Category Archives: Travels

Hospital bacteria: in my blood, in my IV.

I recently had a run-in with some bacterial cousins, courtesy of a small post-surgical wound. The bacteria were winning, so I spent a few days in the hospital where attentive medical staff mainlined antibiotics into my arm. The treatment worked, I’m all healed up, and the hospital guards set me free.

There were some interesting lessons in the wheeled tree of bags and bottles that was my shadow, my daemon, my constant umbilical companion.

IMG1107The molecules flowing into me were labeled and bar-coded. As was I. Both patient and bag were laser-scanned with every fresh dose of fluid. Just like the supermarket checkout: Beep-beep. And thereby, errors avoided, we hope.

But the names and numbers hid a deeper history. Each one of the antibiotics that I received was a synthetic derivative of a drug derived from a living organism. In other words, scientists took an antibiotic produced by a bacteria or fungus, then synthesized a new molecule that was modeled on the original chemical structure but with some extra added molecular tails and loops. Why bother with the modifications? Sometimes the synthetic version is more potent; sometimes it is a replacement for the original, a replacement necessitated by the evolution of antibiotic resistance in the pathogenic bacteria.

These drugs therefore belong to the second generation of antibiotics. The first generation were derived from other species, mostly from soil bacteria. These eventually lost their effectiveness as evolution did its work. The second generation of antibiotics take the original “scaffolds” or shapes, then tweak them to develop chemicals that are new, but not very different from the originals. This usually means that these second generation antibiotics have a limited lifetime of medical utility. The pathogenic bacteria, having found ways to dodge the first versions take little time to develop resistance to these new, rather similar synthetic versions. For drug companies working to make a profit, this is a bad investment strategy: why invest money and time developing products that will be useless, or nearly so, in the short or medium term? There is much more money to be made in convincing men that they need more testosterone. (The idea that the world might be better with a little less testosterone is unprofitable, it seems.) For the rest of us, none of this is good news. Bacterial evolution threatens to outpace the rate of development of new antibiotics.

I had the latest copy of Nature to keep me entertained during my stay and, by coincidence, it had a great article about a new avenue in drug development, an avenue that also promises to give us some fabulous insights into soil biology. Rather than move further down the path of synthetics, Ling et al., the paper’s authors, returned to the soil. Science’s initial foray into soil antibiotics was able to examine only one percent of the organisms that dwell in the soil. The other ninety nine percent died when brought into the lab. The first generation of antibiotics, in other words, was built on a tiny fraction of the soil’s potential pharmacopeia.

Instead of bringing soil to the lab, Ling’s team brought the lab to the soil. They buried a small “iChip,” a rectangular device filled with tiny bore holes, in the soil. The chip had previously been soaked in a diluted sample of soil. Bacteria colonized the holes and, because they were returned to their habitat in the soil, many of them thrived. Instead of one percent, the researchers managed to culture fifty percent of the soil microbes. Kaboom: That’s one small borehole for a bacteria, one giant leap for humankind.

Once the bacteria colonized and grew in the chip, they were presented with pathogenic bacteria like Staphylococcus aureus (“staph”) or Mycobacterium tuberculosis (“TB”). Using this method, Ling’s group discovered a new antibiotic that they named teixobactin. Importantly, this chemical is not structurally similar to existing antibiotics and the researchers have so far been unable to find any bacteria that can resist its attack. No doubt the same method will yield more drugs as we learn to converse with the mysteries of the soil. Excellent news indeed.

Surely it is time to honor the soil bacteria with little drawings of their habitats alongside the barcodes?

Nature News has an interesting commentary by Heidi Ledford, with photos, interviews, links, and technical details.

Christmas’ long strange trip to oil towns in the Amazon

A Christmas nativity scene in Coca, Ecuador. Coca is a rough, booming oil town on the edge of the Amazon, one of the hubs of the rapidly expanding oil and mineral extraction industry in the region.

Coca sits almost exactly on the equator, yet the nativity scene carries marks of the temperate zone: the meandering, anastomosing cultural rivers of Christmas. One stream was born in the deserts of the Levant, another in the forests of Northern Europe, yet another in the imaginations of department store marketing executives in the US. They all wash against the shores of Coca’s Napo river, merging into wells of local culture and the flow of five hundred years of Christian colonialism in the region.

The main tableau features Middle Eastern figures with Old World farm animals, set against a backdrop of the Andes. Some tundra animals also make an appearance: reindeer arranged along the Andes’ foothills.

cocaMore reindeer, dressed in European holly and pine, hang from plastic boughs of boreal spruce:

reindeerSnowy European gingerbread houses intermingle with post-colonial Andean villages:

snowhousesvillageIn a town just down the road, the total lack of snow in this ever-hot climate has not prevented creative constructions of snowmen at many street corners:

snowmanLike Christmas celebrations everywhere, people have created a cultural syncretism, a mash-up of our inheritances. Christianity has some opinions about its own power and the status of other systems of belief. Therefore Christmas nativity scenes in Coca, as is true around the world, exclude many dimensions of local human and non-human diversity of life. So syncretism has its limits, and these limits deracinate Christmas from local soil.

In the Western Amazon, this unrooting has profound political and ecological consequences (more on these later). It also results in a great loss of aesthetic opportunity for community celebrations. The tropical forest could add some spectacular local color to a manger scene. Might a tapir or shaman be allowed into the picture? Might we, in North America, let bison and medicine women into the circle? Locavore religion? We shall see.

sunrisesunsrise2And a clearwing butterfly, surely a suitable symbol for a tree angel?


The dancing oysters of Hiroshima’s market

oystersThese oysters were harvested in the Seto Sea off the coast of Hiroshima. This sea has thousands of bamboo rafts floating on its surface, each raft home to huge colonies of oysters dangling from ropes in the water below. The region produces tens of thousands of tons of oysters every year, a large portion of total Japanese production. There are so many of these oyster farms that the filter-feeding activities of the oysters have a significant cleaning effect on water pollution in the region. Unfortunately, the accumulated toxins mess with the sex lives of the bivalves (an aphrodisiacal irony?) and possibly the health of those who eat them. Fortunately, in the last few decades, wetland restoration efforts have helped to restore vitality to the sea and reduce these problems.

Back to the market: The oysters were not just quietly lying on ice, as oysters so often tend to do. Not only were the oysters decorated with miniature representations of the torii gates at Itsukushima Shrine, these oysters had a funky groove. I took a short video of this zoological son et lumière show.

乾杯, 高貴なカキKanpai, noble oysters!


The city of Jericho is most famous for the unkind things that Joshua is reputed to have done to Jericho’s populace after God gave him the nod to move in. But Jericho’s history is far more complicated than the Biblical story. Jericho is likely the oldest continually inhabited city in the world and archaeologists have unearthed more than twenty distinct physical “layers” of remains, evidence of dozens of city cultures that waxed and waned over ten thousand years. Old stone tools show that before the cities, hunter-gatherers lived in the region, extending human habitation of the region back another thousand years or so.

All this history literally heaped upon itself and built a hill, Tell es-Sultan, a mound that seems like a natural dome, but is in fact built entirely from the accumulated stone and sand of these cultures accreting on the remains of their predecessors.

towerThe photograph above looks down about twenty meters into a trench that has exposed walls that date to 8000 BCE. At that time Jericho was already a fortified city. People appear to have lived in and around ever since. Why? Water. The Ain es-Sultan spring runs year-round and has given life to Jericho for thousands of years, supporting agriculture in a landscape that is otherwise astoundingly dry for much of the year. The spring is sometimes called “Elisha Spring,” for the prophet who we’re told sweetened its waters. The archaeological evidence, though, suggests that the water was good before Elisha wandered past.

springThe fountain above uses a small portion of the water from the spring, the main outflow is contained within a building a few steps from here. The dragonflies that visit are separated from their kin by many, many miles. And because Jericho sits more than two hundred meters below sea level, these may be the lowest dragonflies on the planet:

dragJoshua was hardly the last person to clear a city in God’s name (although Jerusalem must surely beat Jericho in the league table of crusades and other bids for the “promised” land). After Israel’s declaration of independence in 1948, a portion of the seven hundred thousand refugees from the newly formed state moved to a camp in Jericho. In the 1967 war, many of these refugees relocated to Jordan, so the Jericho camp is one of the smaller remaining refugee camps.

Jericho has also been the site of violent attacks from both sides in the ongoing conflict over the West Bank. The city is currently run by the Palestinian Authority, under the eye of the Israeli army (who carry guns called “Jericho 941“). An Israeli army post sits just outside the city. During my brief visit, Palestinian men were lined up outside, summoned by the Israeli military for interviews.

Tell es-Sultan has yet to see the end of layers upon layers.

Sounds from the edge of Boreas’ kingdom

A raven flies to its roost at dusk, wingbeats audible between the calls. Just before this flight, the bird was amusing itself with half a dozen others of its kind by harassing a sluggard-winged eagle. The ravens wove and swooped; the eagle flopped its great wings, finally passing out of sight on the horizon.

I think the squealing call at the end is a younger raven, greeting its homeward-bound parent.

Spectrogram of the same sound. Time moves left to right, pitch increases along the vertical.

Spectrogram. Time moves left to right, pitch increases along the vertical. “Stacked” lines are harmonics.

Night came and with it a frost.

Fir at nightI lingered and was rewarded by the sounds of Northern Saw-whet Owls. These tiny owls are common in dense forests of Canada and the Western US, especially forests with rotten trees to supply nesting holes. In the winter, some birds move south, so Saw-whets can be found all the way to Florida in the right season. The bird gets its name from the supposed resemblance between its repeated whistled call and the action of whetting a saw. The analogy is stretched, unless your saw comes with a flute.

The owls were a distance away, so the following recording has some lower and higher sounds filtered out to make the call come through more clearly.


Move over Gutenberg: Carved movable type from China

In the Western world, Johannes Gutenberg is widely celebrated for his invention of the movable type printing press. Gutenberg’s work certainly produced a major leap in the mechanization of the printing process, but movable type itself was invented four hundred years earlier by Bi Sheng who lived during China’s Northern Song Dynasty, just after the turn of the first millennium. He used both carved wood and fired clay to create his type, which he then temporarily fixed to an iron plate using resin and other glues.

Bi Sheng’s craft lives on in the work of a small number of wood carvers in China. At the IUFRO World Congress, the International Wood Culture Society invited Jianming Zou from the Ninghuan Cultural Center in Fujian Province to demonstrate and exhibit his work.

2014-10-10 Chinese block print 006The translator said that each block is hand-carved from walnut wood. The blocks were certainly hand-carved, but they did not look like walnut; the program notes indicated that pear and jujube are often used.

Unlike the limited number of graphemes in Latin alphabet, a complete collection of Chinese movable type includes thousands of logograms, 汉字. These displays show just a small selection:

2014-10-10 Chinese block print 0012014-10-10 Chinese block print 004A large brush made from palm fibers is used to transfer ink to the frame of blocks:

2014-10-10 Chinese block print 010Printing onto bamboo paper, with the help of a smaller brush:

2014-10-10 Chinese block print 007Jianming Zou signs each printed sheet in red ink:

2014-10-10 Chinese block print 011Would — wood — that all this craftsmanship was brought to you by hand-carved liquid crystals, illuminated by the glow of a polarized palm fire.

In moving away (for much of our writing at least) from direct sensory connection to paper, block, and ink, we’ve lost that beautiful congruence of botanical and zoological talents — wood, inks, our minds — and moved to something that makes the community of life harder to sense. Old, fossilized sunlight, turned to plastic, coal, and mining equipment is still “natural,” but those connections are mightily well hidden.

Take my word for it, I stamped my screen with a block of wood right here:





Largest, oldest creature on Earth?

I took a circuitous route to a conference in Salt Lake City. One of my stops was in south-central Utah at Fishlake National Forest, home to a trembling aspen (Populus tremuloides) grove that we 20th Century humans call “Pando” (meaning “I spread” in Latin). The aspen probably has another name for itself. The root system of Pando may be eighty thousand years old, about thirty or forty times as old as Latin.

2014-10-08 Pando aspen 004This aspen grove covers about 44 hectares (108 acres) and is comprised of one “individual.” Through clonal growth, a founder seed has spread, amoeba-like, over the mountainside to create a forest of nearly fifty thousand stems, which look separate, but are in fact a single organism. The grove is reputed to be the heaviest and oldest creature on the planet, although some fungi likely nudge the aspen out of first place.

2014-10-08 Pando aspen 016

The story is not quite as simple as I have described, though. Through a few mutations in the clone (for biojargon lovers: somatic mutations) and perhaps a little sex, the spreading tree has managed to diversify its genetics. Like other big aspen clones, Pando also has an extra set of chromosomes (making it “triploid” instead of the usual “diploid”), all strategies that may have allowed it to defy one of ecology’s more rigorous rules: huge genetically uniform clones don’t last long in the face of environmental stress and disease (e.g., monocultures of agricultural clones are helped along by pesticides and herbicides; if left alone, they’d be eaten alive by fungi, viruses, and bacteria).

When this tree germinated, modern humans were found only in Africa (or so many think, our travel dates are hazy). The last ice age was just getting going. Now, though, the world is truly changed. Heavy grazing by cattle on National Forest land mows new sprouts (cows and their dung pats are everywhere); deer are also abundant. Humans have changed the rhythms of fire and animals. So, the old feller (yes, he’s a male clone), is now in a zoo-like exclosure fence and land managers are encouraging new sprouts to grow by cutting older trees. A flush of new growth has emerged from one of these zones.

He-whose-name-we-do-not-know is being taken firmly in hand, gardened and managed, by the recently-arrived primates from Africa. Check back in 80,000 years to see who is still around.

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2014-10-08 Pando aspen 0522014-10-08 Pando aspen 043


One tiny part of the rainforest song

Twilight is brief in the tropics. The sun drops with none of the lingering obliqueness of its behavior in temperate and polar areas. My visit to Ecuador placed me almost directly on the equator, so after I watched the sunset from a tree canopy, I hustled to get back to the camp. The trail turns completely dark within a few minutes of sunset.

As I jogged along, a song stopped me in my tracks: a pure tone from the rainforest, then another seemingly in answer, then one more from far across the stream. I’d never heard such a sound. The purity of a thrush, the loudness of a goose. Close.

I captured a few seconds (turn up your volume!):

Here are the spectrograms, with time moving horizontally and pitch (frequency) increasing vertically. The whistles are the low dark marks; all the rest of the sounds are insects and distant birds:

TinSpec2These are the calls of tinamous, ground-dwelling birds found only in the New World tropics (first, the variegated tinamou, then the great tinamou, I believe, but neotropical bioacousticians please feel free to correct me). When I studied their biology in zoology classes I never thought I’d be in their presence. Here they were, though, singing within a few meters of me in the Ecuadorian Amazon. Stunning.

Tinamous have strange habits, at least by the standards of other birds. The males defend nests into which multiple females lay astonishingly glassy eggs. The male incubates the eggs, broods the hatchlings, and guards the young. The females wander from male to male laying more eggs. Tinamous seldom fly, and then rather poorly, preferring to strut in the undergrowth of their forested territories.

Recent molecular research strongly suggests that tinamous are the relatives of the extinct New Zealand moas. This grouping is clustered within the larger “family” of ostriches, emus, rheas, kiwis, and cassowaries. So tinamous are a zoological echo of the ancient southern continent of Gondwanaland, a continent now fragmented into many parts, each carrying biological stowaways. The tinamou song is the closest we’ll come to hearing a moa.

In their biogeographic wanderings, the tinamous seem to have picked up the quena from the mountains to the west, slicing through the acoustic tumult of the Amazon with their melodies. Or perhaps the quena, a recent arrival by zoological standards, is inspired by the Andean tinamous?

Tinamous sing at dawn and dusk, so their music rings out only briefly, bracketing  Amazonian nights and days.





Eastern Ecuador: Amazonian forest

Leaving the frontier town of Coca, our journey took us several hours by motorized canoe and truck, following roads built by the oil companies and rivers built by the prodigious rains. After a day’s travel, we arrived at Tiputini Biodiversity Station, located in what ecologists believe is the richest place on the planet for plants and animals. In one hectare of forest, a team of good taxonomists can find more species of plant than live in all of North America. A walk along a kilometer of forest trail will yield the same for birds. Nine or ten species of primate live here. Invertebrate animal diversity is phenomenal, but mostly unquantified. Humans have lived here for thousands of years, building cultures beautifully adapted to the forest. And now: oil. This area, along with similar places in Peru and other parts of the western Amazon, sits atop some impressive reserves of fossilized sunlight, a commodity valuable to any country, but especially to places that are not wealthy and are striving to keep their economies and governments thriving. So human culture, the forest, and all the connections within and among these are in rapid transition.

A few images from my visit:

Flaring gas from an oil production plant on the banks of the Napo River:2014-09-01 Ecuador 034

Climb the tower to the rainforest canopy, forty five meters up:

2014-09-02 Ecuador 022Looking down from high in the canopy:

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Rainforest vista refracted through a water drop: 2014-09-04 Ecuador 061i

Zebra bromeliad in canopy:

2014-09-02 Ecuador 033

Toads the size of dinner plates:

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2014-09-04 Ecuador 130

“Scorpion spiders” the size of Thanksgiving serving platters (unless I have misidentified this, the common name belies its taxonomy; the creature is neither scorpion or spider, but and amblypygid, or “tailless whip scorpion,” a member of a strange and ancient order of arthropods):

2014-09-04 Ecuador 141Ants of many kinds, including leaf-cutters:

2014-09-03 Ecuador 120

And bullet ants, reputed to be the most painful of all insect bites, a hypothesis I was able to test when one dropped down my shirt collar and nailed me (they sting and bite simultaneously), then got me again on my finger as I yanked the ant off my shoulder.

But bullet ants are not quite as painful as rainforest DIY dentistry:

2014-09-04 Ecuador 181Back in the canopy, a cocoon spun by a moth larva:

2014-09-02 Ecuador 373Saki monkey (genus Pithecia), seldom seen here. Primatologists disagree about which species this is:

2014-09-03 Ecuador 248Woolly monkeys:

2014-09-02 Ecuador 252Crested owl:

2014-09-02 Ecuador 196Paradise tanager:

2014-09-03 Ecuador 363Young caiman in the Tiputini River:

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Huck Finn’s spirit is still alive on the Napo River:

2014-09-05 Ecuador 085Oil depots are expanding, as Ecuador moves ahead with opening Yasuní National Park and surrounding areas to road-building, seismic exploration, and drilling.

2014-09-01 Ecuador 067Much of the oil will reportedly be used to pay down high interest loans from China (Ecuador has, in the past, suspended paying part of foreign commercial debt, so now enters into these other forms of borrowing). The oil also fuels human motion, making photos like this possible, the Andes on my return:

2014-09-05 Ecuador 182My thanks to Universidad San Francisco de Quito and the Tiputini Biodiversity Station for their welcome. Especially Dr. Esteban Suárez, Pablo Negret, José Macanilla, Mayer Rodríguez, and the students from the Institute for the International Education of Students, led by Eduardo Ortiz, René Bueno, and Gladys Argoti in Quito and Lee L’Hote and Melissa Torres in the US. All the opinions expressed here are my own, not those of hosting institutions.

Young vertebrates enjoying the South Platte River in Colorado

High in the mountains, in Eleven Mile Canyon:

A Common Merganser with her brood. She incubated the chicks in an old woodpecker hole and will stay with them as they learn to forage. These “sawtooth” ducks dive under the water to snatch fish. They’ll also feed on invertebrates such as snails and mayflies.


American Dipper fledgling. This young bird left the nest a week or so ago. It waits for the parent to appear…

dipper1…from beneath the fast-flowing water. Dippers dive into mountain streams and walk along the bottom, gripping with their toe-nails for all they’re worth, plucking stream insects from rocks. Once emerged, the adult is met with the youngster’s loud whistles, sounds that cut through the roar of the water. When food is stuffed into the gullet of the noisy birdchild, the sound changes to delighted chirping.



And when the feeding is done, it is time for more piercing begging cries, delivered at the water, below which the parent feeds.

dipper3Another gullet-stuff, another flurry of chirps:


Downstream, in the heart of Denver:

At Confluence Park, in the center of the city, the South Platte has been engineered to provide a series of chutes and rapids for the amusement of Denverites. In the photo below a youth leader takes one of several disabled kids on a paddle ride down the rapids. I’ve blanked the faces because I was not able to ask whether it was OK to post these two water-lovers’ faces on my blog (sorry, dippers and mergansers, speciesism…). As he lurched through the spray, the kid’s face went from apprehensive frown, to a big O of surprise, to a grin of delight. A (mile-)high-five ended the ride.


In the 1960s and 1970s, this stretch of river was the most junky, polluted part of the whole city. Old cars, tires, and mattresses were heaped along the banks; factories piped effluent directly into the river; oil oozed from every bank. Thanks to the very hard work of the Greenway Foundation, The City of Denver, and many other partners, this is one of the most popular places in town for people of all races, incomes, and levels of physical ability. One hundred miles of riverside trails radiate out from here, punctuated with parks of all kinds.

The river flows onward from here, east through Colorado and Nebraska, hopefully encountering a few more young lifeforms reveling in its waters.