Monday, January 31, 2011

W. B. Yeats Had it Right.

    Corrupt and ineffective regimes persist as long as they do only because people tend to be apprehensive towards what might replace them.  The devil which you know is always preferred to the devil that you don't know.  In the last 250 years, most of the old corrupt institutions of power have been overthrown, often to be replaced by even worse arrangements.  And this lesson has not been lost on any who've watched it.
    In the last dozen years, few people, inside or outside of Egypt have been particularly enamored of the Hosni Mubarak regime.  Yet who can know what will actually replace it, and whether it will be an improvement?   Yeats had it right:
   "What rough beast, its hour now come round, slouches toward Bethlehem, waiting to be born?"

Friday, January 28, 2011

Neanderthals--the Cat's Book Review

The Humans Who Went Extinct:  Why Neanderthals died out and we survived.
By Clive Finlayson.

            The prevailing dogma in paleontology has it that Neanderthals were less intelligent, or at least less adaptable than our own ancestors, and that’s why they are gone and we are still here.  We replaced them; perhaps we killed them--maybe even killed them and ate them.  Or perhaps they simply could not compete once our ancestors had entered the game. And of course, since we are the survivors, we must be superior.  So the only question remaining is what makes us so wonderful and how did we get that way.  (A recent NOVA program, The Spark of the Human, consisted of modern humans asking other modern humans just what makes us so wonderful.)
            As comforting as we may find such an analysis, it is probably not the whole story. And about a decade ago, Dr. Clive Finlayson began to suspect that it may not be true at all.  Dr. Finlayson is an evolutionary ecologist with a DPhil from Oxford.  He is the director of the Gibraltar Museum and adjunct professor at the University of Toronto.  His work has focused on Pleistocene caves in Gibraltar, and his specialty also has been the study of climate change and its effect on the survival of bird species.
            When Dr. Finlayson began to have doubts about the conventional views on Neanderthal extinction, he asked just how much evidence supports these views, and discovered that there was little or none.  Scientists had merely assumed that since the Neanderthals are gone and we are still here, we must be in some way superior.  But this raises some awkward questions, such as, why did Modern Humans reach Australia 15,000 years before they entered Europe, unless the Neanderthals were keeping them out.  And if the Neanderthals were able to keep us out, then that would indicate our inferiority, not theirs.  And if they were able to survive for over 300,000 years in Europe and in Siberia, though extremely challenging climate conditions, how could they be so inferior?
            Dr. Finlayson takes the view that the course of evolution is shaped by random events, mostly climate change.  Continents move, mountains grow, ice caps come and go, sea levels rise and fall, and land masses become wetter or dryer.   Whenever a radical climate change occurs, many species go extinct, to be replaced by successful new species.  Finlayson says that all of the many types of humans which at one time simultaneously existed (Modern Humans, Neanderthals, Hobbits, Late Homo Erectus, and who knows how many others) were all examples of relatively new species exploiting fairly recent climate changes.  And except for us, all these species eventually went extinct, which is normal.  But there are always a few species which survive the changes without going extinct—and these are the lucky ones, not the superior ones.   He presents the case that survival is mostly a matter of being in the right place at the right time.  Our ancestors were in the right place at the right time—and the Neanderthals weren’t.
            Species are shaped by their environment.  A lucky species is one that is shaped by its present environment, either genetically or culturally, in ways that also happen to work perfectly well in its next environment.  This does not happen often, but when it does happen it is pure luck, and it’s what happened to us.  The Neanderthals were not that lucky.
            It has been argued that the Neanderthals perished because they lacked adaptability, but this is doubtful.  The last known population lived in a cave at Gibraltar about 24,000 BCE.  Although Europe was very cold at that time, Gibraltar was about as warm and wet as it is today, and the area was host to about the same plants and animals. The bones unearthed in this cave show that these Neanderthals hunted both small and large mammals,  ate 145 species of birds, collected birds’ eggs, took shellfish from the beach, caught fish, ate tortoises, ate small reptiles, monk seals, and two species of dolphins. They were very opportunistic general purpose foragers.  Modern humans who occupied the same cave four thousand years later left about the same array of animal bones, and even built their hearth in the same spot in the cave.  They made their living about the same way that Neanderthals had.  Finlayson says this shows that the variety of food sources which a population depends on is determined by what’s available—not how adaptable they are. 
            Neanderthals had never been mammoth hunters or reindeer hunters.  These are fauna of the steppe tundra, and no part of Eurasia was ever steppe tundra at the same time that Neanderthals were living there.  Neanderthals practiced ambush hunting, which requires a good thrusting spear, strength, courage, and cover.  There is an abundance of edible animals on the steppe tundra, but no cover—just a vast treeless wasteland. This land would have grass and lichens beneath the snow for any grazing animal able to paw through the snow to get it. But these animals could only be killed if attacked from a distance.  
            The Neanderthals never lived on the steppe.  They always lived in the band of woodland just south of the steppe, and they killed mostly red deer because that’s what was there.  As the climate turned colder, couldn’t the Neanderthals have modified their technology so as to make throwing spears, and either bows or throwing sticks? Actually, they were probably experimenting in that direction. At one point, a “transitional technology” the Chatelperronian, began to appear in Europe.  Earlier it was thought that these tools were made by modern humans.  But the fact is, we have no idea who made them. It may have been the Neanderthals, or moderns, or both.  But whoever made them died anyway.  While the general trend of the temperature in Europe was downward, there were variations in both directions superimposed on this pattern.  Often, a particular region would go from woodland to treeless steppe tundra in less than 150 years, and then go back to woodland in another 150 years.  Any change of technology made for hunting reindeer would become useless when the reindeer were gone and the woodland deer were back.  And a throwing spear is useless in heavy brush.  Europeans were subjected not only to a cooler and dryer climate, but to rapid, random changes, which makes any kind of adaptation nearly impossible.
            Eventually Europe was depopulated of nearly all humans, both Neanderthal and whatever moderns may also have been there, except for tiny populations clinging to small refuge areas in southern Iberia, Italy, and the Balkans.  Then Europe was repopulated by people who could not only survive on the steppe tundra, but who had learned thrive there.  But they did not learn to do this in Europe.  These immigrants did not come up from the south—they came in from the east—from central Asia.  And that’s where they learned to live on the treeless frozen waste.  These people happened to be modern Homo sapiens.
            Why was a central Asian population able to adapt to the new environment, whereas no humans in Europe had been able to do so?  Because in central Asia, the climate change had been slow and gradual, and consistent.  Eventually, the treeless, frozen steppe extended from France to Siberia, a thousand kilometers wide.  The central Asians had been living on the edge of the tundra for a long time, and eventually learned to survive there.  Then they simply expanded their range in every direction—west to Europe, northeast to Siberia, and eventually to the new world.
            The Central Asians, our ancestors, were in the right place at the right time. The Neanderthals and any modern humans who were in Europe along with them, were in the wrong place.  The author says that often a population living on the margins of the core area of their species will experience certain unfavorable climate conditions and have a chance to adapt to them, long before such conditions become widespread and engulf the whole core area.  Those in the core area are wiped out, but those out on the margins, who have always had to deal with these climate difficulties survive.  He cites as an example the population of nineteenth century Gibraltar.   The Island has very little fresh water. The upper classes owned cisterns for storing rainwater, and a few had wells, but the poor had neither.  In normal times, the rich had a much lower infant mortality rate than the poor. But in times of extreme drought, the poor, who had always drunk contaminated water, got on about as they always had, while the rich died like flies.  The author calls this “the survival of the weakest.”
            Did Neanderthals interbreed with modern humans?  Recent DNA studies, published since this book was written claim that all modern humans from outside Africa carry between 1% and 4% Neanderthal DNA.  Findlayson guessed that there was probably some interbreeding, but not enough so that modern humans carried very much Neanderthal DNA. He says that the problem was that the main group of moderns who would have had access to Neanderthals died along with them.  The central Asian moderns all moved in after there were no more Neanderthals present, nor any moderns who had ever interbred with Neanderthals.  The interbreeding probably occurred in the Middle East, just after our ancestors left Africa, because the DNA trace is found in all non African humans. 
            The Neanderthals were not dumb brutes.   They used fire, they made tools, they buried their dead, in fact, when burying children, the graves were often strewn with flowers.  They apparently did not use jewelry, but neither do I.  I’ve never seen the point of body ornaments. But does my lack of jewelry make me intellectually inferior to someone who would prefer to wear a bone in his nose?  Neanderthals were very much like us.  They had the same range of hair coloring, including red hair.  Red hair indicates fair skin, which would be required to make vitamin D in cold high latitudes.  They had the same version of the FOXp2 gene as we have.  This gene is involved in the development of the brain structures which process language.  Modern humans with a defective FOXp2 gene can speak but cannot process syntax. The fact that we and Neanderthals share this same gene indicates not only that Neanderthals could speak, but that our common ancestor, Homo Heidelbergensis, could also speak.
            Is there any way at all in which we moderns are superior to Neanderthals?  Well, there is no way to be certain, but we might just have a superior ability to take credit for events we had nothing to do with.  

Sunday, January 23, 2011

Limerick of the Day, Jan 23

There once was a linguist named Cindi
Who spoke both Bengali and Hindi,
With fluency such
That she spoke them too much,
And was generally thought a bit windy.

Monday, January 17, 2011

limerick of the day, Jan 17

I'm a patriot, sir, through and through.
I stand for the red, white, and blough.
But if some monkey hollers
About "saving tax dollers,"
Let's return the poor beast to the zough.

Sunday, January 16, 2011

The Last of the Bananas

                     Bananas around the world are dying.

                  There’s an article in the Jan 10, 2011 issue of New Yorker magazine by Mike Peed entitled “We Have No Bananas.”  It happens that 99% of all bananas produced for export are of a single cultivar—the Cavendish.  And a fungus which attacks and kills this variety, called Tropical Race Fungus Four (TRF-4) is spreading worldwide. This pathogen has already wiped out the plantations of Asia and has spread to Australia.  Most experts agree that it’s only a matter of time before it becomes established in Latin America.  (Technically, a “banana tree” is not actually a tree—but I will call it a tree for this post.)
                  How did the industry become dependent on a single cultivar?  There are over 1000 varieties of banana.  But most are wild bananas whose fruit is tiny, filled with seeds, and in most cases inedible.  And most of the domesticated varieties are sterile, which makes cross breeding nearly impossible, and most are either too fragile to ship, too small, or can be eaten only if cooked.  The Cavendish is the only game in town.
                  No chemical spray or antibiotic has any effect on this fungus.   TRF-4 kills banana trees by entering the root system and then invading cells and switching on a gene already present within the cell, causing the cell to commit suicide, through apoptosis (programmed cell death).  The fungus then feasts on the dead cells, continuing until the tree trunk is consumed from within.  Yet apoptosis is a common defense mechanism which most organisms possess.  If something goes wrong with a cell, the cell is supposed to remove itself and make room for its replacement, or at least remove itself before the problem spreads to the rest of the organism.  Yet TRF-4 turns this defense against its owner.
                  The only way to stop the disease would be to start growing varieties that have natural resistance to it. To do this would mean finding a wild plant, preferably a banana plant, that has resistance, and then cross this plant with a Cavendish or some other marketable variety—to somehow insert a gene that tells the cells not to kill themselves.  But crossing anything with the Cavendish might not be possible because the Cavendish is sterile.  It bears fruit without fertilization, and it produces no seeds.  (In fact, its lack of seeds is what makes it marketable).  It is sterile because it has three sets of chromosomes. It is a triploid.  It originated from an accidental cross between two normal, seed producing wild varieties.  New Cavendish trees are grown from suckers which remain when a banana tree is cut down.
                  Although Alexander the Great introduced some kind of banana to Europe in 327 BC, the banana as we know it was brought to the United States in 1870.  The cultivar was from Jamaica and was called the Gros Michel. It was well received and by 1910 Americans were eating 40 million bunches a year, and vast tracts of South American jungle had been planted with Gros Michel bananas.  But in the mid 1920s, these plantations were being attacked by a fungus, TRF-1, and in about thirty years they were mostly destroyed.   What saved the industry was the Cavendish.  This plant, growing in the private greenhouse of the Duke of Devonshire, was from a cutting in a nineteenth century garden in China. 
                  The Cavendish was in most ways less desirable than Gros Michel.  The fruit was harder to ship, spoiled more quickly, was less tasty, required artificial ripening with ethylene gas, and the plants required heavy pesticide use.  But it was resistant to Tropical Race Fungus One, so it was used.  If only the Cavendish were also resistant to Tropical Race Fungus Four.   Eighty-seven percent of all bananas grown are not for export.  They are eaten locally, and they are of many different cultivars, so fungus is not much of a problem. 
                  In 1960, United Fruit Company, seeing that a replacement for the Cavendish would eventually be needed, opened a research center in Honduras, headed by Phil Rowe.  They hoped to develop a cultivar that would be marketable, shippable,  could be grown efficiently, and would be fungus resistant.  After 40 years of effort, Mr. Rowe had made little progress, and in 2001, he hanged himself.  The center he founded is now a non-profit and is continuing his work, headed by Juan Fernando Aguilar. They are still using conventional plant breeding techniques and have not lost hope.  But plant breeding with plants presumed to be sterile is not easy.  About one Cavendish banana out of every 10,000 will actually produce a seed, if you expose Cavendish plants to massive amounts of wild pollen.  So you must sort through tons of banana pulp, running it all through a sieve to find that one seed, and then get it to grow.
                  In Brisbane, Australia, a team led by James Dale of Queensland University of Technology is trying to solve the problem with genetic engineering. They hope to find a plant with resistance to TRF-4, and splice its resistance gene into a common soil bacterium. Then they will allow the bacterium to invade banana cells in a culture, so as to place the gene within the banana cell. They will then kill the bacterium with an antibiotic.   If a live plant could then be cultured from this altered cell, they will have what they want.
                  But even if they succeed, they will still have two problems:  First, present technology would only allow a transgenic plant in which the foreign genes would be expressed throughout the whole plant, not just in the roots.  So it’s not clear that the resulting fruit would be demonstrably safe to eat. (And even if it could be proven safe, most consumers might wish to avoid it.)  Second, we would still have the main problem, which is monoculture.  These fungi have been around for thousands of years.  As long as banana trees were scattered throughout the jungle, no one fungus that specialized in attacking one kind of plant could ever become a pandemic. But when the same cultivar is planted for thousands of square miles, then once a pathogen gets started there is nothing in its path to stop it.

Thursday, January 13, 2011

Shop Class as Soul Craft, a Review

     I have just finished reading a book which I wish to recommend.  The book is Shop Class As Soulcraft, by Matthew B. Crawford. If you liked Zen and the Art of Motorcycle Maintenance, then you'll love this book. It's a study of what's wrong with work in the modern world, and why most workers aren't very happy.  The author has an interesting background. As a child, he was raised in a hippie commune in Berkeley, CA.   He got a BA in physics, and then a PHD in philosophy, and worked for a while in a Washington think tank. But he quit that job to open a motorcycle repair shop.  And for many years, before he finished his PHD, he had worked off and on as an electrician's helper.
    He concludes that as we move away from work using tools to solve "one of a kind," hands-on problems in the real material world, we move away from the only kind of work that every gave workers a sense of personal empowerment or pride of workmanship.   He says that the skilled trades are the last refuge of meaningful work, and goes on to prove this with both practical examples and persuasive philosophical arguments. 
  This is a guy who says some of the things I have always said--only says it beautifully.   You're going to love it.  

Thursday, January 6, 2011

None Wept For Cahokia

            If you’ve never heard of Cahokia, it was a large pre-Columbian city located across the Mississippi river from present day St. Louis, Missouri.  In the eleventh century CE, it was larger than any city in Europe at that time.  But it was abandoned sometime after 1250 CE, and by the time Europeans arrived, except for several huge earthen pyramids and other massive earthworks, there was almost no trace of it.
            I’ve just finished reading CAHOKIA, by Timothy Pauketat.  Mr. Pauketat, an archaeologist, provides the story of the modern archaeological studies of these ruins, and what he believes we have learned about this ancient city. 
            Even before the Lewis and Clark expedition about 1803, European explorers noticed these gigantic earthworks and found them extremely puzzling.  The largest pyramid, a flat-topped rectangular pyramid now called Monk’s Mound, was over 100 feet high, had a volume of 25 million cubic feet, and covered 15 acres.  It was immediately apparent that building these things would require the organized labor of thousands of people, perhaps tens of thousands.  But in the early nineteenth century, most tribes in Mid-North America were hunter-gatherers who were at least semi-nomadic, who rarely lived in groups of more than a few hundred, and who had little in the way of any hierarchical political structures.  Most Americans of European descent assumed that this had always been the case, so many argued that these flat-topped earth pyramids must be natural land forms.  Others, noting that even though badly eroded, one could see that they had originally been laid out in perfectly straight lines, and aligned with the four cardinal directions, conceded that they were made by man, but refused to believe that the Native American tribes could have done it.  So they began speculating about some “lost civilization” that might have built them.
            By the mid-nineteenth century, many earthworks had been dug up by amateur pot hunters, and human bones had been unearthed.  By then, the pyramids were being leveled to make room for cities and roads and farms.  The next explanation, one that persisted for a century, was that Indian Tribes (Native American Peoples) had indeed built them, but not as part of a city. The whole complex, they said, was merely a place where many tribes would meet for some annual festival, like an Indian version of Woodstock.   Not until the 1950s did the archaeology of the site progress to the point that the foundations of thousands of single-family sized huts were unearthed.  These huts, complete with hearths and storage pits, established that tens of thousands of families had lived there.  When this information was published, most archaeologists were reluctant to believe it, since it totally contradicted everything that had been taught about Native American life before Columbus.
            What appears to have happened at Cahokia, according to Pauketat is this:  Most parts of the U.S. that are being farmed today, were being farmed by about 800 CE, though usually not very intensively. And the main crop was corn (maize), just as it is today.  At about 800 CE, a small city was established on the Mississippi flood plain near the confluence of the Mississippi and Missouri rivers, and was supported by adjacent farm fields also located on that flood plain.  Then about 1054, the entire city was razed and a new city, four times as large, was built on top of the old Cahokia.   The new town could hold at least 10,000 residents within its wooden walls.  But counting the suburbs, the city was five times that big.  And this population center was fed and supported by innumerable peasant farmers spread out fifty miles in every direction, with some farms that had a clear connection to Cahokia located well over one hundred miles away.           
             Along with the temples and houses were huge courtyards and playing fields. The largest was 900 feet by 1600 feet.  Cahokians danced, played at sports, feasted, and also conducted ritual human sacrifices--regularly, and on a grand scale.  In one burial vault, a high-status male was buried with 52 young females, aged 15-20 years.  Often, sacrificial victims were killed by having their skulls bashed in with a blunt instrument, probably a stone mace.  Analysis of the teeth showed that these young female victims were of a different ethnic group than the Cahokians.  The captives were probably taken from one of the subject peoples who lived on their periphery. 
            Sometimes a ritual slaughter seemed to involve the deliberate extinction of an entire blood line. There, the victims were other Cahokians, and probably very high status Cahokians.  Men, women, children, and even infants were decked out in ritual finery, and then bludgeoned to death.   
            Analysis of the bones of Cahokians shows that the residents of the city were well fed and healthy; but the same cannot be said about some of the peasant farmers in the surrounding countryside. Small farms were found not only in the flood plain, but on upland prairies over a hundred miles from the city.  And objects found there show a direct connection with the city. Analysis of the bones buried there showed signs of the kind of extreme malnutrition which would occur when people are fed a diet of only corn (maize.)  So while life was good in Cahokia (if you weren’t part of the sacrifice),  life was miserable in the small farmsteads which provided Cahokia its food, and also wove its cloth.  This means that Cahokia was not just a city, but an empire, or at least a city-state with imperial pretensions.  If Cahokians could not project military power for a hundred miles in every direction, then it is unlikely they would have been able to confiscate food from farmers located that distance from the city, especially if these farmers were nearly starving themselves.   And these small farming villages would not have voluntarily surrendered their daughters to be ritually slaughtered--unless they were being crushed under the heel of an unimaginably repressive empire.
            When the facts about Cahokia became clear in the 1960s and 1970s, no one was really happy to hear them.  Most Americans of European descent would prefer to think that the owners of the continent they had appropriated were simple, child-like folk—not the engineers of an empire.  And most Native Americans were saddened to discover that their own ancestors had been capable of such unspeakable cruelty to their own people.  So nothing that was learned was what anyone wanted to hear.
            But Cahokia went as suddenly as it had come. Some time about in the late thirteenth century, the city was abandoned as was the surrounding farmland.  And the entire region remained nearly devoid of humans for two centuries.  The author does not speculate as to why this happened, but one reason would seem obvious.  If you grow maize year after year, the soil, not matter how rich it was to start with, will eventually become depleted. There are areas in Oaxaca and Chiapas, where maize was originally domesticated, where the same plots have been farmed for 4,000 years and are still fertile. But they use a multi-culture.  Maize, beans, squash, and chilies are grown at the same time in the same field.  The beans fix nitrogen for the maize; the maize provides a pole for the beans to climb; and the squash leaves provide a ground cover to mulch out the weeds.  And a diet of this combination of plants provides a nearly balanced diet.   And if the food is consumed locally by those who produce it, and if all animal and human wastes are returned to the field, then no minerals leave the farm.
            But if you grow only maize and send most of it to a far away city to be eaten by others, then the nitrogen, phosphorous, and potassium in this maize is making a “one way trip” away from the farm, and sooner or later there is so little left in the soil that nothing will grow. This is the most economical explanation of the death of Cahokia.
            The author finds it interesting that none of the tribes of Native Americans today have any tales, songs, or folklore of any kind which seem to mention this city. He says that it seems that they made a conscious effort to forget it. But why wouldn’t they?  For masses on the bottom of the system, the whole thing probably seemed like a bad dream and when it was over they wanted to forget it had ever happened.  And for the elites—we don’t know how it all ended.  But the elites may have fled for their lives.  If so, they would have spent the rest of their lives denying that they had ever been Cahokians, lest they be torn limb from limb by former peasants.  No one wept for Cahokia.