The Language of Heritability

“The Minnesota twin study raised questions about the depth and pervasiveness of qualities specified by genes: Where in the genome, exactly, might one find the locus of recurrent nightmares or of fake sneezes? Yet it provoked an equally puzzling converse question: Why are identical twins different? Because, you might answer, fate impinges differently on their bodies. One twin falls down the crumbling stairs of her Calcutta house and breaks her ankle; the other scalds her thigh on a tipped cup of coffee in a European station. Each acquires the wounds, calluses, and memories of chance and fate. But how are these changes recorded, so that they persist over the years? We know that the genome can manufacture identity; the trickier question is how it gives rise to difference.”
~Siddhartha Mukherjee, Same But Different

If genetics are the words in a dictionary, then epigenetics is the creative force that forms those words into a library of books. Even using the same exact words in the genomic code from identical twins, they can be expressed in starkly different ways. Each gene’s expression is dependent on it’s relationship to numerous other genes, potentially thousands, and all of those genes together are moderated according to epigenetics.

The epigenome itself can be altered by individual and environmental factors (type of work, exercise, and injuries; traumatic abuse, chronic stress, and prejudice; smoking, drinking, and malnutrition; clean or polluted air, water and soil; availability of green spaces, socioeconomic class, and level of inequality; etc). Then those changes can be passed on across multiple generations (e.g., the grandchildren of famine victims having higher obesity rates). This applies even to complex behaviors being inherited (e.g., the grandchildren of shocked mice, when exposed to cherry blossom scent, still jumping in response to the shock their grandparents experienced when exposed to the same scent).

What is rarely understood is that heritability rates don’t refer directly to genetics alone. It simply speaks to the entire package of influences. We don’t only inherit genes for we also inherit epigenetic markers and environmental conditions, all of the confounders that make twin studies next to useless. Heritability is only meaningful at a population level and can say nothing directly about individual people or individual factors such as a specific gene. And at a population level, research has shown that behavioral and cultural traits can persist over centuries, and they seem to have been originally caused by distant historical events of which the living memory has long since disappeared, but the memory lingers in some combination of heritable factors.

Even if epigenetics could only last several generations, though at least in some species much longer, the social conditions could continually reinforce those epigenetic changes so that they effectively become permanently set. And the epigenetics, in predisposing social behaviors, would create a vicious cycle of feeding back into the conditions that maintain the epigenetics. Or think of the centuries-long history of racism in the United States where evidence shows racism remains pervasive, systemic, and institutional, in which case the heritability is partly being enforced upon an oppressed underclass by those with wealth, privilege, and power. That wealth, power, and privilege is likewise heritable, as is the entire social order. No one part can be disentangled from the rest for none of us are separate from the world that we are born into.

Now consider any given disease, behavior, personality trait, etc might be determined by thousands of genes, thousands of epigenetic markers, and thousands of external factors. Change any single part of that puzzle might mean to rearrange the the entire result, even leading to a complete opposite expression. The epigenome determines not only if a gene is expressed but how it is expressed because it determines how which words are used in the genomic dictionary and how those words are linked into sentences, paragraphs, and chapters. So, one gene might be correlated as heritable with something in a particular society while correlated to something entirely else in a different society. The same gene could potentially have immense possible outcomes, in how the same word could be found in hundreds of thousands of books. Many of the same words are found in both Harry Potter and Hamlet, but that doesn’t help us to understand what makes one book different from the other. This is a useful metaphor, although an aspect of it might be quite literal considering what has been proven in the research on linguistic relativity.

There is no part of our lives not touched by language in shaping thought and affect, perception and behavior. Rather than a Chomskyan language organ that we inherit, maybe language is partly passed on through the way epigenetics ties together genes and environment. Even our scientific way of thinking about such issues probably leaves epigenetic markers that might predispose our children and grandchildren to think scientifically as well. What I’m describing in this post is a linguistically-filtered narrative upheld by a specific Jaynesian voice of authorization in our society. Our way of speaking and understanding changes us, even at a biological level. We are unable of standing back from the very thing about which we speak. In fact, it has been the language of scientific reductionism that has made it so difficult coming to this new insight into human nature, that we are complex beings in a complex world. And that scientific reduction has been a central component to the entire ruling paradigm, which continues to resist this challenging view.

Epigenetics can last across generations, but it can also be changed in a single lifetime. For centuries, we enforced upon the world, often violently and through language, an ideology of genetic determinism and race realism. The irony is that the creation of this illusion of an inevitable and unalterable social order was only possible through the elite’s control of environmental conditions and hence epigenetic factors. Yet as soon as this enforcement ends, the illusion drifts away like a fog dissipated by a strong wind and now through clear vision the actual landscape is revealed, a patchwork of possible pathways. We constantly are re-created by our inheritance, biological and environmental, and in turn we re-create the social order we find. But with new ways of speaking will come new ways of perceiving and acting in the world, and from that a different kind of society could form.

[This post is based on what is emerging in this area of research. But some of it remains speculative. Epigenetics, specifically, is still a young field. It’s difficult to detect and follow such changes across multiple generations. If and when someone proves that linguistic relativity can even reach to the level of the epigenome, a seeming inevitability (considering it’s already proven language alters behavior and behavior alters epigenetics), that could be the death blow to the already ailing essentialist paradigm (Essentialism On the Decline). According to the status quo, epigenetics is almost too radical to be believed, as is linguistic relativity. Yet we know each is true to a larger extent than present thought allows for. Combine the two and we might have a revolution of the mind.]

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The Ending of the Nature vs Nurture Debate
Heritability & Inheritance, Genetics & Epigenetics, Etc
Identically Different: A Scientist Changes His Mind
Epigenetic Memory and the Mind
Inherited Learned Behavior
Epigenetics, the Good and the Bad
Trauma, Embodied and Extended
Facing Shared Trauma and Seeking Hope
Society: Precarious or Persistent?
Plowing the Furrows of the Mind

What If (Almost) Every Gene Affects (Almost) Everything?
by Ed Yong

But Evan Boyle, Yang Li, and Jonathan Pritchard from Stanford University think that this framework doesn’t go far enough.

They note that researchers often assume that those thousands of weakly-acting genetic variants will all cluster together in relevant genes. For example, you might expect that height-associated variants will affect genes that control the growth of bones. Similarly, schizophrenia-associated variants might affect genes that are involved in the nervous system. “There’s been this notion that for every gene that’s involved in a trait, there’d be a story connecting that gene to the trait,” says Pritchard. And he thinks that’s only partly true.

Yes, he says, there will be “core genes” that follow this pattern. They will affect traits in ways that make biological sense. But genes don’t work in isolation. They influence each other in large networks, so that “if a variant changes any one gene, it could change an entire gene network,” says Boyle. He believes that these networks are so thoroughly interconnected that every gene is just a few degrees of separation away from every other. Which means that changes in basically any gene will ripple inwards to affect the core genes for a particular trait.

The Stanford trio call this the “omnigenic model.” In the simplest terms, they’re saying that most genes matter for most things.

More specifically, it means that all the genes that are switched on in a particular type of cell—say, a neuron or a heart muscle cell—are probably involved in almost every complex trait that involves those cells. So, for example, nearly every gene that’s switched on in neurons would play some role in defining a person’s intelligence, or risk of dementia, or propensity to learn. Some of these roles may be starring parts. Others might be mere cameos. But few genes would be left out of the production altogether.

This might explain why the search for genetic variants behind complex traits has been so arduous. For example, a giant study called… er… GIANT looked at the genomes of 250,000 people and identified 700 variants that affect our height. As predicted, each has a tiny effect, raising a person’s stature by just a millimeter. And collectively, they explain just 16 percent of the variation in heights that you see in people of European ancestry.

An Enormous Study of the Genes Related to Staying in School
by Ed Yong

Over the past five years, Benjamin has been part of an international team of researchers identifying variations in the human genome that are associated with how many years of education people get. In 2013, after analyzing the DNA of 101,000 people, the team found just three of these genetic variants. In 2016, they identified 71 more after tripling the size of their study.

Now, after scanning the genomes of 1,100,000 people of European descent—one of the largest studies of this kind—they have a much bigger list of 1,271 education-associated genetic variants. The team—which includes Peter Visscher, David Cesarini, James Lee, Robbee Wedow, and Aysu Okbay—also identified hundreds of variants that are associated with math skills and performance on tests of mental abilities.

The team hasn’t discovered “genes for education.” Instead, many of these variants affect genes that are active in the brains of fetuses and newborns. These genes influence the creation of neurons and other brain cells, the chemicals these cells secrete, the way they react to new information, and the way they connect with each other. This biology affects our psychology, which in turn affects how we move through the education system.

This isn’t to say that staying in school is “in the genes.” Each genetic variant has a tiny effect on its own, and even together, they don’t control people’s fates. The team showed this by creating a “polygenic score”—a tool that accounts for variants across a person’s entire genome to predict how much formal education they’re likely to receive. It does a lousy job of predicting the outcome for any specific individual, but it can explain 11 percent of the population-wide variation in years of schooling.

That’s terrible when compared with, say, weather forecasts, which can correctly predict about 95 percent of the variation in day-to-day temperatures.

Complex grammar of the genomic language
from Science Daily

Each gene has a regulatory region that contains the instructions controlling when and where the gene is expressed. This gene regulatory code is read by proteins called transcription factors that bind to specific ‘DNA words’ and either increase or decrease the expression of the associated gene.

Under the supervision of Professor Jussi Taipale, researchers at Karolinska Institutet have previously identified most of the DNA words recognised by individual transcription factors. However, much like in a natural human language, the DNA words can be joined to form compound words that are read by multiple transcription factors. However, the mechanism by which such compound words are read has not previously been examined. Therefore, in their recent study in Nature, the Taipale team examines the binding preferences of pairs of transcription factors, and systematically maps the compound DNA words they bind to.

Their analysis reveals that the grammar of the genetic code is much more complex than that of even the most complex human languages. Instead of simply joining two words together by deleting a space, the individual words that are joined together in compound DNA words are altered, leading to a large number of completely new words.

“Our study identified many such words, increasing the understanding of how genes are regulated both in normal development and cancer,” says Arttu Jolma. “The results pave the way for cracking the genetic code that controls the expression of genes. “

Dietary Health Across Generations

It’s common to blame individuals for the old Christian sins of sloth and gluttony. But that has never made much sense, at least not scientifically. Gary Taubes has discussed this extensively, and so look to his several books for more info about why applying Christian theology to diet, nutrition, and health is not a wise strategy for evidence-based medicine and public health policy.

Yes, Americans in particular would be wise to do something about their health in a society where 88% of the adult population has one or more symptoms of metabolic syndrome with about three-quarters being overweight and about half diabetic or prediabetic (Joana Araújo, Jianwen Cai, June Stevens. “Prevalence of Optimal Metabolic Health in American Adults: National Health and Nutrition Examination Survey 2009–2016”; for more info, see The University of North Carolina at Chapel Hill or Science Daily). Consider, these statistics are even worse for the younger generations. But let’s put this in even greater context. It’s not only that each generation is unhealthier than the last for this declining health is being inherited from before birth. There is now an obesity epidemic among 6 month old babies. I doubt anyone thinks it’s reasonable to blame babies. Should babies eat less and exercise more?

This goes back a while. European immigrants in the early 1900s noticed how American children were much chubbier than their European counterparts. By the 1950s, there was already a discussion of an obesity epidemic, as it was becoming noticeable with the younger generations. We are several generations into this modern industrialized diet of highly processed starchy carbs, added sugar, and seed oils. Much of this is caused by worsening environmental conditions, from harmful chemicals to industrial food system. The effects would begin in the womb, but the causality can actually extend across numerous generations.

This is called epigenetics, what determines which genes get expressed and how. And this epigenetic effect is magnified by the microbiome we inherit as well, since microbes help determine some of the epigenetic effect, involving short-chain fatty acids that can be obtained either through plant or animal foods (Fiber or Not: Short-Chain Fatty Acids and the Microbiome). This is important, as it is easier and more straightforward to manipulate our microbiome than our epigenetics, or at least our knowledge is more clear about the former. By changing our diet, we can change our microbiome. And by changing our microbiome, we can change our epigenetics and that of our children and grandchildren.

The dietary aspect is the most basic component, in that some diets seem to have an effect directly on the epigenome itself, however the microbiome may or may not be involved — for example, there is “recent evidence that KD [ketogenic diet] influences the epigenome through modulation of adenosine metabolism as a plausible antiepileptogenic mechanism of the diet” (Theresa A. Lusardi & Detlev Boison, Ketogenic Diet, Adenosine, Epigenetics, and Antiepileptogenesis). It’s been proven for about a century now that the ketogenic diet is the most effective treatment for epileptic seizures, but there has been much debate about why. Now we might know the reason. The mechanism appears to be epigenetic.

This is not exactly new knowledge (Health From Generation To Generation). Such cross-generational influences have been known since earlier last century, but sadly such knowledge is not epigenetically inherited by each succeeding generation. Francis M. Pottenger Jr studied the health of cats on severely malnourished and well-nourished diets — by the third generation the malnourished cats were no longer capable of breeding and so there was no fourth generation. This doesn’t perfectly translate to the present human diet, although it does make one wonder. Many of our diseases of civilization seem to be at least partly caused by malnourishment. This is a public health epidemic as national security crisis.

Here is the question that comes to mind: In this modern industrialized diet, what generation of malnourishment are we at now? And if as a society we changed public health policies and medical practice right now, how many generations would it take to reverse the trend and fully undo the damage? To end on a positive note, we could potentially turn it around within this century: “Dr. Pottenger’s research also showed that the health of the cats could be recovered if the diet were returned to a healthy one by the second generation; however, even then it took four generations for some of the cats to show no symptoms of allergies” (Carolyn Biggerstaff, Pottenger’s Cats – an early window on epigenetics).

So, what are we waiting for?

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To give you some idea of how long our society has experienced declining health, check out some of my earlier posts:

Malnourished Americans
Ancient Atherosclerosis?
The Agricultural Mind

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Videos, podcasts, and articles on epigenetics as related to diet, nutrition, microbiome, health, etc with some emphasis on paleo and ketogenic viewpoints:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Nutriepigenomics
from Wikipedia

Changes in the diet affect epigenetics via the microbiota
from EurekAlert!

Diet and the epigenome
Yi Zhang and Tatiana G. Kutateladze

Dietary Epigenetics: New Frontiers
by Austin Perlmutter

RHR: The Latest Discoveries in Evolutionary Biology, Genetics, and Epigenetics
by Chris Kresser

Epigenetics, Methylation, and Gene Expression
by Kevin Cann

Epigenetics: Will It Change the Way We Treat Disease?
by Kissairis Munoz

Hacking Your Genes Through Epigenetics and Targeted Nutrigenomics
by Daniel Rash

The Promise of Paleo-Epigenetics
by Jennifer Raff

Dawn of Paleoepigenomics
by Zachary Cofran

37: Robb Wolf – Diets, Epigenetics, Longevity, and Going Foodless for 9 Days
by Andy Petranek

Epigenetics and the Paleo Diet
from The Paleo Diet

Paleo, Epigenetics, and Your Weight
from Paleo Leap

EP157: Improving Mental Health with Epigenetics, Diet & Exercise with Alex Swanson
from Paleo Valley

Epigenetics Warning: Are You Wrecking Your Kids’ Health?
by Louise Hendon

EPISODE 64: Epigenetics 101 with Bailey Kirkpatrick
from Phoenix Helix

Episode 90 – Dr. Lucia Aronica studies keto and epigenetics
by Brian Williamson

Can Keto Affect Your Genes?
from KetoNutrition

Energy & Epigenetics 1: The Infant Brain is Unique
by Jack Kruse

Dr. David Perlmutter: Intermittent Fasting, Epigenetics & What Sugar Really Does To Your Brain
by Abel James

Epigenetic Explanations For Why Cutting Sugar May Make You Feel Smarter
by Caitlin Aamodt

Eating Sweet, Fatty Foods During Pregnancy is Linked to ADHD in Children
by Bailey Kirkpatrick

High Fat, Low Carb Diet Might Epigenetically Open Up DNA and Improve Mental Ability
by Bailey Kirkpatrick

A Child’s Mental Fitness Could Be Epigenetically Influenced by Dad’s Diet
by Bailey Kirkpatrick

Dad’s Drinking Could Epigenetically Affect Son’s Sensitivity and Preference for Alcohol
by Bailey Kirkpatrick

B Vitamins Protect Against Harmful Epigenetic Effects of Air Pollution
by Bailey Kirkpatrick

Vitamin D Adjusts Epigenetic Marks That Could Hinder A Baby’s Health
by Bailey Kirkpatrick

Could We Use Epigenetics and Diet to Fix Binge Eating?
by Bailey Kirkpatrick

Early Epigenetic Nutrition ‘Memory’ Could Program You for Obesity Later in Life
by Bailey Kirkpatrick

The Consequences of a Poor Diet Could Epigenetically Persist Despite Improving Eating Habits
by Bailey Kirkpatrick

Epigenetic Transfer of Nutrition ‘Memory’ Ends Before Great-Grandchildren
by Bailey Kirkpatrick

How your grandparents’ life could have changed your genes
by Tim Spector

Nutrition & the Epigenome
from University of Utah

The epigenetics diet: A barrier against environmental pollution
from University of Alabama at Birmingham

How Epigenetics May Help Explain the Complexity of Autism Spectrum Disorder
from Zymo Research

Epigenetics, Health and the Mind
from PBS with John Denu

Eating for two risks harm to the baby
by Laura Donnelly and Leah Farrar

Micronutrients in Psychiatry: Sound Science or Just Hype?
by Seth J. Gillihan

Epigenetics: A New Bridge between Nutrition and Health
by Sang-Woon Choi and Simonetta Friso

Role of diet in epigenetics: a review
by Abhina Mohanan and Raji Kanakkaparambil

The science behind the Dutch Hunger Winter
from Youth Voices

Epigenetic Marks From Parents Could Influence Embryo Development and Future Health
by Tim Barry

Can Your Diet Epigenetically Shape Your Child’s Health?
by Janeth Santiago Rios

Epigenetic Insights on Nutrition, Hormones and Eating Behavior
by Janeth Santiago Rios

Paternal Environmental and Lifestyle Factors Influence Epigenetic Inheritance
by Estephany Ferrufino

How Diet Can Change Your DNA
by Renee Morad

Food that shapes you: how diet can change your epigenome
by Cristina Florean

The Unknown Link: Epigenetics, Metabolism, and Nutrition
by Nafiah Enayet

Obesity, Epigenetics, and Gene Regulation
by Jill U. Adams

Epigenetics and Epigenomics: Implications for Diabetes and Obesity
by Evan D. Rosen et al

Epigenetic switch for obesity
from Science Daily

Epigenetics between the generations: We inherit more than just genes
from Science Daily

Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes
by R. Lambrot et al

Diet-Induced Obesity in Female Mice Leads to Offspring Hyperphagia, Adiposity, Hypertension, and Insulin Resistance
by Anne-Maj Samuelsson et al

Maternal obesity increases the risk of metabolic disease and impacts renal health in offspring
by Sarah J. Glastras

Transgenerational Epigenetic Mechanisms in Adipose Tissue Development
by Simon Lecoutre et al

Your Grandma’s Diet Could Have Made You Obese, Mouse Study Suggests
by Kashmira Gandery

Your Diet Affects Your Grandchildren’s DNA, Scientists Say
by Christopher Wanjek

You Are What Your Grandparents Ate
by Maria Rodale

People who eat too much fast food could cause heart disease in their great grandchildren by Jasper Hamill

Eating Badly When Pregnant Might Make Your Kid Fat
by Zak Stone

Perinatal Western Diet Consumption Leads to Profound Plasticity and GABAergic Phenotype Changes within Hypothalamus and Reward Pathway from Birth to Sexual Maturity in Rat
by Julie Paradis et al

A Maternal “Junk Food” Diet in Pregnancy and Lactation Promotes Nonalcoholic Fatty Liver Disease in Rat Offspring
by S. A. M. Bayol et al

Exposure to a Highly Caloric Palatable Diet during the Perinatal Period Affects the Expression of the Endogenous Cannabinoid System in the Brain, Liver and Adipose Tissue of Adult Rat Offspring
by María Teresa Ramírez-López et al

A maternal junk food diet alters development of opioid pathway in the offspring
from Science Daily

‘Junk food’ moms have ‘junk food’ babies
from Science Daily

Born to Be Junk Food Junkies
by Linda Wasmer Andrews

Reality check: Do babies inherit junk food addictions from their moms?
by Carmen Chai

Bad Eating Habits Start in the Womb
by Kristin Wartman

Could Over-Snacking While Pregnant Predispose Children to Be Obese?
by Natasha Geiling

Overeating in pregnancy could lead to child obesity
by John von Radowitz

Eating for two puts unborn child at risk of junk addiction
by James Randerson

Craving for junk food ‘inherited’
from BBC

Craving for junk food ‘begins in the womb’
by Fran Yeoman

Hooked on junk food in the womb
by Fiona MacRae

How pregnant mums who ‘eat for 2’ can make their babies fat
by Victoria Fletcher