#40. The 1950 Ramp [population, genetics, evolutionary psychology, engineering, neuroscience]

PO     EN     EP     NE     GE     

Red, theory; black, fact.

6-01-2018; Since about 1950, the world population has been increasing along a remarkably steady ramp function with no slackening in the rate of increase yet apparent, although one cycle of oscillation in the slope occurred during the Sixties. Malthusian reasoning predicts an exponential increase, which this is not. From several lines of evidence, I keep coming back to the idea that humans must have a subconscious population controller in their heads, and yet such a controller would have leveled out the increase by now. Until now, no theory has sufficed to explain the facts.

I here propose that the natural population curve for humans in good times is a saw-tooth waveform, with population ramps alternating with political convulsions that result in a large group being expelled permanently, resulting in the precipitous but limited drop in local population density that ends the saw-tooth cycle. This cycle accomplishes the ecological dispersal function to which I allude many times in these pages. The population must ramp up for a time to sustainably create the numbers needed for the expulsions. The WHO population curve shows only a ramp because it is a worldwide figure and therefore population losses in expelling regions are balanced by population increases in welcoming regions. This also implies that human population has been increasing in a way unrestrained by food or resource availability or any other external constraint since 1950, to now.

Clearly, human population is being controlled by instinctive factors, but not to a constant absolute density, but rather to a constant rate of increase. Population density would go up along the much faster, steeper, and more disastrous exponential curve of Malthus if there were actually no controller.

My formal training in engineering and neuroscience justifies a bit of speculation as to mechanisms at this point. Look first for such a controller in the hypothalamus, already known to control other variables, such as temperature, by feedback principles.

In school, I was taught that nature does not reinvent the wheel, which I understand to mean that once a brain structure evolves to serve a particular computational function, it will be tapped for all future needs for such a calculation. This process may make it grow larger or develop sub-nuclei, but additional, independent nuclei for the same computation will never evolve.

I will continue to assume that the controller is a conventional PID controller, as in previous posts. To make it control rate of increase rather than absolute population density, you put a differentiator in the feedback pathway. Look first in the amygdala for such a differentiator. If you are of the opinion that human population control is urgent, then you must knock out this differentiator and replace it with a simple feed-through connection. Fortunately, one common way for evolution to implement differentiation in mammals is to begin with such a feed-through connection and supplement it with an inhibitory, slow, parallel feed-forward connection. If this is the case here, then you just inhibit the feed-forward pathway pharmacologically as specifically as may be, and the job is done. Subjectively, the effect of such a drug would be to take away people's ability to get used to higher population density in deciding how many children to have. An increased propensity to riot should not occur.

I assumed in the last post that the political convulsions that produce dispersal are triggered by the value on the integrator of the PID controller rising above a threshold. However, in the above design solution, the convulsion would be triggered by the raw, undifferentiated population-density signal rising above some threshold. Look in the amygdala for this signal as well. Consistent with this, bilateral removal of the amygdalae and hippocampi in monkeys is known to have a profound taming effect accompanied by hypersexuality, known as the Kluver-Bucy syndrome.

6-17-2018: To be consistent, I would have to say that the differentiator for the population signal is more likely to be in the hippocampal formation by the argument of nature not reinventing the wheel, because in an earlier post, I interpreted the hippocampus as the site of four successive differentiations that carry out a Fourier transform by mapping sinusiodal waves back onto themselves at a particular best frequency, in the presence of a map of such best frequencies.

However, this setup would require the creation of two neuron-to-neuron connections for its evolution; a first connection to send the amygdalar raw population signal to the hippocampus, and a second to send the differentiated result back for further processing. At best, this would require two simultaneous mutations. Either change by itself would be at best useless and could never be selected. This appears to be another example of irreducible complexity requiring the bi-mutation mechanism described in the previous post. 

The mechanisms usually offered to explain cases of apparent irreducible complexity, such as spandrelling, exaptation, and scaffolding, all appear to lack time efficiency and processiveness. I previously said that in evolution there are no (absolute)  deadlines, but relative deadlines can easily be created by an interaction of processes. In the presence of relative deadlines, such as adaptive footraces to be the first clade to exploit a newly-habitable area or a new niche, time is of the essence and selection for speed and evolvability can be expected. Such selection will create mechanisms such as crossing over that enhance evolvability.

#39. Can Irreducible Complexity Evolve? [genetics, evolution]

EV     GE     

Red, theory; black, fact.

5-26-2018: Influential biologist Richard Dawkins wrote in "The God Delusion" that a genuine case of irreducible complexity will never be found in biology. A case of irreducible complexity would be some adaptation that would require an intelligent designer because it could never evolve one mutation at a time, and Dawkins believes there is no such intelligent designer in biology.

In classic natural selection, each mutation must be individually beneficial to its possessor in order for selection to increase its prevalence in the population to the point where the next incremental, one-mutation improvement becomes statistically possible. In this way, all manner of wondrous things are supposed to evolve bit by tiny bit.

However, I am seeing irreducible complexity all over the place these days. For example, your upper-jaw dentition must mesh pretty accurately with that of your lower jaw or you can't eat. Thus, the process of evolutionary foreshortening of the muzzle of the great apes to the flat human face could never have happened, assuming that a single mutation affects only the upper or lower jaw. But it did. (Let us gloss over the fact that that is an assumption, because the contrary seems to require non-local rules in development.)

Furthermore, how can any instinctive signaling system evolve one mutation at a time? At a minimum, you always need both the transmitter adaptation and the receiver adaptation, not to mention further mutations to connect the receiver circuit to something useful. The evolution of altruism presents a similar problem. The lonely first altruist in the population is always at a disadvantage in competition with the more selfish non-mutants unless it also has a signaling system that lets it recognize fellow altruists (initially, close relatives) and a further mutation that places the altruistic behavior under the control of the receiver part of this system. Thus, altruists would only be altruistic to their own kind, the requirement for altruism to be selected in the presence of selfishness. Finally, the various parts of this system must be indissolubly linked in a way that the non-altruists cannot fake.

My solution is to label the crossing-over events that occur during meiosis as "tetra-mutations." In crossing over, two homologous chromosomes pair up along their length and swap a long segment of DNA, a process requiring four double chain breaks and their corresponding repairs. Because of the presence of single-nucleotide polymorphisms, the homologous chromosomes are not exactly the same, so that each of the upstream sides of the four chain breaks ends up in a subtly different genetic environment. If the break point falls between a cis-acting regulatory element and the corresponding structural gene, for instance, the former may now control the expression of a slightly different protein. Thus, there could be as many as four distinct functional consequences of one crossing-over event. Why not call that a tetra-mutation?

In this way, a concerted change affecting four distinct sites becomes possible. The two ends of the recombinant segment can in principle be functionally unrelated initially. They become related if both are affected by the same tetra-mutation and the entire change increases fitness and is thus selected.

A single tetra-mutation could in principle produce viable altruism at one stroke because of the number of simultaneous changes involved. 

The probability of a combination of simultaneous local changes being beneficial to the organism is much smaller on mathematical grounds than is the probability of a given single-nucleotide change being beneficial. However, these unfavorable statistics are at least partly offset by the existence of a dedicated system for producing tetra-mutations in large numbers, namely meiosis, part of the process of maturation of egg cells and sperm cells.

In the big picture, tetra-mutations provide a way for a species to discontinuously jump into new niches as they open up, possibly explaining how a capacity for this kind of mutation could spread and become characteristic of surviving species over time. This idea also provides a ready explanation for the lack of transitional forms in the fossil record.

5-30-2018: Here is the search description again, in case you missed it or could not see all of it: Sexual reproduction may allow the evolution of irreducible complexity by increasing the intrinsic complexity of the basic building block of change, the mutation.

6-12-2018: Upon further reflection, it seems that the tetramutation construct described above lacks validity because during gamete maturation it falls apart into two bi-mutations, both of which cannot contribute to the same zygote. The bi-mutation is stable, however, because of the intervening translocated DNA segment. It is harder to see how a complex adaptation like altruism could evolve out of nothing but mono-mutations and bi-mutations, but that does not mean the theory put forward in this post is necessarily wrong. One must not argue from lack of imagination. It is an interesting question, actually, what is the minimum set of all mutation types necessary to account for all known adaptations.

8-27-2019: In my ignorance, I have undersold the bi-mutation idea. A very far-reaching change to the genetic information can occur during crossing-over that is not at all subtle and is termed unequal crossing-over. This form of the process arises because of inaccuracies, sometimes major, in the initial alignment of the homologous chromosomes prior to crossing-over. When the process is finished, one chromosome has been shortened and the other has been lengthened, with gene duplication. This is the major source of gene duplication, which, in turn, is a major source of junk DNA, the part that is classified as broken genes. Two questions come to mind. The first is, are anatomical features such as jaw length and axon targets somehow controlled by variations in gene dose? The second, which is a tangent, is, are broken genes really broken or just temporarily switched off by genetic drift at some mutational hot spot in the recognition site of some transcription factor? The analogy here is to a generator in a power plant that has been placed in stand-down mode because of a temporary decrease in the demand for electrical power.

#38. The Fallacy of Justice [evolutionary psychology]

EP

Red, theory; black, fact.

4-04-2018: In my treatment of evil and criminality so far, I have tried to show that they sub serve either dispersal or preemptive population reduction, both valuable biological processes that tend to prolong the survival of species. 

The algorithms for achieving these ends would have been created over time by some form of evolution, with probably a large component coming from a hypothetical, fast form of evolution I call post-zygotic gamete selection (PGS), where gametes -- individual cells -- are effectively the units of selection. In general, the smaller the unit of selection, the faster the adaptation. PGS may have accelerated evolution to the point where it could be detected by simple record-keeping technologies, which may have led to the first record-keeping peoples eventually realizing that "someone is looking out for us," leading to the invention of monotheism.

The genetically inherited parts of our behavior enter consciousness as emotions, and can therefore be easily identified. The main outlines of civilization are probably due to the inherited behavior component, and not to the reasoning, conscious mind, which is often just a detail-handler. How could civilization rest on a process that can't even remember what happened last weekend?

Thus, humans have a dual input to behavior, emotion and reason. The above arguments show that evil and criminality come from the emotional input. Yet the entire deterrence theory of justice assumes the opposite, by giving the person a logical choice: "You do this, we do that, and you won't like it. So you don't do this, right?"

I'm not so sure. People commit crimes for emotional reasons. As usual, the criminal's reasoning faculties are just an after-the-decision detail handler. The direction that this detail handler then takes is fascinatingly monstrous, but this does not mean that crime begins in reason.

Conclusion: the deterrence theory of justice is based on a category error.

Religion, with its emphasis on emotion, was all the formal "law enforcement system" anyone needed up until only about 200 years ago, at the industrial revolution. We may be able to go beyond where religion takes us by means of a disease model of criminality.

It does make some sense to lock criminals up, because with less freedom they cannot physically commit as many crimes. Many prisons become dungeons, however, because of the public's desire for revenge. However, all revenge-seeking belongs to the dispersal/depopulation dynamic and is thus part of the problem. A desire for revenge may follow a crime very predictably, but logically, it is a non-sequitur.

4-30-2018: A more nuanced theory of crime prevention is possible, where logical and technological constraints on behavior complement efforts to reduce the motivation for committing crimes at the source: the individual's perception of the fairness of society. However, I originally wrote as I did because I don't think that the former is the squeaky wheel at the moment.

#34. Emotions [evolutionary psychology, genetics, neuroscience]

EP    NE    GE

Red, theory; black, fact.

12-17-2017: In previous posts, I theorized that humans, along with all other sexually-reproducing species, have a long-range guidance system that I called proxy natural selection, or preferably, post-zygotic gamete selection (PGS), that is basically a fast form of evolution in which individual cells, the gametes, are the units of selection, not individuals. Selection is conjectured to happen post-zygotically (i.e., sometime after the beginning of development, or even in adulthood) but is retroactive to the egg and sperm that came together to create the individual. Each gamete is potentially unique because of the crossing-over genetic rearrangements that happen during its maturation. This theory explains the biological purpose of this further layer of uniqueness beyond that due to the sexual mixing of chromosomes, which would otherwise appear to be redundant.

Our emotions are conjectured to be programmed by species-replacement group selection and to serve as proxies for increases and decreases in the fitness of our entire species.

A further correlate of an emotion beyond the cognitive and autonomic-nervous-system components would be the neurohumoral component, expressed as chemical releasing and inhibiting factors that enter the general circulation via the portal vessels of the hypothalamus, blood vessels which are conventionally described as affecting only the anterior pituitary gland. These factors are theorized to reach the stem-like cells that mature into egg and sperm, where they set reversible epigenetic controls on the level of crossing-over that will occur during differentiation. Large amounts of crossing-over are viewed as retroactively penalizing the gametes leading to the individual by obfuscating or overwriting with noise specifically the genetic uniqueness of said original gametes. In contrast, low levels of further crossing-over reward the original gametes with high penetrance into the next generation. Here, I believe you have all the essential ingredients of classical natural selection, and all the potential, in a process that solves problems on an historical timescale.

Crossing-over happens only between homologous chromosomes, which are the paternal and maternal copies of the same chromosome. Human cells have 46 chromosomes because they have 23 pairs of homologous chromosomes. The homologous-chromosome-specificity of crossing-over suggests that the grand optimization problem that is human evolution has been broken down into 23 smaller sub-problems for the needs of the PGS process, each of which can be solved independently, without interactions with any of the other 22, and which involves a 23-fold reduction in the number of variables that must be simultaneously optimized. In computing, this problem-fragmentation strategy greatly increases the speed of optimization. I conjecture that it is one of the features that makes PGS faster than classical natural selection.

However, we now need 23 independent neurohumoral factors descending in the bloodstream from brain to testis or (fetal) ovary, each capable of setting the crossing-over propensity of one specific pair of homologous chromosomes. Each one will require its own specific receptor on the surface of the target oogonia or spermatogonia. Check this out in the literature, and you will already find a strange diversity of cell-surface receptors on the spermatogonia. (I haven't looked at oogonia yet.&&) I predict that the number of such receptors known to science will increase to at least 23. None of this is Lamarkism, because nervous-system control would be over the standard deviation of behavioral traits, not their averages.

1-09-2018: Naively, this theory also appears to require 23 second messengers to transfer the signals from cell surface to nucleus, which sounds excessive. Perhaps the second messengers form a combinatorial code, which would reduce the number required by humans to log2 (23) = 4.52, or 5 in round numbers. This is much better. Exactly five second-messenger systems are known, these being based on: cyclic AMP, inositol triphosphate, cyclic GMP, arachidonic acid, and small GTPases (e.g., ras). However, many mammalian species have many more than the 32 chromosome pairs needed to saturate a 5-bit address space.

1-10-2018: If we expand the above list of second messengers with the addition of the calcium/calmodulin complex, the address space expands to 64 pairs of homologous chromosomes, for a total ploidy of 128. This seems sufficient to accommodate all the mammals. Thus, a combinatorial second-messenger code representable as a five- or six-bit binary integer in most organisms would control the deposition of the epigenetic marks controlling crossing-over propensity.

If the above code works for transcription as well as epigenetic modification, then applying whatever stimuli it takes to produce a definite combinatorial second-messenger state inside the cell will activate one specific chromosome for transcription, so that the progeny of the affected cell will develop into whatever that chromosome specifies, be it an organ, a system, or something else. And there you may have the long-sought key to programming stem cells. You're welcome.

Each pair of homologous chromosomes may correspond to what in an earlier post was called a "PNS focus." The requirement that the evolution of each chromosome contribute independently to the total increase in fitness suggests that a chromosome specifies a system, like the nervous system or the digestive system. We seem to have only 11 systems, not 23, but more may be defined in the future.

A related concept is that a chromosome specifies an ancestral, generic cell type, like glial cells (4 subtypes known) or muscle cells (3 subtypes known). The great diversity of the neurons suggest that they must be reclassified into multiple basic types, perhaps along the lines suggested by the functional classification of the cranial nerves: general somatic, general visceral, and special somatic (i.e., specific senses).

1-09-2018: A third concept for function assignment to homologous pairs of chromosomes postulates a hypothetical maximally divided genome in which each cell type has its own chromosome pair, a state conjectured to seldom occur in nature. Co-evolution of clusters of cell types (e.g., neurons and glia; bone and cartilage) would create selection pressure for the underlying cell-type-specific chromosomes to become covalently linked into the larger chromosomes that we see in the actual karyotypes. Thus, each observed homologous pair would correspond to a few cell types that are currently co-evolving, which seems to return us to the system or organ concept. 

01-08-2019: The system specified by a chromosome may be called a cooperation system, and these may be organized in a hierarchy, following the general principles of spatial organization outlined in my post: "The Pictures in Your Head." Chromosomes activated earlier in development will specify system-like entities and those activated late in development will specify organ-like entities. Only the first-activated chromosome will apply to the entire organism.

Humans depend on complex social structures for their survival, and this comes out of our individual behavioral tendencies. Probably, most PGS adaptations to environmental fluctuations involve modifying these structures, which would come out of subtle modifications of individual behaviors. I think I am just repeating E.O. Wilson here. Our hard-wired species-fitness definitions would give rise to the primary emotions, perhaps in the hypothalamus or limbic system, by connecting specific stimuli to primary emotions in the manner of an if-then rule. 

Further out on the cortex, the specific stimuli being connected would get progressively more complex and learning-dependent, and progressively less concerned with the "what" of behavior (i.e., our species-specific taxes) and more with the "how" of behavior. In "how" mode, the complex stimuli become more like signposts to be consulted on a journey. PGS adaptations of our behavior would affect the hardwired aspects of this hypothetical transition zone. The primary emotions would then be like the highest hierarchical level of our motor program, or like the least-indented instructions of a conventional high-level computer program.

I conjecture that religion is important because it goes straight for this highest level. We all know that religion is kind of an emotional business, what with the organ music and the stained glass and all such as that, and this is why. I therefore conjecture that words spoken often from the pulpit, such as God, sin, forgiveness, devil, angel, soul, salvation, etc., all enclose a secret that writers such as Dawkins do not grasp: the emotions are the message. To illustrate this, let us attempt an emotional definition of the master symbol, "God."

God: feeling loved and secure to the point of invulnerability; feeling small in an agreeable way, as in the presence of mountains; feeling brotherly/sisterly towards one's fellow humans; blossoming in confidence into one's full potential; fearing nothing.

Perhaps that's enough to give the general idea. No doubt a whole dictionary could be compiled along these lines. When the priest strings these emotion-words together, he creates an experience for the congregation that could fairly be called a form letter from "God," assuming that the word "God" points to the PGS process itself. The job of the priest is to help the congregation relate on a deep level to the sacred texts and to see/feel how they apply to the challenges of the here and now.

7-05-2018: Another term for PGS would be "Yahwetion," from "Yahweh," the conventional modern spelling of the name of the god of ancient Israel, and the "tion" ending indicating a process, like evolution. This neologism advantageously steers people away from category errors like attempting to worship it, or appease it, or what have you.

The conventionally religious will complain that this would make prayer to God impossible, but not if prayer itself is re conceived as "auto socialization," following the educational theory of prayer. Then prayer becomes a fantasy conversation with anyone, living or dead, that you would like to have as a mentor, if it were possible.

#27. Why Organized Religion? Theory Two [evolutionary psychology]

EP

Red, theory; black, fact.

My last post about proxy natural selection (PNS) has directed me to emphasize emotion more in seeking explanations for human behavior. I now think of emotions as an "endophenotype," to use a term from functional magnetic resonance imaging, that provides a useful stepping stone from evolutionary arguments to explanations of our daily lives. I recently applied this insight to obtaining a second explanation of religion, alternative or parallel to the first one that I give in a previous post.

What is the mood or feel as you enter a place of worship and participate in the ceremonies conducted there? More than anything else, the mood is one of great reverence, as though one is in the presence of the world's most powerful king. Kings are supposed to "represent their race." However, I want to translate that statement into a sociobiological function assignment. My discussion "Proxy Natural Selection from the Inside" suggests a problem: if the emotional outlines of people's behavior is being partly randomized in each generation by recombination-type mutations, a consistent moral code seems impossible if we assume that morality comes mostly from peoples' inborn patterns of emotional reactivity, that is, the sum total of everyones' betes noir. The purpose of a king may be to find or at least coincide with societies' moral center of gravity, around which a formal, if temporary, moral code can be constructed. In a complex society, everyone must be "on the same page" for efficient interaction. 

The same problem no doubt recurs each time organisms come together to form a colony, or super-organism: the conflict between the need of a colony for coordination of colonists and the need of evolution for random variability. Such variability will inevitably affect the formulation and interpretation of the coordinating messages that the colonists exchange, like all their other inborn characteristics. 

Kingship comes the corrupting influence of personal power, leading to destructive, tyrannical governments. Replacing a real king with a pretend-king named "God" would seem to be the solution that accounts for organized religion, but then one loses all flexibility, the flexibility that goes with having a flesh-and-blood king who can change his predecessor's laws based on current popular sentiment.

However, human nature may well have a core-and-shell structure, with an "unchanging" core surrounded by a slowly changing shell. The former would be the species-specific objective function previously alluded to in post #16, and produced by species-replacement group selection within the genus, and the latter would be due to PNS, and would represent the stratagems hit upon by our ancestors to meet the demands of the objective function in our time and place. This shell part may account for cultural differences between countries. The core may be implemented in the hypothalamus of the brain, whereas the shell may be implemented in the limbic system. The core, being unchanging, could be taught by organized religion, whereas the shell could be codified by the more flexible institution of government. Though the core is unchanging overall, specific individuals will harbor variations in it due to point mutations (not part of PNS), necessitating the standardizing role of religion. Synaptic plasticity would then be used to cancel the point-mutational variation in the objective function.

This core  consists of four pillars, or themes: genetic diversity, memetic diversity, altruism, and dispersal. Our energetic investment in obtaining each item is to be optimized. To produce this, the church of my acquaintance is continually emphasizing, respectively, tolerance, creating beautiful things, charity, and justice. It's almost too neat, especially if we adopt the deeply cynical-sounding position that the demand for "justice" only polarizes groups to the point of schism and diaspora.

#23. Proxy Natural Selection: The God-shaped Gap at the Heart of Biology [genetics, evolution]

EV    GE    

Red, theory; black, fact.

2-06-2017

As promised, here is my detailed and hypothetical description of the entity responsible for compensating for the fact that our microbial, insect, and rodent competitors evolve much faster than we do because of their shorter generation times. In these pages, I have been variously calling this entity the intermind, the collective unconscious, the mover of the zeitgeist, and the real, investigable system that the word "God" points to. I here recant my former belief that epigenetic marks are likely to be the basis of an information storage system sufficient to support an independent evolution-like process. I will assume that the new system, "proxy natural selection" (PNS) is DNA-based.

11-20-2017

The acronym PNS is liable to be confused with "peripheral nervous system," so a better acronym would be "PGS," meaning "post-zygotic gamete selection."

2-06-2017

First, a refresher on how standard natural selection works. DNA undergoes point mutations (I will deal with the other main type of mutation later) that add diversity to the genome. The developmental process translates the various genotypes into a somewhat diverse set of phenotypes. Existential selection then ensues from the interaction of these phenotypes with the environment, made chronically stringent by population pressure. Differential reproduction of phenotypes then occurs, leading to changes in gene frequencies in the population gene pool. Such changes are the essence of evolution.

PNS assumes that the genome contains special if-then rules, perhaps implemented as cis-control-element/structural gene partnerships, that collectively simulate the presence of an objective function that dictates the desiderata of survival and replaces or stands in for existential selection. A given objective function is species-specific but has a generic resemblance across the species of a genus. The genus-averaged objective function evolves by species-replacement group selection, and can thus theoretically produce altruism between individuals. The if-then rules instruct the wiring of the hypothalamus during development, which thereby comes to dictate the organism's likes and dislikes in a way leading to species survival as well as (usually) individual survival. Routinely, however, some specific individuals end up sacrificed for the benefit of the species.

Here is how PNS may work. Crossing-over mutations during meiosis to produce sperm increase the diversity of the recombinotypes making up the sperm population. During subsequent fertilization and brain development, each recombinotype instructs a particular behavioral temperament, or idiosyncratotype. Temperament is assumed to be a set of if-then rules connecting certain experiences with the triggering of specific emotions. An emotion is a high-level, but in some ways stereotyped, motor command, the details of which are to be fleshed out during conscious planning before anything emerges as overt behavior. Each idiosyncratotype interacts with the environment and the result is proxy-evaluated by the hypothalamus to produce a proxy-fitness (p-fitness) measurement. The measurement is translated into blood-borne factors that travel from the brain to the gonads where they activate cell-surface receptors on the spermatogonia. Good p-fitness results in the recombination hot spots of the spermatogonia being stabilized, whereas poor p-fitness results in their further destabilization. 

Thus, good p-fitness leads to good penetrance of the paternal recombinotype into viable sperm, whereas poor p-fitness leads to poor penetrance, because of many further crossing-over events. Changes in hotspot activity could possibly be due to changes in cytosine methylation status. The result is within-lifetime changes in idiosyncratotype frequencies in the population, leading to changes in the gross behavior of the population in a way that favors species survival in the face of environmental fluctuations on an oligogenerational timescale. On such a timescale, neither standard natural selection nor synapse-based learning systems are serviceable.

2-07-2017

The female version of crossing over may set up a slow, random process of recombination that works in the background to gradually erase any improbable statistical distribution of recombinotypes that is not being actively maintained by PNS.

7-29-2017

Here is a better theory of female PNS. First, we need a definition. PNS focus: a function that is the target of most PNS. Thus, in trees, the PNS focus is bio elaboration of natural pesticides. In human males, the PNS focus is brain development and the broad outlines of emotional reactivity, and thus behavior. In human females, the PNS focus is the digestive process. The effectiveness of the latter could be evaluated while the female fetus is still in the womb, when the eggs are developing. The proxy fitness measure would be how well nourished the fetus is, which requires no sensory experience. This explains the developmental timing difference between oogenesis and spermatogenesis. Digestion would be fine tuned by the females for whatever types of food happen to be available in a given time and place.

8-18-2017

Experimental evidence for my proposed recombination mechanism of proxy natural selection has been available since 2011, as follows:

Stress-induced recombination and the mechanism of evolvability

by Weihao Zhong; Nicholas K. Priest

Behavioral Ecology and Sociobiology, 03/2011, Volume 65, Issue 3

permalink:

http://ncsu.summon.serialssolutions.com/#!/search?bookMark=ePnHCXMwfV1NS8QwEC2yBz9-gxL0JgTytUl7EUQU767nkDQJeCgu7uLv903SVlEQepx0pmky8yaTvJx3G-StuZsLiKLydSpLO8QEx8Ry3J3QgR9Nmx6t2tAivxGcaNhOFw9qZd-fdXcv9bQER26Kr0yMMsQJ6WK1mCHPZoBIbMp0QvbtMLH3wjKm9GfjtwbEen163D088_lSAT4i9js-xgi_DdSQBplcwQhXIQSggNjHVEpwUlIlK-uSyJI4JMRspZKKymyzTfqiu27vXVy3n__6wQO9GARIQVXsqyZEbt7TWDl-hNEj1wHg2A5EOiqbwBIM_b6xS_iVR7h2mxcNpTtPN7vf_NIcIq2HjEeotopifT_8L_XDwNsmtZR_V_2ECDxpxqOr6m9j_wpDiOrp_r6N82bqPhW0uWxt6i7PtYGRhgh9lP4C2uagLw

Abstract:

"The concept of evolvability is controversial. To some, it is simply a measure of the standing genetic variation in a population and can be captured by the narrow-sense heritability (h2). To others, evolvability refers to the capacity to generate heritable phenotypic variation. Many scientists, including Darwin, have argued that environmental variation can generate heritable phenotypic variation. However, their theories have been difficult to test.

 Recent theory on the evolution of sex and recombination provides a much simpler framework for evaluating evolvability. It shows that modifiers of recombination can increase in prevalence whenever low fitness individuals produce proportionately more recombinant offspring. Because recombination can generate heritable variation, stress-induced recombination might be a plausible mechanism of evolvability if populations exhibit a negative relationship between fitness and recombination. Here we use the fruit fly, Drosophila melanogaster, to test for this relationship.

We exposed females to mating stress, heat shock or cold shock and measured the temporary changes that occurred in reproductive output and the rate of chromosomal recombination. We found that each stress treatment increased the rate of recombination and that heat shock, but not mating stress or cold shock, generated a negative relationship between reproductive output and recombination rate. The negative relationship was absent in the low-stress controls, which suggests that fitness and recombination may only be associated under stressful conditions. Taken together, these findings suggest that stress-induced recombination might be a mechanism of evolvability."

However, my theory also has a macro aspect, namely that the definition of what constitutes "stress," in terms of neuron interconnections or chemical signaling pathways, itself  evolves, by species-replacement group selection. Support for that idea is the next thing I must search for in the literature. &&

#22. The Cogs of Armageddon [evolutionary psychology]

EP

Red, theory; black, fact.

1-27-2017

This is a "just-so story" about how I believe everyday human behavior eventually accomplishes the all-important biological function of dispersal for the human race. A future post will attempt to explain how the "just-so story" got written in terms of natural selection and possible faster-acting proxies thereof needed by organisms with long generation times.

Dispersal is things like dandelions shedding airborne seeds, slime molds developing into spore cases on stalks and releasing the spores into the wind, territorial systems of birds and mammals forcing the unlanded young to seek widely for their own territories, and humans going into space because our science fiction writers keep scaring us about the possibility of meteor crashes wiping out life on Earth. To paraphrase the latter, a way to avoid extinction, long-term, is not putting all your eggs in one basket, geographically speaking.

The slime mold dictyostelium is triggered into its dispersal program by the food supply running short; I will adopt the assumption that the human dispersal program is also triggered by the end of the good times, that is, the price of bread rising relative to wages.

I conjecture that human neural pathways potentiate aggression when the hard times come, but of an elaborate kind adapted for ensuring efficient dispersal (i.e., with minimal loss of life). It begins with a two-person feud of the sort illustrated in cultural references too numerous to mention. In Canada, where I live, a cough accompanied by an angry expression plays the role of the instigation. The arbitrary stimulus, made offensive by some piece of Pavlovian conditioning, is traded back and forth with rapidly increasing energy. The process is remarkably like flirting, not surprising since the ultimate purpose has commonalities with reproduction--but of an entire society. 

However, the emotional component is strongly threatening rather than rewarding, because the participants must be induced to seek allies, which people do when threatened, until all of society is eventually polarized. The acts of provocation being traded back and forth become progressively more outrageous, as they must, to keep the polarization process going. Eventually, one side gets the upper hand and forces the other to flee.

The result is a diaspora, i.e., dispersal. Because of the long polarization process, an entire group is expelled, not single individuals one at a time. Thus, members of such a group can assist each other to survive and relocate, thereby reducing the mortality associated with dispersal, thereby making the dispersal event more efficient in terms of number of people relocated. The group who flees is then seen by the international community as the blameless victim, and the group who stays is seen as the unprincipled aggressor. This tends to elicit a sheltering of the refugees and an intimidation of the "aggressor," who is deterred from pressing his advantage, that is, pursuing the refugees and slaughtering them to the last man, which is what each side would dearly like to do to the other by this point. This, again, is an efficiency from the point of view of producing dispersal.

However, if each side is continually threatening the other, why don't they flee each other's presence during the very early stages? The answer seems to be that humans have a reflex that converts feeling threatened into a wish to injure the threatening party, possibly a behavioral leftover from some earlier adaptation, such as an anti-predation defense; to injure, you have to stick around. (Leftovers such as these form the building blocks of future just-so plots.)

Finally, settled refugees usually do not integrate completely into the host society, instead forming ethnic neighborhoods. This increases the resemblance to an entire society reproducing itself. However, the growth phase following reproduction in individuals seems to be lacking at the society level. However, being seen as ethnic by the host society, due to slow integration, could improve individual-level reproductive success of refugees because of disassortative mate-choice effects evolved to favor genes that produce dispersal.

2-24-2017

The dispersal-producing dynamic just outlined is fantastically powerful, as it must be to overcome all the reasons you would not leave your homeland forever at some arbitrary time: expense, risk of mortality in transit, opportunity costs, temporary loss of livelihood, need to learn a new language and customs, vulnerability to exploitation in the new country, etc., etc.

This dynamic is basically what theologians call evil, for which I propose the less judgmental, substitute term "dispersalism." If this is truly an insight, it should have a liberating effect on your life, even if you just remember that one word, but with the price of always being population-conscious: always trying to see what is happening at the population/zeitgeist level, and reading the paper every day at the very least.

At least one "just-so story" could probably be written for each of the pillars of the human species-specific objective function mentioned in previous posts, these being as follows: dispersal, genetic diversity, memetic diversity, and altruism. (The latter has not been mentioned until now.) Each of these must be optimized, not blindly maximized, for each comes at a cost. In terms of neurobiology, each pillar is probably a family of functionally related likes and dislikes wired up in the hypothalamus, but not obviously related to individual-level survival or reproduction.

#19. Explaining Science-religion Antipathy also Explains Religion [evolutionary psychology]

EP

Red, theory; black, fact.

I will be arguing here that the Darwinian selective advantage to humans of having a propensity for religion is that it regulates the pace of introduction of new technology, which is necessitated by the disruptive side effects of new technology.

If this sounds like a weak argument, perhaps people have been chronically underestimating the costs to society of the harmful side effects of new technology, ever since there have been people. Take the downside of the taming of fire, for instance. You can bet that the first use would have been military, just as in the case of nuclear energy. Remember that everything was covered in forests in those days; there must have been an appalling time of fire until kin selection slowly put a stop to it. The lake-bottom charcoal deposits will still be there, if anyone cares to look for them. (Shades of Asimov's story "Nightfall.")

The sedimentary record does not seem to support the idea that the smoke from such a time of fire caused a planetary cooling event sufficient to trigger the last ice age. However, the mere possibility helps to drive home the point, namely that prehistoric, evolutionary-milieu technology was not necessarily too feckless to produce enough disruption to constitute a source of selection pressure.

Natural selection could have built a rate-of-innovation controller by exaggerating people's pleasure at discovering a new, unexplored phenomenon, until they bog down in rapture at that moment and never progress to the next step of actually experimenting or exploring. The latter activities would be just upstream of the nominally controlled process, the introduction of new technology. People's tendency for "rapture capture" would be causally linked via genetically specified neural pathways to the kinds of hardships caused by technological side effects, thereby completing a negative feedback loop that would work like a steam engine governor.

I conjecture that all present-day religions are built on this phenomenon of "rapture capture." This may explain why the most innovative country, the USA, is also the most religiose, according to Dawkins, writing in "The God Delusion." An Einsteinian sense of wonder at the cosmos that, according to Dawkins, most scientists feel, could be a mild, non-capturing version of the same thing. The unlikely traits attributed to God, omnipotence, omni this and that, could have instrumental value in intensifying the rapture.

Another possible name for what I have been calling rapture could be "arcanaphilia." A basic insight for me here was that religion is fundamentally hedonistic. I do not seem to be straying too far from Marx's statement that "Religion is the opiate of the people."

These ideas help to explain why some sciences such as astronomy and chemistry began as inefficient protosciences (e.g., astrology, alchemy): they were inhibited from the start by an excessive sense of wonder, until harder heads eventually prevailed (Galileo, Lavoisier). Seen as a protoscience, the Abrahamic religions could originally have been sparked by evidence that "someone is looking out for us" found in records of historical events such as those the ancient Israelites compiled (of which the Dead Sea Scrolls are a surviving example). That "someone" would in reality be various forms of generation-time compensation, one of which I have been calling the "intermind" in these pages. Perhaps when the subject of study is in reality a powerful aspect of ourselves as populations, the stimulus for rapture capture will be especially effective, explaining why religion has yet to become an experimental science.

By the way, there is usually no insurmountable difficulty in experimenting on humans so long as the provisions of the Declaration of Helsinki are observed: volunteer basis only; controlled, randomized, double-blind study; experiment thoroughly explained to volunteers before enrollment; written consent obtained from all volunteers before enrollment; approval of the experimental design obtained in advance from the appropriate institutional ethics committee; and the experiment registered online with the appropriate registry.

Religions seem to be characterized by an unmistakable style made up of little touches that exaggerate the practitioner's sense of wonder and mystery, thus, their arcanaphilic "high." I refer to unnecessarily high ceilings in places of worship, use of enigmatic symbols, putting gold leaf on things, songs with Italian phrases in the score, such as "maestoso," wearing colorful costumes, etc. I shall refer to all the elements of this style collectively as "bractea," Latin for tinsel or gold leaf. I propose the presence of bractea as a field mark for recognizing religions in the wild. By this criterion, psychiatry is not a religion, but science fiction is.

It seems to me that bractea use can easily graduate into the creation of formal works of art, such as canticles, stained glass windows, statues of the Buddha, and the covers of science fiction magazines. Exposure to concentrations of excessive creativity in places of worship can be expected to drive down the creativity of the worshipers by a negative feedback process evolved to regulate the diversity of the species memeplex, already alluded to in my post titled, "The Intermind: Engine of History?"

This effect should indirectly reduce the rate of introduction of new technology, thereby feeding into the biological mission of religion. Religion could be the epi-evolutionary solution, and the artistic feedback could be the evolutionary solution, to the disorders caused by creativity. Bractea would represent a synergy between the two.

#16. The Intermind, Engine of History? [evolutionary psychology]

EP

Red, theory; black, fact.

9-21-2016

This post is a further development of the ideas in the post, "What is intelligence? DNA as knowledge base." It was originally published 9-21-2016 and extensively edited 10-09-2016 with references added 10-11-2016 and 10-30-2016. Last modified: 10-30-2016.

In "AviApics 101" and "The Insurance of the Heart," I seem to be venturing into human sociobiology, which one early critic called "An outbreak of neatness." With the momentum left over from "Insurance," I felt up for a complete human sociobiological theory, to be created from the two posts mentioned.

However, what I wrote about the "genetic intelligence" suggests that this intelligence constructs our sociobiology in an ad hoc fashion, by rearranging a knowledge base, or construction kit, of "rules of conduct" into algorithm-like assemblages. This rearrangement is (See Deprecated, Part 7) blindingly fast by the standards of classical Darwinian evolution, which only provides the construction kit itself, and presumably some further, special rules equivalent to a definition of an objective function to be optimized. The ordinary rules translate experiences into the priming of certain emotions, not the emotions themselves, 

Thus, my two sociobiological posts are best read as case studies of the products of the genetic intelligence. I have named this part the intermind, because it is intermediate in speed between classical evolution and learning by operant conditioning. (All three depend on trial-and error.) The name is also appropriate in that the intermind is a distributed intelligence, acting over continental, or a least national, areas. If we want neatness, we must focus on its objective function, which is simply whatever produces survival. It will be explicitly encoded into the genes specifying the intermind, (For more on multi-tier, biological control systems with division of labor according to time scale, see "Sociobiology: the New Synthesis," E. O. Wilson, 1975 & 2000, chapter 7.)

Let us assume that the intermind accounts for evil, and that this is because it is only concerned with survival of the entire species and not with the welfare of individuals. Therefore, it will have been created by group selection of species. (Higher taxonomic units such as genus or family will scarcely evolve because the units that must die out to permit this are unlikely to do so, because they comprise relatively great genetic and geographical diversity.* However, we can expect adaptations that facilitate speciation. Imprinted genes may be one such adaptation, which might enforce species barriers by a lock-and-key mechanism that kills the embryo if any imprinted gene is present in either two or zero active copies.) Species group selection need act only on the objective function used by epigenetic trial-and-error processes.

In these Oncelerian times, we know very well that species survival is imperiled by loss of range and by loss of genetic diversity. Thus, the objective function will tend to produce range expansion and optimization of genetic diversity. My post "The Insurance of the Heart" concluded with a discussion of "preventative evolution," which was all about increasing genetic diversity. My post "AviApics 101" was all about placing population density under a rigid, negative feedback control, which would force excess population to migrate to less-populated areas, thereby expanding range. Here we see how my case studies support the existence of an intermind with an objective  function as described above.

However, all this is insufficient to explain the tremendous cultural creativity of humans, starting at the end of the last ice age with cave paintings, followed shortly thereafter by the momentous invention of agriculture. The hardships of the ice age must have selected genes for a third, novel component, or pillar, of the species objective function, namely optimization of memetic diversity. Controlled diversification of the species memeplex may have been the starting point for cultural creativity and the invention of all kinds of aids to survival. Art forms may represent the sensor of a feedback servomechanism by which a society measures its own memeplex diversity, measurement being necessary to control.

A plausible reason for evolving an intermind is that it permits larger body size, which leads to more internal degrees of freedom and therefore access to previously impossible adaptations. For example, eukaryotes can phagocytose their food; prokaryotes cannot. However, larger body size comes at the expense of longer generation time, which reduces evolvability. A band of high frequencies in the spectrum of environmental fluctuations therefore develops where the large organism has relinquished evolvability, opening it to being out competed by its smaller rivals. 

The intermind is a proxy for classical evolution that fills the gap, but it needs an objective function to provide it with its ultimate gold standard of goodness of adaptations. Species-replacement group selection makes sure the objective function is close to optimal. This group selection process takes place at enormously lower frequencies than those the intermind is adapting to, because if the timescales were  too similar, chaos would result. For example, in model predictive control, the model is updated on a much longer cycle than are the predictions derived from it.

12-25-2016

Today, when I was checking to see if I was using the word "cathexis" correctly (I wasn't), I discovered the Freudian term "collective unconscious," which sounds close to my "intermind" concept.

* 3-12-2018

I now question this argument. Why can't there be as many kinds of group selection as taxonomic levels? Admittedly, the higher-level processes would be mind-boggling in their slowness, but in evolution, there are no deadlines.

#15. The Insurance of the Heart [evolutionary psychology]

EP

Red, theory; black, fact.

8-29-2016

We live in an uncertain world, the best reason to buy insurance while you can. Insurance is too good a trick for evolution to have missed. When food is plentiful, as it now is in my country, people get obese, as they are now doing here, so that they can live on their fat during possible future hard times. They don't do this consciously; it's in their genes.

However, eating has only an additive effect on your footprint on society's demand for resources; how many kids you have affects your footprint multiplicatively. Thus, the effectiveness of biological insurance taken out in children foregone during times of plenty would be greater than that taken out in food consumed. Such a recourse exists (See Deprecated, Part 8); how well and long remembered the family name you bequeath to your children affects your footprint exponentially. (I assume that a good or bad "name" affects the reproductive success of all your descendants having that name until you are finally forgotten.) Compared to exponential returns, everything else is chump change. ("Who steals my purse steals trash." - Shakespeare)

There remains the problem of food going to waste during times of plenty because social forces prevent a quick population increase. I conjecture that the extra energy available is invested by society in contests of various sorts (think of the Circus Maximus during the heyday of ancient Rome) that act as a proxy to evolutionary selection pressure, whereby the society accelerates it's own evolution. Although natural selection pressure is maximal during the hard times, relying on these to do all your evolving for you can make you extinct; better to do some "preventative evolution" ahead of time.

Postscript 3

Since future environmental demands are partly unforeseeable, a good strategy would be to accelerate one's evolution in multiple directions, keeping many irons in the fire. Indeed, in the Olympics just concluded, thirty-nine sports were represented.

The power of these contests is maximized by using the outcomes as unconditioned stimuli that are associated with the family names of the winners and losers: the conditioned stimuli. In this way, one acquires a good or bad "name" that will affect the reproductive success of all who inherit it, an exponential effect. To ground this discussion biologically, it must be assumed that the contests are effective in isolating carriers of good or bad genes (technically, alleles), and that the resulting "name" is an effective proxy for natural selection in altering the frequency of said genes. To keep the population density stable during all this, winners must be balanced by losers. The winners are determined and branded in places like the ball diamond, and the losers are determined and branded in the courts.

#14. Three Stages of Abiogenesis [evolution, chemistry]

The iconic Miller experiment on the origin of life

Abiogenesis chemistry outside the box

EV    CH    

Red, theory; black, fact

Repair, growth, reproduction

"Abiogenesis" is the term for life originating from non-life.

Self-repair processes will be important in abiogenesis because life is made of metastable molecules that spontaneously break down and have to be continually repaired, which results in continuous energy dissipation. I will assume that self-repair in non-reproducing molecules is what eventually evolved into self-replication and life.

I also assume that the self repair process was fallible, so that it occasionally introduced a mutation. Favorable mutations would have increased the longevity of the self-repairing molecules. Nevertheless, a given cohort of these molecules would relentlessly decrease in numbers, but they would have been continuously replenished in the juvenile form by undirected chemistry on the early Earth. Eventually, at least one of them was able to morph self-repair into self-replication, and life began. I call this process of refinement of non-reproducing molecules "longitudinal evolution" by analogy to a longitudinal cohort study in medical science. The process bears an interesting resemblance to carcinogenesis, where an accumulation of mutations in long-lived cells also leads to an ability to self-replicate autonomously. Carcinogenesis is difficult to prevent, and so must be considered a facile process, suggesting that longitudinal evolution to the threshold of life was also facile.

A simple self-repairing molecule

The "enzyme ring" shown above is an example of a possible self-repairing molecule that I dreamt up. It is a ring of covalently-bonded monomers that are individually large enough to have good potential for catalyzing reactions, like globular proteins, but are small enough to be present in multiple copies like the standardized building blocks that one wants for templated synthesis.

If the covalent bond between a given pair of monomers breaks, the ring is held together by multiple, parallel secondary valence forces and hydrophobic interactions, until the break can be repaired by the ring's catalytic members. With continuing lack of repair, the ring eventually opens completely, and effectively "dies." To bring the necessary catalysts to the break site reliably, no matter where it is, I assume that multiple copies of the repair enzyme are present in the ring, and are randomly distributed. I also assume a temperature cycle like that of the polymerization chain reaction technology that repeatedly makes the ring single-stranded during the warm phase and allows it to collapse into a self-adhering, linear, double-stranded form during the cool phase. This could simply be driven by the day-night cycle. In the linear form, the catalytic sites are brought close to the covalent bond sites, and can repair any that are broken using small-molecule condensing agents such as cyanogen, which are arguably present on the early Earth under Miller-Urey assumptions. When the ring collapses, it does so at randomly selected fold diameters, so that only a few catalytic monomers are needed, since each will eventually land next to all covalent bonds in the ring except those nearby, which it cannot reach because of steric hindrance and/or bond angle restrictions. The other catalytic monomers in the ring will take care of these.

How it would grow

The mutation process of the enzyme ring could result from random ring-expansion and ring-contraction events, the net effect being to replace one kind of monomer with another. Expansion would most likely begin with intercalation of a free monomer between the bound ones at the high-curvature regions at the ends of the linear conformation. The new monomer would be held in place by the multiple, weak parallel bonds alluded to above. It could become incorporated into the ring if it intercalates at a site where the covalent bond is broken. Two bond-repair events would then suffice to sew it into the ring. The ring-contraction process would the the time-reversed version of this. 

In addition, an ability to undergo ring expansion allows the enzyme ring to start small and grow larger. This is important because, on entropy grounds, a long polymer is very unlikely to spontaneously cyclize. The energy-requiring repair process will bias the system to favor net ring expansion. Thus, we see how easily self-repair can become growth.

How it would reproduce

If large rings can split in two while in the linear conformation, the result is reproduction, without even a requirement for templated synthesis. Thus, we see how easily growth can become reproduction.

Onward to the bacterium

To get from reproduction-competent enzyme rings to something like a bacterium, the sequence of steps might have been multiplication, coacervate droplet formation, cooperation within the confines of the droplet, and specialization. The first specialist subtypes may have been archivists, forerunners of the circular genome of bacteria; and gatekeepers, forerunners of the plasma membrane with its sensory and transporter sites. Under these assumptions, DNA would not have evolved from RNA; both would represent independently originated lines of evolution, but forced to develop many chemical similarities by the demands of templated information transfer.

Back to chemistry

During the classic experiment in abiogenesis, the Miller-Urey experiment, amino acids were formed in solution, but no-one has been able to show how these could subsequently have polymerized to functional protein catalysts. The origin of the monomers in my enzyme ring thus needs to be explained. However, the formation of relatively large amounts of insoluble, dark-colored "tars" is apparently facile under the Miller-Urey reaction conditions. The carbon in this tar is not necessarily lost to the system forever, like a coal deposit. In present-day anoxic environments relevant to the early Earth, at least three-quarters of modern biomass returns to the atmosphere as marsh gas. The driving force for these reactions seems to be not enthalpy reduction, but entropy increase.

Seen in the library of the University of Ottawa

Retrofractive synthesis

I therefore propose that if you wait long enough, and a diversity of trace-metal ions is present, then the abiogenesis tar will largely break down again, releasing large, prefab molecular chunks into solution. Reasoning from what is known of coal chemistry, these chunks may look something like asphaltenes, illustrated above, but relatively enriched in hydrophilic functional groups to make them water soluble. Hydrolysis reactions, for example, can simultaneously depolymerize a big network and introduce such groups (e.g., carboxylic acid groups). I propose that these asphaltene analogs are the optimally-sized monomers needed to form the enzyme ring.