WHAT IS A MINERAL AND WHAT DOES IT MEAN?

Sometimes a silly question turns out to be a revelation.  I was reading about the "mineralome" of the human body and about the mineralization of the Cambrian one-celled creatures when it struck me that I don’t really know what a mineral “is.”  It turns out that it depends.  The thumbnail is five criteria:

To meet the definition of "mineral" used by most geologists a substance must meet five requirements: 

• naturally occurring

• inorganic

• solid

• definite chemical composition

• ordered internal structure

Steel is not a mineral because it is an alloy produced by people. "Inorganic" means that the substance is not made by an organism. Wood and pearls are made by organisms and thus are not minerals. "Solid" means that it is not a liquid or a gas at standard temperature and pressure. 

"Although liquid water is not a mineral, it is a mineral when it freezes. Ice is a naturally occurring, inorganic solid with a definite chemical composition and an ordered internal structure.”  But ice cubes made by humans are no longer mineral.

This is mind-blowing stuff, because we think there are only three categories: animal, vegetable and mineral — but it turns out this idea is “old science” (archaic, says one source!) from “the Linnaean taxonomy in which all things can be assigned to the animal, vegetable and mineral kingdoms.”  “The Linnean Society of London is the world’s oldest active biological society. Founded in 1788, the Society takes its name from the Swedish naturalist Carl Linnaeus (1707–1778) whose botanical, zoological and library collections have been in its keeping since 1829.”  Nice website.

They are newly relevant since the recent revolutionary and sometimes disturbing information from DNA needs to be reconciled with the Old Science idea of direct experience, palpable and comparable.  That is, if it looks like a duck, quacks like a duck, smells like a duck — the New Science says it still might not turn out to be a duck.  The Linneans had saved a drawer of duck hides (study skins), just in case. 

These ducks are hybrids.

Mineral “is used in reference to the many inorganic chemicals that organisms need to grow, repair tissue, metabolize and carry out other body processes. Mineral nutrients for the human body include: iron, calcium, copper, sulfur, phosphorus, magnesium and many others.”  That list is the “mineralome”, so-called to align it with the terms for the genome, the epigenome, the proteome, et al.  But once a mineral is in the body, it can’t by definition be a mineral anymore, can it? 

“The word "mineral" is also used inconsistently in geology. In mining, anything obtained from the ground and used by man is considered to be a "mineral commodity" or a "mineral material". These include: crushed stone, which is a manufactured product made from crushed rocks; lime, which is a manufactured product made from limestone or marble (both composed of the mineral calcite; coal which is organic; oil and gas which are organic fluids; rocks such as granite that are mixtures of minerals; and, rocks such as obsidian which do not have a definite composition and ordered internal structure.”

“There are approximately 4000 different minerals and each of those minerals has a unique set of physical properties. These include: color, streak, hardness, luster, diaphaneity, specific gravity, cleavage, fracture, magnetism, solubility and many more. These physical properties are useful for identifying minerals. However, they are much more important in determining the potential industrial uses of the mineral.”

Around here, if we could figure out how to market gumbo, a major feature of our soils, we’d have a new industry.  This has been investigated because gumbo is an excellent lubricant that some say is the secret to creating the Egyptian pyramids and the standing stones of Europe.  It’s also an ingredient in cat litter and used for plugging exhausted oil wells.  In fact, if you put cat litter down your toilet, which seems logical, it will seal off your sewer system.  The problem with marketing is transportation of something so heavy and slippery.

So minerals are as inconsistent as the rest of life, dancing in and out of the definition.  Some suggest that the mineral composition of clays along waterways were what provided the scaffolding for the first genome to begin organizing.  Lately I was absorbed by an article detailing how evolution began in the Cambrian Era.  Those little softies in the sea, one-celled eukaryotes, learned how to use minerals to create hard structures: skeletons, shells, teeth and at that point the Hobbsian principal of survival of the fittest in conflicts became relevant. The evolution of bones made it possible to leave the support of the sea and climb onto land, beginning the long evolution to us.

He won't get far on land.

Now I’m going to append a long quote from Eliade. One of the purposes of this blog is to simply put things where I can find them.  I will come back to talking about bones on another post later, because it strikes me that minerals, which we think of as solid and unchanging, are in fact transformed and transforming like everything else in the New Science world of quantum physics and “-omes”.  This is key to our present thinking paradigm.

Myths, Dreams and Mysteries by Mircea Eliade

PP. 83-84

This mystical experience (qaumeneq) is related to the contemplation of his own skeleton, a spiritual exercise of great importance in Eskimo shamanism, but which is also found in Central Asia and in Indo-Tibetan Tantrism.  The ability to see oneself as a skeleton implies, evidently, the symbolism of death and resurrection; for, as we shall not be slow to see, the “reduction to a skeleton,” constitutes, for the hunting peoples, a symbolico-ritual complex centred in the notion of life as perpetual renewal.  

Unfortunately, the information that we have about this spiritual exercise of the Eskimo shamans is rather lacking in precision.  Here is what Rasmussen reports of it:  “Although no shaman can explain how or why, he can, nevertheless, by the power that his thought receives from the supernatural, divest his body of flesh and blood, so that nothing of it remains but the bones.  He then has to name all the parts of his body, mentioning each bone by name; and for this he must not use ordinary human language, but only the special and sacred language of the shamans that he has learned from his instructor.  While seeing himself thus, naked and completely delivered from the perishable and ephemeral flesh and blood, he dedicates himself, still in the sacred language, to his great task, through that part of his body which is destined to resist for the longest time, the action of sun, wind and weather”

Such a spiritual exercise implies the “exit from time”, for not only is the shaman, by means of an interior vision, anticipating his physical death, but he is finding again what one might call the non-temporal source of Life, the bone.  Indeed, for the hunting peoples the bone symbolizes the ultimate root of animal Life, the matrix from which the flesh is continually renewed.  It is starting with the bones that animals and men are re-born; they maintain themselves awhile in carnal existence, and when they die their “life” is reduced to the essence concentrated in the skeleton, whence they will be born anew according to an uninterrupted cycle that constitutes an eternal return.  

It is duration alone, time, which breaks and separates, by the intervals of carnal existence, the timeless unity represented by the quintessence of Life concentrated in the bones.  By contemplating himself as a skeleton, the shaman does away with time and stands in the presence of the eternal source of Life.  So true is this, that in the ascetic technique of mysticisms as highly developed as Tantric Buddhism and Lamaism, meditation upon the image of one’s skeleton, or divers spiritual exercises done in the presence of corpses, skeletons or skulls, still play an important part; such meditations, among others, reveal the evanescence of temporal duration and, consequently, the vanity of all incarnate existence.  

But evidently this “going out of time” by means of the contemplation of one’s own skeleton is different evaluated among the shamans of hunting and pastoral peoples, and among the Indo-Tibetan ascetics; for the former, its aim is to re-discover the ultimate source of animal life and thence to participate in Being; while, for the Indo-Tibetan monks, it is to contemplate the eternal cycle of existences ruled by karma; and hence to dispell the Great Illusion (maya) of Cosmic Life, striving to transcend it by placing oneself in the unconditioned, symbolized by Nirvana.

"Soul-Catcher"

CENTER VERSUS EDGE

I remarked earlier that we need to think about defining groups by their outliers, where things fuzz out into the next group or no group, versus defining a category by its nucleus.  Or what about variegated categories where components mix to make a kind of striped group?  Then what holds them together.  What is their axis mundi?

We’ve broken down the sharp lines between male and female, between the many kinds of desire, between various races -- esp. the ones defined by appearance whether skin color or epicanthal fold.  DNA smashes so many of our cultural and governmental categories.  One of the reasons I watch CSI is that it is an easy way to consider what the show writers have already debated over a coffee-stained table and defined for reflection.  What technical tools have reframed the same questions over and over?

Should we each get a genomic printout attached to our birth certificates?  Or should one be made in the womb so that “faulty” or stigmatized elements can allow an abortion of the fetus before it makes trouble?  Or, since CRISPR allows genes to be replaced rather accurately, should we just do that ?  If we can closely control who we are, what will we do?

What does that imply in terms of demographics -- not who prevails so much as how it will confuse the bean-counters.  Now it appears that everyone is “metis,” mixed.  There’s no such thing as a purebred human -- what a scandal to discover Neanderthal genes -- but, in fact, there’s no such thing as “purebred” anywhere anything, not even in a lab where an impure mix of e-coli strains can abort your doctoral thesis.  Even sitting there isolated in a petri dish, the little bugs mutate.

But history has insisted on sorting everyone by appearance and location.  And using location means drawing boundaries, which means the possibility of gating, controlling who can enter or leave.  Of course, a cell and a body MUST do that -- there MUST be a way to keep out poisons and eject debris.  

Recently the most paradoxical use of face-scanning recognition technology is using it to filter who may attend church services.  Troublemakers?  Heretics?  The disobedient?  Someone with a gun?   In the early days of Christianity there was a phenomenon called "fencing the Communion."  That little rail where you kneel and rest your elbows?  It's meant to prevent you from just walking up and helping yourself.  

Or it could exclude some people from the inner chambers where decisions are made and study becomes more intense.  It took me a while to realize the Board of Trustees of the seminary was mostly for show, to identify people with a lot of money, so as to keep them in mind of the next pledge drive.   The real decisions were made by a sub-group.  In the old days, they were men who retired for whiskey and cigars; naturally, rich widows did not attend.

Who's in, who's out.

Maybe you’ve never participated in a pledge drive in a big church.  The committee -- carefully chosen -- sits down with a set of cards or a list of members and guesses the income of each formal member and then informal Sunday attendees.  (There’s always a banker on the committee.) An estimate is made of the capacity of that person to pledge.  (Kid in college?  House burned down?)  Canvassers are each assigned a certain number of people to visit.  The idea is to remind them what good things generous pledgers had made possible in the previous years and then to hint a bit about “norms.”  One of the men I visited -- wives often weren’t present -- was an important doctor.  He knew I was not making a lot of money.  All I had to do was mention the amount I was pledging to cause him to blush and raise his pledge.  

So a lot of norming -- doing what others are doing -- is based on guessing secrets, which money matters normally are.  DNA suggests belonging to a population whose norm is attendance at a good school and many connections among themselves that will help to attract job offers and provide support after getting the job.  DNA counts more than IQ.

Schisms and eccentricities are bad for business, bad for research, bad for strategies -- IF your goal is to perpetuate an institution.  What kind of institution could be defined by it’s core?  Medicins sans Frontiers seems obvious.  No doubt there are differences among them, but the axis of it all is to heal as many as possible.  They have preserved the original pledge of doctors.

Of course, there are always many forces that are uncontrollable.  Even DNA is constantly being changed by the environment -- providing new opportunities or damages and, more subtly, turning various genes on and off.  Genes don’t necessarily control something like coloring but rather things like the timing of maturation or the interaction of sets of linked genes.  If some CRISPR enthusiast knocks out the gene for something linked to, for instance, metabolism, the person may fail due to its own attempt to succeed.

There are many subtle, internal, unseen dynamics of the code that is each of us.  But ethnic populations of many people also operate as codes, esp. when governments are trying to keep track, politicians are trying to persuade, and advertisements are trying to re-norm us so that we just MUST have some gizmo.

After I read about a lot of this teeny stuff, I love to read the macro research.  Like this quote:

“Until about 9,000 years ago, Europe was home to a genetically distinct population of hunter-gatherers, the researchers found. Then, 9,000 to 7,000 years ago, the genetic profiles of the inhabitants in some parts of Europe abruptly changed, acquiring DNA from Near Eastern populations.

“Archaeologists have long known that farming practices spread into Europe at the time from Turkey. But the new evidence shows that it wasn’t just the ideas that spread — the farmers did, too.

“The hunter-gatherers didn’t disappear, however. They managed to survive in pockets across Europe between the farming communities.

“ ‘ It’s an amazing cultural process,’ said David Reich, a geneticist at Harvard Medical School who led the university’s team. ‘You have groups which are as genetically distinct as Europeans and East Asians. And they’re living side by side for thousands of years.’

“From 7,000 to 5,000 years ago, however, hunter-gatherer DNA began turning up in the genes of European farmers. “There’s a breakdown of these cultural barriers, and they mix,” Dr. Reich said.

“About 4,500 years ago, the final piece of Europe’s genetic puzzle fell into place. A new infusion of DNA arrived — one that is still very common in living Europeans, especially in central and northern Europe.”

Dr. David Reich

So this population, possibly sheep herders on horseback, came in from the high north and their clue DNA is present in North American Indians!  Is this an example of NA’s infiltrating Eurasia through Russia?  

“The Ancient North Eurasian line was not present in either the 8,000-year-old hunter-gatherers or the 7,000-year-old farmer, so researchers believe it represents a migration into Europe sometime after those individuals lived but before recorded history in the region.

“These Ancient North Eurasians must have spread into Europe at a later time, and so encountered early farmer- or hunter-gatherer-type populations and mixed with them,” Lazaridis said. “It’s definitely, chronologically, the last thing that arrived in most of Europe.”

“Lazaridis said the period of approximately 4,500 years ago appears likely for the influx, because that is when new types of mitochondrial DNA appear in the genetic record. Reich added that there are hints from other disciplines, including linguistics, that point to migrations during that time span.”

A far more controversial and politically incorrect study suggests:

“A team of scientists at the University of Utah has proposed that the unusual pattern of genetic diseases seen among Jews of central or northern European origin, or Ashkenazim, is the result of natural selection for enhanced intellectual ability.

“The selective force was the restriction of Ashkenazim in medieval Europe to occupations that required more than usual mental agility, the researchers say in a paper that has been accepted by the Journal of Biosocial Science, published by Cambridge University Press in England.

“He and two colleagues at the University of Utah, Gregory Cochran and Jason Hardy, see the pattern of genetic disease among the Ashkenazi Jewish population as reminiscent of blood disorders like sickle cell anemia that occur in populations exposed to malaria, a disease that is only 5,000 years old.

“In both cases, the Utah researchers argue, evolution has had to counter a sudden threat by favoring any mutation that protected against it, whatever the side effects. Ashkenazic diseases like Tay-Sachs, they say, are a side effect of genes that promote intelligence.”

Tweets between @DavidQuammen and @Dr. Neil Bodie:

 "Why has there never been an outbreak of #Ebola in Pygmies? Very low rate of serious malaria? Genetic protection?"

Now consider what HIV and addiction are doing to the DNA of America.  Which is the center?  Maybe it is NOT entitled white men.  Maybe this winnowing will create a concentration of something new.  The name of the game is survival.

http://video.pbs.org/video/2365516010/     First peoples.  So far, so good.  Maybe.

"BACKDOOR JOHNNIE'S DNA BIZ": Fiction

“Downton Abbey” with all its Edwardian glamour probably introduced more nice ladies to the idea of anal intercourse than “Oz” did, because nice ladies don’t watch “Oz.”  Of course, some of those nice ladies had to have the exotic prince’s way of having sex without breaking a hymen explained to them.  If they were smart, they asked their kids who undoubtedly knew.  Hopefully not because they had tried it.

As with so many “forbidden” practices, the actual act is embedded in a context of other forces which are sometimes more damaging than the bad thing.  Anal intercourse is a staple of cop shows where prison is made more threatening by promising that the perp will be subjected to regular rape.  It features -- along with oral sex -- in shocking media stories about what teenagers are “up to” or “down to” these days.  And then there are the drug related stories about cavity searches.  Or maybe anal matters come up at public health seminars where the subject is handled with latex gloves and statistics gathered in dubious ways.   I mean, who was asked and why did they answer? 

Rarely are such matters handled frankly lest they be labeled pornography.  Or for fear the usual jump to blaming the messenger will mean that someone just trying to address the subject will be labeled a practitioner.  Which is even more problematic when something has been criminalized, meaning that it has been reduced to code and written down in a way that authorizes penalties.  Not just natural consequences or health advisories, but things that will cause a person to be incarcerated and “you know what will happen there.”  (The context is private prisons, underfunded, accountable to no one and overcrowded.)  Or maybe linked to illegal immigration so that it means deportation.

Rarely do people think of something like this as an opportunity, but I thought I’d try to create a story that would point out a different possibility.  One of the good things about being an eclectic reader is that ideas sometimes crossover.  I call this story:  “Backdoor Johnnie’s DNA Biz.”

In fact, Johnnie had that printed on a calling card for his business.  The joke among he and his confidants was “just leave your calling card at the back door.”  Having been a guy who considered the angles all his life, he thought up this business.

It all started when Johnnie read a story on the internet about independent biolabs, probably the same one I read. (Or did we hear about it on NPR?)  He had not realized that this movement meant that these days most cities had spaces for rent that were equipped for biological laboratory bench work, stuff like figuring out a person’s DNA.  The procedures had gotten simple enough by now for a smart computer whiz like Johnnie to pick up the basics pretty easily.  

Johnnie didn’t make his living the standard conventional admirable way -- he was a male whore, sexy and careful enough to make money.  That is, he took precautions so he wouldn’t be beaten up (ruins your pretty face) and he found a friendly doc.  But the virus got him “in the end” so to speak.  For a while he’d been worried because HIV was as bad as a heroin addiction in terms of needing pills and newer, more expensive treatments all the time.  True enough, the pills got better in terms of side-effects and numbers, but they also required constant testing of ALL body fluids and tied him even tighter to that doc.  So many lab tests meant more people could identify him.  He could do some of them himself, but not all.  When they invented a private HIV self-diagnosis test, like a pregnancy test, it was great, but he was past that.  He knew he could make more money barebacking [no condom], but he also knew that doing it when he was infected -- even though his numbers were below  what was proven contagious -- would expose him to really harsh penalties because it was criminalized.  People still thought the virus was a death sentence when -- for someone with money -- it was more like an eternal debt.  It was a money-making bonanza for pill-pushers.  He wasn’t quite to the level where he could make antiretroviral drugs in his lab, though he had ways to import them from countries where they were produced cheaply.

But when he realized that he could actually learn to sequence DNA -- it’s just a code, after all -- he knew he had a product.  That very night he began to “stock his shelves.”  He went straight to the lab after his trick, cultured the “sample,” and the next day sequenced it, filed it, and identified it with a physical description of the guy, including the intimate details.  He learned ways to pick up names and addresses, both email and physical.  

When he had archived several hundred of these code sequences, he took a SVU detective out for a few drinks.  It didn’t take the guy long to see the possibilities. Johnnie had to do a bit of dickering to get the price he wanted for access to his DNA info, but that wasn’t hard for a guy like him.  Suddenly the cops were finding perps a lot sooner than before and they had DNA evidence to nail a lot of bad citizens.  Stupid ones who never watched CSI shows.  Both Johnnie and the cops were not exactly forthcoming about where they were getting their DNA samples.

Of course, Johnnie had some favorite clients and he let it be known that if they wanted their DNA code to be, you know, “protected,” it would only take a little investment in his business.  At first he thought he might clean up the town so much that it would be bad for his collection enterprises, but there were always enough randy guys coming along to keep things going.  In fact, in time he stopped doing tricks himself and paid whores for samples.  He gave out free self-diagnosis kits for the virus, plus -- for cautious types -- reservoir-tipped condoms and baggies to put them in once they held the sample.  He was trying to run a business, not create an epidemic, which was already underway anyhow.

It did surprise him a little bit to realize who some of these tricks were.  Even the cops hadn’t quite realized how many of the Public Health suits were doing first hand research into the problems of HIV-AIDS.  Not at a lab bench.  Maybe they just thought about it too much on all those panels.  Got obsessive.  But most of them had no intention of ever having first-hand contact with the losers they talked and wrote about, since they were demonstrating what winners they themselves were, what privileged knowledge they had.