Tuesday, July 31, 2018

My Green, Green Happy Place

Sometimes I like to go to my happy place. This time, it was so that I could relax and enjoy my happiness at being a new grandfather. For some people, their happy place is a fantasy inside their minds. But for me, it is an actual place: the forest. In particular, the forest on Turkey Mountain outside of Tulsa.

The forest is a place with layers upon layers of stories. It is a palimpsest, that is, a document with layer upon layer of writing. On this particular like, I already knew almost all of the stories. One story was the geological history of the landscape. As I looked down from the mountain onto the Arkansas River, I remembered that this mile-wide river was once ten miles wide, as the glaciers up north melted. Another story was about human impact. The forest all around me grew in just the last century, since the time when this mountain was covered with oil derricks. Each species of tree, and each tree, had its own story: an evolutionary story of adaptation, and a developmental story of how each individual tree adjusted to its immediate environment of shade and sun, of deep soil or rock outcrop. The story is written from moment to moment. When I hiked, a drought was underway, and many leaves were wilted. Wilting is not completely a bad thing; by drooping down, a leaf has less of a heat load from the sunlight and avoids some of the damage it would otherwise experience. There are also many stories of food webs, whether it is of insects that have eaten the tender leaf tissue between the veins, or fungi eating dead branches. There is the story of the hard, green, inedible persimmon fruits that keep animals away until the seeds are ready to disperse, and only then do the fruits become ripe and delicious. There is the story of stumps sprouting back to life.

I knew all of these stories, but I just wanted to see them again on this hike. But I kept my eyes open, just in case there was a new story. And I found one—just one. A mimosa sampling was hit hard by the drought. Mimosas have lots of little leaflets which, after being held horizontally to face the sunlight in the day, close upward at night for reasons that nobody knows for sure. The leaflets also close upward during moderate drought, thus reducing their solar heat load. The leaflet movements are caused by bags of water called pulvini (singular pulvinus). When the bags of water exert pressure, they push the leaflets; when the bags lose pressure, the leaflets return to their original position.

But what I did not know was, are the pulvini on the top of the leaf or the bottom? If they are on top, then the water pressure pushes the leaflets open; their nocturnal closure represents only a loss of pressure, a relaxation, going to sleep. If this is the case, then the closure of the leaflets at night does not need an explanation. The plant is saving energy by letting the leaves relax. But if the pulvini are on the bottom, then the nocturnal closure demands an explanation: why would the mimosa leaf deliberately close its leaflets at night? This requires the expenditure of energy. The same is true for leaflet closure during moderate drought. If the pulvini are on the top, leaflet closure is merely the result of drought; but if they are on the bottom, then leaflet closure is a deliberate act to prevent drought damage. Of course, the pulvini are too small for me to see.

But I saw one leaf that was so stressed by heat and drought that the leaflets were starting to curl up and die. And in this leaf, the leaflets were horizontal. This tells me that the pulvini are on the bottom. I know this because, when severe drought causes the pulvini to stop working, the leaflets are horizontal, not vertical. In the photo, the drought-damaged leaflets are on top, the leaflets that are actively responding to drought are on the bottom. The damanged leaflets are horizontal, and the responsive leaflets are almost vertical.

To me, this was a new story that I learned on my hike. But I enjoyed re-experiencing the thousand other stories in the forest that I already knew.

Wednesday, July 25, 2018

A Genetic Record of Conquest and Dominion: A Cherokee Story

Here are further thoughts that came to me as I read David Reich’s Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past (Pantheon, 2018). See my previous essay for more about this book.

All of human history has consisted of conquest and dominion. One human group, whether tribe or nation, has conquered one or more others for as long as there have been humans. And in the course of these conquests, the conquering men have had children by the conquered women.

That is certainly what happened in America. Europeans came to America and started conquering Native Americans. Except when they intermarried with them. When they did so, it was usually a white man with a Native woman. This happened over and over again in my family. My sixth great grandmother, Nancy Ward, was a full-blood Cherokee who married a white trader, Bryan (Bryant) Ward. Their half-Cherokee daughter, Betsy Ward, married the white general Joseph Martin. Their quarter-Cherokee daughter Nancy Martin married a rich white (German) ferryboat owner named Hildebrand. Their one-eighth Cherokee daughter Elizabeth Hilderbrand (somewhere along the line the r was added to the name) married a white man, James Pettit. Then things reversed temporarily when their one-sixteenth Cherokee daughter Minerva Pettit married Usquuh-ne, a.k.a. Lewis Hicks, who may have been full-blood Cherokee. But at least on the maternal Cherokee side of my family, it has mostly been white men and Native women. The picture is of Elizabeth's grave in Ft. Gibson, Oklahoma (1801-1887).

This is also what happened to black people. Most American blacks (except the Gullah speakers from the islands off the coast of South Carolina) have partial European ancestry, mostly from white men, many of them slave owners.

The historical evidence for this is reflected in the genetic evidence. In your cells, the Y chromosome (if you have one) came only from your father, and your mitochondrial DNA (abbreviated mtDNA) came only from your mother. In a perfectly fair admixture (in which, for example, white-mother-Native-father pairings were as common as white-father-Native-mother pairings), the Y:mt ratio would be 1:1. But among American blacks, the ratio is 4:1 white to black. In some populations in Central America, as in Colombia, the ratio is as high as 20:1.

To put it in personal terms for me: Up to my great grandfather Andrew Hicks, all of the mtDNA was native. At that point, beginning with my white great grandmother Mary Franklin Hicks, all of the mtDNA was white. My grandfather married a white woman too. I got all my mtDNA from my mom, but it was probably all white. Therefore, perhaps all of my Y chromosomes, and all of my mtDNA, are white. My native genes are mixed into the other chromosomes somewhere.

Back to the white Y chromosomes. Did the white Y chromosomes in my family, and maybe yours as well, come from white men raping dark women, or from dark women choosing white males in order to get some of their wealth and status? Undoubtedly some of both. Both of these Y sources constitute oppression of women: rape is absolutely direct oppression, while the appeal of white wealth and status is an indirect, and possibly subconscious, oppression. In the case of white male owners and black female slaves, it is difficult to see it as anything except rape, since the woman had literally no choice in the matter.

But in my family, things were a little more complicated. As musician Becky Hobbs wrote in her musical Nanyehi, which was about our shared ancestress Nancy Ward, “Cherokee women have always done and will always do whatever they want.” Bryan Ward did not rape Nancy. But the white connection gave Nancy Ward status and respect in the eyes of the white conquerors, and she used this status to her advantage. (She already had status in the eyes of Cherokees.) One of the things she did was, I believe, to arrange to have her half-white daughter Betsy married to Joseph Martin, later a general. This gave Betsy influence in the white world far beyond what a full-blood Cherokee was likely to have. General Martin did not rape Betsy. The trader Bryan Ward and the general Joseph Martin got advantages among the Cherokees because they had Cherokee wives, and Nancy and Betsy got advantages from Betsy marrying the general who was in charge of Cherokee-white relations. All of this status and advantage came to a screeching halt when Elizabeth Hilderbrand Pettit, one-eighth Cherokee and Nancy’s great-granddaughter, had to go on the Trail of Tears to Indian Territory along with all the full-bloods, and take little Minerva with her.

But here is the most complicating factor. In three of the Cherokee-white marriages in my family history, the Cherokee woman was the squaw wife of a man who already had a white family. Bryan Ward had a white family down in Georgia, outside of Cherokee territory, and he eventually returned home to his white wife. General Martin had a white wife and family back in Virginia. Apparently, in both cases, the Cherokee women knew that they were second wives. Nancy’s great granddaughter Elizabeth Hilderbrand, however, did not. By Cherokee law, after about 1829, polygamy was illegal in the Cherokee Nation. When Elizabeth found out her white husband James Pettit had a white family in Missouri, she sued the crap out of him in the Cherokee Supreme Court and won. She was the only woman to do this in the history of the short-lived Cherokee Supreme Court. I’m proud of her. You can read about this in Theda Perdue’s Cherokee Women (University of Nebraska Press, 1998, page 151).

The biggest example of male warrior conquerors inseminating female victims was the empire of Genghis Khan. In some areas of western Asia that were once part of his empire, up to eight percent of males carry what was likely to be Genghis Khan’s Y chromosome, many centuries later. But this was not all rape. Genghis and Kublai Khan established empires that produced a lot of public works and other benefits for the conquered people. The men who ruled the empire must have been much in demand by the native women.

In all these cases, it was conquest and dominion, even if the dominion was one that the conquered women thought that they consciously chose. We just need to admit this fact about ourselves, our human species.

Thursday, July 19, 2018

Human Racial History

There are some conservatives who believe in the superiority of European genes. But this is impossible. The reason is there are few if any European genes.

What we call “European” is a mixture of several different races, all of which were distinct from one another in the past but which, today, have blended together. Five thousand years ago, there were European races that do not resemble any modern races. One race had dark eyes, dark hair, and white skin; another had blue eyes, dark hair, and dark skin. These races did not become extinct, but all of their genes have been mixed together in Europeans. In addition to different Homo sapiens races, European ancestors also included some Homo neanderthalensis.

Take, for example, the famous “ice man” mummy Ötzi who got shot by an arrow as he crossed the Alps 5,000 years ago. He was a member of a race that no longer exists but was widespread in Europe 5,000 years ago.

At one time, Europe was the home of hunter-gatherers. Then people migrated from the middle east, bringing agriculture with them. In a separate migration, horsemen and herdsmen from western Asia brought Indo European languages. Europeans are the mixture of at least three human races, maybe more.

So, you Eurocentric racists, show me: will the real European please stand up?

The migration and subsequent blending of ancient races helps to explain some genetic anomalies from ancient times. The modern Europeans most closely related to Ötzi are the native people of Sardinia. How did that happen? Did Ötzi’s clan embark on an expedition to Sardinia, or maybe the Sardinians invaded Europe? Not at all. Ötzi’s race lived throughout Europe, but as later races migrated into Europe and intermixed, this intermixture did not occur in Sardinia. Sardinia contains a little remnant of Ötzi’s race. But even there, the Sardinians who most closely match Ötzi have mostly non- Ötzi genetic origins.

Such migrations and intermixtures have occurred throughout human history. People scratched their heads in confusion when it was announced that the natives of Papua New Guinea had up to six percent of their genes from the Denisovans, which were a race of Neanderthals who lived in what is now Siberia fifty thousand years ago. (Unlike European Neanderthals, who had red hair and light skin, the Denisovans were darker.)

I know that I, like others who are not expert geneticists, wondered if some Denisovans got on a boat and sailed down to Southeast Asia. But I should have known better, if only because the Papuans live not just in New Guinea but in the highlands, which is largely a world apart from the coastal plain. Any Denisovan voyagers would probably have left their genes among lowland populations. Instead, what probably happened is that people similar to the Denisovans lived throughout Asia, not just Siberia, and that the Denisovan genes were swamped out by human migrants everywhere in Asia except remote places like the New Guinea highlands.

That is, populations such as in New Guinea and Sardinia have remained partially genetically isolated. There are even some Amazonian tribes who have a little bit of Australian ancestry, even though they are mostly descended from migrants who came from Siberia. This suggests that, when the ancestors of Native Americans arrived, there were already some people living in the New World. This pre-Amerindian ancestry was swamped out everywhere except a few scattered tribes.

I got these ideas by reading David Reich’s book Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past (Pantheon, 2018). His main point can be summarized in this way, largely from his own words: The Tree of Life concept does not work for humans, because the branches of the tree keep rejoining. There has never been a single “trunk” of the tree in the past; it is mixtures all the way down (or up).

So the next time you start feeling racial pride (white power, black power, or frybread power) just remember who you really are.

Monday, July 16, 2018

There Are a Lot of Scientific Questions a Citizen-scientist Can Answer

To get answers to some of the biggest questions in the world today, we need to have literally millions of data points and analyze them with large computers. The best example is global climate change. In order to say that the Earth is getting warmer, we must have measurements from almost everywhere, all year, for many years. You can’t just stick your head out the window and tell if global warming is happening or not.

But there are some scientific questions you can answer by just looking out the window.

One of them is the question about whether there is an infinite number of stars in the universe. Now, we have all heard about the astronomers who have looked far out into space and, starting with Edwin Hubble, reconstructed the history of the universe. But what if you don’t have a big telescope? You can answer the question anyway.

The brightness of a star decreases as the square of the distance; a star twice as far away is four times dimmer. Therefore, very faraway stars are practically invisible to most of us. But if there were truly an infinite number of stars, their light, however faint, would add up to an infinite brightness. (Hard to believe? Well, what part of infinite do you not understand?) When you look out the window and see that the sky is dark at night, you know that the universe is finite.

You could solve the problem by putting it into the form of integral calculus. Maybe I could have done so back in 1976 when I understood calculus. But you don’t need to.

There are probably lots of other fascinating scientific questions that do not require equipment, a budget, or expertise to answer.

Monday, July 9, 2018

Fiction: A (Potentially) Long-Lasting Record of the World

Non-fiction, especially science, is an indispensable window on the world. But non-fiction generally has a short shelf-life. They become outdated quickly. For example, Steve Olson’s Mapping Human History, which explained how DNA technology allows scientists to figure out human history (origins, migrations, etc.) was published in 2002. However well-written Olson’s book was, it has been totally eclipsed by books such as David Reich’s 2018 Who We Are and How We Got Here, in which the author explains his own research in this same area but which is based on massive numbers of entire genomes, ancient and modern, from around the world and using new kinds of analysis. Compared to Reich’s work, Olson’s seems based on a mere handful of observations. And however well-written was John Gunther’s 1958 Inside Russia Today, the only people who read it now are professional and amateur historians who wonder what the old communist state was like. Some of the best popular sociology books were the ones written by Vance Packard, but they contain very little information that is relevant today. Old biology textbooks are outdated since they contain no mention of CRISPR-Cas9 systems which are already revolutionizing biotechnology.

Where, then, can one preserve the knowledge of the past, and especially the sense of adventure that the old scientists had in discovering that knowledge?

A few works of non-fiction are still in print after almost two hundred years, not because of their science but because of the authors’ enthusiasm. The example that first comes to mind is Darwin’s Voyage of the Beagle. You can read it and relive the excitement of a time in history when the evolutionary history of the Earth, and even the Earth itself, were largely unknown. It reads like a story.

Which brings me to my point. It is fiction that can preserve the knowledge of previous generations and the sense of scientific adventure. Perhaps the best example is Jules Verne, as explained by Rosalind Williams in The Triumph of Human Empire. Most of Verne’s novels introduced as much scientific and geographical knowledge, as it was known in the nineteenth century, as possible. What was the bottom of the sea like? The middle of Africa? It wasn’t always Verne’s science fiction that explored the world; Michael Strogoff is not science fiction but introduced readers to the vast regions of Siberia with which they were likely to be unfamiliar. Even as Verne wrote about these places, the blank spots on the map, the realm of the unknown, was being filled in. If Verne had written non-fiction books (and some parts of Twenty Thousand Leagues almost sound like a textbook being recited by the scholarly servant Conseil), they would have fallen off the edge of the world at most twenty years after they were written. But in Verne’s novels, we readers willingly assume the mantle of limited knowledge, we pretend that we really don’t know what is under the sea, and we relive the adventure. We are even willing to overlook Verne’s errors that were based on a total ignorance of undersea plate tectonics (we know Atlantis is not really there).

Even the best works of non-fiction get replaced by new discoveries, just as Carl Sagan’s still-famous Cosmos has largely been replaced by the one by Neil DeGrasse Tyson. Few scientists could match Peter Medawar’s thrill of scientific discovery, but when I looked through his Threat and Glory, based on his writings from the 1960s, I found almost nothing with which I could connect.

As I hiked along a trail in an oak forest near Tulsa, as I have done many times, I felt a billowing of enthusiasm about all of the trees, all of the other organisms, and all of the ecological processes that I could see. How could I convey this enthusiasm to others? I could write (and probably have to self-publish) The Flora of Turkey Mountain, which a few people would look at and which would survive, if at all, in a library vault. I could write a more popular book on the same subject. Or I could make it the setting of one of the scenes of a novel, in which the characters advance the plot by exploring the forest. With luck, the novel in which I did this will remain part of the corpus of American literature long after I am gone, assuming it gets published. In non-fiction, I would describe and explain the forest; in fiction, my characters live in it.

Therefore, I hope that, as an aspiring novelist, I can help preserve the history of scientific discovery and enhance the popular appreciation of science.

Friday, July 6, 2018

A Beautiful Scientific Mind: Charles Darwin and His Fossils

I recently skimmed through Adrian Lister’s book Darwin’s Fossils: The Collection that Shaped the Theory of Evolution (Smithsonian Books, 2018). I am not aware that any previous book has gone through all of the specimens that Darwin collected while traveling around the world on H.M.S. Beagle in 1832-1835. Nearly every science-literate person has heard about the finches Darwin saw on the Galápagos Islands, and how these observations eventually led him to think of natural selection. But what about the fossils that he collected and sent back to England?

Previous authors such as Niles Eldredge have noted that Darwin’s fossils included the bones of numerous large extinct mammals from South America, and that it was from this that Darwin concluded what could be called the succession of forms. That is, in the past, the kinds of fossilized mammals lived in the same locations that they are currently found. Glyptodonts (giant armadillos) lived in South America; armadillos lived there today. Giant llamas lived there in the past; llamas live there today. Giant sloths lived there in the past; sloths live there today. Darwin concluded, and scientists widely agreed, that when species become extinct, they are succeeded by similar species in the same location. Today, we can hardly force ourselves to avoid saying that modern species live in the same places that their ancestors lived. But “ancestors” means “evolutionary ancestors” and this is the very thing that Darwin eventually concluded from his observations. But he had to gather the evidence first.

Darwin collected a lot of other fossils as well. He collected petrified wood. He found a petrified forest in Patagonia. He noted that the bases of the trunks were inclined away from the Andes, and so were the sedimentary layers in the rocks, which implied that the Andes had been pushed up out of the Earth since those sedimentary layers had been formed. He also found a few carbonized leaves such as those that can today be found near Clarkia, Idaho, about which I wrote in 2014.

Darwin also found fossilized seashells far above the high tide line, some of them even high in the Andes. The conclusion that was obvious to him, as to us, is that land that was once below the sea has risen. But Darwin was not satisfied with drawing the obvious conclusion. He wanted to eliminate other possible explanations, and to do so before his critics might attempt it in print. Suppose, for example, that the fossilized seashells above high tide were not actually fossils, but were modern middens? That is, what if fishermen hauled seashells up onto land (which they did in fact do) and that what Darwin was seeing was just a pile of leftover shells? Darwin observed midden heaps that were produced by fishermen, and found that the shells were in piles, while the putative fossil shells were individually spaced out, not in piles. In fact, when Darwin asked local fishermen if the putative fossils could have put the shells there, they laughed at the idea.

Darwin suspected that the fossil seashells far above high tide were not deposited in the places where they had lived but had been dead at the time the waves deposited them on an ancient beach. He needed evidence for this. He saw that some of the shells had dead barnacles on the inner surface, which means the shells had been dead for a while before being buried in sediments. If Darwin had not looked for this evidence, he might not later have been able to distinguish fossil shells from an ancient seashore vs. fossil shells from an ancient shell bed.

Darwin also thought that earthquakes caused the successive stepwise uplift of land in South America. But he wanted evidence for this. He got it. In 1835, he witnessed a severe earthquake in Concepción on the Pacific coast of Chile. This one earthquake lifted the land surface at least eight feet. Such earthquakes happen about every century; these earthquakes could easily have produced the Andes. If Darwin had not seen one of these earthquakes for himself, he would have had to depend on second-hand accounts. In fact, an earthquake at least as strong as the 1835 quake, in almost exactly the same place, occurred in 2010.

My point is that while he was on his voyage, Darwin was not just collecting fossils but testing scientific hypotheses about them while he was there rather than wishing he had done so when he got back home. Until I looked through Lister’s book, I had not known this.

Lister’s book also told the story of Darwin’s discovery that coral atolls formed as volcanoes subsided in the ocean floor. This would explain not only their roughly circular shape but also why the atolls were not perfectly circular, like volcanoes, and why they were much larger than volcanoes. The new corals built their reefs on top of old reefs, each new reef being in a slightly different location from the old reef. (A delightful story: When prominent geologist Charles Lyell read Darwin’s theory of coral reefs, he danced around with wild contortions. I’d always thought Lyell was kind of a stick-in-the-mud but I was wrong.) Darwin could not actually prove that there were volcanoes at the bases of coral atolls, however. This was first done in 1952 when geologists drilled a hole down into a coral reef, piercing through thousands of feet of coral limestone, until they hit volcanic rock.

I would not recommend buying this book, unless you are a paleontologist, because it is heavy reading for the rest of us. But it is well illustrated and taught me some new things that, even though I have read dozens of books about Darwin, I’d never known. Get it from your library.

Darwin had a beautiful mind. He was always questioning everything, including his own assumptions. This made him a happy man, because he noticed so many beautiful details of the natural world that he might otherwise have overlooked. The natural world is full of surprises, but only to the person who looks closely and thinks carefully.