TWO DISCONCERTING STUDIES

Ruefully, true scientists admit that every answer asks a thousand new questions.  “Let's map the human genome?” they said, assuming that genes explain everything and that there are a hundred thousand of them.   And they did.  The map part.  But then it turns out that only about a third of that many are code for making protein and the rest were -- um, “junk.” (The map is not the territory.)  But then it turned out that they WERE code, but code for turning the other genes on and off, genes for timing, coordination, and so on.  One third of the genes were the keys of the piano -- the others were the sheet music.  The result was the creature, which was a symphony.  And which has a personal style because every individual "plays" its chromosomes differently.

Ah, that explains it all!  But then there turned out to be annotations to the notations of the notes.  “Epigenes” are little methyl snippets that attach to genes here and there.  (Epi= on top of, like epi-dermis is "on top of skin.")  Like the pedals of the piano, they can mute.  They turn the gene off and on throughout the process of gestation, but also the environment can create some, early parental actions can create some.  Some can be inherited and some cannot.  They can create or prevent gestative mistakes that result in things like Down Syndrome.  They mysteriously interact with one's sexual nature.  (Sharps and flats?  Minor and major chords?)

Here’s the high tech Wiki, presumably written by Someone Who Knows, so I left the links:

DNA methylation is a biochemical process whereby a methyl group is added to the cytosine or adenine DNA nucleotides. DNA methylation stably alters the expression of genes in cells when cells divide and differentiate from embryonic stem cells into specific tissues. The resulting change is normally permanent and unidirectional, preventing a cell from reverting to a stem cell or becoming a different cell type. DNA methylation is typically removed during zygote formation and re-established through successive cell divisions during development. Some methylation modifications that regulate gene expression are heritable and cause genomic imprinting, and hydroxylation of methyl groups occurs rather than complete removal of methyl groups in zygote.[1][2]

DNA methylation suppresses the expression of endogenous retroviral genes and other harmful stretches of DNA that have entered the host genome. DNA methylation also forms the basis of chromatin structure, which enables a single cell to grow into multiple organs or perform multiple functions. DNA methylation also plays a crucial role in the development of nearly all types of cancer.[3]

DNA methylation at the 5 position of cytosine has the specific effect of reducing gene expression and has been found in every vertebrate examined. In adult somatic cells (cells in the body, not used for reproduction), DNA methylation typically occurs in a CpG dinucleotide context; non-CpG methylation is prevalent in embryonic stem cells,[4][5][6] and has also been indicated in neural development.

Epigene “annotations” exist in all forms of life -- including plants -- and operate separately from the mutations of the nucleic instructions in the way we call “evolution.”  Instead of making changes over millennia by creating populations with variations in them and then “cooking them down” by attrition of those that don’t quite fit, the epigenes are more immediate.  In fact, at the one-cell microbe level, the genes and epigenes are swapped across the cell boundary so much that their merry multiplicity prevents them from going into the careful classification boxes invented by 19^th century Euros.  It’s a mosh pit out there.  Um, down there.  Uh, in there.  (We’re full of ‘em.)

A starving boy in Holland during WWII.

Here’s an account of a study that threw all the strict evolutionists into a tizzy.

Summary. A historical birth cohort study of 1116 women born between August 1 1944 and April 15 1946 in the Wilhelmina Gasthuis hospital in Amsterdam, the Netherlands, was set up to study the short- and long-term effects of a limited period of extreme nutritional deprivation in the winter of 1944–1945 in the Western Netherlands. The degree of food deprivation is evidenced by a dramatic decline in third trimester pregnancy weight gain and infant birthweight. All women were traced and 84% (683/813) of survivors presently resident in the Netherlands agreed to be interviewed in their homes. There were no differences in characteristics at birth between interviewed and uninterviewed survivors. The women who were interviewed had 1299 offspring and were able to recall birthweight of all of them. Additional birthweight information from hospital and well-baby clinic (WBC) records is available for about half of the offspring. Since the famine was imposed on the entire population of a well-defined area, whose opportunities to obtain food elsewhere were severely restricted, and the women from this hospital cohort were predominantly lower middle class, the relationship between fetal nutrition and subsequent health outcomes in this cohort is not likely to be confounded by unmeasured attributes related to social class. In addition, selective losses to follow-up could be excluded, which makes the Dutch famine birth cohort a valuable resource for future studies in perinatal epidemiology.

Radiolab is an excellent way to acquire scientific sophistication because it is cheerful, funny, accessible, and rests your computer-sore eyes.  Try these links:

http://www.radiolab.org/story/251876-inheritance/  This is the link for the whole sequence of stories about DNA.

http://www.radiolab.org/story/251885-you-are-what-your-grandpa-eats/  This link is for the grandpa story.

So, it appears that we’re talking about an aspect of the “epigenome” -- that is, things that affect the “expression” of the genes so that the molecular reactions that the gene encodes is different.  Different chords on the keys. The mechanism is sometimes called “methylation,” which appears to be a little add-on bit, involving methane, that says, “on” or “off” or “only in certain cases.”  

what goes on in seminiferous tubules

This research story above suggests that at the ages of 9 to 12, just before adolescence, a boy’s gonads are developing.  Among them are the “nurse cells” in the testicles that make sperms.  They are little templates for sperm. In one super-microscopic picture of them I saw, the nurse cells look as though they have their arm around the growing sperm.  (It's mitosis, "budding.")  In the case of the starving boys, something molecular in the template was changed that was beneficial to the results of the eventual receivers of the sperm (which were the ova in girls).  These starved boys turn out to produce boys who do better than usual: fewer heart attacks, less diabetes, and so on -- both in the children and grandchildren of that man.  Maybe the more vulnerable or flawed nurse cells were culled some way.  No one knows.

On the other side of the gender equation, rat mom’s at McGill were distributed over a spectrum from bad-rat-mom, who rarely licks her babies, to good-rat-mom, who licks her babies all the time.  The baby female rats grew up to be as maternal as their mothers.  (No surprise.)  Turns out that motherliness was molecular: “mom protein” (genetically controlled) is what carries signals to lick.  Somehow.  It turns out that it’s erotic!  The licking stimulates a thyroid hormone which turns on the neurochemical serotonin ("pleasure"), which turns on bits of stuff that peel off any methylation that has been closing off some healthy genes.

http://www.radiolab.org/story/261176-the-great-mother-switcheroo/

http://learn.genetics.utah.edu/content/epigenetics/rats/   This is an interactive website that lets you play “mother rat.”

It turns out that “lovin’ on your babies” will make them smart, relaxed, and happy.  BUT, is that any way to survive in a hostile environment?  NOT.  Shrewd, tense, restless rats may be the best survivors in the Darwinian sense, fit for sliding along walls in the dark and jumping-full of adrenaline at the slightest threat.  Wild rats are just like that.  Tame rats are not.

It's not just rats -- it's a mammal thing.

METAGENOMICS: GENERATING NEW IDEAS

http://www.genomicsnetwork.ac.uk/egenis/

I'm considering  the manifesto of the organization whose website is linked above, which describes itself as doing “metagenomics.”  It appears to be a little bit like the Bioneers and interests me from at least four points of view: 

1.  As a context for science-based “religious” concepts in something like the way that Bertrand Russell tried to reconcile Christianity with physics, which turned out to be a clumsy failure IMHO, but suggested useful ideas like “process theology” and interactions with Zen or Tao.

2.  As a “way in” to discussion of how a little virus (gene code) from the jungle of Africa jumped from chimps to humans, spread around the world, and has changed everything by eliminating whole generations of people in African countries and on the American arts scene, to say nothing of the SF gay renaissance, by propelling research on the processes in cells and immunity systems, and by affecting earmarked international assistance for disease as a way of controlling populations politically.  Always just under the surface are suspicions that HIV-AIDS clinics have made it possible to eliminate stigmatized groups within the US by only pretending to provide antiretrovirals.  The poorer, sicker, more rural you are, the harder it is to get care.  The wealthy, healthy, urban politicians do not "care."

3.  Metagenomics provides an interface for creating a morality of science in terms of how every ordinary action and small life decision affects all the rest of the planet.

4.  It asks what is the function of membranes, boundaries, between creature and environment or within the creature or within the environment, particularly in terms of evolution that is horizontal instead of vertical down the generations, jumps sideways instead of advances.

THE MANIFESTO OF THE METAGENOMICS

"Recent developments in molecular biology imply that classic distinctions between nature and nurture or biology and culture are not applicable to the human ecological niche. Research in epigenetics shows that the effects of culture on nature go all the way down to the gene and up to the stratosphere, and the effects of  biology on culture are similarly inextricable. Living systems almost invariably involve the interaction of many kinds of organisms with a diversity of technologies. The anthropocene—the age of human cultures and technologies interacting with natural environments—changes rapidly, and to understand and manage its functioning requires perspectives from each domain. We propose  the study of Symbiology, the post-organismic study of relation.  [The biology of symbiosis.]

The kinds of relations we study include:

mutualism, 

parasitism, 

domination, 

recognition, 

separation, 

solubility, 

symmetric mutuality (relations among equals in power or status), 

asymmetric mutuality (relations among unequals such as parents/offspring or teacher/pupil), 

reciprocity, 

alienation, 

isolation, 

autonomy, and so forth, and these relations are discernible throughout  nature and all cultures." 

(Regenia Gagnier, Egenis, the Centre for the Study of Life Sciences, University of Exeter)

In my own terms, everything is connected, it’s all moving, and there is no escape or apartness.  It saturates us all, IS us and our thinking.  "Us" includes all plants and animals.

Much of my thinking about it so far as been in terms of boundaries, in the sense of biological boundaries or the legal borders of countries, and how an abundance on one side but a shortage on the other will create a value differential that can be exploited.  I come at this in terms of art and groups like Native Americans or at-risk boys, but also in terms of something like a religious congregation that promises health and prosperity -- even eternal life in an afterworld -- to the people who come “into” the group.  Their worst punishment then is expulsion, but also they may leave voluntarily.  Empty pews mean a dead church.  What fills the pews is effectiveness, safe haven, powerful ideas.  Good for countries, too.

Sometimes countries control the crossing of their borders by banning anyone who cannot prove they don’t have HIV in their bodies, which gives border officials the justification for invasive procedures that break the privacy of the individual as well as his or her skin in order to get blood to test.  The drive to convert a person’s genome into an identification algorithm like a grocery store bar code makes science into politics on the spot.  Television crime shows spin plots around it.  But too soon!  Now that we can look at individual cells, we find chimeras -- people who have two separate genomes in one body, perhaps because of absorbing a twin early in gestation, and we discover that mothers can have cells from the fetus in the womb migrated through their own bodies, even to their brains.  Genetic mosaic.  We lurch from one assumption, seemingly so firm and useful, to its discrediting, to the next shaky idea -- often overlooking the assumption that might truly be effective.

One of the most compelling ideas is that our individual bodies are really communities in process, some cells leaving, some cells arriving, changing their nature according to what resources are available, so that we only have the illusion of being ourselves over time even though we continually add exo-beings to our bodies.

Now I’m going to repeat the list of processes while adding definitions, because I’m not exactly sure what each of them means.  Yet.

Mutualism, the way two organisms of different species exist in a relationship in which each individual benefits.  An economic theory and anarchist school of thought that advocates a society where each person might possess a means of production, either individually or collectively, with trade representing equivalent amounts of labor in the free market.

Parasitism is a non-mutual symbiotic relationship between species, where one species, the parasite, benefits at the expense of the other, the host.  (The 1% problem.)

Domination is control or power over another or others.

Recognition is an act of recognizing or the state of being recognized. The identification of something as having been previously seen, heard, known.  Social approval.

Separation is the act of separating people or things or the state of being separated

Solubility, The solubility of a substance is the amount of that substance that will dissolve in a given amount of solvent. Solubility is a quantitative term. 

Symmetric mutuality is relations among equals in power or status. 

Asymmetric mutuality is relations among unequals such as parents/offspring or teacher/pupil.

Reciprocity is the practice of exchanging things with others for mutual benefit, esp. privileges granted by one country or organization to another.

Alienation is a withdrawing or separation of a person or a person's affections from an object or position of former attachment : estrangement. 

Isolation is the state of being in a place or situation that is separate from others. 

Autonomy is independence or freedom, as of the will or one's actions: the autonomy of the individual.

As I think about these terms, many of the examples that come to mind are political, as in the current situation between Ukraine and Russia, which seeks to alter the boundary between the two countries.  In fact, borrowing from the gender terminologies, Ukraine is not cis-identified:  It is legally not Russia, emotionally is Russia, mixed in terms of religion and language, asymmetrically mutual, and internally alienated.  In a word, askew.

The present political situation on the reservation is also more easily described if one has a grasp of these terms, but they can be less emotionally discussed in terms of the metagenomic code and the way it both determines and responds to its environment.  Without good terms, carefully defined, it is too easy to misunderstand what is going on or to overlook dynamics that aren’t obvious to an outside observer or to a person who is emotionally involved, living in the turbulent situation.  Much of the evolution of the rez population has been horizontal: pulling in people and culture from other places, or -- in the case of the half of the tribe that lives elsewhere -- dissolving into the larger culture.