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The Hidden Half of Nature: The Microbial Roots of Life and Health
David Montgomery and Anne Biklé
WW Norton, 2016

The authors began a journey into examining the role that microbes play in our lives by reconstituting the soil in their yard. They discovered the soil was brought back to life with relatively little effort. This lead to a lot of research into what, exactly what going on, and learning about the rhizosphere, the wealth of bacteria and microbes that surround and enrich the roots of plants. When Biklé contracted cancer, they embarked on a similar journey into the depths of the colon and the microbial life we support and which supports us. Both systems are bewilderingly complex, and there is much more cooperation and symbiosis than we thought. In both cases, a healthy microbial environment provides strength and immunity to the host (either the plant or us).

A few things prevented us from seeing these communities and benefits earlier. Our lab practices were focused on the “germ theory,” that microbes were inherently harmful and needed to be eradicated. This lead to studying only pathogenic microbes that could be easily cultured in labs. DNA sequencing allows us to study microbes that aren’t culturable outside their host environment. Further, relationships between organisms were viewed through the lens of Darwinian competition, which is only recently being challenged by new views on cooperation and symbiosis.

This is leading to a revolution in our approach to both farming and nutrition. For the second half of the 20th century, agribusiness concentrated on ever-higher doses of fertilizers and biocides for the short-term benefits of yield increase, ignoring the long-term problems of soil depletion, adaptation of pests, and destruction of helpful microbes and insects. A similar practice was happening in medicine, with a reliance on antibiotics that provided untold benefits, but which led to a larger problem we now face.

The farming practices, combined with dietary changes (and convenience foods) led to diets filled with nutritionally poor but high calorie foods. Meanwhile, our helpful gut flora were being destroyed by the antibiotics that were otherwise saving our lives. New research indicates that over-use of antibiotics is leading to both an increase in disease-resistant bacteria and chronic auto-immune and inflammation diseases.

“The Hidden Half of Nature” is filled with interesting stories about research into soil health that contradicted the agrichemical practices that was ignored, or research into gut health that went a little past the ability to visualize or quantify why things worked the way they did. One particularly fascinating story is that of Ignasz Semmelweis, who in the late 1840s noticed that the wards in his hospital run by midwives had significantly less mortality than the wards run by doctors. Why? The doctors wore their bloody coats with pride, and went between patients or autopsies and patients without washing their hands. Montgomery and Biklé say that by insisting the doctors wash their hands and change their lab coats, mortality in the doctor-run wards was reduced to the same as the midwife wards. This infuriated the doctors, Semmelweis was fired from that hospital, fired from another for instituting the same changes, and was so hounded by the medical establishment that he died in an asylum. Philosophers of science now use the term “Semmelweis reflex” to describe the autocratic rejection of new knowledge that contradicts established paradigms.

The authors are careful not to ignore the good results of agribusiness or antibiotics, but they fully acknowledge that it is crucial to adapt our practices to new realities. More careful administration of antibiotics, removing antibiotics from use as animal growth promoters, and more attention to prebiotics and foods that improve our gut flora are among their recommendations for human health. They also recommend farming practices that concentrate on soil health, such as returning stubble to the field after harvest, no-till farming, and organic farming. They acknowledge where research is still inconclusive, such as whether organically farmed plants are more nutritious than conventionally farmed plants.

“The Hidden Half of Nature” is informationally dense – the “Sources” section has pages of citations for every chapter – but is so clearly presented that at first I thought it almost felt like it was aimed at a young adult audience. Once they got onto things I didn’t know, however, I was fascinated by their stories. They mix personal experience with research in a way that brings the research into focus. The few notes are amplifications of the text that would have gotten in the way of their main point. There is also a good index.

I think this book makes a good companion to The One-Straw Revolution. Fukuoka’s book is much shorter, and focuses on his personal experience with restoring pre-agribusiness farming practices to his farm in Japan. Montgomery and Biklé present the history of the science of microbes, looking at European research into farming and medicine.

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The One-Straw Revolution: An Introduction to Natural Farming
Masanobu Fukuoka
New York Review Books, 1978

Masanobu Fukuoka proposes a method of farming timed to natural sequences of plants. Cover crops and food crops are sown in sequence such that weeds are kept down. Straw and plant waste is returned to the field after harvest, returning most of the nutrients to the soil. This is a no-till method that builds the soil up year after year with no amendments. The soil is increasingly healthy, which prevents plant disease. The diversity of the crops prevent crop pests from taking over. Not spraying also allows the beneficial insects to live and protect the crops. The plants themselves are more resistant to pests and diseases because they are growing in healthier soil, and are consequently healthier. The healthiness of the soil and the extensive use of straw and plant waste as mulch greatly decreases water use. In general, Fukuoka used a method of farming that had been developed over time by the indigenous farmers of his region, before Western agrichemical practices took over. This method of farming is as productive as Western agrichemical farming, but with healthier soil and stronger, more nutritious plants.

This method of no-till agriculture and crop rotation would work in any location, but would need to be adapted to local growing seasons and crops. He also espouses a philosophy of being in touch with the earth and its cycles. In some ways, his method of farming reminded me of the Bradley method of restoration, in that both of them look to the cycles of plant life and soil health and ecology to accomplish their goals. This book left me wishing I had some land — even a back yard would do — to practice his method and adapt it to PNW climate.

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Tristan Donovan
Chicago Review Press, 2015.

An engaging read about the wild animals that live in cities with us — from raccoons in Berlin to leopards in Mumbai, rattlesnakes in Phoenix and African land snails in Miami, to foxes in London and subterranean crabs in Rome.

These animals have come to be in cities in many ways. Raccoons are not native to Berlin, but were escapees after the brief fad for raccoon coats in the early days of automobiles. Foxes in London had the city built up around them – it’s not that they were pushed out of the city and moved back, but they stuck around when new food sources presented themselves. African land snails were imported by accident.

Living in the city affects the animals in many ways, — good, bad, and neutral. Bird song has to change to adapt to city noise, such as getting louder, changing pitch, or both; birds colliding with skyscrapers is a problem for Chicago, which is on the Great Mississippi flyway. In many cases, such as coyotes and foxes, the animals live longer, healthier, and with much smaller ranges than in the wild. The smaller ranges happen because food is more abundant; this results in greater density, which can be a problem if there’s an infectious disease outbreak such as mange. Another change that happens across many species is animals becoming nocturnal in the city, as that helps them avoid humans.

Donovan talks to people doing on the ground research and control of animal species, and examines the issues using references that range from scholarly articles and to general interest books, news articles, and blog posts. In the final chapter (which provides a good, inspiring end to the book), he looks at how we can use cities as conservation agents and not only improve them as homes for the animals that live with us, but bring more animals into the city.

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Alan de Queiroz
Basic Books, 2014

How do species disperse – how do they get from one place to another? This is the kind of question that appears to have a ready answer, but experts can spend a lifetime debating. It’s easy to see birds flying in their migrations, or mammals moving across continents. How did trees get across oceans? How did amphibians get to islands? How did monkeys get to South America? The answer to these questions not only has ramifications to evolution, but to the history of life on Earth. And scientists have been debating them since the beginning of the study of evolution.

Although perplexing and difficult to imagine, before we knew about plate tectonics, ocean crossings were the only possible choice. Darwin did some experiments in seed viability, and a lot of people talked about land bridges that no longer existed.

As we learned more about plate tectonics and the deep past of the Earth, it became obvious that most of the dispersal happened by species being isolated by Gondwana (the supercontinent) breaking up. No ocean crossings necessary. Soon enough, the idea of life as a relic of the Gondwanan break up was pervasive to the point of becoming a truism. Ocean crossings were dismissed as almost magical. The incompleteness of the fossil record was no help: the oldest fossil of a species only tells us how old a species might be; it could have been around for a long time before the unlikely set of events that create fossils happened.

Now, scientists studying the question of dispersal use DNA analysis and the molecular clock to provide new evidence that weighs more strongly in favor of ocean crossings. The molecular clock, despite its limitations, can provide more statistical evidence as to when speciation occurs than the fossil record or any other tool we’ve had to date. This statistical evidence can be combined with improved dating, greater knowledge of the continental positions in deep time, and other evidence to build convincing cases for oceanic dispersal. The hypothesis that monkeys rafted from Africa to South America may not ever be “falsifiable” in the way that mathematics or physics hypotheses are falsifiable, but enough evidence can be built in its favor to show that despite improbability, given enough time, it’s the most likely explanation.

This is the “plot synopsis” version of de Queiroz’s book, and like all plot synopses makes a tapestry into a threadbare towel. In examining the basic question of how life disperses, de Queiroz looks at aspects of the philosophy and history of science, how science is engaged by its practitioners – in the field, in academic journals, and in the realm of personal politics. It looks like there is finally enough agreed-on evidence to provide basis for further research.

This is the kind of science book that I like because it engages me in a subject I had little knowledge of, and thought I had little interest in.

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1493: Uncovering the New World Columbus Created (Vintage)
Charles C. Mann
Alfred A. Knopf, 2011

Before Columbus landed on Hispaniola, China was the most technologically advanced country in the world. Tenochtitlan (now Mexico City) was larger and cleaner than any Spanish city. There were empires and pig iron in Africa, and empires across the Americas. Europeans were malnourished, disease ridden, and living in filth.

But there was no contact. For better or worse, that contact was established by Columbus. That contact set off an exchange of produce, metals, commodities, cultures, and perhaps most important, diseases, that continues to this day. Globalization has been happening for more than 500 years, and only accelerates.

I was stunned repeatedly while reading this book. Particularly intriguing to me were the stories of 16th century Mexico City, the first global city. Silver from South America was counted there and sent to China and Spain. Porcelain and silk came from China before going on to Europe. The trade and peoples of the world flowed through Mexico City.

This is only one chapter in a long book that sets the received stories of the colonization of the Americas on its head. It wasn’t an orderly colonization of a nearly-empty continent. The very first settlers found a populous, healthy land. Smallpox, malaria, and other diseases endemic to Europeans needed to depopulate the continents to make European conquest possible. Even so, it was the 19th Century before there were more Europeans than Africans in the Americas.

Frequently I felt as if no good has come from the Columbian exchange, even though I’m a product of it. So many wars, famines, plagues. It’s brought vast wealth for a few kings and individuals, but complete social destruction for many cultures.

That was my own agenda in reading 1493, though, not Mann’s in writing it. He takes scrupulous care to be evenhanded, to not make judgments to one side or the other, just to show objectively the effects of the Columbian exchange. There’s a lot to talk about, and this long, invigorating book ranges over the centuries and the planet.

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Words by Lynda V. Mapes
Photography by Steve Ringman
Mountaineers Books, 2013

The Elwha River flows out of the Olympic Mountains north to the Strait of Juan de Fuca on Washington’s Olympic Peninsula. It’s wild and steep, and until dammed in the early 20th century was known for its dense fish runs.

This book tells the story of the Elwha, from the time the dams were built until the beginning of their removal. The history of the dams is excellently covered, and the reporting of the efforts to remove the dams – who wanted them removed, who wanted them to stay, how they were to be removed, who did the pre-removal baseline monitoring of the ecosystems, who would do the post-removal restoration – gives I think a fair credence to all sides of the story.

There’s no question that the dam removal was necessary. They were built without even the few safeguards and fish passage required in the early 20th Century, making them basically always illegal. The Olympic National Park boundaries later included the upper dam. In both cases, removal was cheaper than updating and refitting for new licensing compliance.

In the meantime, the power they provided to Pt. Angeles and its lumber mills was replaced by power from the Bonneville Power Administration, so they were not only illegal but irrelevant. There’s a large emotional aspect to dam removal, on all sides of the issue. People like me, who feel “it’s the right thing to do” as strongly as we can point to river warming, blocked fish passage, silt-transport blockage, and so on. Or people who feel “they should stay” as strongly as they can point to power provided, dam maintenance jobs, and even novel ecologies that will be lost when the lakes are drained. I think Mapes, in fact, could have covered the anti-removal side of the story in a little more depth; it might have helped me understand it a little better.

This is a minor lack in otherwise excellent coverage. The writing verges on the poetic when describing the “Niagara of the West,” and just as easily switches to conveying scientific details. The words and pictures unite to tell us just about every aspect of the story: The politicians and activists who worked for and against removal; the people it would benefit; the scientific research being done under sometimes very trying conditions (such as dry-suit snorkeling in shallow tributaries fresh off the glacier).

The Elwha dam was completed in 1910, with no fish passage. The Glines Canyon dam was completed in 1927. The first movements to remove the dam began in 1986. The upper dam is still being removed in 2013. The project, because of obstructionism, became vastly more expensive than originally estimated, and left almost no one satisfied with the process. The restoration is vastly underfunded, partly because the purchase price of the dams became so inflated.

Despite the difficulties of removal, I think it’s a success story: for the environmental and social justice of the Lower Elwha Klallam Tribe, for the ecologies of the river and the forest it drains, and the fish that can now swim to their spawning grounds.

The book ends with a moving depiction of the ceremony at the very start of removal (September 2011), and a ritual of the Lower Elwha Klallam to call the fish back to their home. This is an appropriate and optimistic place for the book to end, but the story continues, and will continue, for at least as many generations as it has already.

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James Barilla
Yale University Press, 2013

When most people think about creating backyard habitat, they probably imagine an almost Disneyfied picture of inter-species harmony and cooperation. The reality is much messier. On the one hand, the human desire to live with animals is strong; that’s why we have pets. On the other, we would like the boundaries to be distinct.

This messiness is what Barilla explores. So you want to create a backyard that’s welcoming to squirrels. What about when they’re eating your peaches? What about when rats and opossums come into this big hollow tree that’s warm and full of great nooks and crannies? You want animals close, but not too close.

Barilla looks at many different cities and how they’re coping with the encroachment of supposedly wild animals. Vervet monkeys in Dania, FL; rhesus macaques in New Delhi, India; black bears in Northampton, MA; and tamarins in Rio de Janeiro, Brazil. Dealing with the animals is hindered by many factors. The tamarins of Rio are an invasive pest where they are — but endangered in their home range. It would seem simple to just capture them in Rio and transport them to their home range. But they’re separated by thousands of miles. Have the urban tamarins picked up new parasites or diseases that will affect the wilderness tamarins? How has their genotype altered in response to city living over the generations? Can they still survive in the wilderness? One of the reasons they do so well is the prevalence of jackfruit trees, which are themselves an invasive species.

Another reason they do so well is because people feed them. Barilla feeds a vervet monkey in Florida, and describes the experience in great detail. It’s much different than putting out a feeder for birds, or kibble for a dog. He feels a transcendent connection to the wild, to the “us and not us” of a primate.

Barilla’s depiction of his personal experiences in his research is one of the strengths of the book. I wish he’d taken a little more time to talk about the process of building a backyard habitat, but there are plenty of books on that subject. This book, as I said, explores the messier territory. The animals we invite into our backyards have their own agency, their own desires, which do not always neatly align with ours.

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by Russell Link

One thing I didn’t mention when talking about Bringing Nature Home is the production. The book is illustrated throughout with hundreds of full-color photographs by the author, all illustrating important points from the text. The pages are thick, opaque, and glossy, which makes the photos really pop out. This makes it a great reference book as well as an interesting read.

If “Bringing Nature Home” is a reference book, then Landscaping for Wildlife in the Pacific Northwest is a workbook. This is a book made for marginal notes, comments, post-its, multiple bookmarks, working in the field, cross-referencing, and all-in-all giving it the provenance of a book that shows it’s well-loved by being well-used. Most of the pages (except for a color photograph section) are newsprint. There are line illustrations throughout, of plants, water flows, landscape designs, and more.

There are five parts to the book, each at least four chapters long: habitat design and maintenance, pacific northwest wildlife, special features of a wildlife habitat, and co-existing with wildlife. Part five is a long section of appendices that includes information on PNW habitats; plant lists, tables and maps; wildlife information for specific plants; and construction plans. The last appendix is a list of resources for each specific topic (ie, birds, wildlife maintenance, reptiles and amphibians, etc.). This book was published in 1999, with a third printing in 2002, and to my knowledge hasn’t been updated. The organizations and books listed in the resource section are still around, but the list of native plant nurseries in particular should be double checked. If anything, there are likely to be more specialized native plant nurseries supporting the restoration industry.

But that slight caveat aside, this is a book that belongs in the work room or greenhouse of anyone interested in landscaping for wildlife. As “Bringing Nature Home” demonstrates, landscaping with native plants in home gardens can go a long way towards restoring some of the imbalances and destruction of nature our sprawl is creating. “Landscaping for Wildlife in the Pacific Northwest” gives you the specific tools and resources to do that in our region.

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Jon R. Luoma
foreword by Jerry Franklin
© 1999, Jon R. Luoma
Oregon State University Press, Corvallis, 2006

The Hidden Forest, originally published in 1999, shows that everything we thought we knew about forests – how they grow, how they could be best managed for wood, how they work, etc. – is wrong. Although much of what is discussed here has become common knowledge since 1999, none of it would have become common knowledge without the Andrews Forest Long-Term Ecological Research Station in the Andrews Forest, OR. Beginning as a small venture with a brief flash of opportunistic funding from the International Biological Program, the research station has grown to produce numerous studies that shook forestry to its very basis.

It was a literal case of being unable to see the forest for the trees. The trees that produce our wood – yes, we see them and harvest them. The forest – that is, the web of life at the roots and canopies of the trees – happens at timescales that some ecologists call “the invisible present” – that is, within our lifespans, but long enough that the changes can only be shown by collecting data carefully for decades. The other end of the scale is the brief lives of the almost-invisible mites that live on the needles and in the roots.

These long-term processes require long term research. How does the warming planet affect budding of plants in the spring? How does that interact with the lifecycles of over-wintering insects and migratory birds? To answer these questions – even to propose them in an answerable form – you need decades of observation. This goes against the grain of the short-term focus of most research, the three to five year grant cycles (if that long), and the demand for publishable results.

And yet, even in the relatively short time the Andrews research base has existed, it’s completely changed the way forestry is practiced. Not just the maintenance of national lands, but the corporate-owned lands as well.

The story here is not just the patient research: the political struggles, particularly around the spotted owl, have their share of cliffhangers, false hopes, and final resolutions. And if the “once in a lifetime” storm shows up on your watch, then by gum you get out in it.

The story here is also the evolution of techniques, using canopy cranes to explore the canopy (and discover the importance of Lobaria oregana, a nitrogen-fixing moss that lives in the canopies. And the development of remote sensing techniques using LIDAR (laser interferometry) and GIS (Geographic Information Systems) to gather data about otherwise nearly-inaccessible locations without having to build roads.

And the story is also one of the great, continuing stories of science, whatever branch or method it follows: The stories of people being intensely curious about something, and trying to learn as much about is as they possibly can – as excited by their ignorance as what they know, because the ignorance gives them opportunities to learn more.

All in all, this was a great book to read. I’d like to see a follow up. How did the Andrews research base survive the Bush years? How is it doing today? What new has it learned? This kind of long-term research is needed not only for commercial forestry, but for restoration and conservation as well.

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Emma Marris

I’ve read this book twice.

The first time, I thought it was going to affect my approach to restoration as deeply as Crow Planet had (which was my first encounter with a critique of the false dichotomy of the urban/nature divide). I even said to myself (rather embarrassing to admit) “How shall we tend the rambunctious garden of this crow planet?” Everything felt like a revelation, this was a manifesto that was going to crumble the walls of the prison and free all within.

The second time, I did get a deeper understanding of the ideas of the book, and why the author presented them.

One important challenge is the idea of the “baseline.” How far back do we reach? The problem of “the baseline” is a difficult one. In North America, it appears easy: first European contact. But “first contact” might be after smallpox had wiped out most of the population; Europeans making first contact were already finding degraded cultures with most of their practices reduced or even lost. First contact might have included some botanic experts, but as often as not, it was fur trappers. If the first attempts at scientifically describing the landscape occurred after fur trapping wiped out the beavers, the hydrology has already been severely disrupted. Between smallpox and beaver extirpation, we have two layers of disruption before our supposed baseline.

Let’s not forget the racist implications of thinking that pre-European contact the Americas existed in a state of nature. Increasing evidence indicates that, in fact, in North America lands were settled soon after glacier retreat and were managed right from the start. One of the habitats that people are putting a lot of effort into restoring, Garry Oak savannah, is completely anthropogenic. The idea that the Americas, before Europeans, were “pristine” and unmanaged excludes the roles that Native Americans and First Nations peoples played in managing the environment.

The baseline for park restoration efforts is 1850. This is after smallpox and beaver extirpation, true; but it’s between botanizing and settlement. It’s a useful fiction because it gives us a target, but it’s not an absolute truth.

Once we realize that the “baseline” is a useful fiction, then we need to think about novel or hybrid ecosystems – that is, ecosystems based on combinations of native and introduced species, or completely new assemblages. What if a tree is a weed in one ecosystem but endangered in its native range? What about plants that have no native range as such? Is there value to the increasing expense of fighting back the increasing list of invasive species?

These are only some of the questions that Marris raises in “Rambunctious Garden.” Each chapter looks at a different aspect of restoration – restoring to a baseline; natives vs. introduced; pristine vs. modified – looking at what people are doing, what the challenges are, how problems might be approached differently.

For my own part, all I can say is “the journey continues.” I’m more interested in getting ivy, blackberry, and other monocultural weeds out than I am in meeting a “baseline” community or replicating an historical example.

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