Journeys Written in DNA

Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past by David Reich. Pantheon. 2018.

Image: pixabay.com and pmgimage.com

When I spent a summer on the campus of Saint John’s College in Santa Fe, New Mexico, in 1987, one of the groups meeting there was comprised of researchers working on planning the Human Genome Project. The project, which ran for about fifteen years, starting in 1990, cost several billion dollars and produced a single composite DNA sequence for Homo sapiens. Hard to believe that today, thousands of sequences are run routinely at a cost so low that you can get your own sequence in one to two days for $1000.

David Reich provides an account of the recent developments in studying ancient DNA, which is beginning to provide a picture of the evolution of our genus, Homo, over the last 50-150 thousand years, roughly the time that enough DNA remains in old bones or teeth to allow sequencing. The field is rapidly expanding, as more labs open across the world to explore the accumulated human remains in museums, as well as newly excavated material.

Among the findings he reviews are the discovery that early modern humans did indeed hybridize with the archaic populations of Homo that were already in Europe and Asia when the first Homo sapiens moved out of Africa. These earlier people included the Neanderthals and the newly recognized Denisovans. Another finding is that the spread of Indo-European language and culture was indeed accompanied by a spread of people with steppe genotypes into Europe as far west as the British Isles ( see my post on The Horse, the Wheel and Language) The modern human population of Europe turns out to have been the result of multiple waves of migration, bringing not only cultural innovations like farming, but also new human lineages that displaced or blended with the earlier people.

In fact, everywhere that geneticists examine ancient genomes, they find that multiple migrations have shaped human destiny. In North and South America, the most recent areas of human occupation, at least three different migrations can be seen in the genes, and there is still much more work to be done. Likewise, the Indian subcontinent holds a story of migration of Indo-European speakers from the steppes of Central Asia, displacing and blending with the earlier Dravidian language speakers. East Asia has similar patterns, spilling out into the Pacific. These are truly epic journeys of the human species.

Reich discusses the implications of these findings at length. The chapter on genetics and inequality was particularly interesting. The subject is the differences between and within sexes in numbers of offspring produced, as shown by the frequency of distinct gene sequences from a single ancestor among descendent populations. Because men can produce offspring with very little direct effort compared to women, it is possible for men to have many more children in a lifetime. I recall my world history teacher in high school saying that Augustus the Strong of Saxony, “only had about four hundred children.” Circumstantial evidence suggests that Genghis Kahn, thirteenth century Mongol conqueror is the male ancestor of millions, though this is disputed. Certainly, powerful rulers, if fertile and with access to a succession of willing or unwilling consorts, can father many, many sons and daughters.

Reich cites data that indicate that a number of individuals were the fathers of similarly large numbers of descendants during the period between five thousand and three thousand years ago as Neolithic farming peoples began to feel the effects of new technologies: pastoralism, the horse, the wheel and metalworking. In The Horse the Wheel and Language, David Anthony discusses the idea that the new technologies made it possible for tribal chiefs to accumulate power, wealth and prestige. Such men may have led aggressive expansions into new territory, like Genghis, fathering enough descendants for their distinctive Y-chromosomes to show up in genetic analyses. When peoples mix by this mode of male driven conquest, the result is that Y- chromosomes are from the conquering group, while mitochondrial DNA, which is maternally inherited, is from the original inhabitants.

I heard a similar idea many years ago in a seminar on the shift from mother goddess based religion to male sky god religions. Anthony suggests this too in his account of the steppe peoples whose culture and Indo-European language spread widely in this period. The long ago speaker attributed it to mining for metals de-sanctifying the earth, but I suspect it more likely related to the technologies listed above allowing a subset of males to accumulate power. There are now many other cases, from ancient China to medieval Ireland documented by genetic researchers.

Another point Reich makes is that genomics can become a very touchy issue for contemporary descendants of our diversified ancestors. Ethnocentrism is alive and well, from scientists from India who maintain that there were no migrants from the Asian steppes to Navajo elders who refuse to countenance genetic testing arguing that they already know how the Dine were created. Origins are disputed territory: how many Americans still believe in Adam and Eve? Reich points out the falsity of the politically motivated myths of Aryan origins promulgated by German nationalists and still alive today. These crumble in the face of incontrovertible evidence that the modern inhabitants of Northern Europe originated from an amalgam of previous populations with invaders from Central Asia. Migration and mixing of populations and cultures, as we know only too well, is often seen as a threat.

Reich is sensitive to the ethical issues raised by these powerful technologies. He finally consulted a rabbi on the question of whether it was morally right to disturb the dead to obtain genetic material from bones. The answer: only if the knowledge gained will contribute to human  understanding. On the even more fraught question of what population wide genetic studies may reveal about average differences between identifiable groups of people, Reich says two things: First, the question must be faced with accurate data, lest it become the province of pseudoscientific or politically motivated interpretations. Second, whatever the facts are, we know that all groups contain a wide range of potentialities, all of which deserve a chance to be fully realized. Even if a person is not in the upper percentiles of learning ability or athletic ability, the human capacity for hard work makes it possible to succeed. I think Reich means that while  admire the extreme standouts, the Einsteins and Usain Bolts, the bulk of the useful work in the world gets done by those of us closer to the average.

Finally, Reich discusses individual genetic testing. He is in favor of the study of DNA at the population level for medical reasons and also at the individual level, if this helps reduce the incidence of illness caused by recessive mutations. He doesn’t object to individual testing to discover ancestry, but he is not interested in learning about his own genetic background. He seems to feel that focusing on our own unique genomes distracts us from the heritage we share with everyone else, of which the most important part is non-genetic. The simple fact that we are alive tells us that we come from an unbroken genetic line of survivors. Being able to claim descent from particular populations really doesn’t prove much of anything about your own worthiness. Moreover, making such claims can lead to embarrassment, as Elizabeth Warren has discovered.

Humans have been evolving culturally for much longer than the period for which we can get DNA data. Given how much of our behavior is learned, it is likely that our cultural milieu has been a major part of our environment for a long time. Cultures evolve. In doing so, they change the selective environment for humans and the things that live with them. Cultural change drives natural selection. That is, culture shapes our genes indirectly through natural selection as much as genes shape our culture.

As a social species, cultural traditions matter as much or more than our particular DNA in shaping how we live. Many of us, however, know very little of that tradition, or only slivers of it, dependent on our nationality, ethnicity, religion or profession. Too many people grow up with almost no knowledge of any tradition. Even though he professes no religion now, Reich was raised in a deep cultural tradition, Ashkenazi Judaism. He recognizes that all human populations have come out of similarly rich traditions. Together, they represent the most important heritage of the human species; as much as DNA, they are who we are and how we got here.

The Journeys of Holling C. Holling

Paddle to the Sea. 1941. Tree in the Trail. 1942. Seabird. 1948. Minn of the Mississippi. 1951

Each of these books tells a story about travelers. Paddle to the Sea is a small wood carving of a Native American in a canoe, placed by its maker into the water north of Lake Superior. Paddle finds his way to the Gulf of St. Lawrence after years of travel through each of the Great Lakes in turn. Seabird follows the career of a boy named Ezra on a New Bedford whaler and his son’s on yankee clippers, accompanied by a carving in walrus ivory of an ivory gull. Father and son grow to manhood in the age of sail, but the story ends with Ezra’s great-grandson still carrying the white bird as he pilots airplanes over the ocean.  Minn is a snapping turtle, who hatches in Lake Itasca, headwaters of the Mississippi, and who travels slowly south, ending up as a moss covered ancient in the deep backwaters of the Delta. Only the tree in the trail stays put; it begins as a young cottonwood sapling by a tributary of the Arkansas River near present day Great Bend, Kansas. It is witness to generations of Native American Buffalo hunters, the arrival of the Spanish and then the Americans – trappers, traders, settlers and all along the Santa Fe Trail. After hundreds of years, the dead tree is carved into an ox yoke and travels the Santa Fe trail at last. All the books are filled from beginning to end with the natural and human history of the places the travelers pass through. These books are about journeys, but even more about the passage of time.

As a child, I loved Holling’s illustrations, both the large color ones on nearly every other page and the monochrome drawings that filled the margins – maps and diagrams of everything from whales to ships to arrowheads and rivers. I’ve never had difficulty picturing the outlines of the Great Lakes, because Holling, in Paddle to the Sea, provided an object to fit each shape: A wolf’s head for Superior, a summer squash fruit with leaves for Michigan, a trapper carrying a pack of furs for Huron, a lump of coal for Erie and a carrot for Ontario. The forms connected to the regional economies: trapping in the north woods around Superior and Huron, farming in  the midwest around Lake Michigan and in the lake plain of central New York, heavy industry from  western Pennsylvania through northern Ohio to Michigan. Even Lake St. Clair, by Detroit, had a shape like a heart: that region was at the time Holling wrote and illustrated, the industrial heart of the continent.

His marginal illustrations include beautiful maps, both historical and contemporary of the regions his travelers pass. He shows how glaciation shaped the upper Mississippi and the Great Lakes. Showing the history of Minn’s evolution, he goes back to the age of dinosaurs, and there are numerous geological diagrams. his painting of the 1811 New Madrid Earthquake in Minn of the Mississippi is unforgettable.

He illustrations and drawings take you back in time through the history of the regions he depicts.  He illustrates whaling ships and steamboats and covered wagons, often in great detail, showing the different types and how they were used. There are diagrams, beautifully lettered, showing the parts of tools and machines, plans for corrals, sawmills, river locks and how pearl buttons were cut from mussel shells.

In his scenes of life, whether aboard ships at sea or in the bayou country of Louisiana, Holling illustrates the people with sympathy and an absence of satire or irony (he studied anthropology as well as art).  He draws plants and animals in great detail (he was a taxidermist at the Field Museum in Chicago when he was young) and with the same sympathy as his people. Landscapes, wild, rural or industrial are usually shown from a human perspective, as if one were in the scene, with dramatic effect when he shows storms, floods or wildfires. Much of what he depicts he had seen firsthand; he and his wife and collaborator, Lucille Webster Holling, were great travelers themselves.

The Hollings left a legacy of beautifully illustrated books for children. While in many respects, the world they show has changed tremendously since they were published in the 1930s to 1950s, they are still wonderful. There is a love of the natural and the human  coming through these pages that is impossible to miss.

[Here’s another fascinating bit from Wikipedia: “Holling wrote and illustrated a full-page Sunday comic strip titled The World Museum. Each strip included a diorama, which could be cut out and assembled into a 3-D scene of, for example, a buffalo hunt or an undersea panorama.”]

Note: I first found Holling’s books when I was in grade school in the Mary Bailey Pratt Children’s Library in Chapel Hill NC. The library was housed on the upper floor of the elementary school on Franklin Street. It was there, as well as at home, that my love for books developed, thanks to the librarians, especially Mrs Hardee. I worked for her at least one summer, learning how to care for the books. Books with pictures by great American illustrators from N. C. Wyeth to Doctor Seuss, made up a large part of the collection, and two large, framed watercolors, done years before by a student, hung on the wall opposite the desk. One was of Ichabod Crane, walking down the road, reading a book, the other was of Tom Sawyer, heading off to go fishing. After the old school was demolished in the late 1960s, I wondered what had become of those pictures. Years later, I was delighted to find them hanging in the new Chapel Hill Public Library children’s section.

Looking for the Logos of Life VIII: Organism and Superorganism

I Contain Multitudes: The Microbes within us and a Grander View of Life by Ed Yong. Harper Collins. 2016.

IMAGE: Wolbachia inside an insect cell

Who are we really? A question with a thousand answers, one being that we metazoan animals are large collections of cells, descended from a single fertilized egg cell, and organized into tissues, organs and systems, forming an individual. But, like any other object that contains nutrients and and energy ( and we contain a lot of both) we are also a good habitat for other kinds of living things, especially small, unicellular ones. In fact, there are more cells in our body of other kinds, with different DNA and different ancestry, than there are human cells. Most of them live in our intestines, but there are lots in and on every surface exposed to the outside, from our scalp to our toes.

What are they doing? Until 1676, when van Leeuwenhoekdescribed seeing microbes for the first time, we knew nothing of these guests on and within us (nor our own cellular structure) Cell theory did not become a standard tenant of biology until the mid-nineteenth century, and the germ theory of disease followed decades later. For a considerable period after that, microbes enjoyed very bad press, but it gradually emerged that these organisms were in fact mostly benign and possibly even essential to our well being.

We are not alone, of course: microbes are everywhere on and in plants and animals, including in microbes themselves. This book nicely recounts what has been learned about the manifold, complex ways microbes, especially bacteria, are woven into the fabric of the biosphere.

From the way bacteria form the luminescent organs of squid to how the sugars and antibodies in mothers’ milk regulate development of human infants’ digestive and immune systems, nourishing some bacteria and discouraging others, Yong shows the many ways animals depend on symbionts.

With the development of fast and cheap genome sequencing techniques, we can now characterize the microbiome, as it is called, for many organisms in detail. What has emerged is what Darwin described in his famous image of the tangled bank: an intricate network of ever evolving relationships among multitudes of actors, all struggling to survive and replicate under varying circumstances. Since we also know that gene sequences are exchangeable, just like energy and nutrients, from one organism to another, it is not too surprising to read of frequent exchanges among the microbes and sometimes between them and their hosts.

We also know, thanks to Lynn Margulis, that we still carry the highly evolved symbionts that first came together to build our eukaryotic cells from prokaryotic bacterial cells, a billion and more years ago. Our energy transforming mitochondria are the best known example, along with plants’ chloroplasts.

Not all relationships are benign: apart from acute and chronic infections, some fatal, there are lots of suggestive associations between for example, gut microbes and obesity, autoimmune disease and cancer. But at least we aren’t insects or worms, who frequently have their tiny lives disrupted by the almost ubiquitous Wolbachia, a bacterial symbiont that can twist their sex and reproduction in bizarre ways, but in other cases provides essential nutrients the host can’t make or facilitates the bugs’ own parasitic relations to plant or animal victims.

All this has practical implications, of course. If we could understand the workings of our relationships to microbes, we might be able to control some of the pathologies mentioned above. We might be able to provide better alternative nutrition for infants whose mothers can’t or won’t nurse them. We might be able to modify other organisms or build artificial ones to better suit our needs (see the review of Underbug in Science) for chemicals, food, etc. Of course, a little knowledge can be a dangerous thing, as witness the current interest in “probiotics,” whose benefits are largely unproven, or the even grosser move to fecal transplants. I’m not sure we are ready to safely manipulate our own microbiomes yet.

On a sounder footing, there are pilot studies of using Wolbachia to control the spread of dengue fever by mosquitos. Wolbachia prevents mosquitoes from carrying the virus, so releasing Wolbachia infected mosquitoes has been successful in reducing transmission of the disease. On the other hand, using antibiotics to kill symbiotic Wolbachia that enable filariasis worms to attack humans has resulted in the first successful treatment for elephantiasis.

The key thing, as my microbiologist father passed on to me from his idol, Theobald Smith, is to understand the ecology of the symbiotic relationship. In the Wolbachia-filaria relationship, there is a bit of love hate. Specifically, the worm has to have its own ways of stopping Wolbachia from becoming a parasite instead of a mutualist. If we could learn to manipulate those natural controls, we might have a way to trick the worm into eliminating Wolbachia and hence, ending its own ability to survive in its human host. Then even people who can’t take a long course of powerful antibiotics could be cured.

So much for the practical implications, of which these examples are just the tiniest hint. What does this new understanding tell us about the logos of life? Are there profound consequences for our self understanding in the realization that we contain multitudes?

I think that nothing here undermines the basic Darwinian conception of evolution by natural selection. Exponential growth (resulting in a struggle for existence) and genetic variation in populations lead to natural selection within these communities of organisms. The question seems to be what are the units on which selection acts? In the case of symbionts transmitted from parent to offspring and that can’t be expelled, it is likely, as is obvious with mitochondria, that the partnership as a whole must be what is acted on. Where the partners are acquired from the environment and can be lost and replaced, it seems to make more sense to think of coevolution, with each as a component of the environment of the other.

It’s reasonable to think that there must be a spectrum of such relations from purely casual and opportunistic to completely integrated. Is there a tendency for relationships to evolve towards complete integration? Lynn Margulis seemed to think so; she believed that such symbiogenesis was a more significant phenomenon than natural selection. I think that the logic of the process indicates otherwise. Self replication is the fundamental process; integration occurs when divergent lineages converge because of mutual advantage in the struggle for existence.

The accompanying loss of independence doesn’t matter. Very few organisms are totally independent of others. Research suggests that most animals are parasites, if we include plant parasitic herbivores, and so they require a host or hosts to survive. Even scavengers and plants rely extensively on fungi and bacteria to release nutrients. Many fungi, in turn, are dependent on symbiosis with plants. That’s probably the main lesson here: the biosphere is a web of interdependent organisms, and the best way to live is with as much help as possible. As Red Green says, “we’re all in this together.”

Note: Underbug: An Obsessive Tale of Termites and Technology by Lisa Margonelli, Scientific American/Farrar, Straus and Giroux, 2018, also deals with symbiosis and the lives of some of the most socially integrated of organisms, the termites. Termites provided some of the earliest studied examples of complex symbiotes: the amazing protists in their guts possess a whole array of bacterial symbiotes themselves that enable them, and hence the termites, to digest wood. The so called advanced termites have gone another route, letting gardens of fungi in their giant nests do the work of digestion, just like the equally remarkable leaf cutter ants.

This book deals mostly with the many lines of research inspired by termites, more so than the details of their ecology and evolution. Still, it is a fascinating story about how we humans are expanding our own possibilities by looking closely at complex organisms. For more, see the review in Science.

Life with Lepidoptera

Peter Marren. Rainbow Dust: Three Centuries of Butterfly Delight. University of Chicago Press. 2016.

This was subtitled “Three Centuries of Delight in British Butterflies,” when it was first published in the UK in 2014. The Chicago edition has a preface for American readers, making some comparisons between the American and European faunas. He briefly mentions the great American collectors of the nineteenth century (see my post from February 2015) and introduces his favorite butterfly lover, Vladimir Nabokov, to whom he will return  throughout.

Marren begins with personal recollection and reflection on his early days as a butterfly collector: the joys of pursuit and capture, the thrill of discovering a new species to add to his collection and the less easily expressed delight of simply being alive and out in a world inhabited by beautiful, delicate beings.

In discussing this aesthetic joy and recounting the history of the long fascination that butterflies have exerted on the minds of human beings, Marren does a great job of presenting the collectors, artists and writers who left behind a record of their pursuits. Among those he most admires are the Rothschilds, who have probably done more for entomology than any of the other great families of England. Nine different members are listed in his index. His account of the lives and works of the many notable painters and engravers of butterflies, from the late Renaissance to the 21st century, reminds us of the enormous labor involved and the many disappointments and financial failures that dogged their efforts. It is very helpful to have a computer or tablet handy while reading this chapter, so you can search out examples of work by Moses Harris (see example above) Henry Noel Humphries, F.W. Frohawk, Richard Lewington and David Measures. The book itself has only monochrome illustrations of butterflies in the chapter headings.

I was rather less taken by Marren’s attempt to write a literary, cultural and psychological history of the passion for butterflies. The familiar identification of the soul (psyche) with a butterfly and the various ways butterflies appear in poetry do not seem to add up to much in terms of understanding human responses to the natural world. Nor do his forays into mythology make compelling reading for me. His accounts of the people who established our understanding of the lives of butterflies are much more interesting. The tribulations of women who shared the passion are especially telling: from Lady Glanville whose interest in butterflies was grounds for suspecting her sanity and thus contesting her will, to her successors in the eighteenth and especially the nineteenth century, who contributed much to entomology, despite a “men only” attitude among most organizations and institutions.

One of the best features of this book is Marren’s fascination with the names that people have given to butterflies over the centuries and in different parts of the world. Here, I think his cultural reflections are on firmer ground. Besides, the names are just amazing and fun to wonder about. Why is a beautiful flying insect called a red admiral or a golden hog? He also comments on how names and naming conventions have changed over the centuries. Luckily, we have the Linnean system to impose a more or less uniform system so serious students can keep things straight.

Marren also does a fine job of describing the butterflies themselves and their habitats all across England and Scotland. He talks about the plants they rely on and the plant communities they inhabit, with much attention to how changing ecology, driven by modernizing agriculture and the rise of suburbs, have affected species, some for the better, but more for the worse. His 12th chapter on butterfly monitoring and preservation efforts is one of the best reflections on the dilemmas of trying to maintain and protect natural habitats that I have read in a popular work.

Marren chronicles the decline of butterfly collecting as a hobby and even as a scientific endeavor in Great Britain. More and more areas prohibit collecting, and more and more of the public is openly hostile to the idea of killing and preserving butterflies. Marren’s own collection from his youth in the 1950’s and 60’s was accepted by the Natural History Museum, because well-documented specimens from the latter part of the 20th century are scarce and valuable records of the state of the fauna, which help scientists today understand how things have changed. The anti-collecting bias of many current environmentalists and natural history enthusiasts is understandable, given the decline of so many species, but largely misguided, at least if they care as they claim to, about protecting these natural wonders. We need more solid documentation, not less, for butterfly populations, and although photographs and even unvouchered reports can be helpful, serious conservation needs specimens to verify what it is that is there and to enable us to trace the shifting makeup of populations. As Marren makes clear in his chapter on efforts to save England’s butterflies, simply trying to freeze things in place is a sure route to failure. Too many organizations and agencies, at least here in my home state, still seem to think that way, though.

 

 

Moth Lady

Moths of the Limberlost by Gene Stratton Porter. Doubleday, Page and Co. 1921. I listened to the Librivox version, beautifully read by J M Smallheer.

I would not have thought that listening to a book about insects, least of all large moths, without being able to see the illustrations, could be utterly absorbing, but Gene Stratton Porter’s descriptions of the finding and rearing of some dozen species certainly is. All of them came from from around her home near the great Limberlost Swamp of northeast Indiana, found by herself, her husband and numerous friends and neighbors, some of whom went miles out of their way to bring her specimens. Besides her accounts of the finding of the adults or caterpillars and her meticulous descriptions of each species behavior and development, there are her minute descriptions of the patterns and colors of all stages, carefully based on the freshest individuals. As a photographer and painter of birds and insects in the days of black and white glass plates, she had to be a very close observer and recorder of colors, if she wanted to get good illustrations based on her photos. A look at the illustrations from the book shows that she did extremely well.Moths_of_the_Limber crop

Her life history observations, such as how hawk moth larvae pupate, burying themselves in the ground and then wriggling back to the surface, posterior end first, while still in the pupal case, so they can spread and dry their wings upon emergence, are fascinating. I like her attitude towards the published literature on moths. She mentions many famous lepidopterists (see my post from on Butterfly People from last February) has read their work, but is willing to point out the shortcomings of their accounts of the actual lives of the insects they describe and illustrate.

Her anecdotes of catching and keeping moths are delightful. Her home must have seemed like more of an insectarium at times, with moth eggs carefully marked and protected on the floors and carpets, because a gravid female escaped and could find no host plant to lay them on. The effort put into successful rearings and the failures that invariably accompany attempts with unfamiliar species must have been very demanding, and the moths were not even her chief occupation. Her novels, the most famous being A Girl of the Limberlost, 1909 and bird photography and illustration took even more time.

Even as she studied them, species like the Cecropia moth and the Polyphemus were losing out to expanding agriculture, lumbering and drainage of swamps like the Limberlost. Later would come DDT and street lights to put still more stress on their populations. Parasites introduced to control gypsy moths have added to the widespread decline, especially in the Northeast. Today, aerial images of the Limberlost show mostly agricultural fields and only a few remnant woodlands, including one small restoration site on Loblolly Creek. We can be grateful that Gene Stratton Porter left us such a beautiful record of what was there before.

Death Valley Days

Land of Little Rain by Mary Hunter Austin, first publication 1903 by Houghton Mifflin.

The Librivox recording of this wonderful book from the first decade of the twentieth century is a pleasure to listen to. Mary Austin’s descriptions of the desert country east of the southern Sierra Nevada are beautifully clear, evoking the harsh land, the hardy plants and animals and the various humans who live among them. My favorite was the pocket hunter, a prospector traveling with his burros and a gold pan that is cleaner than his cooking pots, and who dreams of finding a strike rich enough to allow him to set up as a middle class Londoner. Twice, he made enough to visit England, but each time he returned, with only a pair of elegant green canvas traveling bags to show for the trips. He told how once in a blinding snowstorm he sought shelter with what he thought were a flock of domestic sheep. Looking about in the morning, he saw he had slept among wild mountain bighorns. They bounded away through the drifts like God’s own flock. Breathtaking.

Whether it is the denizens of a mining town or the native Paiute, among them the blind basket weaver and the Shoshone exile medicine man, who must be killed when he can’t prevent an epidemic of pneumonia from taking away a third of the band, Austin tells the stories simply and with evident deep compassion.

She has a soft spot for the coyote, that butt of Warner Brothers cartoons, but in her view far from a fool. She gives loving descriptions of the numerous desert rodents and the jackrabbits whose tracks lead to the waterholes like the spokes of giant wheels, along with their enemies the birds of prey and the scavengers who watch all that goes on from far above, waiting for the predator’s kill or the dying gasp of the starving.

Plants get just as careful attention, some of the best botanical description I’ve read. Whether in her neighbor’s field or on the mesa, she evokes the marvels of the California desert flora with its tough shrubs and delicate ephemerals that blossom only in years when enough rain falls to waken the seeds out of dormancy.

Everything about this book makes me want to visit this land.

Looking for the logos of life VI: Gaian analysis

Williams, G. R. 1996. The Molecular Biology of Gaia. Columbia University Press. 210 pp.

This is a book I wish I had read when it was first published. Williams lays out so many interesting scientific problems so clearly that I would have expected that it would have considerable influence on subsequent research, somewhat as Schrodinger’s What is Life? the subject of the first post in this series. I was somewhat surprised that Google Scholar only finds a few citations of this book. Perhaps William’s scholarly papers have been more extensively cited.

William’s goal is to see why the famous Gaia hypothesis has attracted so much popular interest, while receiving little positive notice from practicing biologists. He wants to determine whether the hypothesis is actually useful, either as a metaphor or a verifiable model of the function of the biosphere. The central question is whether it can explain why the Earth has remained habitable throughout the several billion-year history of the biosphere. That it has is not in question: all evidence points to the occupation of Earth continuously by the descendants of the first living things, which originated 3.5 billion years ago. This strongly implies that the earth has not frozen or boiled and that life has not otherwise been poisoned or starved during that time. Some factor or factors has kept the conditions on at least some of the Earth within the ranges essential to living organisms of some kind. In fact the conditions have not become intolerable to land plants and metazoans at least for hundreds of millions of years. The concept of the continuity of descent, expressed beautifully by Loren Eisley’s image of each of us trailing a long chain of ghostly ancestors, stretching back to those first living things, is to me one of the most useful ways to imagine what evolution is all about. If there had ever been a break in that chain, you and I would simply not exist.

The Gaia hypothesis states that this stability is the result of homeostasis: the regulation by negative feedback (like a thermostat) of a living super organism, Gaia. In its strongest form, the hypothesis is that life on the planet, the biosphere, regulates itself just as a single organism, whether a single cell or a multicellular individual, does. This idea has an obvious appeal: just as networks of interacting macromolecules make up a cell, which is capable of regulating its internal environment, so do networks of interacting cells make up tissues, organs and whole organisms that are able to regulate their internal environment. At least some organisms, like ants and bees, live in self-regulating colonies. Why shouldn’t all the organisms on earth form a self-regulating system?

Williams answers that for biologists the problem is how such a self-regulated super organism could be put together in the first place. Natural selection can explain how self-replicating systems can evolve, because natural laws can discriminate among multiple variant copies that compete for limited resources. The Earth is not self-replicating. There are no variants among which nature can select. There is only one. This problem led Lynn Margulis to argue that Darwinian evolution was not really that important, and that symbiogenesis was the true explanation. Margulis’s great contribution was the discovery that certain cellular organelles, chloroplasts and mitochondria, were once free-living organisms. More broadly, she showed that evolutionary advances by the incorporation and integration of separate living parts were behind the origin of the eukaryotes and that similar processes continue to operate in the form of horizontal gene transfer. The trouble with claiming that symbiogenesis is a replacement for Darwinian natural selection is that it appears obvious that all such new combinations remain subject to survival of the fittest.

Would it be possible for a Gaia-like system to arise in part of the biosphere and then spread, supplanting the less effective parts? Only if it’s self-regulating effects were confined to where it first existed, as might work for something like the terrestrial nitrogen cycle. It seems less likely where the atmosphere and oceans are involved, since they carry the products all over the planet.

Williams also points out that there is more than one possible explanation for the continuous suitability of the Earth for living things. He lists four: luck, inertia, equilibrium, and homeostasis. He analyzes each possibility in turn, and shows how each may contribute to the persistence of habitable conditions. In the case of homeostasis, he distinguishes between negative feedbacks from purely physical and chemical forces involving the lithosphere, atmosphere and hydrosphere and ones that require the biosphere. It is possible that even if there were no life on Earth, the temperature would stay within habitable limits (basically the range where liquid water can exist) just because of feedback among the temperature and the release and sequestration of carbon from air, ocean and rocks.

According to Williams, if you try to assess this possibility, the difficulty is that today the rates of almost all steps in this process, except volcanism, are under catalysis by organisms. We don’t know what an abiotic planet would be like. As of the time he wrote this book, not enough was known about the global chemical cycles at the molecular level to settle the question how much life matters. He gives an example of what was known about the molecular biology of nitrogen to show how complex the regulation of these cycles is likely to be. Nutrients move among four pools: inorganic forms in the lithosphere, hydrosphere and atmosphere; nutrients in forms available for uptake by organisms in the same three spheres and the biosphere itself as accumulated by organisms; nutrients incorporated into living cells and tissues; and bio products, from the cellulose of wood in trees to dead plants and animals to dissolved organic compounds to fossil fuels. All these are connected by flows and many of those flows (mobilization, assimilation, regeneration, sequestration and excretion) are controlled by living organisms, via enzyme-catalyzed, energy-requiring reactions.

I like this book because Williams thinks about Earth and ecology very much as I do. I learned from my professors at Cornell in the early 1970s about five processes of ecology: population dynamics, natural selection, energy flow, nutrient cycling and cultural evolution. These are closely interrelated ways of looking at the overall phenomenon of life on earth, or as I like to define ecology, the structure and function of the biosphere. Is the function of the biosphere to regulate the habitability of the planet, or does the planet have the property of remaining a stable habitat for life without life being involved? You can’t really answer that question with only one habitable planet and one biosphere to study.

I will add that I tried to read another account of the same problem of why the Gaia hypothesis had been largely criticized by biologists while being so well received by non-biologists: The Gaia Hypothesis: Science on a Pagan Planet by Michael Ruse (University of Chicago Press, 2013) I did not find it helpful, being mostly a historical narrative, with a focus on a wide variety of –isms, such as Platonism, Mechanism, Organicism, Hylozoism (the belief that all matter possesses life) and Paganism. I have never been much interested in –isms or cultural explanations for why people accept of don’t accept given ideas. Williams gives us a scientific way of thinking about the problem.