Tuesday, August 15, 2017

The zoo beneath our feet: We’re only beginning to understand soil’s hidden world




The gardener has a long, touchy-feely relationship with the soil. As every good cultivator knows, you assess the earth by holding it. Is it dark and crumbly, is there an earthworm or beetle in there, is it moist, and when you smell it, are you getting that pleasant earthy aroma?
All these signs are reassuring, and have been through the ages, but they are mere indicators of something much greater and infinitely mysterious: a hidden universe beneath our feet.
This cosmos is only now revealing itself as a result of scientific discoveries based on better microscopic imaging and DNA analysis. There is much still to learn, but it boils down to this: Plants nurture a whole world of creatures in the soil that in return feed and protect the plants, including and especially trees. It is a subterranean community that includes worms, insects, mites, other arthropods you’ve never heard of, amoebas, and fellow protozoa. The dominant organisms are bacteria and fungi. All these players work together, sometimes by eating one another.

The awareness of this biosphere should change the way gardeners think about cultivating plants and heighten everyone’s understanding of the natural world. In other words, don’t ever call it “dirt” again.

The sheer vitality of it is mind-bending: A teaspoon of good loam may contain a billion bacteria, yards of fungal strands, several thousand protozoas and a few dozen nematodes, according to Jeff Lowenfels, a garden writer based in Anchorage and co-author of “Teaming With Microbes.”
This is, basically, how it works: Plants manufacture carbohydrates through photosynthesis, but not just for themselves. They release some of their carbon sugars into the soil, which causes the bacteria and fungi to show up to feed. The bacteria crowd around the root zone, and the fungi form vast networks of interlocking strands that often link one plant to another. The bacteria convert nitrogen and other nutrients into forms the plants can use, often by getting devoured by other microbes.

The fungal strands, the mycelium, effectively increase the root mass of its host plant by as much as a thousand times and transport a bevy of goodies to the host plants, including phosphorus, copper, calcium and zinc. There is also evidence that trees use this network to send signals to one another if, say, leaf-eating pests have arrived. In his Ted Talk, mycologist Paul Stamets referred to mycelium as “Earth’s natural Internet.”

Although some plant (and human) diseases are caused by soil-borne fungi and bacteria, most of these microbes are beneficial and keep the bad ones in check. The organisms assist in other ways, by increasing the size of soil particles, which improves the ability of the soil to hold water and air. Even in the middle of a city, the subterranean world is thriving.
Scientists took almost 600 soil samples from across New York’s Central Park and discovered a surprising diversity and richness. They identified more than 120,000 types of bacteria and more than 40,000 species of fungi, protozoa and arthropods. Among the unexpected findings: The microbial species were the same, more or less, as those found in parts of the world with dramatically different flora and climates from New York’s, including Antarctic cold deserts, tropical forests and grasslands.

There was a strong association between the diverse organisms in each sample. “Unravelling these relationships will be critical to building a more integrated understanding of below-ground ecology,” the researchers wrote in a paper published by the journal for the British Royal Society. “Our work highlights that most of the diversity found in soil remains undescribed.”

Enough is known, however, to create a 21st-century subset of farming known as regenerative agriculture. The farmers have discovered that if you foster this biosphere, you don’t need expensive fertilizers because the microbes repay the plants with nutrients. They also, for obvious reasons, avoid pesticides that would kill this soil life.

The farmers do as little soil digging as possible because traditional tillage destroys the fungal networks and the desirable soil structure. Cover crops keep the soil life happy between growing seasons.

Advocates of this low-impact farming say it can restore soil carbon lost by the historic conversion of forest and prairie to farmland and help to mitigate greenhouse gases. In the 1990s, an Agricultural Research Service scientist in Beltsville, Sara F. Wright, discovered a sticky coating to fungal threads named glomalin that, it turns out, is a major reservoir for carbon.

Lowenfels says it’s also time for gardeners to adopt practices that nurture the soil biosphere. To say he thinks deeply about this subterranean world is an understatement. In addition to “Teaming With Microbes,” he has written “Teaming With Nutrients.” His latest title is “Teaming With Fungi,” which dwells on the type of fungi that directly associate with plant roots. They are known as mycorrhizal fungi, and he’s a big fan of adding them to his plants when they are installed, either as a spray or in powdered form available from the garden center. “It works. My tomato plants are bigger than the control, they’ve got more fruit on them, the plants are so healthy,” he told me. “My carrots are unbelievable this year.”

Some gardeners turn to compost tea to build soil microbes. This is made by aerating sugars, compost and humic acids in non-chlorinated water and then spraying the brew on plants and soil. Others are not convinced that this is needed, though everyone agrees that the way to foster the soil food web is to top-dress growing beds and lawns with organic matter such as shredded leaves or finished compost.
James Nardi, a biologist at the University of Illinois in Urbana, offers this advice: “Work with your fellow non-human gardeners. I never use synthetic fertilizers, and I never use pesticides.” Nardi’s 2007 book, “Life in the Soil,” remains an excellent introduction to the subject.

In the fall, he mixes horse manure with fallen leaves, shreds the mixture and applies it as a mulch to his growing beds. “In the spring, I have this lovely, spongy soil,” he said. Lowenfels shreds autumn leaves on his lawn and lets the biosphere use them over the winter. The organic gardener’s mantra has never seemed more appropriate. Feed the soil, not the plant.

● Earthworms: Earthworms (and other worms) play an important role in the hidden biosphere. Most worm species in the garden were imported by Old World settlers, and some worms in certain regions have caused a problem by processing organic matter too efficiently. The latest culprit is a creature called the Japanese crazy worm (Amynthas agrestis), which multiplies like, er, crazy and damages the soil structure through mass feeding. It is long established in parts of the Southeast but has spread recently to Wisconsin and Illinois, where it is causing problems. But the European earthworms familiar to most gardeners are helpful.
Worms provide critical assistance to smaller organisms by breaking down and incorporating leaves into the soil, so all may eat. Worm castings are rich in nutrients, including calcium, nitrogen, phosphorus and potassium. The most famous observer of earthworms, Charles Darwin, estimated that they could add as much as 40 tons of casts per acre annually.

● Insects: Thousands of insects (and spiders) live in a patch of soil. Some are considered pests by humans — Japanese beetle grubs, termites and weevils, for example — but others are beloved or at least beguiling and include the larvae of lightning bugs and cicadas. Dung beetles convert animal waste into humus, a service we take for granted. Ants are the most abundant soil insect. Although some species are pests or nurture pests such as aphids, ants with their highly organized colonies are essential members of the soil biosphere. They assist in the conversion of litter to humus, move and mix large quantities of soil, and spread the seed of bulbs and other desirable plants.

● Other arthropods: The more conspicuous of these include millipedes and centipedes, as well as woodlice. Millipedes feed on plant debris and microbes; centipedes eat other arthropods. Woodlice, or sowbugs, are crustaceans that like soft plant debris and make quick work of green plant material and newly fallen leaves.

One of the most abundant, but barely visible, arthropods in the soil are springtails. They are named for a tail-like structure that allows them to jump when threatened. As many as a billion or more can live in an acre of soil. Depending on species, they cycle plant debris or feed on fungi, algae or other springtails.

Mites are generally regarded by gardeners as pests, and some are — sucking sap from plants and spreading disease. But the soil houses an immense community of non-pest species that are essential to the cycle of life. Half the known species of mites live in the soil, where they feed on decaying plant litter. Nardi writes that they “set the stage for smaller decomposers like bacteria and fungi to free most of the energy and nutrients stored in those leaves.” Some mites are predatory and attack nematodes and other small creatures.

● Nematodes: Nematodes are tiny wormlike creatures that have traditionally been viewed in agriculture as serious pests that harm plants by feeding on their roots. More recently, the view of nematodes has become more nuanced because some species are now commonly used (and purchased) as predators of garden pests such as slugs, vine weevils and white grubs, to name a few. In truth, the world of nematodes is much greater and can only be imagined. Experts believe there may be close to a million species, of which only a fraction have been described scientifically.
Some nematodes eat soil bacteria and fungi, while others prefer to consume other soil arthropods and protozoa. Their value to the garden is in converting nitrogen into a form that plants can use.

● Protozoa: Protozoa are microscopic creatures that live in vast numbers in the film of water between soil particles. The most well-known is the amoeba, but these microbes come in several forms, including species that move with a single flagellum or with hair like cilia.
They are the major predator of bacteria, and in consuming them they release nitrogen and other nutrients to plants. Protozoa, in turn, are eaten by nematodes and other small arthropods.

● Bacteria: Historically, bacteria have been associated with germs. Some of the nastiest human diseases — anthrax, typhoid, tuberculosis and syphilis, for example — are the result of bacterial infections. But we have come to know too that our guts are full of beneficial bacteria and essential to our health.

The soil is the same way — the bad actors are outnumbered and usually outwitted by the good ones. Healthy soil is loaded with bacteria, and because they’re not very mobile, they tend to hang out in vast numbers on and around the roots of plants, a zone known as the rhizosphere. There can be as much as 100 times more bacteria around plant roots than elsewhere in the soil, and with good reason. The plants feed them carbon sugars. The microbes give back nitrogen.

● Fungi: Fungi break down organic matter, which is why you will see mycelium strands in compost piles and under leaf litter. Two basic forms of fungi form a symbiotic relationship with plants. One exists in proximity to root tips and associates with hardwood trees and conifers. The other penetrates the cell wall of the roots and is found in plants of the domestic landscape — flowers, shrubs, grasses and vegetables.
The fungi grow tiny, fragile strands called hyphae. They are a tenth the thickness of human hair, but there are so many of them that they form a vast network, effectively extending the reach and efficiency of plant roots. In her book “The Soil Will Save Us,” science writer Kristin Ohlson says there can be as much as 320 miles of hyphae in a cubic foot of soil. At least 80 percent of the plants on Earth connect to these fungal partners.

“Gardeners need to know this stuff,” Lowenfels said. “A thinking gardener is a better gardener.”

Friday, May 5, 2017

Understanding What Makes Plants Happy



A dense carpet of woodland perennials. Thomas Rainer, a landscape architect, calls plants “social creatures” that thrive in particular networks. Credit Mark Baldwin
 Thomas Rainer and I have both been doing the botanical thing for decades; we know, and use, many of the same plants — and even much of the same horticultural vocabulary. But what he and I see when we look at a butterfly weed or a coneflower, or what we mean when we say familiar words like “layering” or “ground cover,” is surprisingly not synonymous.

It turns out I’ve been missing what the plants were trying to tell me, failing to read botanical body language and behavior that could help me put plants together in combinations that would solve challenges that many of us have: beds that aren’t quite working visually, and garden areas that don’t function without lots of maintenance.
As we gardeners shop the catalogs or the just-opening local garden centers with an eye to finally “fixing” that bed out front that has never quite cooperated, I asked Mr. Rainer, a landscape architect based in Washington, D.C., to lend us his 3-D vision.
In his career, Mr. Rainer has designed landscapes for the United States Capitol grounds, the Martin Luther King Jr. Memorial and the New York Botanical Garden, as well as gardens from Maine to Florida. He is an author with Claudia West of the 2015 book “Planting in a Post-Wild World: Designing Plant Communities for Resilient Landscapes.” He is a principal in the firm Rhodeside & Harwell, but will leave soon to start a new firm with his wife, the landscape architect Melissa Rainer, and Ms. West. He advocates an ecologically expressive aesthetic that interprets rather than imitates nature.

Q. You visit a lot of gardens, and probably hear from gardeners like me with beds that just aren’t working. What’s the most common cause?

Traditional garden design often isolates plants, setting them “as individual objects in a sea of mulch,” Mr. Rainer said. “We place them in solitary confinement.” Credit Thomas Rainer
A. First, we have to understand that plants are social creatures. Our garden plants evolved as members of diverse social networks. Take a butterfly weed (Asclepias tuberosa, named this year’s Perennial Plant of the Year by the industry group the Perennial Plant Association), for example. The height of its flower is exactly the height of the grasses it grows among. Its narrow leaves hug its stems to efficiently emerge through a crowded mix. It has a taproot that drills through the fibrous roots of grasses. Everything about that plant is a reaction to its social network. And it is these social networks that make plantings so resilient.

So if we think about the way plants grow in the wild, it helps us understand how different our gardens are. In the wild, every square inch of soil is covered with a mosaic of interlocking plants, but in our gardens, we arrange plants as individual objects in a sea of mulch. We place them in solitary confinement.

So if you want to add butterfly weed to your garden, you might drift it in beds several feet apart and tuck some low grasses in as companions, like prairie dropseed, blue grama grass or buffalo grass.

Start by looking for bare soil. It is everywhere in our gardens and landscapes. Even in beds with shrubs in them, there are often large expanses of bare soil underneath. It’s incredibly high-maintenance. It requires multiple applications of bark mulch a year, pre-emergent herbicides and lots and lots of weeding.

The alternative to mulch is green mulch — that is, plants. This includes a wide range of herbaceous plants that cover soil, like clump-forming sedges, rhizomatous strawberries or golden groundsel, and self-seeding columbine or woodland poppies.

Intermingling plants can also foster more flowering plants in a smaller space. Credit Thomas Rainer
Q. If I want to try to do it more as nature does, what am I aiming for? Where do I take my cues?

A. The big shift in horticulture in the next decade will be a shift from thinking about plants as individual objects to communities of interrelated species. We think it’s possible to create designed plant communities: stylized versions of naturally occurring ones, adapted to work in our gardens and landscapes. This is not ecological restoration, it’s a hybrid of ecology and horticulture. We take inspiration from the layered structure in the wild, but combine it with the legibility and design of horticulture. It is the best of both worlds: the functionality and biodiversity of an ecological approach, but also the focus on beauty, order and color that horticulture has given us. It’s possible to balance diversity with legibility, ecology with aesthetics.

And it is a shift in how we take care of our gardens: a focus on management, not maintenance. When you plant in communities, you manage the entire plantings, not each individual plant. This is a pretty radical shift. It’s O.K. if a plant self-seeds around a bit, or if one plant becomes more dominant. As long as it fits the aesthetic and functional goals. We can do much less and get more.

Q. Sort of gives new meaning to the phrase “community garden,” doesn’t it?

A. Yes. And plants each also have particular behavior — whether it wants to hang out with other plants of its own species or not. So many gardening mistakes are a result of not paying attention to this.

Q. You make them sound like social animals, which makes me think I’ve been shallow, objectifying plants — choosing among them for just another pretty face, instead of reading their body language to get at their true nature.

A. One of the most useful ideas that came out of our research was this German idea of sociability, developed by Richard Hansen and Friedrich Stahl. They rank a plant’s predilection to spread on a scale of 1 to 5. A low-sociability plant is one that in the wild is almost always found by itself (Panicum virgatum, for example, is almost always found by itself in a meadow). A high-sociability plant is one that spreads into large colonies (Epimedium or Tiarella cordifolia are Level 4 plants; Carex pensylvanica and Packera aurea are Level 5). You arrange plants according to their sociability level: Plants of lower levels (1 and 2) are set individually or in small clusters. Plants of higher levels (3 to 5) are set in groups of 10 to 20-plus, arranged loosely around the others.

A meadow-like display of greenery on an urban deck designed by the HM White landscaping firm. Credit Aaron Booher
It sounds geeky, ranking plants on a scale, but it’s useful because it informs which you should mass, and which you should mingle. It’s why a mass of 50 echinacea (Level 2) tends to flop. They’re just not meant to cover ground. But if you scatter a handful of echinacea in a mass of prairie dropseed or sideoats grama, it will look great.

For years, I would pack together large grasses like switchgrass, or flowers like garden phlox (both Level 1 plants) and wonder why they got rust or powdery mildew. But if you find phlox in the wild, it will never have mildew. It’s growing out of a lot of lower plants, so it gets good air circulation. This idea changed the way I look at plants and pay attention to how they behave.

Q. I know that nature doesn’t plop a 50-foot tree in a mowed lawn (or mow its lawn at all, actually), so that’s not the winning design tactic. I also know that more diverse layered designs are richer ecologically — and now you are saying they are easier to manage, too. But how do I figure out how to fit the right plants together?

A. We need to start thinking about how, not what. So many garden books focus on what to plant, but so few focus on how to arrange plants to fit together in ecological combinations. When we fit our plants together like a tight jigsaw puzzle, the maintenance goes way, way down. They start becoming resilient systems rather than random objects.

To do this, we need to pay attention to a plant’s shape. Its shape is often an indication of where it grows in the vertical strata of a plant community. Upright plants with low or minimal basal foliage like Joe Pye weed (Eutrochium) or spiky upright plants like beargrass (Nolina bigelovii) have adapted to growing through other plants. Horizontally spreading rhizomatous plants like Pennsylvania sedge (Carex pensylvanica) or beach strawberry (Fragaria chiloensis) have adapted to grow underneath others. You almost have to look at a plant from the vantage point of a chipmunk to see its shape.

A grouping of plants by sociability: Foamflower (a very sociable Level 5) dominates, followed by wild ginger and trillium (Levels 2 to 3) and just a few ferns (more independent at Level 1). Credit John Roger Palmour


What I love about this layering idea is that it gives gardeners flexibility. Those lower layers should be very biodiverse: lots of different plants covering the ground and providing stability. But diversity in this layer does not really look messy, because most of these plants are growing underneath our taller ones, so you don’t really see them.

In my garden, I have a corner with dry shade where I have a handful of shrubs that screens a busy road. Lately I’ve been adding white wood aster (Eurybia divaricata), Appalachian barren strawberry (Geum fragarioides) and Pennsylvania sedge and watching them fill the gaps. Upper layers, on the other hand, are the ones I consider the “design” layers because they shape your impression of the planting. You can arrange them naturalistically, or in neat clumps — whatever style you like. That’s the flexibility: The order and legibility of the upper layers combines with the diversity and functionality of the lower ones.

The really cool thing is you can combine this layering idea with the sociability idea. Those Level 1 and 2 sociability plants tend to be those taller upright plants you use in the top layers of your garden because they like to grow through others. The Level 3 to 5 plants tend to be your lower spreading ground-hugging species.

Q. So I am not shopping for plants solely as decorative objects, but for plants with a purpose — for instance, as a living mulch or a good companion to others. Of course none of that, neither the “sociability” nor the plant’s layer, is on the plant labels. A tag might say “for containers or landscapes” or that the plant is “trailing” or “upright” or “mounding,” but that’s about it. What should the label say to help me put plants together successfully?

A. My dream label would describe things that are actually useful to understanding how it grows. It would describe its shape, its root system (taprooted, deep fibrous roots, shallow horizontal roots); its life span (a short-lived pioneer like columbine, or a long-lasting lavender); its sociability level; its adaptation to stress (quick-establishing, but short-lived ruderal species like Gaura lindheimeri or Nassella tenuissima; a thuggish, fast-spreading competitor like Monarda didyma; or a slow but steady stress-tolerator like Hosta or Calamintha). These are really the factors that explain how it will grow in our gardens.

Q. Where can we learn more? Being Northeastern, I love studying plants on the Go Botany plant finder from the New England Wildflower Society, for instance.

A. The Mt. Cuba Center, the Lady Bird Johnson Wildflower Center and the California Native Plant Society websites all have excellent information about how a plant grows in the wild and what it grows with. But mostly, I think gardeners can get to know their plants by going outside and getting reacquainted. Take a look at their shape, how they spread and see what they are trying to show you. You can learn a lot.


Tuesday, March 21, 2017

The Japanese practice of ‘Forest Bathing’ is scientifically proven to improve your health


The tonic of the wilderness was Henry David Thoreau’s classic prescription for civilization and its discontents, offered in the 1854 essay Walden: Or, Life in the Woods. Now there’s scientific evidence supporting eco-therapy. The Japanese practice of forest bathing is proven to lower heart rate and blood pressure, reduce stress hormone production, boost the immune system, and improve overall feelings of wellbeing.
Forest bathing—basically just being in the presence of trees—became part of a national public health program in Japan in 1982 when the forestry ministry coined the phrase shinrin-yoku and promoted topiary as therapy. Nature appreciation—picnicking en masse under the cherry blossoms, for example—is a national pastime in Japan, so forest bathing quickly took. The environment’s wisdom has long been evident to the culture: Japan’s Zen masters asked: If a tree falls in the forest and no one hears, does it make a sound?

To discover the answer, masters do nothing, and gain illumination. Forest bathing works similarly: Just be with trees. No hiking, no counting steps on a Fitbit. You can sit or meander, but the point is to relax rather than accomplish anything.
“Don’t effort,” says Gregg Berman, a registered nurse, wilderness expert, and certified forest bathing guide in California. He’s leading a small group on the Big Trees Trail in Oakland one cool October afternoon, barefoot among the redwoods. Berman tells the group—wearing shoes—that the human nervous system is both of nature and attuned to it. Planes roar overhead as the forest bathers wander slowly, quietly, under the green cathedral of trees.

From 2004 to 2012, Japanese officials spent about $4 million dollars studying the physiological and psychological effects of forest bathing, designating 48 therapy trails based on the results. Qing Li, a professor at Nippon Medical School in Tokyo, measured the activity of human natural killer (NK) cells in the immune system before and after exposure to the woods. These cells provide rapid responses to viral-infected cells and respond to tumor formation, and are associated with immune system health and cancer prevention. In a 2009 study Li’s subjects showed significant increases in NK cell activity in the week after a forest visit, and positive effects lasted a month following each weekend in the woods.
This is due to various essential oils, generally called phytoncide, found in wood, plants, and some fruit and vegetables, which trees emit to protect themselves from germs and insects. Forest air doesn’t just feel fresher and better—inhaling phytoncide seems to actually improve immune system function.

Experiments on forest bathing conducted by the Center for Environment, Health and Field Sciences in Japan’s Chiba University measured its physiological effects on 280 subjects in their early 20s. The team measured the subjects’ salivary cortisol (which increases with stress), blood pressure, pulse rate, and heart rate variability during a day in the city and compared those to the same biometrics taken during a day with a 30-minute forest visit. “Forest environments promote lower concentrations of cortisol, lower pulse rate, lower blood pressure, greater parasympathetic nerve activity, and lower sympathetic nerve activity than do city environments,” the study concluded.
In other words, being in nature made subjects, physiologically, less amped. The parasympathetic nerve system controls the body’s rest-and-digest system while the sympathetic nerve system governs fight-or-flight responses. Subjects were more rested and less inclined to stress after a forest bath.

Trees soothe the spirit too. A study on forest bathing’s psychological effects surveyed 498 healthy volunteers, twice in a forest and twice in control environments. The subjects showed significantly reduced hostility and depression scores, coupled with increased liveliness, after exposure to trees. “Accordingly,” the researchers wrote, “forest environments can be viewed as therapeutic landscapes.”
 Berman advised the forest bathers to pick up a rock, put a problem in and drop it. “You can pick up your troubles again when you leave,” he said with a straight face.

 City dwellers can benefit from the effects of trees with just a visit to the park. Brief exposure to greenery in urban environments can relieve stress levels, and experts have recommended “doses of nature” as part of treatment of attention disorders in children. What all of this evidence suggests is we don’t seem to need a lot of exposure to gain from nature—but regular contact appears to improve our immune system function and our wellbeing.
Julia Plevin, a product designer and urban forest bather, founded San Francisco’s 200-member Forest Bathing Club Meetup in 2014. They gather monthly to escape technology. “It’s an immersive experience,” Plevin explained to Quartz. “So much of our lives are spent interacting with 2D screens. This is such a bummer because there’s a whole 3D world out there! Forest bathing is a break from your phone and computer…from all that noise of social media and email.”

Before we crossed the threshold into the woods in Oakland, Berman advised the forest bathers to pick up a rock, put a problem in and drop it. “You can pick up your troubles again when you leave,” he said with a straight face. But after two hours of forest bathing, no one does.
Joy Chiu, a leadership and life coach on the forest bath led by Berman, explained that this perspective on problems lasts long after a bath, and that she returns to the peace of the forest when she’s far from here, feeling harried. “It’s grounding and I go back to the calm feeling of being here. It’s not like a time capsule, but something I can continually return to.”

https://qz.com/804022/health-benefits-japanese-forest-bathing/?utm_source=atlfb

Wednesday, April 20, 2016

A Computer with a Great Eye is About to Transform Botany

By Margaret Rhodes

My dad is a wildlife biologist, and during road trips we took when I was growing up he spent a lot of time talking about the grasses and trees along the highway. It was a game he played, trying to correctly identify the passing greenery from the driver’s seat of a moving car. As a carsick-prone kid wedged into the back seat of a Ford F150, I found this supremely lame. As an adult—specifically, one who just spoke with a paleobotanist—I now know something about my father’s roadtripping habit: Identifying leaves isn’t easy.

“I’ve looked at tens of thousands of living and fossil leaves,” says that paleobotanist, Peter Wilf of Penn State’s College of Earth and Mineral Sciences. “No one can remember what they all look like. It’s impossible—there’s tens of thousands of vein intersections.” There’s also patterns in vein spacing, different tooth shapes, and a whole host of other features that distinguish one leaf from the next. Unable to commit all these details to memory, botanists rely instead on a manual method of identification developed in the 1800s. That method—called leaf architecture—hasn’t changed much since. It relies on a fat reference book filled with “an unambiguous and standard set of terms for describing leaf form and venation,” and it’s a painstaking process; Wilf says correctly identifying a single leaf’s taxonomy can take two hours.

That’s why, for the past nine years, Wilf has worked with a computational neuroscientist from Brown University to program computer software to do what the human eye cannot: identify families of leaves, in mere milliseconds. The software, which Wilf and his colleagues describe in detail in a recent issue of Proceedings of the National Academy of Sciences, combines computer vision and machine learning algorithms to identify patterns in leaves, linking them to families of leaves they potentially evolved from with 72 percent accuracy. In doing so, Wilf has designed a user-friendly solution to a once-laborious aspect of paleobotany. The program, he says, “is going to really change how we understand plant evolution.”

The project began in 2007, after Wilf read an article in The Economist titled “Easy on the eyes.” It documented the work of Thomas Serre, the neuroscientist from Brown, on image-recognition software. Serre was at MIT at the time and had taught a computer to distinguish photos with animals from photos without animals, with an 82 percent rate of accuracy. That was better than his (human) students, who only only pulled it off 80 percent of the time. “An alarm went off in my head,” says Wilf, who cold-called Serre and asked if this computer program could be taught to recognize patterns in leaves. Serre said yes, and the two scientists cobbled together a preliminary image set of leaves from about five families and started running recognition tests on the computer. They quickly achieved an accuracy rating of 35 percent.

By now, Wilf and Serre have fed the program a database of 7,597 images of leaves that have been chemically bleached and then stained, to make details like vein patterns and toothed edges pop. Small imperfections like bug bites and tears were purposefully included, since those details provide clues to the plant’s origins. Once the software processes these ghost images, it creates a heat map on top of them. Red dots point out the importance of different codebook elements, or tiny images illustrating some of the 50 different leaf characteristics. Together, the red dots highlight areas relevant to the family the leaf may belong to.

This, rather than detecting species, is the broader goal for Wilf. He wants to start feeding the software tens of thousands of images of unidentified, fossilized plants. If you’re trying to identify a fossil, Wilf says, it’s almost always of an extinct species, “so finding the evolutionary family is one of our motivators.” Knowing the leaf’s species isn’t as helpful as knowing where the leaf came from or what living leaves it’s related to—invaluable information to a paleobotanist.

In this way, Wilf and Serre’s tool creates a stronger bridge between the taxonomical aspects of paleobotany and the ecological side of things. Ellen Currano, an assistant professor in the Department of Geology and Geophysics at the University of Wyoming, says that bridge has been sorely lacking. “You could go into a herbarium and look at leaves, or say, ‘I see big leaves, it must be from a wet place,'” but that’s less than efficient.” Currano, who has studied with Wilf in the past but did not work on this study, also points out that modern botanists can often discern a leaf’s taxonomy by looking at the flower or the fruit, but that those often get fossilized separately from each other. “It’s a tremendous challenge to have the leaf, but not flower or fruit,” she says. “So [Wilf’s tool] is an important breakthrough in that it’s taxonomy based on leaves.”

It’s also taxonomy based on machine learning and image recognition. “Everyone”—at least, every paleobotanist—“has had that dream in their head, if only I could just take a picture of this, and get an identity,” Currano says. In seeking to fulfill that wish, Wilf has taken the same approach to studying fossils that Google engineers have taken to streamlining your search results, or teaching a computer to dominate at Go. Wilf even goes so far as to call his tool “an assistant.”

“Assistant” is an apt description. After all, Wilf’s creation doesn’t always provide hard answers (the software, he reiterates, is 72% accurate, not 100%), but it does serve up helpful prompts and ideas. The computer can quickly, and without bias, see what a well-trained botanist might otherwise overlook—and once the computer presents a promising line of inquiry, human analysis can resume. It’s the kind of tool that Wilf is optimistic will unleash “a flood of new botanical information”—but he’s definitely not worried about his job. “It’s not going to replace botanists,” he says, “but it is going to show them where to look.”

http://www.wired.com/2016/03/computer-great-eye-transform-botany/

Wednesday, March 23, 2016

Leading by the Nose

For humans, walkable neighborhoods and commercial hubs reward strolling with varied architecture, safe street crossings, and a mix of things to do and see on foot. For dogs, there is a much larger world of scent. Can our canine companions guide us to a richer walking experience?

Frank Edgerton Martin

Dogs and other animals understand sidewalks and parks not as visually ordered settings but as shifting islands and drifts of smells. When we humans step out the door, it’s basically the same outdoors we left behind. But for the dog with us on a leash, a street is like a flowing stream filled with the scent trails of passing people and dogs. It’s an ever-changing place.

In 2003, I adopted a yellow Labrador named Samson from the Hennepin County Humane Society. When I first saw him, he struck me as quiet and observant as he sat there upright, regarding the other dogs as they barked and whimpered. For years, Samson spent his days sitting Sphinx-like on the front steps, left paw crossed on right, surveying passersby. He became famous among the neighbors for wanting to sit outside even on the coldest January days.

Samson loved meeting people and other dogs. He was a natural greeter, but we found little social life along the roads and subdivisions of our Lake Minnetonka neighborhood. And because I myself was more interested in architecture than in exercise, I often found our walks boring. But Samson and I both needed exercise and to get outside for strolls. Over the years we developed a set of alternative suburban environments that made sense for both of us.

Instead of walking by lawns and large houses, we got in the car (a thrill for Samson) and drove to denser places where we could do the things we liked, such as: smelling other dogs, visiting antique shops, sniffing sidewalk trees, and sitting in outdoor caf├ęs while greeting people and watching traffic. We often went to downtown Excelsior, a 19th-century town where we could do all of these things. But we also made new discoveries. For some reason, Samson loved outlet malls, perhaps because the long sidewalks afforded him the chance to meet a lot of people.

I took him to Tonkadale Greenhouse and other nurseries where we could walk among the plants in winter, admiring shoppers could pet him, and we could take in the fragrances and humidity. In summer, we went to public docks on Lake Minnetonka, where Samson greeted those departing from the tour boats. Seniors and teenage girls particularly loved him.

TALKING SCENTS

In her collection of essays On Looking: Eleven Walks with Expert Eyes, Alexandra Horowitz takes us along on eleven treks, mostly in Manhattan, with experts in a variety of different fields—graphic design, geology, entomology, and so on. Another one of the experts is her dog Flip, who reminds me of a more citified version of Samson.

Horowitz is a cognitive psychologist who writes extensively on dogs and how they perceive the world. In describing her walk with Flip, she notes that “smell, like memory, is entirely personal. It cannot be shared with the ease that an image, rendered in ink or oils, can be experienced by hundreds of millions of viewers.”

Smells are not easily communicated in words; we humans have only vague olfactory classifications such as “sweet,” “earthy,” or “pungent.” But dogs like Flip and Samson experience nuanced smells in thousands of variations. They may not have a word for each, but they have recognition all the same. For dogs, smells form an unfolding map of information about specific places and other animals and people. “Their world has a topography wrought of odors . . . the landscape is brightly colored with aromas,” writes Horowitz.

ARBY’S

When touring a neighborhood, we humans use visual classifications such as “late Victorian” or “New Urbanist.” Dogs, of course, could care less. From my walks with Samson, I learned more about the experiences that mattered to him, and, in doing so, I began to appreciate suburban landscapes in a different way.
I learned that busy places like Main Streets and public parks have a smell history. Huge parking lots can be bleak for all. Samson and I agreed that big-box stores and malls were the worst—visual and olfactory deserts unsuitable for a hike. But a parking lot at Arby’s could be a sacred place.

At least it was for Samson, who generally refused to leave after we sat on the grassy suburban berm and shared a bag of curly fries. After snacks, I would walk with him around the building—along the lane leading to the drive-thru, past the drive-thru window (with faster sniffing because much is dropped there), and around to the back where the exhaust fans are (a kind of climax). This circuit never tired him, and he would tug billy-goat-like on the leash when I tried to get him back into the car. Inevitably, I would have to pick him up, all 75 pounds, and dump him in the backseat.

A dog can sniff fast when there is much to take in, like at a drive-thru window—up to seven times per second. Humans can only take in a new scent about once every two seconds. We have about five million olfactory sense receptors; a bloodhound can have 300 million. A dog can gauge a smell’s strength by its variance between nostrils.

Samson and I had many kinds of walks, the hardest being the “process of elimination” at 7:00 on January mornings. When it was 20 degrees below zero, he always sniffed too long. But sometimes we both liked to linger in a place. We might sit in a park, Samson sniffing with darting nose the scents of other dogs flowing from upwind. With my eyes and ears, I observed things too—where people gathered, the shouts of children, and impromptu soccer games on an open patch of grass.

TAKING THE TIME

In an interview with the National Canine Research Council, Horowitz put into words what I intuited from Samson: We need to value our dogs’ “dogness.” This “means appreciating that they get bored, and working to give them things to do; it means celebrating their perceptual abilities, and letting them smell the well-marked spots at length,” she explained.

By following our canine companion’s lead, we two-legged animals can rediscover important things—the fragrances of childhood, so deeply implanted that they seem like they occurred only yesterday. From my walks with Samson, I recalled the smell of leaves burning on an October afternoon; the peonies in June that my mother floated in a crystal bowl; what a pumpkin smells like when you carve it. No matter how boring a place may seem, a dog can open up a new journey. If I’d never had my walks with Samson, I may never have lingered, pausing to discover scents and other creatures hidden in a world we mostly see.

http://www.aia-mn.org/leading-by-the-nose/