nucleus, and the cytoplasm contains the most conspicuous cytoskeletal structures. The template idea is similar to but goes beyond the already-established idea that lncRNAs act as scaffolds for ribonucleoprotein complexes. Since cytoskeletal elements are made from monomers of few kinds, we would expect the template to be highly repetitious, and lncRNAs are decidedly repetitious. Indeed, transposons and tandem repeats are thought to drive lncRNA evolution. See https://doi.org/10.1038/s41598-018-23334-1, in Results, subsection: "Repetitive sequences in lncRNAs," p. 4 in the PDF.>

An uncertainty principle for molecular biology?

09-02-2022: These ideas call into question the assumption that all biological order stems from primary amino acid sequences and that a glorified bacterial genome, if artfully regulated, can produce a human. Is there a fundamental limit on how high an amino acid residue can extend its influence in the structural hierarchy of biology? Even something as big as a ribosome appears to need help from ribosomal RNAs to keep its act together. However, perhaps the issue is coding parsimony.

Two more biological questions:

1. Does a cell in a multicellular organism run a metabolic simulation of the whole organism to help it carry out its specialized role more efficiently? Are these little guys thinking of us?

2. Is immune cycling the answer to preventing cancer? Let’s say you deliberately take a drug to suppress your immune vigilance for one month out of each year, then discontinue the drug to let it rebound. During suppression, the micro cancers run wild for a short time, thereby growing large enough for the immune function to easily detect them upon its return. They get whacked, of course, and the immune system learns something in the process, making it a more effective anti cancer system going forward. The analogy here would be a cat playing with a mouse it has caught. Since it is play, it is a learning activity; the cat is working on its game. Pre-civilization, human immune suppression would have happened regularly due to prolonged  environmental stressors, leading to cannier immune systems and lower cancer rates than we now experience.

This agrees with the impression I have that cancer is a disease of modern lifestyles. The following article may or may not be relevant: Coventry, B.J., Ashdown, M.L., Quinn, M.A. et al. CRP identifies homeostatic immune oscillations in cancer patients: a potential treatment targeting tool?. J Transl Med 7, 102 (2009).  https://doi.org/10.1186/1479-5876-7-102 

#74. Extended Theory of Mind [Evolution]

EV

Red, theory; black, fact.

Where is evolution going at the moment? Pretty good question. Let us look around, then. I am writing this in a submarine sandwich joint where one sandwich maker is serving two customers. The radio brings in a ballad by a lady vocalist at a tempo suggestive of sex. Now a DJ (Mauler or Rush) is amusing the listeners with some patter. The window shows that rush hour is over and only a few home-bound stragglers are in the street. If I crane my neck, I can see the green beacon on the new electric charging station. 

That will do for starters. Sandwich maker, pro singer, DJ, bureaucrat, electrician—I couldn’t do any of that. We are a society of specialists, and such societies feature differentiation with integration. So, how far back does this go? At most, nine millennia; about 450 generations. Time enough for evolution? Doesn’t matter; we want direction here, not distance.

Contemporary natural selection of humans will therefore reward differentiability and integratability.

Differentiability: vocational choices often begin in childhood with hobbies, and there is a certain frame of mind associated with hobbies called “flow.” I therefore suggest that we are being selected for a susceptibility to flow. 

Integratability: society is held together by our ability to coordinate with others, and the key ability here is thought to be “theory of mind,” or the ability to infer the mental states of those with whom we interact. Likewise, we are being selected for theory-of-mind ability.

I would like to suggest that there is something higher than theory of mind, which not everyone possesses at this time: extended theory of mind: inferring the mental states of those not present, and whose very existence is itself inferred. A society strong in this trait will appear to be communicating with one another through solid walls, as if by ESP. 

Who are these Chosen? Probably military generals, politicians, and the executive class. Go figure.

However, the human cranium is probably as voluminous as it can get and still allow childbirth, so the gray matter subserving the new ability will have to be included at the expense of some other, preferably obsolete ability, like accuracy in spearing game animals.

So challenge your mayor to a game of darts and see how he does. This theory is falsifiable.

Photo by Le Vu on Unsplash

#73. How Enhancers May Work [Biochemistry]

 CH

Red, theory; black, fact.

Background about enhancers

Enhancers are stretches of DNA that, when activated by second messengers like cyclic AMP, enhance the activity of specific promoters in causing the transcription of certain genes, leading to the translation of these genes into protein. Enhancers are known for causing the post-translational modification of the histones associated with them. Typically, lysine side chains on histones are methylated, doubly methylated, triply methylated, or acetylated. Serines are phosphorylated. In general, phosphorylation condenses chromatin and acetylation expands and activates it for transcription. Methylation increases positive electric charge on the histones, acetylation decreases positive charge, and phosphorylation increases negative charge. The enhancers of a promoter are usually located far away from it measuring along the DNA strand, and can even be on different chromosomes ("in trans"). 

The mystery of enhancer–promoter interaction

How the distant enhancer communicates with its promoter is a big mystery. The leading theory is that the enhancer goes and sticks to the promoter, and the intervening length of DNA sticks out of the resulting complex as a loop. This is the "transcription hub" theory. 

My electrostatic theory of enhancer–promoter interaction

I propose a far different mechanism: when activated, the multiple enhancers cause modification of their associated histones that place the same electric charge on all of them, which is also of the same sign as the charge on the promoter region. Mutual electrostatic repulsion of all these regions then expands the chromatin around the promoter. This effect reduces the fraction of the time that the RNA polymerase II cannot move down the DNA strand because unrelated chromatin loops are in the way, like trees fallen across the railway tracks. (Each "tree" eventually moves away because of Brownian motion.) This could also be the mechanism of chromatin decondensation generally, which is known to be a precondition for the expression of protein-coding genes.

05-28-2022: The mutual electrostatic repulsion of enhancers does not necessarily accomplish decondensation directly, but may do so indirectly, by triggering a cascade of alternating chromatin expansions and histone modifications. Furthermore, this cascade is not necessarily deterministic. These ideas predict that raising the ionic strength in the nuclear compartment, which would tend to shield charges from each other, should inhibit gene activation. This manipulation will require genetic knockout of osmolarity regulating genes.