Showing posts with label metagenomics. Show all posts
Showing posts with label metagenomics. Show all posts

Saturday, March 22, 2014

SUPERPERSON UNCLOAKED


For most of history what you saw is what you got:  but like the fellow who married a showgirl and on the first night witnessed her get ready for bed by removing a wig, a corset, “falsies,” fake eyelashes and fingernails, a layer of makeup . . . there were surprises. Then there’s the story about the NA chief who ordered a nice big sturdy woman from the Monkey Wards catalog and was disappointed when the package that came only contained a strong corset.  "She escaped," he said, shaking his head.

Scientists begin to realize that a person is more than they might seem.  In fact, the metagenomic people are suggesting that gut biota and the other microbes and viruses that find our bodies a very nice place to live are not just passive dwellers, but actively interact with our own cells to do us both good and harm. 



Years ago I read an article describing how intimate bodily contact with another human being (lovers, mothers, nurses, masseuses) meant a storm of migration back and forth until both bodies were colonized by the microbes of the other.  And all the others with whom that other has been intimate, some of them historic enough that their carriers were dead.  Sometimes the crossover entities were what had killed their previous carrier!  In the case of really troublesome diseases, this seems obvious, but to sleep with someone who has gut bacteria possibly beneficial to you is still a very strange idea.  The tiny beings who live in your eyelashes or your armpits don’t generally come to our attention.  

But now our ability to investigate the teeny-tiniest of genomic sequences lets us even distinguish among the strains of HIV that arose from chimp SIV, gorilla SIV and gibbon SIV; lets us trace waves of smallpox infection and their origins; lets us map the Great Spanish Flu Epidemic as it marched across the planet.  Now we know that a person might have HIV, but what KIND of HIV?  And what if now you’ve just required a NEW kind of HIV that will react with your old kind -- the consequences unknown?

The evolutionary change twins are Darwin and Lamarck, one saying it’s all about long time survival on an island (those finches whose bills adapted according to what they ate) and the other saying it’s all about behavior, like giraffes stretching their necks to eat the top leaves."  Sensible people say,  “Okay, kids.  Let’s try to get along -- it’s gotta be both/and.”  (Bibfeldt was very sensible.  That’s because he’s not real -- he was invented by students at the U of Chicago Div School in the early Eighties.)  Let’s just accept that both/and stuff.  Let’s apply that to HIV and “gay” -- just for the helluvit.  Let’s accept the idea of the “super person,” including what may be mutations and may be epigenetic, acquired since birth.


Superpersons are the total of DNA, the added annotation of the epigenome; the contributions of maternal gestation support; the nurturing care in the first few years after birth (rat moms' licking); events during the “latency” period (starved grandpas); community context in childhood; family context; education in fashion at the time (culture); early work (culture); and more.  You can’t be “gay” unless the category exists (culture).  You can’t be “Native American” unless the category exists (culture). “Super” should probably be spelled “supra” since is not about heroes with extraordinary powers, but rather about the many forces that amount to overlying identity in the human individual.

We look to biographies, autobiographies, and memoirs in hopes of discovering ways to make persons (like ourselves and our children) more “super.”  Genealogy studies and nationalism also take a close interest in what might make their members extra potent, effective, praiseworthy and otherwise reflecting well on us.  Members who are defective are quietly cloaked.  Achievements are cheerfully exaggerated.  Descendants are urged to improve the previous generations' reputations by being more super superpersons.  This burden might weigh down the descendants so much that they can sink or they can become defiant and refuse to comply -- this may save them.  Or they may be goaded into being more super.


So far no one has decided to starve their pre-adolescent boys in order to improve their grandchildren, but if people will castrate boys of that age in order to improve their singing, they probably just haven’t thought of it yet.

The Netherlands study was possible because such careful records were kept, but there have been many many people starved in those crucial development years, including Blackfeet.  What if it is the epigenomic adaptation of their descendants that has caused the present fat explosion?  What if the economic Depression across America created a generation of starved grandfathers?  How old was your grandpa in the Thirties?

The epigenome is of particular interest because methylation -- which is what controls it -- can be turned on and off, which means that one can indirectly turn a gene on and off -- in an easier way than trying to deliberately mutate a specific gene.   In fact, epigenome methylation somehow controls the status of a stem cell, so we could use it to create a precious stem cell from skin maybe, potentially the kernel of a new heart or lung.   We DO know how to make a break in the double helix and insert new code.  We aren’t too accurate yet, so trying to do this might knock out code for something vital.

About one in a hundred persons has a natural immunity to HIV.  This comes from the affected cells necessarily having two little ports or points of attachment and entry for the virus.  That “one percent” population’s genome gives mutated instruction that fails to create either both or one of those points. They are missing from the white blood cells.  (We don’t know what else the ports do besides accommodate HIV.  There must be something or why would they be there?)  Conceivably, those ports could be shut off with methylation.


Difficult as that might be, there is another side of the superperson that’s much more difficult: the social part, the cultural part, the political part.  These are what support the “ports” for stigma (fear, rage, hate).  Stigma is as deadly -- maybe more deadly -- than HIV.  HIV is a vulnerability disease: it doesn’t affect the red blood cells of the blood, but rather the white blood cells that manage immunity.  Without the response of white blood cells, infections and trauma cannot heal.  There is no white blood cell that can protect from the vulnerability of stigma, but there ARE social equivalents to methylation.  (Friendship, knowledge, joy.)

To cure the social/cultural/political dimension of HIV-AIDS would mean somehow curing stigma:  hatred, competition, permission to victimize, neglect and abuse of children, unjustified violence, and the monetizing of stigma to capture free labor and sexual objects.  It might mean removing the ports for aggression, male virility, combat, physical competition, war -- all the things we blame on testosterone. At the dimension of culture, that could mean the elimination of a whole population that cannot defend itself or compete.  Culture becomes custard.  Could a culture where people are too nice to reproduce be regenerative enough to keep their population high without resorting to capturing the children of others -- which isn’t very nice but has proven to be effective in the past, even for primates?


From an exhibit by holly-anstiss.co.uk

What do we do about the culturally vulnerable that is NOT based on stigma -- just being in the wrong place at the wrong time?  Crop failure, tsunami, volcano.  Stigma is simply an evil way to manage the distribution of food, shelter, education, access to medical care.   If there is enough of all those things, stigma is unnecessary.  

And put a rat on that committee:  people need affection and emotional development.  But rats don’t pay taxes.  It’s an economic problem.  And it’s a competition problem.  Which makes it a territory and resources problem.  Now we’re beginning to talk planet.  In the end, vulnerability is a planetary problem.  It’s vital to include the microbes in our thinking, but we hardly recognize that territory, much less are able to map it or begin to draw blueprints.





Wednesday, March 19, 2014

METAGENOMICS: GENERATING NEW IDEAS




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 c
ontrol 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.