Friday, September 30, 2011

My DNA -- a personal story

I couldn't have written this a few years ago. Recently I sent in DNA samples to two organizations to see what they could find. The first one was National Geographic's Genographic Project which geographically traces either the paternal or maternal line back to Eastern Africa about 50,000 years ago, about the time homo sapiens took the "Great Leap Forward," developed language and culture and distinguished themselves from the other hominoids, and left the continent.


National Geographic use genetic markers, mutations on the Y chromosome, to track the male lineage. For females, they use the mitochondria. I ran the test for my Y chromosome which, because only males have one, is transferred intact from the man to his son. No shuffling like the other chromosomes; they only change by mutation.

A few weeks later I received my map, below

My ancestor crossed the Red Sea 40-50,000 years ago, and moved either northeast into modern day Pakistan or northwest into modern Turkey, My haplogroup -- my "tribe," as best as they can tell, is G-M201 of the more ancient M168, P143, and M89 lineage. Today, thirty percent of men in the Caucus Mountains, 14% in Sardinia, 10% in northern Italy, 8% in northern Spain, and 7% of Turkish men are my haplogroup brothers.

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Now I'll share a little family secret, or least a family suspicion. Some of us have noticed what appear to be African facial features in some relatives, and by induction my paternal grandmother's line seems implicated. At times, in certain light, she looked like a black woman. And I remember doing a double take on a photo of Mobutu Sese Seko, infamous leader of Zaire, thinking it was my uncle in a funny hat. I'll admit there was a little inclusive pride surrounding this family curiosity.





With National Genographic Project I thought, here is an opportunity to see if it was true. My grandmother, you see, had come from  Kentucky and although they weren't wealthy and I've never heard rumor, it's possible that one of her ancestors at some point owned slaves. There would have been slaves in that area, at any rate.  I've read that if a white man impregnated a black slave and the children were light enough skinned they were sometimes raised in the father's home. This would be great taboo for all sorts of reasons, of course, and it seems likely in the prim southern culture such a secret could die within a generation or two, leaving just the genetic trace which I have mentioned.


Her maiden name couldn't be more Scotts/Irish: O'Bannon but surnames were almost always attached to the Y chromosome, not to the mitochondria which I could now trace.

A short biology lesson.   Mitochondria are the little "cells-within-our-cells," at one time actually invading bacteria, most people believe. They create heat and more important, they package up energy as adenosine triphosphate (ADP), which is sent around the body to do work. The mitochondria are essential to almost all organisms with a nucleated cell: the "eukaryotes."

For the present purpose two things are most relevant. One is that the mitochondria only get passed on from the mother. Males get them, and they become the organelles which propel sperm, but jettison before entering the egg. Matt Ridley, in his excellent "The Red Queen," explains that, in essence, male and female organelles will fight (chemically) if they encounter one another in the egg, so have come to an agreement -- so to speak -- that the males' will not enter. The second thing about mitochondria is that they carry their own DNA. It's circular and there are up to ten copies in each cell, but for reasons explained above it's passed on intact -- except for mutations. National Geographic is able to trace the female line back through time this way, using the mutations or "markers" to do so.

My grandmother is no longer living. But note that while mitochondria are not passed on through males it is passed on to males, so I asked my father to swab his cheek to have her mitochondria genographed, and he did.

Our reasoning went like this: 1) IF there was black blood in the genome it probably happened during slavery. 2) it probably would have been between a white man and a black woman, and 3) if the lineage from that event to my grandmother involved only daughters, then the Genographic Project would trace my father's maternal line back through the black woman in recent history and straight to Africa from there. We might stand to learn which part of Africa some of my ancestors may have come from.

My father's maternal "haplogroup" was U4. It didn't come straight from Africa.

My grandmother's female heritage moved north to Eastern Europe about 50K years ago. So while we don't know there was an interracial affair on my grandmother's side we still don't have any evidence that there wasn't one; a single male along that lineage would sever the mitochondrial chain.

Another thing I didn't learn was much about myself. In each generation, each parent passes on half their DNA to child and the other half comes from the other parent. Of course. So, using the mitochondria test for example, the entire male half of my heritage is lost -- 50% right away. But not only is the father is ignored, so are both of his parents and all their ancestors too. And the mother's father and all his heritage is trimmed off and this happens for every generation -- so what National Geographic has done is lay down a single rather arbitrary thread of ancestry for me, among many pruned branches. All I know is one of my ancestors seemed to have traveled out of Africa 50,000 years ago, moving north.

But at a generous average of 20 years a generation, in 50,000 years there've been 2,500 generations. Raise 2  to the power of 2,500 and you get 375 followed by 749 0's , each of whom would be just as relevant to my own genome as the woman who first rafted across the Mediterranean.  But oddly, back then humans numbered in just tens of thousands.  How do we reconcile these two numbers?  In a word, as Bill Bryson put it in A Short History of Neary Everything: incest, naturally.  And a lot of it. Fortunately most of it was so far removed to not matter a whit, but all told we can conclude that my ancestry is much more convoluted than the thread National Geographic was able to trace, but it's still of academic interest and that's good enough for me.

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This brings me to the next study of my genome, done by a company called 23andme which focuses on health. Their report is even more impressive. By referencing medical literature they report how likely the average person is to get any of almost 200 hundred diseases. They indicate how inheritable each disease is, and how much is environmental or behavioral and how certain scientists are of these measures. Then, after looking at your genome they report how susceptible you are, compared to average, and how certain they are of that! Some diseases are highly heritable, the relevant genes few and obvious, the studies are highly reliable, the diseases are devastating, and there's nothing you can do about it. I figured if I had one, I'd recalibrate my personal clock. If you are brave enough to look, I think it's a valuable service.

But I'm concerned here with a minor report from 23andme, a map of my "haplogroups" set at 500 years ago. That is, a map showing where "my people" were living before they could travel intercontinentally with relative ease. Like the Genographic Project, and with a similar method, 23andme did this for both my maternal and paternal sides.

So, before they could sail, my mother's mother's people were scattered around northern and eastern Europe. This sounds plausible; my mother is 100% Czech. My father's father's side was scattered in smaller more concentrated groups in southern and Eastern Europe, western Asia, the Middle East (he claims to be German, Irish, and Scottish). Interesting, they are also in northern Africa.

Well I might have found where those admirable black features came from, after all.

Saturday, September 24, 2011

"Lying" is [never] Good (book review)

I downloaded Sam Harris' latest book Lying on my kindle today for under $2.00.  This is his fourth book following the brilliant End of Faith and its companion Letter to a Christian Nation.  These are essential reading for anyone seriously weighing the arguments for and against religion.  The Moral Landscape was, in my opinion, more uneven.  In it, Harris argues that science has the potential to define an objective moral ground.  Harris' debates and talks are always interesting to follow, so I was eager to read his latest short digital book Lying.


It's hard to judge the length of a kindle book, but this one is short enough to be considered a good chapter. It's Sam Harris, so it's well put, succinct, and a pleasure to ponder. He makes some excellent points about the effects, costs, and alternatives to lying - even small lies - and I believe I may become an even more honest person because of it.


Lying, he says, is "almost by definition a refusal to cooperate with others. It condenses a lack of trust and trustworthiness into a single act. ... To lie is to recoil from relationship." This is a brilliant observation, and it's almost seems like common sense. Harris goes on to make a case for vigilant truth-telling, quite well.


It is a strong argument, but it's not airtight. State secrets present an exception, he points out; espionage sometimes requires a complex set of lies. But spies, Harris says, operate under the ethics of war and therefore the "ethics of emergency," and are therefore not only exempt from the golden rule of truth-telling, they are irrelevant exceptions. "We can draw no more daily instruction from the lives of spies than we can from the adventures of astronauts in space. Just as most of us need not worry about our bone density in the absence of gravity, we need not consider whether our every utterance could compromise national security." This begs a question. Without a limiting definition of "emergency," emergency ethics *are certainly relevant to daily life. There is a spectrum of emergencies. I've had emergencies. If on one end lying is ok, the other end not -- doesn't that suggest a spectrum of wrongness to lying, as well?


As I read through it, interesting questions arose for me which unfortunately were not addressed. If lying is, as Harris explains, closely related to selective omission and calculated deception, how would this bear on the ethics of attorneys, of politicians, or to anyone engaged in debate? Can't truth emerge from biased perpsectives bearing down on each other from various angles? Harris, an expert in debate, would be the one to comment. In  field of deception, especially if the audience is half-attentive (this may include politics, and advertising), does it become more acceptable to be deceiptful in return? To counter deception with deception? He addresses this to some extent, but not to my satisfaction.
What of implicators -- those crafty, slippery statements which mean two things, each of which can be denied.  They can be false and true at the same time.  Wrong?  Half-wrong?


What about lying in nature? Camoflage or mimicry, for instance, is a lie. But is this not useful to survival? Survival itself, of course, has already answered this question. Now that doesn't make lying the best strategy for success and it certainly doesn't make it right.  Harris points out the long-term costs and short-term risks of lying quite well.  But one must admit -- there's something pretty appealing about camoflage. 


And how about self-deception, lying to one's self.  We're fabulously equipped to do this; it may well explain a good part of how we function..  It's a major theme in evolutonary psychology, but doesn't seem to be addressed.


Finally, many  of Harris' arguments against lying rely on the difficulty of maintaining a lie and the potential cost of being found out.  What then of a lie that has no chance of being detected and has no maintenance needs -- not so bad?  If someone lies in an anonymous chat room, for example.  I'm sure he would say it was wrong, but why?


To conclude, his argument for the personal policy of "never lie" is short, sweet, and thought provoking. And it is Good.  But it didn't have his typical depth, and wasn't quite convincing.

Thursday, September 15, 2011

What you might have wrong about evolution

In my previous blog I mentioned that evolution is misunderstood by most people – even those who do believe in it.  There is an excellent FAQ on this topic at Berkeley, but I’ll take a moment and try to clarify some things. Most of this is well agreed; some is my current opinion within an existing controversy.  I hope it is interesting to a casual reader.
First, the main reason most Americans don't believe in evolution has nothing to do with reasoning; evolution just comes up against preexisting beliefs, depending on their culture, and probably from childhood.  To the argument that complex life could not have "just occurred" without a conscious designer, I must simply wonder how would that designer (who would be much more complex than his creations) have come into being.  Wouldn't that be less likely still?  And to the argument that gaps in scientific record discredit evolution, yes there are gaps in our knowledge.  Of course.  The gaps just get smaller. 

Natural selection prefers survivors, who pass on their traits to offspring. Thomas Malthus wrote about 1800 that population naturally grows exponentially while food supplies increase much more slowly, and so there is a lot of premature dying that happens.  Malthus had a big influence on Darwin, and on Wallace, it turns out.  Creatures which don't perish often survive for a practical reason, which is often inherited, and so that trait becomes more common. That much is now common knowledge. 

But, there are the misconceptions too, like thinking evolution always drives toward complexity.  Bacteria have evolved by going in the opposite direction; they have stripped down rather than tooled up.  They adapt to single specific niche rather than become adaptable to various environments.   Although we are doing well now, in the long run the bacteria will probably out survive us.

Then there's the idea that what evolves is always better, that evolution is a drive toward perfection.  A lot of things evolution comes up with are not optimal, because they must always result from cumulative changes.  Sometimes traits are lost due to disuse and random deterioration (we've nearly lost our sense of smell, for example).  Some traits are poorly done to begin with.  Our eyes are poorly designed, for example -- we have a blind spot which other animals don't have.  And some were once useful, and now work against us.  We crave sugar, salt, and fat because they were so hard to find that we didn't need a good regulator.  Now we have an overcharged appetite and we're surrounded by sugar, fat, and salt.  We overeat these things simply because we still want to, and now we can.
There's a simplistic model in which genes are little switches for discrete things, like height or alcoholism.  Some do work this way, but not many.  We do have just 25,000 genes or so, but they work in combination.  And they interact with the environment.  Many genes influence a single trait, and each gene influences many traits.  Imagine an immense Rube Goldberg  machine; that's more or less how it works.

A very common misunderstanding is that evolution works at the level of the species -- that animals do what is best for the group.  Not so.  An individual who "cheats" the group for his/her own selfish benefit will likely out survived the others, and to the extent that genes contributed to the cheating behavior those genes will be passed on.  What is more controversial is whether or not the organism is the unit of selection.  I'll use an example: a fierce lion or a camouflaged moth out compete other less aggressive or more obvious peers.  The lions get tougher and moths get darker.  It seems as simple as that, but I think Richard Dawkins (in The Selfish Gene) probably has it right:  The competition actually takes place at the level of the gene, the code which simply makes proteins which eventually have an outward effect (sharper claw, darker wing).  In this way of thinking the organism is just the result of a group of genes working together; the individual parts -- the genes -- are being naturally selected.  

The book I mentioned and Dawkins' subsequent Extended Phenotype  explain this in detail.  Others writers, like Stephen J. Gould, say it happens at the organism or at the group level.  I'll explain by example why I have thing Gould is wrong.   Human males may produce 350 million sperm a day while females incubate one fertilized egg for a long long time. So if one male can impregnate thousands of women, wouldn't the group do better if there were 95 women for every man?  Any population with a gender ratio like that would grow a lot faster and out compete other groups.  But gender ratios in almost all animal species are about 50-50.  This is because within a female-heavy population any male would successfully spread his genes widely.  So a mutation which produced a Y chromosome would end up being copied many times. Although this is by mutation and not design, I like the way Dawkins puts it: They cheat.  
 
Maybe because of this selfishness aspect, there is a common misperception that evolution lends itself to amoral behavior.  Doesn't evolution suggest we shouldn't care about others?  No, it doesn't.  Just as there was an advantage for cells teaming up into multicelluar organisms, people do better for themselves by joining groups.  Working well with others -- and hence, caring about them -- is naturally selected. 

Dawkins wrote something else in The Selfish Gene which has really resonated with me.  Natural selection comes into play when three things are in place: 1. something replicates (copies itself), 2. it sometimes makes mistakes or changes when doing so and 3. it matters in the real world.  Genes do this, with DNA replicating, sometimes mutating, and causing “phonenotypes” such as blue eyes, sharp claws, opposable thumbs, and so on. 
When sophisticated brains are around, information meets these criteria too.  If I think up a good idea and tell you, you may find it interesting enough to tell others.  Someone along the line will change or improve the idea and some of these changes will make the idea more likely to be shared, and some less so.  The idea, in other words evolves.  

A joke spreads, sometimes getting funnier by embellishment or adaptation, but sometimes it's told poorly and falls flat.  Humor has its component parts -- I've read that jokes often involve something tragic, separated by time or distance.  Some use words with two meanings where one interpretation is the opposite of the other.   Dawkins suggested calling these idea-particles "memes," a sort of counterpart to genes  If a meme is something like a gene, then a group of memes may make something like an organism.  It could be a political system, the scientific method, a concept of fairness, an ideology, a religion, a culture.  Take the scientific method -- at its core you'll find evidence-based reasoning, conjecture, hypothesis, statistical testing, random samples, theory building, accumulation of knowledge, peer review, etc.  These ideas have worked very well together.  Ever since language has allowed us to share thoughts, the thoughts in essence, have moved among us, not unlike viruses; they are not living in themselves, but come "alive" in our minds.  You could say they use us.  Just like genes do.
Some people, like Stephen J. Gould, consider science and religion to be in "non-overlapping magisterial,"  completely compatible with one another -- even complementary. I think that's wrong, unless we're talking about a religion with a completely non-interventionist deity.  An intervening God introduces the supernatural, which is simply not allowed in science.  Moreover, evolution has quite a lot to say about consciousness, perception, morality, free will, spirit, human behavior, and the origin of life.  It's not just that science does well without religion.  Science and supernaturalism contradict one another.   It's a matter, I believe, of choosing to believe something because you choose to, or because it is probably true.  

Evolution is a theory, but being a theory does not in itself cast any doubt upon itself; it simply means that the idea is held to a high standard -- it is subjected to evidence-based testing.  Religions are not theories in this way; they are assertions, although some assertions can be -- and I would suggest should be -- tested anyway.  The power of prayer, for example, telepathy, divine predictions.  Anyone who supports the rigorous testing of religious claims has elevated their religion from an assertion to a theory, and that is commendable.  And for theories, to survive, they must be supported by evidence.  When there is vast evidence (as for evolution or for gravity), the theory becomes -- though never immutable truth -- highly, highly, reliable.   

Yet I do believe there is some faith in the scientific method: faith in reason.  Before they have any evidence to support the idea, scientists must have faith in evidence-based reasoning itself -- that is, they must have faith that one can learn by careful observation.  In comparison to religious faith, though, as Dan Dennett has pointed out, this is puddle jumping.  It's not like walking on water.
So far I've been referring to the natural sciences but when it comes to evolution there is quite a lot of disagreement among social scientists - whether or not evolution affects the way we think and act (via our neurology of course).  Some people disparage evolutionary psychology as a collection of "just so" stories.  I don't think it's wise to dismiss it out of hand. 

Why do we fall in love?  Robert Wright, in his excellent book The Moral Animal puts it this way, and I'll risk oversimplifying it. In terms of finding mates (and in human interaction generally) we have developed excellent bullshit detectors, because being tricked is often costly or dangerous.  This is why it's difficult to conceal a lie.  A woman, for example, may be woo'd by a male who pretends to be more devoted than he actually is. She may pay for her mistake with a pregnancy and single motherhood.   His genes are passed on -- an evolutionary win!

When a woman is impregnated and then abandoned is usually not a good thing for the child's survival, so by now her B.S. detectors are so keen that she is unlikely to fall for a faker.  In order to convince her that he is devoted, it is quite useful if he actually feels it, first.  So he falls in deeply in love, it's an infatuation that at the time feels boundless, which is a self-deception of course but it allows him to honestly look deeply into her eyes and tell her with all his heart, in a thousand ways, that she is perfect, perfect, perfect.  She will see that he does really feel that way and perhaps she may be convinced, and a child may be born and if it is, the child will likely have the innate inclination, when it reaches a certain age, to fall in love too.  Just so.

The lesson here is simply that our genes may incline toward behaviors that help our genes, and that emotions can be an effective way to do this.  In other situations they may give us the confidence to face down an intimidating opponent.  They may cause flight at the right moment, empathy, and so on.  The whole range of emotions may exist to push us this way and that.

This is evolutionary psychology, and at its root I think you will find the biggest question of all: do we have free will?  If we are programmed by genes, if we are vessels for memes, and if we are manipulated and deceived by our emotions, what is left of self-determination?  Sam Harris has the best answer I've seen.  Maybe nothing.  It's possiblel that we only think we have free will because we can rarely predict what we're going to decide next.
So to summarize, common misperceptions about evolution include the simple ones based on an aversion to contradictory life perspectives.  Evolution is not a drive toward complexity or toward perfection.  It doesn't happen to groups and probably not even to organisms -- it's simply genes and traits at play.  Evolution is just a theory -- which makes it much better than an assertion but more reliable too.  It does not naturally lead to immorality.  It probably applies to ideas and behaviors just as it does to genes and physical characteristics.  And -- I think --- it is sufficient to explain life as we know it.  Not only is no supernatural intervention necessary, unfortunately, it's not allowed.

Tuesday, September 13, 2011

Everything Equals Everything

Hey, this is not bad!  First I tried Everything is Everything, that was my first choice.  Taken, 2004.  Then Everything means Everything ... 2005.  So I got Everything is Still Everything, but then it occurred to me Everything Equals Everything is better than any of them.  Available!  Who would have thought such a sweet name would still be free for the taking.

I am starting this blog on the advice of a friend who noticed that I have a lot of book reviews on Amazon.com.  Yes, I read books and review them for fun.  My genre is not strictly my own field (geography) per se, though it includes some excellent geographers.  My reading is non-fiction, to be sure, mainly science, including the natural and social sciences and tapping into philosophy, biology, brain neurology, physics, theology, geology, ethics, anthropology, history, political science, geography ...

You see, my passion is evolution.  The link to geography is clearly biogeography, and I am working up a course by that name to teach between my GIS and Cartography.  But this reading is all in my spare time -- I like other fields too.

I think I'll comment on evolution mainly, one way or another.  For better or for worse, and at the risk of sounding like an absurd scientific reductionist, I think evolution pretty much explains every living thing on Earth and elsewhere -- the origin of life, human consciousness, and much of thought and behavior.  Many people in the U.S. don't even believe in evolution or dismiss it as just a theory.  Even a few people I know have expressed their doubt (that's an embarrassment I must live with).  But most of the rest of us believe it, but have just a weak understanding.  I was a little fuzzy on evolution myself until I starting reading up.

There is something I need to say, and first I feel that I should throw up a bunch of caveats and apologies before I move forward because things that interest me include some things that are controversial.  The meaning of life, purpose, truth, right and wrong to name a few.  Though I love the words, I eschew obfuscation and wishy-washy implicators.  I try to be clear, I make mistakes, and am open to being wrong.  There.

Although I am atheist, I like to engage in conversations with devout believers when they will have me.  I entertain the Jehova's Witnesses when they come to the door, and I even welcomed some Unification Church folk too.  Nice people, I thought, and I enjoyed disagreeing with them.  Lo, they seem to like me too and sometimes even return with gifts!  A Jehova Witness friend sent me a book, and a Moonie gave me one to read as well. 

I read them both, as I've read the dominant religious scriptures.  When I was young I went through the Old Testament page by page, and the New, and with an open mind too.  I met with a Rabbi/scholar with a long agenda of topics that interest me, and recently I shared thoughts with a theologian and professor of religious studies.  I know I'm not going to convince anyone already so committed as they are; it wouldn't mean that much to me anyway. But I like to use these conversations to deepen my understanding -- to test the validity of my views and to refine them.  I try to gather evidence (including contradictory evidence) and adjust my beliefs accordingly.  That's the scientific method; no faithful shortcuts to understanding for me, thank you very much.  I am pedisposed, however to what Daniel Dennett wrote, encapsulating what made (and still makes) Darwin's idea so explosive: no "skyhooks," no devine intervention.  None of that is necessary to get us where we are right now.

I'm also agnostic, of course -- it's the only reasonable position.  All believers should be agnostic too, it's simply admitting you really don't know.  Atheism means you don't believe, agnosticism admits you don't really know.  So that's where I am about that, and it colors my views about everything.

.. which brings me to the name of my blog.  In a recent and thoughtful dialog with a theologian, he posited that viewing God as a "creature" or a "being among beings" is not a very sophisticated perspective.  People who do that are looking for straw dogs, he said, the sort that Richard Dawkins, Sam Harris, Christopher Hitchens, and Daniel Dennett knock down so easily.  God, he said, is not the man in the clouds with the flowing beard.  That might as well be Santa Claus.  God is the "ground of being itself."  Without God we would not be able to know anything at all because God is a precondition for all existence.  Therefore he found no contradiction between science and religion, God includes ALL truth, you see ... including scientific truth.
 
I thought it was a nice perspective -- a God of that sort could be inspiring to contemplate.  It reminded me of what I have frequently heard growing up in a liberal Quaker household: God is Love. God is the spirit of love, which radiates from being to being. It warms the heart, it's infectious, you pass it around and all sorts of good things come of it. Yes, love actually does that, and so the argument resonates. It sits well with me.  No "creature," no supernatural force necessary, nothing patently absurd.  Just true pure love.

Except we already have a word for love. It's "love." Love is love.  And tying it up with the language and imagery, myth and ritual, contradictions, mystery -- the obfuscations, or the religious straw dogs (who I consider "absurdly religious") is completely unnecessary.  Associating something so real, beautiful, simple, and pure as love with those firestorms of ideas even seems a little dangerous even, for love.

But I have gotten carried away.  He did not say God is Love, it was other people who said that.  He was referring to something much bigger, much greater, much more beautiful than love.  His concept included all of science, all of existence, it was the "ground of being," without which nothing is possible, nothing exists. It includes all things and all meaning.  Even when biochemists discover how life began (and there are four interesting theories that I know of so far), it won't matter.  God will include first life and everything else too. Even a deist God, which set everything in motion and then stepped back, so to speak, could have set it in motion before first life, and He/It would still deserve the credit for everything.

That comes back to the problem I had when God was just Love. We also have a word for Everything.



And so that's where I guess I'll begin.  Religion is not something I intend to dwell on, but hey ... if you have clear thoughts and questions about life, the universe, and everything, it informs just about everything else.