AND NOW THE HOLOGENOME . . .

The genome.  Then the connectome.  The epigenome.  And now the hologenome, which is the creature plus all the other microbial life forms that cuddle down with us.  Maybe feed on us.  Insert their genes in among the spirals that we thought were only ours, because they were the plan for us.  We think of them as infections but they are elaborations.  The holobiont is the “whole shebang,”  connected and dynamic.  It’s all ecology: the logic of interactions and fittingness.

http://nautil.us/issue/29/scaling/when-evolution-is-infectious

I suppose we ought to include the molecules we ingest as medicines, escapes, food, and — well, just accidental soak-ups from breathing, bathing, rubbing up against things.  This is an Age of Inclusion despite our complaints and rejections, our attempts to insist on boundaries.

So the docs talk about leverage, probiotic epidemics, niches, dysbiosis, protective commensals, and fecal transplants.  Mucus earns a new respect because it harbors so much.  Then there’s the “envirome” where the creature grapples with and seduces what’s around it on every level, including the emotional.  This is why I’m an “everythingist.”

Dr. Stan Rowe, U of Saskatchewan faculty

In 1988 in Saskatoon, Stan Rowe was one of my heroes.  He was proposing this point of view explored by Max Tegmark, as linked below, one of the constant attempts to unite science, religion, and human experience (philosophy included).  I think a lot of people think this way, quietly in order to avoid the yapping opportunist media.  Stan talked about “slices of space/time” and I tried to pass on his thoughts in Sunday sermons.

I copied and pasted these from amazon.ca, in case the US site doesn’t show them.

Home Place: Essays on Ecology, new revised edition  Oct 16 2002  by Stan Rowe

Earth Alive: Essays on Ecology  Apr 15 2006  by Stan Rowe

http://nautil.us/issue/29/scaling/life-is-a-braid-in-spacetime-rp

Max “the braidman” says, “Some people find it emotionally displeasing to think of themselves as a collection of particles. I got a good laugh back in my 20s when my friend Emil addressed my friend Mats as an “atomhög,” Swedish for “atom heap,” in an attempt to insult him. However, if someone says “I can’t believe I’m just a heap of atoms!’’ I object to the use of the word “just”: the elaborate spacetime braid that corresponds to their mind is hands down the most beautifully complex type of pattern we’ve ever encountered in our universe. The world’s fastest computer, the Grand Canyon or even the Sun—their spacetime patterns are all simple in comparison.”

Articles like these two in nautil.us make me dizzy with the joy of insight.   

http://www.nytimes.com/2013/05/07/science/a-glossy-science-magazine-or-living-fossil.html  Dennis Overbye explains in this linked NY Times article that the ‘zine is a bit of a throwback to a time a few decades ago when there were more magazines like it.

1991

At the time, mostly ’70’s, the one I went absolutely crazy over was “The Sciences” published by The New York Academy of Sciences.  I kept breaking my rule about not hoarding magazines because the issues were both so amazing and so beautiful.  In fact, my use of images on prairiemary is inspired by “The Sciences” though they used contemporary art and abstract impressionist paintings, very sophisticated.  This frame of reference that unites art with science is one of my affinities to Tim Barrus and Aad de Gids. I suppose it’s structuralist and deconstructive at once.  Open to argument and the startling.

Ralph Burhoe, founder of Zygon

These days I admire the online magazine Aeon, which is peripherally connected to Nautil.us through the Templeton Foundation, which gave its very first prize to Ralph Burhoe, then associated with Meadville/Lombard.  We weren’t very appreciative of Burhoe and his magazine.  Maybe because, in Gertrude Stein terms, there was no “there” yet in his attempt to unite science and religion.  In 1980 it was just early "process theology".  My problem was that I never could see the difference between science and religion in the first place and don’t appreciate math at all, but Burhoe loved all that stuff, all the apparatus of thought.

Spencer Burhoe, sexy male model

My complaint about Aeon has been that it’s too Anglican culture-bound.  They’ve never gotten down to the homonin layer because they are always in their pre-frontal cortex hobnobbing with respectable libraries.  I like a little porn in my spirituality.  They manage to talk about generations without ever really getting to full-frontal sex.   Less Buddhism, more Hindu!  More autonomic juice!

This vid is pretty seductive:  http://nautil.us/issue/1/what-makes-you-so-special/what-would-buddha-say    It’s Uma Thurman’s dad.  I love the short vids on Aeon.

In the end, in terms of congregations and the paranoid threat of being “religious”, or “institutional” or “dogmatic,” I think — not to worry — but some kind of “denomination” (group with a name, nomenclature) is forming now with many small starts here and there, maybe not understood as religious and maybe not much more than a “house church” that meets in someone’s home.  

Some will consider it “post-Christian” but that’s just because they are as Christocentric as they are anthropocentric.  They don’t frame life in cosmic terms yet.  Or even consider the planetary.  I think this nascent movement is simply a response to the Kuhnian phenomenon of re-organizing thought and belief because of the need to accommodate new information.  

This time it’s pretty extreme because there is so much knowledge and it’s so counter-intuitive.  But I do not think that anyone will be prepared to torture those who refuse to admit that there is a genome.  Well, maybe if they realize it’s a description of how we evolved from monkeys.

Just now in one of those Sharia nations a man who blogged about atheism has been condemned to decades in prison, 2,000 lashes of flogging and a huge money fine.  The people who have the power to do this are showing that they have no power except the power of fear and paranoia.  Their rifle has a barrel that turns back on their own faces.  I doubt they have enough time left in their regime to carry out the sentence to the end.  

Even if they do, their insane reaction will recruit many others to follow the informed man.  That’s the way human culture works.  You can’t resist the whole planet anymore because you can’t put up walls against ideas when people have smart phones in their pockets.  But I ache for the guy.  Like everything else, we’re connected.  Also to the floggers, of course.

THE DOUBLE HELIX AND ITS TANGLES

My niece's AI biz is for cows -- NOT pigs.

CSI television series, like “CSI Miami” or “CSI New York” or “Bones”, are a quick and easy way to pick up information about high tech or edgy or just surprising subjects.  The episode of “CSI Miami” that I watched last night was about a subject my niece knows very well, except that she knows about it in terms of cows.  I’m talking about the management of fertilized ova so that they produce live birth of healthy babies.  Last time I talked to her she was in her pickup on the way to an exceptionally good cow.  On the seat beside her was a cooler of high quality bull sperm which she would put into that mother.  In a few days an attending veterinarian would wash the resulting embryos out and implant them in other cows who would carry the calves to term.  Her AI business is in Oregon, but ranchers around Valier do this.

But the television program was looking at human consequences.  I can imagine the writing team sitting around a table imagining and debating each step after the original concept of exploring human artificial insemination.  This time the story -- “ripped from the headlines” --  began with a man whose sperm had resulted in more than a hundred children.  (The real life version was based on a doctor who thought, “Why pay for donated sperm when I have a little factory right at hand?”)  The donor in the story had a fatal flaw:  “Wilson’s syndrome.”  It means an accumulation of copper in one’s system.  Not necessarily fatal, but that weakened the story which turned on the kids all getting sick and needing liver transplants, so that they used the relaxed disclosure laws to find each other and their father.

Exasperated by the father -- who was not very nice -- the offspring had motives for killing him, which did indeed happen.  In the investigation of that, identical twins turned up.  And then it developed that a surrogate mother gave birth to them and kept one for herself.  In the story she had successfully carried to term some incredible number of implanted zygotes.  They were not biologically related, so the story didn’t follow them looking for each other.  But as it turned out, the sperm donor’s wife was the one who did him in -- he refused to inseminate her and she really wanted a baby.  The law favors people who marry in the expectation of children, which is considered a key purpose of marriage.

Leia and Luke

By now there have been many stories of people who fall in love, unaware that the sympathy they feel for their loved one comes from sharing genes.  (“Star Wars,” for instance.) The ability to move living beings around from conceiving mother to gestating mother, to discover the markers for biological fathers, and to gestate someone else’s zygote as a paid service, is great plot fodder, but also challenges our legal and ethical assumptions and strategies, to say nothing of jangling emotions.  

The closest precedents come from cultures where an important woman can cause her husband to inseminate a servant and then take the baby as her own.  That leaves out the laboratory and includes fleshly contact (i.e. sex), but presumably, technically, the semen donor could be in one room, the ovum donor could be in a second room, and the conception could be in a third. They need not meet each other.  No freezer storage necessary.  Now it is possible to transplant the mitochondria (little sub-cells that manufacture energy) of one woman’s ovum into a recipient, causing even more social puzzles.  Or two women could impregnate each other, taking a nucleus from each ova and combining them.

A cluster of storage "straws" -- each one a potential person

The possibility of storing these germ cells over time also creates problems, though the benefits might be great, for instance, if someone were facing disease or enormous risk, their genes could be saved, so that a woman could create a baby from her husband posthumously.  Sometimes the conceived blastosphere (early stage of development) is frozen for later implantation.  This has created a new CSI scenario over the issue of whether to treat these little blobs as human children with custody and legal costs of maintenance.  If someone unplugs the freezer, is that murder?   If someone sells someone else that tiny undeveloped embryo, have they kidnapped a baby?  As I type, the news comes that a California court decided that the embryos of a woman rendered sterile  by chemotherapy must be destroyed, because the father who was now divorced from her, has a “right NOT to have children.”  Indeed, he might be forced to pay to raise them.

Laws also have to struggle with marriage between closely related people since there are laws against such a thing that are based on the danger of in-breeding, probably much exaggerated unless there is a fatal flaw in the genome.  Luke and Leia might marry on a permissive planet.  But over time “sameness” works against the creative randomness that keeps the whole of the population adapting and creative.

Still, parallel research is showing that a child is as much a product of its environment and human interactions in its early years as it is created by the “simple” genome.  We’ve found the epigenome -- the genome is the piano keys, the epigenome plays the keys, and the environment is, um, the vibrating strings under the lid.  Fun to play with this idea.  Maybe a person is a concerto.

Someone's genetic code

For quite a while Native Americans and other indigenous people have resisted giving blood for genomic analysis. Some groups, due to being separated from other populations, have developed unique gene codes that might have such precious abilities as immunity to HIV or Ebola.  If such a person has blood that might save people, should they be forced to donate it, even if it will endanger their own health or make their lives miserable?  What if their blood is only studied, maybe against their will, using trickery to collect samples?

Apart from that, a genome is like a fingerprint.  The ability to identify individual people has huge implications, not all of them about health which is the way they are usually represented.  As CSI watchers know, it greatly increases criminal detections.  In the past. rape -- for example -- has been hard to prove, not just because the line between consent and force is blurry, but because one individual male couldn’t be identified.  Similarly, child support depends on identifying the actual father.

So the “rape kit” was developed that could take timely evidence from a woman or man to convict a rapist.  The trouble is that enough people don’t see rape as a crime to motivate them to store evidence carelessly and never provide the funds to do the genomic work.  Increasingly, rape is being used as a war weapon.  Viagra reinforces the adrenaline of violence.

One entering wedge is through the military, which agrees to identification partly because of motivation to keep track of many people who are “unitized” and arranged in a hierarchy which is monetized.  That is, an array of soldiers, some of which are considered more valuable and powerful than others, and which are paid according to rank.  There is a need to identify dead people.  

Feeling around for more justification, the military has tried to evoke the mojo of battlefield blood transfusions which we’ve learned can save lives.  But this time the idea is to bar from enlistment those who might have troublesome tendencies, maybe as ambiguous as a tendency to develop PTSD.  (Actually, no identifiable surefire way to do this exists.  Neither can sexual orientation be detected.)  Army medical insurance has already been accused of retroactively defining people as unsuitable because of pre-existing emotional problems, therefore denying promised benefits for PTSD.

Medical and social support for veterans is a mixture of gratitude and recruitment promises.  Since joining the military is a potent way to escape poor social situations, many people with pretty good genes have had miserable enough childhoods to suffer epigene damage or even parasite issues.  We are discovering that gut biomes have a lot to do with health and even personality.  We are used to people being excluded from the army because of flat feet or tricky hearts (that drives many plots), but might one not qualify because of worms? 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561935/

“The Genetic Information Nondiscrimination Act of 2008 provides new legal protections to Americans by prohibiting the discriminatory use of genetic information by health insurers and employers. Additionally, the United States military recently created new policies for fair use of genetic information in the determination of benefits for servicemen and servicewomen leaving military service.”   What about the worm's genes?

Trying to digest the implications of all this, I asked Carl Zimmer, the outstanding science writer, whether the universal recording of all military personnel genomes could be matched (if funded) with the database derived from rape kits (if funded).  This was his answer:

“Greetings—

“The informed consent that veterans give when they agree to participate in this program does not allow anything like that.

“Best wishes,

“Carl Zimmer”

In other words, the lawyers have already seen this possibility and tried to block it.  But as we know, once there is ANY kind of electronic database, sooner or later it will be hacked.  The worst consequences from all this is that our ethical thinking and our cultural assumptions are nowhere near being able to cope with all this stuff.  The great advantage of CSI video stories is that it helps at least frame up the issues.

The Original Space Suit

But he has no say about his destination.