biology – NearcticTraveller

Looking for the Logos of Life IX: Entangled Life

Entangled Life: How Fungi Make Our Worlds, Change Our Minds, and Shape Our Futures, by Merlin Sheldrake, Random House, 2020, 368 pp. Kindle Edition.

Image: Agaricus bisporus mycelium. Rob Hille. 9 December 2011 from Wikimedia Commons
I would describe this as a tantalizing book. Merlin Sheldrake writes in the mode so common to current popular science books, breathlessly exclaiming that these discoveries change how we think about everything. Boiled down, his message is that fungi created the world we know and continue to underpin its foundations. The case he makes is no better and no worse than most such claims, which I suspect every editor for publishers of nonfiction books tries to attach to every work that crosses his or her desk. Much of what Sheldrake describes is new looks at well known phenomena: the section on psilocybin mushrooms and LSD, for instance. It offers glimpses of a deeper understanding of what the chemicals fungi do to animal nervous systems, but reaches no firm conclusions.

It offers a lot of new information and speculation on the myriad roles that fungi have come to play in the biosphere, and a bunch of interesting potential applications to human problems (you can make, among many other things besides antibiotics, beer, wine and bread, fungal dog biscuits (Mutt-rooms) and packing foam) He also discusses mycoplasma-remediation as a solution to contaminated sites from oil spills to herbicides. They will even break down discarded cigarette filters.

Interesting as these things are, they are not, in my view going to fundamentally alter our view of life.

Nevertheless, this is an enjoyable book. Sheldrake knows his fungi from intimate experience, and he writes well, except for the occasional hyperbolic outburst or awkward analogy. He explains a lot of exciting new research using DNA sequencing, tracer analysis and ingenious lab experiments to understand the role that fungi play in terrestrial ecosystems as decomposes, parasites and symbiotic partners with plants and each other. He spent many hours himself, doing down and dirty work in the forests of Panama, following the roots of a tiny mycoheterotrophic plant and the mycelial network of its fungal associate. He also talked to a wide range of fungus researchers in fields like anthropology as well as biology and shares their insights into the roles fungi play in nature and culture. Some of the most interesting characters are the fungal enthusiasts – mushroom freaks, one might say, truffle hunters and entrepreneurs working to create products from fungus ranging from ersatz leather to bricks. I like this better than 3D printing, with its inputs of resins, metals etc. Also I doubt you can make a fungal firearm at home.

I wish he had been even more comprehensive: for instance he says little about fungi and human illness. His discussions of fungi and food omit such important staples as tempeh. He talks a little about his own work on mycotrophy, but doesn’t mention the possibility that plants may be able to survive mycotrophically when competitions squeeze them out of the struggle for light. How else is it possible for plants in the New Jersey Pine Barrens, like turkey beard (Xerophyllum asphodeloides) pine barrens reed grass (Calamovilfa brevipilis) pine barrens gentian (Gentiana autumnal) and maybe even scrub oak (Quercus ilicifolis) to appear so quickly after fire, after a long interval since the last fire and no individuals could be seen in the unburned forest? Do their mycorrhizal root systems simply live off their fungal partners until a burn clears the space for them to send up shoots, leaves, flowers and fruits?

What do fungi tell us about life in general, if anything? His theme is interconnectedness. The title echoes Darwin’s image of the “entangled bank.” He frequently repeats the view that life is less about individuals than about networks of interaction and exchange, some mutually beneficial, some exploitative, some switching back and forth depending on circumstances. Like like Lynn Margulis, discoverer of the symbiotic origins of cellular organelles and the authors I discussed in my previous post Looking for the Logos of Life VIII: Organism and Superorganism, Sheldrake questions the reality of individuals.

Why the determination to shatter us into fragments? Whatever I mean by “I” doesn’t include the microbes indigenous to my body. I am not them, and it’s arguable whether I am even the parts of my body that are the result of the form encoded in the DNA I got from my parents. When I think of the Pythagorean theorem, it isn’t a soggy collection of bacteria doing that, or sharing in the contemplation. [??] The scientists want to abolish me entirely or reduce me to an aggregation of trillions of cells, of diverse descent. Meanwhile the social theorists would reduce me to nothing but culturally determined categories: white, male, middle class, straight, cis gendered, etc. But what I think about I’m free to select from a vast web of tradition both ancient and up to the minute, delivered to me in multiple modes. That’s the most relevant entanglement: the mycelium of ideas. It’s in the tangled network that is my brain, but it is there because I chose to attend to those ideas as they came to me and because I made the effort, sometimes racked my brain, to connect them to what was already there.

Anyway, fungi are amazing enough in their own right: in their chief domain, the soil, they are virtually sovereign, with allies like bacteria and the numerous arthropods, earthworms, nematodes, etc, that shred and stir the vast amounts of dead plant material that enter their realm every year. Constantly grazed by animals, they regenerate at phenomenal rates in every cubic centimeter of dirt. Without them, dead plant material would pile up, as it does in bogs, where lack of oxygen excludes them. Carbon would be locked away and CO2 levels would fall to the point of global cooling, as they did in the Permian ice ages, which followed the Carboniferous age of coal formation.

In his ecological classic, The Biosphere, V. I. Vernadsky talked about the speed of life – the rate of expansion of a disk of cells, imagined as multiplying to cover the earth. Sheldrake makes an even more startling calculation: according to his reckoning, if all the fungal hyphae that have been produced were laid end to end, they would extend further than the limit of the visible universe, i.e. they would have expanded faster than the speed of light. Even though this is a bit like saying that if one airplane can fly from New York to Los Angeles in five hours, two can make it in two and a half hours, it’s still a remarkable image. It gives some hint just how ubiquitous and prolific fungi are in our world.

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, although recent work suggests there may be more than we suppose, at least where symbiotic microbes are concerned. 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.

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.

Looking for the Logos of Life IV

Pross, Addy. 2012. What is Life? How chemistry becomes biology. Oxford University Press. 200 pp.

Chapter 5: Origin of life

Pross gives a summary of research on this question that seems fairly reasonable, although he clearly doesn’t think much of historical approaches. I wonder whether he is not giving enough credit to geochemical analysis of rocks from the period before we find microfossils, that is to possible evidence of biogeochemistry back before the oldest fossil organisms. Also, he has not mentioned cosmochemistry – what was available in the part of the solar nebula that became the earth? None of that evidence in itself would answer the question, but he earlier talked about how historical studies could supply useful constraints on the free flow of speculative ahistorical studies of prebiotic chemistry.

He says sequence analysis fails on the origin problem because of horizontal gene transfer. If you start to see networks instead of trees, he claims that you can’t tell anything from the results. Is that so, or is that just a further challenge for clever analysts to overcome? After all, trees took a while to be generally useful. There still are lots of difficulties, but horizontal gene transfer isn’t just chaos. The process must have some logic, ultimately controlled by natural selection, like “normal” vertical gene transfer. I think he might be giving these approaches short shrift, because he has his own agenda.

He also assesses RNA world as unlikely, given the failure to create really complex self-catalyzing molecules in decades of lab studies. This despite his earlier claim that negative findings could not be used to rule out this very scenario. Well, if there was an RNA world, we haven’t been able to create a similar thing in vitro.

The other current scenario has a closed metabolic cycle evolving before self-replication kicked in. He calls such a cycle, “holistic autocatalysis.” So far, attempts to develop such systems by evolution in vitro have also not gone very far, according to Pross.

Biology’s Crisis of Identity

Pross asks three questions: what is life? How did it originate? And how would one make it? He says biology has reached a point, with the completion of the human DNA sequence project, that physics had reached in the late 19th century, prior to relativity, quantum mechanics and subatomic particles. How you can judge the state of mind of a body of scientists, I don’t know, but such an assessment feeds into his attempt to portray himself as breaking through confusion and complacency. To him, the problem is complexity. Is complexity a substance? Can there be a theory of complexity, as opposed to a complex theory?

Does all complexity go back to symmetry breaking, like quantum theory says, if I understand correctly? Life’s complexity clearly arises from the pure combinatorial possibilities of sets of fairly simple elements – four nucleotides, twenty amino acids, thousands of enzymes and similar numbers of intermediary products to create all those metabolic cycles. But they wouldn’t be of much use in a totally homogeneous environment. That’s the competitive exclusion principle. Life is complex because it exists in a large and complex environment, whose complexity is the result of irregularities in composition and past impacts, etc. leading to plate tectonics, and the uneven heating of a rotating almost sphere by the sun, leading to circulation of atmosphere and hydrosphere.

Pross says, “It is the organization of life, rather than the stuff of life, that makes life the unique phenomenon that it is.” Well, duh. He says “systems biology,” which tries to explain cells functions using mathematical ideas like “network topology, ” has not produced much in the way of insight. He also says that a holistic approach can be reductionism “dressed up.”

Another favorite of complexity mavens: non-equilibrium thermodynamics. Life, Pross says, can be said to be a dissipative structure, but what further insight comes from that? None, he thinks.

He then turns to John Conway’s Game of Life, the cellular automaton computer program, beloved of Gaia worshipers. These programs illustrate how simple deterministic games can generate complex patterns, but like the physical insights into complexity, there mathematical discoveries don’t seem to throw light on what Pross claims is the tough question about life: how does teleonomy arise within non-teleonomic worlds? I wonder if there is a fallacy in looking for the origin of “apparent purposiveness” when things apparent are clearly in the mind of the beholder. Can science find any sort of purposiveness at all? That’s a philosophic problem, as Socrates pointed out long ago. And as to “apparent purposiveness” is that anything at all? It’s not hard to explain how natural selection acts to give things apparent purposiveness: purposelessness is clearly maladaptive, it is not bothering to try. Is this his great insight?

Biology is Chemistry

The answer, he says, lies in systems chemistry. What defines it is that it deals with simple chemical systems that have life-like properties of self-replication. After dismissing all the previous attempts involving RNA or metabolic cycles, what is he offering that is different? He starts by justifying all over again the utility of simple systems, with the argument that since we think life started from simple stuff it will be informative to experiment with simple systems. This, however, is unproved: what if comets bombarded the proto-earth with really complex stuff, like Buckyballs and other cosmic macromolecules? Also, this comes after he says that we have no idea what sort of simple stuff life came from. I wonder if he’s headed for another case like those he dismisses.

He claims that systems chemistry is like looking at the Wright brother’s flyer to understand flight, as opposed to a 747. That is, if we can strip down to the simplest possible replicating system, we can get somewhere. But he just said that’s not possible because we don’t have any idea what the earliest living organisms were like. As if we did not know anything about airplanes prior to say, WWII, and we’re trying to imagine the ones from1903, could we do it? He seems to be saying both yes and no.

So here comes his “bombshell,” Darwin applies to replicating chemical systems, thus removing the distinction between chemistry and biology. Fine. But if this is really a momentous original discovery, a lot of folks must not have been thinking very clearly. Anyhow, we know Darwinian theory can apply to designing electrical circuits, why not replicating molecules? But can you actually use that to account for life on earth, more than just in principle? Now he brings in competitive exclusion, and we are off to the races. How well can you demonstrate this principle in a purely chemical system? He says replicating RNA molecules competing for different substrates, evolved to optimize their use of two different substrates, thus precisely mimicking the evolution of Darwin’s finches. Well, precisely is putting it a bit strongly. He claims totally without conclusive evidence that the finches are only doing what molecules were doing five billion years ago. He says that somehow replicating molecules transformed into living cells. I agree, but this is no profound insight, just an attempt to dress up a few clever experiments as a major breakthrough. And maybe the fact that a chemist can learn something from paying attention to ecology and evolution.

The earlier chemists, whose work he seems to dismiss, we’re studying the same things as he is, and he still has no idea what molecules to study. It seems exactly like non-equilibrium thermodynamics or systems biology or Game of life: some clever demonstrations, but no meaningful answers. On pages 132-134, he cites experiments that laboriously mimic the process that was already obvious, that evolving systems become more complex over time, but actually the experiment only shows that two interacting molecular species replicate more efficiently than a single species. Cross catalysis, in this case, speeds things up. So is all life one giant cross catalytic system? Of course it is. Herclitus’s ONE:EVERYTHING::EVERYTHING:ONE holds. Yes, it is chemical; life is an interacting system of macromolecules in an aqueous medium, but it is more. For one, it is largely cellular. Why? Can Pross explain that transition from chemistry to biology with more than a somehow?

Pross wants to add complexification into the sequence replication, mutation, selection, evolution. He puts it after mutation, but that makes no sense, and in his experiment it was the experimenter who in effect introduced it. Even the bare sequence is not right. Evolution doesn’t belong. It is not inevitable, it only happens if the frequencies of the interacting elements change, and that requires an outside physical/chemical/biological cause, a selective force. The system only evolves because of some constraint. Complexification is not a force, no more than evolution; it is the outcome of selection operating under varying conditions. It isn’t a cause. Evolution is change. Complexity is variability, they are not causes, they are results. True, it seems as if complexity is somehow auto catalytic, generating more and more complexity, but there is no law that says that has to be. Diversity does not necessarily result in stability or increasing diversity. Those outside constraints ultimately set the limits. Pross knows a little ecology and evolution, but not enough.

Pross says chemistry and biology are connected by a complexity continuum. What does that mean? Just that he’s repeating his claim in a different way? Wouldn’t discontinuity be more complex? His holistic claims seem more like good old reductionism dressed up. Is his bridge between the two more than just analogical? Physically, of course, it is the same stuff, but until you can actually make molecules evolve into living cells, what have you added to our understanding?

Is the first gene or the first enzyme buried somewhere in our cells, still doing a job, albeit not necessarily what it did billions of years ago? Or did it go the way of the protobiont and so many other species that are now extinct? If we could reverse engineer a simple bacterium into an even more minimal creature, would we be replicating our now vanished ancestors, or just making test tube freaks that never could have competed in the biosphere? Pross says the bacteria have remained simple, but how does he know? Is the bacterial component of the biosphere becoming ever more complex, just in a different way, than the higher plants and animals?

Assume he’s right, and some bit of RNA started the whole thing. Did it manage to do this in some primordial soup competing with uncounted numbers of other molecules, or was it in some incredibly sheltered, simplified environment, like those laboratory test tubes? One thing you don’t have to worry about is sufficient numbers to let mutation and selection act on. Enough might be produced in seconds, if you hit on the right mix. Even if it was much less rapid, as Pross notes, there was certainly plenty of time back then.

Natural selection is kinetic selection

Are competing organisms much like competing molecules? That’s a very loose analogy. Organisms don’t just compete for substrate. He claims we have to explain biology in the language of chemistry, but he uses all language very loosely. He really makes an unwarranted jump in equating chemical kinetics with biological reproduction. If you say that one species winning out over another is just chemical kinetics, I think you will get demurrals from most biologists. He’s back to hiding crude reductionism under his holistic claims. What he says about chemical systems being more amenable to mathematical analysis is just wrong, too (p. 139-140).

Fitness equals dynamic kinetic stability

He’s already in trouble by claiming fitness is a population phenomenon, not an individual one. Even chemically, I’d say that’s dubious, although there may be a population aspect. He is shoehorning a biological idea into a much simpler chemical concept. He claims you can focus on the population aspect, evidently without considering the individuals. But that is just wrong. The only real aspect of fitness is which individuals are the parents of future generations. Who is going to have descendants? Perhaps highly predictable with molecules that replicate. Not so easy with organisms. Even in general it isn’t easy. Who would have picked out the ancestors of angiosperms and placental mammals in the Jurassic? Connecting fitness to stability seems hugely wrong. On the level of the persistence of simple forms, maybe. Lots of genes seem not to have changed all that much.

His attempt to explain fitness landscapes and to make an analogy to a flock of birds seeking higher peaks is not particularly helpful, and didn’t that come from Richard Levin’s work in ecology? Actually the Eigen-Schuster Quasispecies concept is a neat mathematical formulation, but it is not clear what it applies to. Maybe viruses, maybe the origins of DNA RNA transcription/translation! maybe sex (see Wikipedia on quasispecies model) Certainly nothing like all evolving species. This is another analogy that seems to break down on close inspection. He’s trying to bridge the gap by forcing these analogies to do more than they are suited to do. After all, the real unification would mean that you can reduce equations of population genetics to chemical equations, doesn’t it?

He ends up not making a clear connection to the quasispecies concept and goes on to talk about his dynamic kinetic stability, which he admits can’t be measured absolutely, just like fitness, which also depends on the environment in which it is measured. Given how vague DKS seems, it does share the character of “fitness,” in as much as both can be what you want them to be. He suggests (p. 146-147) two measures: abundance and persistence, that are like part of Wilson’s definition of ecological success.

Incidentally, why does he not discuss the Eigen-Schuster hypercycle idea, which seems like a real theory of evolution of simple replicating molecules into linked pathways?

He now says that the cause of evolution is the drive toward greater DKS. But isn’t the cause self copying, with imperfections in a variable, limited environment? It’s differential reproduction, not any drive to achieve stability in any sense of stability I understand. A driving force towards something that he admits can’t be quantified and a mechanism that is a process of becoming a mechanism that is made up of more diversely interacting components (complexification) Seems pretty incoherent to me. He can’t put this into an equation, can he?

In arguing for the idea that life has undergone complexification he points to the fragility of self replicating molecules in the lab. I don’t see that that self-evidently applies to the first replicators in nature. Maybe we are all descended from a horrendously tough little replicator that just happened along out of the seemingly infinite possibilities. Maybe there are theoretical limits set by the problem of mutation in a small set of elements, something seemingly discussed by Eigen and Schuster. Small sets are inherently unstable, so it’s hard to conserve the replication when the replicates are too unlike the original. If a sequence is going to assume the role of a template, or even just determine catalytic properties, it can’t vary too much. Isn’t that just a trivial result, though? It sounds more profound if you introduce the term information into the discussion, but is that really necessary? Jacob Klein always denied that what geneticists talked about was information. I’ll stop at this point, because I think I have about reached my limit in thinking about where life comes from. Pross has made an interesting attempt to define a new agenda for research in this area. I don’t think he’s got anything really significant, though. Perhaps if we can ever find another biosphere to examine, we will see just how narrow or how loose the constraints are.

Looking for the Logos of Life III

Pross, Addy. 2012. What is Life? How chemistry becomes biology. Oxford University Press. 200 pp.

Chapter 2 The Quest for a Theory of Life

Pross discusses previous attempts to develop what he calls a theory of life, beginning with Aristotle. The only aspect of Aristotle’s views that he describes, though, is telos. He also characterizes Copernicus, Bacon, Descartes, Galileo and Newton as banishing telos from the universe, instead of only from their philosophical explanations of motion. [It is worth noting that he retrospectively applies the name “science” to what they and others were doing.] Pross quotes Jacques Monod as saying that a purposeless cosmos is the most important discovery of the past 200,000 years. Besides being completely unverifiable and hence clearly unscientific, the supposed discovery doesn’t even seem that obviously useful. I guess you could say it frees us to do destructive experiments on animals, but our current regulations suggest that we don’t think that. Pross says it propels us into a new conceptual reality. What does he mean by that? Pross also adds that Schrodinger, in his What Is Life, said that the explanation of living things would involve as yet unknown laws of physics.

Pross thinks, along with Monod, that teleonomy requires an explanation. Isn’t teleonomy only supposed to be apparent purposiveness? So what is the problem? If we assume organisms lack real purpose and simply obey the laws of chemistry and physics, then there is nothing to explain except our perception of purpose. That may be a problem, the problem of consciousness. Is he going to solve that with his chemistry?

In his section on definitions of life, he carefully distinguishes individual living things, which cannot evolve, from populations, which can evolve, but he then talks about a population of mules, possibly not seeing that there can be no such thing.

He does seem to be on track in suggesting that most attempts to define life fail. The examples given either make mistakes like saying life is self-sustaining without qualification, instead of pointing to reliance on energy inputs, for instance, or only list some characteristics of life as known to us, or seem just ridiculous, like Freeman Dyson’s information definition.

Chapter 3 Understanding “Understanding”

Pross links understanding to induction, citing Bacon. He says all scientific explanations are inductive, being based solely on pattern recognition. True, patterns in some sense must match, but induction is a reasoning process, so it should describe not the explanation but the way it was derived. In that case, it seems clear that deduction plays as great a role as induction in our understanding. In talking about mathematics’ role in explanations, he goes from pattern recognition to pattern formulation, without noting that he’s moving between induction and deduction.

In discussing the problem of where the underlying patterns come from, that is, what is the reality behind them, he denies we can know that scientifically, and he quotes Wittgenstein to that effect. This would seem to put him into the linguistic positivists’ camp, but I doubt he’s that clear about questions like realism vs. anti-realism, although so far, his statements seem consistent with anti-realism. He does however seem to qualify himself at one point by saying that patterns are to some degree subjective. He also distinguishes quantitative, qualitative and statistical patterns. Then we get a dose of pragmatism to the effect that adequate understanding is whatever works. Then, in another twist, he says that the patterns we recognize are only reflections of the underlying reality of nature. Once again, it is not clear whether he’s an anti-realist, as he seemed to say earlier, or some sort of Kantian realist. Could he even be a Platonist? Images of reality?

The reductionism vs holism section doesn’t add anything. The problem is that he’s leaving out any discussion of the environment of life. If you frame the problem as what environment and what inputs do I have to supply to create a self-replicating molecular system that can undergo natural selection, you have a pretty good reductionist program for developing an understanding of life. If by life, you mean the biosphere, then you still have a long way to go, and it becomes necessary to use more complex terminology than what you would use to describe life in a simple experimental system.

Chapter 4 Stability and Instability

Pross agrees with my idea of auto catalysis: if something is auto catalytic the rate of formation increases as there is more of it around: dn/dt = rn provided you maintain steady inputs of reactants, while in a normal chemical reaction with a catalyst dn/dt = r, where n is the concentration of product and r is the rate of conversion of reactants to products. He expresses the idea in terms of the time required to produce a given amount of product, if you have a given amount of catalyst. For the Spiegelman RNA autocatalysis, you should get a logistic growth pattern, because the rate will be constrained by both the RNA and the protein enzyme acting catalytically. This seems like it ought to apply to PCR, for example.

Another thing about the RNA replication reaction is that it is template replication, so it actually yields copies with a highly specific structure – meaning that analogies to information become possible. Is that what all the talk about “information” in biology is, a physical analogy? How would the idea of a physical analogy apply to a computer or a brain? It seems as if information theory is a mathematical formulation applicable to understanding a variety of things, some of which (cells, telephone signals, computers) we think of as physical and others (language) that seem not to be. I would say that what goes on with cells is physical and the information is only metaphorical. A computer seems more problematic, especially since what it does can be represented as a Turing machine, and even though it isn’t a machine but a mathematical hypothesis its relation to meaningful information seems very immediate. Since information theory involves representations in mathematical symbols of concepts that are not physical, why invoke physical analogies? In all the physical systems covered by information theory, is there a point at which a mind is needed to interpret the meaning of the information? That seems to have been the original motivation in fields like cryptography, communications, etc. but in cybernetic systems there may be times when the information is used only by the machine. Still, someone has to eventually determine whether the machine is doing what it is supposed to, at least until we find ourselves in the Matrix, etc. Stephen Hawking apparently worries that this is where Artificial Intelligence is leading us. A biosphere is like that. It doesn’t need to be meaningful to us to be a biosphere.

What about crystal growth? Clonal growth?

What sense does it make to talk about kinetic dynamic stability or about the “efficiency” of maintaining a large population (p. 74) by rapid replication? I would think that in a way, autocatalysis is very unstable, because it tends to exhaust resources so quickly. He talks about Cyanobacteria being around for billions of years. Is persistence of a clade with little obvious development or change the meaning of stability? Success, might be a better term. To me, the Heraclitean flux is the only really persistent feature of the biosphere. Moreover, it looks as if the pace of change is accelerating: metazoans only in the last billion years, a full terrestrial biosphere only in the last 300 million years, hot blooded life only in the last hundred million, and cultural evolution only in the last six million? Is this all the result of auto catalysis? Is dn/dt = rn, where n is “information?”

It seems as if “stability” is not a very good word to encompass the persistence of biological entities through time, given the tremendous range of life histories found among living things. The mathematical complexities are very great (cf. Cole, L.C. The population consequences of life history phenomena. Quarterly Review of Biology Vol. 29, No. 2, Jun. 1954, pp. 103-137) and there are many dimensions to the whole problem of what is it that persists: genes, phenotype, species, clades? What about the stability of Redfield ratios? If true, it is an indication of an extremely widespread pattern. He claims the more stable replaces the less stable. Doesn’t that imply that species should last longer and longer in the fossils record? What is the actual pattern? TO BE CONTINUED