Trauma, Vasana, epigenitics, Fibonacci, Lamarck vs Mendel

Back when I was in school (graduated ’70), the science of genetics was taught as Lamarck versus Mendel, parallel to the political science of communism vs capitalism. Somehow that disappeared from view, I don’t know when or how.

Lamarck’s work was supposedly disproven in that cutting off connected generations of rat tails doesn’t produce tail-less rats. The questionable logic aside, I find it fascinating that Lamarck’s views were preceded, prefaced &/or prefigured in the concept of vassana, and are now being revived (albeit unattributed-ly) in the study of epigenetics. Meanwhile, many have come to see capitalism as dysfunctional and doomed, but seem trained out of any ability to perceive viable alternatives…
Epigenetics is the study of heritable, often regular and natural, changes in gene expression (active versus inactive genes) that don’t involve changes to the underlying DNA sequence — a change in phenotype without a change in genotype — which in turn affects how cells read the genes. It relates to an additional layer of instructions that control how our DNA is interpreted, controlled and expressed. For years, it was assumed that DNA was a product of our heritage, handed down from parents, a rigid pre-determinant of everything from our height to musical skill. But the study of epigenetics has led to the discovery that what we do actually changes the way our DNA is used, and that the choices we make can forever transform our genetic code. This means that the way we interact with the world changes our DNA, not just the other way around.
One major ways we can change our DNA is by diet. Essentially, the idea of ‘epigenetic diet’ is to emphasize compounds like sulforaphane (found in broccoli), curcumin (found in turmeric), epigallocatechin gallate (found in green tea) and resveratrol (found in wine). These chemicals might slow or potentially reverse damage to DNA. The epigenetic activity of these chemicals may both prevent cancer formation and lead to decreased fat cells, as well as generally lower inflammation.
The epigenetic diet is of exciting interest as research suggests that cruciferous vegetables aren’t just an important source of nutrients, but perhaps a key to eliminating cancer as life threatening disease. Cruciferous vegetables like kale, cabbage, cauliflower, Brussels sprouts, and broccoli sprouts contain chemical components, such as sulforaphane (SFN) and indole-3-carbinol (I3C), which regulate microRNAs (miRNAs) and inhibitors of histone deacetylases (HDACs) and DNA methyltransferases (DNMTs). The mis-regulation and overexpression of these genes are responsible for the uncontrolled cellular proliferation and viability of various types of cancer cells. (that last sentence means nothing to me – it’s just something I found on the web while trying to gather information to flesh out what I’m saying here)
And a word of caution: the epigenetic diet if fed to rats might could cause their tails to fall off.


On 25 May 2011 I posted here:
Vasana
Vasana (wassana in Thai) refers to habitual tendencies or dispositions; subconscious inclinations; a term found in Pali and early Sanskrit writings (from vas: ‘living, remaining’). In yoga practice (Yogācāra or yogachara), it denotes latent energy resulting from action, or better, actions. It’s believed a pattern becomes ‘imprinted’ in the actor's consciousness, or storehouse of understandings; accumulation of these habitual tendencies predisposes one to particular patterns of behavior (samskaras).
In short, they’re all the things that go into building individual sense of self or ego. “Vasana” can be translated as mental conditioning, minute tendencies, inclinations, habit proclivities &/or driving forces which color and motivate one’s attitudes and actions. Vasanas are a conglomerate result of subconscious impressions (samskaras) formed by background experience (extending even before birth, to time in the womb, conception and even beyond). Samskaras, experiential impressions, combine in the subconscious to form vasanas, which contribute to mental fluctuations (vritti whirlpools of consciousness, waves of mental activities, thought and perception).
One might have a fearful experience, and the vasana of fear can remain for a long time (as in post-traumatic stress). Vasana influences our actions and behavior patterns (samskaras). Negative vasanas create negative samskaras and vice versa. But you can replace a negative samskara, or behavior, with a positive behavior, which will cause an internal change and ultimately an external change. For example: if you have low self-esteem (a negative vasana), a positive samskara can change your perception of yourself, so that you start behaving in even more positive ways. But you can’t permanently remove a vasana or a samskara - you only replace one with another, and the old samskaras and vasanas can come back.
Vasanas: subliminal inclinations and habit patterns which, as driving forces, color and motivate one's attitudes and future actions; tendencies and impulses; longing. Awareness of previous observations, recollections, trauma's, other states of mind, etc. The conglomerate results of subconscious impressions created through experience. Deep-seated traits or tendencies that shape one’s attitudes and motivations; impressions about action and experience that remain in the mind; latent subtle desires, innate tendencies. These experiential impressions combine in the subconscious, and thereafter contribute to mental fluctuations and subconscious tendencies which color all levels of personality: our perceptions, emotions, thoughts and deeds. Vasana: a pattern of inclinations and subtle desires; a tendency created in a person by the doing of an action, or by enjoyment; it induces a person to repeat the action, or to seek a repetition of the enjoyment. As a subtle impression in the mind capable of developing itself into action; it’s the cause of the nature of impressions of action which remain unconsciously in the mind, producing self-imposed limitations, or forms of attachments, for instance:
• Personal strengths and weaknesses
• Predispositions
• Likes and dislikes
• Habits
• Habitual outlook
• Opinions
Vasana refers to subtle desires which, like seeds, fructify or manifest, accordingly with favorable circumstances, at appropriate times. Karmic energy created in the current lifetime, or past lifetimes, through repeated patterns of behavior can be called habit energies, or vasanas. These are like old, familiar stories: our emotions, self-images, beliefs and reactive patterns that keep us within limited contexts, experiences and configurations. Many, if not most, of us need to breakup and dissolve our old, too often dysfunctional, patterns, imprints, and habits - boundaries of the ego formed by fear, intellect, memory, and will, rather than reinforce them. As everything passes away, even your mind (a structure composed of various impressions and thoughts), it may be best to experience all you can, while you can, and break out of what limitations you can.
Some say the word vasana means impregnation, learning, processing; and that because the consciousness is plastic, it can be conditioned. If we have habit energies and patterns of behavior, that’s because of vasana. We develop those patterns during the first six years of life, and continue to enact them.

People are born with proclivities; other tendencies are reinforced. In both cases, there’s tendency to repetition, and perhaps to insufficiency of exploration. To know that people (and things) act and interact in patterns is to be better able to plan, to properly respond, and to be prepared. Our personalities (personality: the whole nature or character of a particular person, with traits, qualities and individuality) aren’t necessarily locked-in and predictable patterns of attitude and behavior; much as one can quit drinking or smoking, one can change patterns (at least somewhat) – learn a new song, as it were, use another language, live in a different way, even find oneself acting inexplicably when circumstances, or the people around, have changed. But the old melody, or ways, will creep back in – to dreams, conversation, opinions, moods. A vibration will continue to exist long after it is directly perceptible to humans!
Usually vasana is mentioned in context where meditation is espoused and recommended, but maybe internal quiet, centered harmony, is enough. That the vasana patterns start before individuality, before emergence of any “self” – as recent scientific research has shown. A protein sheath around the double helix DNA strands responds to input (emotional, mental, environmental) and determines much of DNA function, acting like a switch to turn on and off genetic cues, or expression. Epigenetics, the study of gene expression and the regulation of genetic activity, particularly methyl groups and histones attached to our chromosomes, the epigenome suite of biochemical signals that determine which genes in an individual’s DNA can be turned on or off, shows that genomes respond to environmental signals, that the epigenome is sensitive to environmental impact (including nutrients, exposure to toxins, and loving mothering). DNA is fixed, and represents only possibilities; while epigenetic changes are potentially reversible, may not be simply on or off, and involve the new concept of the meme.
The term “epigenetics”was coined in 1942 to describe the idea that an organism's experience may alter the effect of (the prefix epi means ‘on’ or ‘over’). Now, it’s defined as ‘the study of heritable changes in genome function that occur without a change in DNA sequence,’ and scientists tend to accept that epigenetic inheritance affects the action of genes in offspring, despite arising from the life experience of parents. These epigenetic changes extend, at least for a small minority of genes, beyond immediate offspring to further generations, but effects seem not to last indefinitely. Epigenetic instructions aren’t found in the DNA itself, but in an array of chemical markers and switches, known as the epigenome, which lie along the length of the double helix. These epigenetic switches and markers help switch on or off the expression of particular genes.
Nutrition and stress can affect the epigenome, but, unlike genetic mutations, epigenetic changes are reversible. Research shows that diet, behavior, and environmental surroundings can have a great impact on the health of descendants. Twins with different environmental experiences display more divergent genetic expressions than do those with similar environment and experience. A common environment results in the genes of a variety of individuals to increasingly act like each other. These epigenetic changes can be inherited. Acquired traits can be passed down the generations, despite what is taught about cutting off rat’s tails (!).

Of course, it’s not just nature versus nurture, programmed clockwork-like progression or adaptive opportunism, manipulation by, manipulation of, inter-connectivity, or faithful but mostly inactive observers carried along in an unpredictable flow - we’re heavily affected by group dynamics from even before our parents were conceived, and so full of influences that we certainly react more than we decide, and are largely just part of an ongoing process. Environment, nutrition and experience of germs, viruses, etc., and also emotions. A luckier child who gets more strokes will pass on some dissimilar traits to what an identical twin not so favored will. It’s not just the sins of one’s fathers, but the fortunes of one’s antecedents, which determine much of one’s character – and even, I suspect, the emotions present at the point of conception, the time of birth, and also around the house… babies pick up on signals very hard to quantify or even describe! But, eventually, they learn some control, to make and keep to some decisions, and exert some influence.
Lawrence Harper, psychologist at the University of California at Davis, has claimed that a wide array of personality traits, including temperament and intelligence, can be affected by epigenetic inheritance, saying, “If you have a generation of poor people who suffer from bad nutrition, it may take two or three generations for that population to recover from that hardship and reach its full potential. Because of epigenetic inheritance, it may take several generations to turn around the impact of poverty or war or dislocation on a population.” Marcus Pembrey, professor of Clinical Genetics at London’s Institute of Child Health, in collaboration with Swedish researcher Lars Olov Bygren, also found strong evidence that famine in the lives of the grandparents can affect the life expectancy of the grandchildren.
Michael Meaney, biologist at McGill University, showed that some epigenetic changes can be induced after birth. With graduate student Ian Weaver, Meaney compared mother rats that licked their offspring after birth and those that neglected their newborns. The licked newborns grew up relatively calm and brave, while neglected ones nervously skittered into the darkest corner when placed in new environments. Analysis of brain tissue from both licked and non-licked rats showed distinct differences in patterns of DNA methylation (methylation: the process by which methyl, or -CH3, amino acid groups are added to compounds) in hippocampus cells of each group. The mother's licking activity apparently had the effect of removing dimmer switches on a gene that shapes stress receptors in a growing brain. The well-licked rats had better-developed hippocampi, and released less cortisol, a stress hormone; neglected ones released more cortisol, had less-developed hippocampi, and, in marked contrast to the others, reacted nervously when startled or in new surroundings. Maternal behavior had shaped the brains of offspring.
The phenomenon has also been detected in chickens, in response to stress caused by abnormal levels of light. Researchers at Linköping University in Sweden reared a group of chickens under normal day and night conditions; others were exposed to randomly varying light. The offspring of the latter group showed impaired spatial learning abilities, were more aggressive, and grew faster. These characteristics were linked to changes in the activity of genes in the hypothalamus or pituitary gland areas.

Elsewhere in the animal, activity of these genes was largely normal, but was changed in areas of the brain responsible for behavioral traits, including spatial learning. This exemplifies a fundamental characteristic of epigenetic inheritance: that even genes handed down quite normally may change in what they express, with resultant change in some behavioral trait or function. A great implication of heritable epigenetic features is that diet and stress can influence genes of children and grandchildren. In the early 1990s the British ‘Avon Longitudinal Study’ surveyed children born to 14,000 mothers and found that, of 5,000 fathers who took part, 166 had started smoking very early, in the so-called ‘slow growth’ period before puberty (between 9 and 12). Sons of these fathers tended to be significantly overweight by the age of nine, ‘though there was no noticeable difference for daughters. This shows a significant link between fathers who smoked early, and above average weight in their sons. Although little’s yet known of how environment shapes gene silencing, there’s evidence that disturbing DNA methylation during development can bring on health problems from cancer to schizophrenia.
Histone, around which DNA winds, is important role in gene regulation. Changes in histones relate to changes in the physical state and function of chromatin (chromatin fibers form chromosomes) in cell division, and thus to transcription of genetic messages (by neutralizing charges of DNA). Genes and environment don't influence development independently. Instead, environmental influences initiate changes in gene expression. Human behavior can influence inheritance, genetically and educationally. Even very high heritability in a behavioral trait doesn’t imply inevitability. One can’t just blame genes, and abdicate all responsibility.
Epigenetic inheritance may be involved in passing down of cultural, personality and even psychiatric traits, which can be regarded as inclinations. For instance, historical events have led to “embedding” of attitudes within affected communities, attitudes which persist for generations. This phenomenon is explained in Richard Dawkins's theory of memes, according to which cultural or intellectual traits are passed down via non-genetic mechanisms. The possibility raised by epigenetics is that cultural transmission may have a genetic component. Traumas like the experience of imprisonment, slavery, forced relocation or war, can leave genetic marks on descendants of those victimized by them, and thus influence - but not force - behavior.

A meme (a clumsy new term pronounced miem) is any idea or behavior that can pass from one person to another by learning or imitation (including thoughts, ideas, beliefs, theories, rituals, gestures, practices, fads, fashions, habits, tunes, songs, and dances). Memes, cultural entities that an observer might consider a replicator propagate themselves, can move through a populace in a way similarly as do viruses. Dawkins, a biological theorist widely known for espousing atheism, coined the word “meme” in The Selfish Gene (1976), where he described how one might extend evolutionary principles to explain the spread of ideas and other cultural phenomena. Dawkins based the word on the Greek “mimeme” (something imitated), making it sound similar to “gene.” The concept of a unit of social evolution called a mneme (from Greek mneme, meaning “memory”) was used in 1904 by German evolutionary biologist Richard Semon; the French adjective même has similarities in meaning to the Greek mīmos, from which the adjective mimesis comes. As Roman satirical poet Horace put it, “things which are repeated are pleasing” - but some of us are more inclined to like some sequencing than others!
According to Dawkins, genes aren’t the only replicators which change in an evolutionary manner. Memes replicate, spreading from consciousness to consciousness; many of the same evolutionary principles that apply to genes apply to memes as well. Genes and memes may at times co-evolve (“gene-culture co-evolution”).
One can’t view memes through a microscope in the way one can detect genes, but a meme is a recognizable pattern, one that serves as a template for its own replication. Language provides the first and most important memetic infection. Memeticians generally regard language as a memetically-evolved phenomenon. For example, even at the level of animals, many species have evolved particular sounds to convey various meanings (“danger”, “hungry”, “aroused”, “go away” or “come here”). Experiments have verified the memetic nature of these noises, showing that they don’t arise when humans raise the animals concerned: they’re not generated by instinct, but learned from other animals.
Some people understood many of these things long ago, much as many farmers hardly needed to be told of Pavlov’s dog salivation response to learned association of a bell sound to feeding. Interesting, isn’t it, how purportedly new, modern ideas can so match ancient understandings?

We have hard wiring, some software-like programming, and also some feedback-loop like self-awareness mechanisms. We must eat and sleep, and are inclined to indulge in some pleasures, but don’t have to be as stupid as we can be. Much of wisdom lies in knowing what we can change, or at least influence, and what not. What’s really important about epigenetcs is that, by showing the nexus and interactivity between genes and genetic sheath, it shows the lack of true viability to the “science” producing GMOs (genetically modified organisms). To replace gene strands with other gene strands makes an imperfectly formatted system – poorly responsive and inflexible, unable to adjust. Without gaining experience from interactivity with environs, genes cannot operate with real efficiency; GMOs cannot but gum up the whole works. Even if they were but food, and not part of our whole ecosystem, if we are what we eat, do we really want to eat dysfunctional food?

Self as Illusion Like other things, we’re but temporary phenomena. Numbers may not be, but they aren’t tangible. There may be other concepts as durable, but I think not many. But the idea of some essence of a person lasting past death is popular. What would that essence be? For me, it’s hard to imagine it caring about a name once used – and as I study history and the world, I learn that for many individual lifetimes of people, there was no lasting name attachment. One was called one thing as a baby, another as an adolescent, and something entirely different when established in regular occupation with skills others might wish to call on.
A ‘self’ has been suggested to merely comprise a collection of memetic stories, or memes… and it may even be that there is no memory until memes – for instance words – are received.

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Human bodies have about 30 trillion cells which hold maybe 40 trillion bacteria – depending some on recent bowel movements (shit’s composed largely of bacteria). That’s up to 1000 different species of bacteria, with 300 times the total DNA as humans. These microbes affect anxiety, mood, stress-response, depression and social behavior. Collectively, they’re termed the microbiome (My-kroh-BY-oam) — a community of microbes that live in and on us. The microbiome affects, some say regulates, how people think and feel; its massive connections between the immune and nervous systems are critical in pain, despondency, and degenerative brain disorders, among other things.
Links between our gut and brain are hormonal, immunological, and neural, via the central nervous system and the enteric nervous system. The brain sends orders via the vagus (VAY-gus) nerve, a long structure that wanders from the very base of the brain down to the gut. Along the way, it touches many other organs. The brain makes hormones — chemical signals that it drips into the bloodstream. These, too, flow to the gut. Both the vagus nerve and hormones can signal hunger and fullness. They can control, too, how quickly food moves through us. The brain and gut send constant cascades of notes back and forth Our guts are home not just to bacteria, but also to viruses — tiny particles made of genes and coated in proteins. Those viruses hijack the cells they infect, and turn them into factories that produce more virus. 95% of the viruses are bacteriophages (Bak-TEER-ee-oh-faaj-uhs) infecting microbes hanging out within us - predators hunting their microbial prey in the savanna of your intestines.
Normal commensal microbiota colonizes the mammalian gut and other body surfaces shortly after birth and remains there throughout an individual’s lifetime. There are 10 to 100 times more bacteria in the gut than somatic cells in humans. Interactions between commensal microbiota and its host are generally beneficial; in healthy people, there’s considerable variability in gut, yet, if a person’s gut bacteria are examined a few months or more apart, they hardly change. In stressful situations, or in response to physiological or diet changes, the microbiota DO change, creating an imbalance in host-microbiota interactions, and these changes affect the person’s health. Gut microbes synthesize vitamins, while those on our skin earn their keep by eating dead cells and transforming oils into natural moisturiser. Microbes everywhere play a role in keeping harmful pathogens at bay, but apparently our stresses can stress them.
Gut microbiota are significant during early development and can influence the wiring of stress circuitry in the brain; a mother’s milk contains some nutrients useless to her baby, but essential for the early microbial colonizers of her baby’s gut. Probiotics, or “good bacteria,” have been shown in animal and human studies to have a beneficial impact on mood symptoms. In a break from working on this today, I went out to make some purchases and asked at half a dozen drug stores if they had any. Aside from an expensive kind at the Italian chain ‘Fascino’ store, everyone know what I was talking about but had nothing in stock. I think it may have been a brief fad, easily determined to be mostly useless.
Mammals and microbes have had an intricate symbiosis for millions of years; the assemblages of species inhabiting each bodily niche represent complex ecosystems that have evolved with us over millennia. Microbes aren’t usually picked up from the environment, but are passed down from generation to generation, and have been for millions of years.
Families of gut microbes living in both us and other apes diverged from a common ancestor some 15 million years ago. Our microbes continue to evolve with us, and in response to our modern lifestyles. People living in industrialized societies have less diverse microbial communities than people in places like Malawi. Microbiome composition ebbs and flows depending on the food we supply and the various chemicals and drugs we send their way. But exactly how the microbes interact with the illness - whether as a trigger or as a shield - remains mostly a mystery. Bacterial strains from Africa and America diverged 1.7 million years ago, around the time early hominids started leaving Africa. Perhaps the history of human migrations around the globe could be traced using our microbiome.
I’d sure like to see THAT done!

We’re born carrying certain tendencies, attitudes, concerns and proclivities. What occurred in our progenitors’ lives we only slowly become at all able to criticize. We expect patterns to be repeated, and they mostly are. It’s difficult to recognize, or realize, what can or should be changed, especially as there are so many limits to what we can have any enduring impact upon. Words are at best only superimposed over natural anticipations, and taken no more seriously than they ought to be. Our feelings we take much more seriously.
Attitudes, both epigenetically derived and experientially received, change best not from presentations of logical syllogisms or scientific demonstration, but from interest in safety, self-preservation and the well-being of family, community and polity. It’s not about money, power or influence, but of maintenance of continuity – we will maintain what we can of what made us ourselves.
To correct the thinking of the wrong-headed, one must play to that, or achieve nothing. Preaching, pleading, brow-beating or diagramming don’t touch emotion, and emotion is the basis of attitude. Display what is desired, they how it can be lost, and what might be retained, and attitude can be influenced. Getting past blinders is difficult in the best of circumstances; too bad that we’ve clearly little chance of retaining ANYTHING through two more generations (for almost all, anyway).


Not All Things Broken Can Be Repaired!

That ontology recapitulates pylogeny, embryological parallelism, may not be quite right, but indeed embryos go through necessary stages, steps, phases, form variations… and one period imperfectly realized impairs the quality and viability of those coming along subsequently. Ontogenetic development involves sequencing, cycles, or spirals rather, often as in Fibonacci numbers, and if in early stages order is disrupted, damaged, full progressive development cannot regain its full impetus, pace, confidence, rhythm, strength, or original tendencies. So, be it from epigenetic ‘memory’ or direct experience, from surfeit or lack, damage leaves fear, awkwardness, reticence, and inability to compete well with the undamaged.

If there is, at all, some kind of parallel between ontology and pylogeny (fetus development and evolutionary development), then one can wonder if a Fibonacci-type sequence to evolutionary development was disrupted causing traumatic damage - perhaps there were less positive incidents coincident with great, important evolutionary leaps, maybe about 3 million years ago, 300,000 years ago and/or perhaps 75,000 years BP and again around 10,000 BCE? Maybe it was earth-axis tilting 40,000 years ago, or some really strong solar flares, that could help explain out present ineptitude. Space monsters and/or earth-center aliens, dude.
Legends of a great flood are many; the Santorini Volcano of Minoan Crete and consequent tsunami, about 1600 BCE, would have been traumatic, as also the Black Plague (although clearly lots of humanity was already pretty well damaged by then). Perhaps the main thing is to accept that we are damaged, as a start to working on the problem. It may well be too late, but those who don’t try achieve nothing.
The implications vis-à-vis democracy are onerous – to recognize impairment for what it is, and it currently threatens human survival, must make us suspicious of egalitarianism and equality under law. Or maybe force us to do more to rescue and revive what can be recovered.