Dead wood and the woodpecker’s g-force

About fifteen years ago, the local electrical company hired a crew of subcontractors to cut and trim any trees that were deemed a threat to powerlines. The crew gave the sugar maple in our front garden a lop-sided haircut, slicing away all the branches on the south side. Regrettably, the equipment they used must have carried spores from a diseased tree: fungus swarmed over the cut branches, then killed the whole maple.

The dead tree stood next to the house, so its upper trunks had to be cut down. We left the lower ten feet standing, though. This part, even if it fell, presented no danger to the house. Ever since, the stump has gradually rotted away, occasionally calving chunks of bark, but mostly turning slowly, slowly to punk and duff.

The birds love to perch atop the tall stump, as have two generations of housecats. Woodpeckers also include the rotting maple on their rounds and this week a pileated woodpecker made a stop. I poked a microphone out of the cat-flap and recorded the bird’s hammering and the powerful sound of its thirty inch wingspan as it took flight.

As you listen, imagine the slamming impact of beak on wood. Human brains are concussed by forces ten times weaker than those that pileated woodpeckers experience. They’d make a fine mascot for a football team. The woodpeckers’ heads attain speeds of 6-7 meters per second before impact, they then hit the trunk and decelerate at 13,000 meters/second^2 or 1000 g (see Wikipedia for interesting comparative examples of “g”).  The birds tolerate this pounding because their multi-million dollar contracts specify that they must. And because they are protected by the angle of beak to brain, the shock-absorbing design of the skull, the tightness of the brain in its case, and the elasticity of muscles.

The spectrogram gives a visualization of the sound, with time moving left to right, and frequency (pitch) shown on the vertical: woodpeckerfull

These two clips show short segments, one from the beginning and one from the end of the recording:knockknock


Posted in Archosaurs, Bioacoustic revelry | Tagged , | 7 Comments

Crash, hop. Inscriptions on flakes.


2015-02-17 snowprints 006The motions of a landing, wing-folding, strutting, tip-toeing, recorded on an icy pond. Most likely a sparrow.

Snow scribing. Here are the plants at work, from last year.

Posted in Archosaurs, Water | Tagged , | 3 Comments

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.

Posted in Microbes, Travels | Tagged , , | 14 Comments

What is a “seahawk” anyway?

A sports team of ambiguous nomenclature and symbolism takes the field today. The seahawk logo matches the appearance of no Seattle bird that I know of. The logo design itself appears not to be a hawk, but an eagle, a design taken from the Kwakwaka’wakw transformation mask of the Coastal Indians. Even though the NFL knows all about property rights and branding, no Indian got any royalties, to my knowledge.

The captive bird that flies out before games is an Augur hawk from Africa, a distant relative of the red-tailed hawk, in the Buteo genus. It is not a seabird, but feeds in mountains and grasslands. Thanks to the Smithsonian Magazine for that interesting tidbit. This captive needed some serious training to prepare it to face the whooping Seattle fans.

“Seahawk” might refer to either an osprey (not a hawk, but a bird in its own family, a relative of hawks and eagles) or a skua (a fierce cousins of gulls). The osprey has a bold eyestripe, not a two-tone head, so the color match with the sports team logo is imperfect, as is the size of the beak. Ospreys feed by swooping down on fish with great skill and elegance. Skuas, our other contender for “seahawk,” look nothing like the logo. They feed by robbing other birds, eating the afterbirth of marine mammals, preying on the eggs and young of other seabirds, scavenging dead meat, and generally scraping the barrel of respectable behavior. We’ll see how the game goes, then decide which bird is the better fit.

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Sandhill Cranes at Hiwassee Wildlife Refuge, TN

2015-01-16 Sandhills 037Tens of thousands of cranes gather at Hiwassee. Gruuu gruuu: sound resonates within the trachea coiled within their sternum. Horn section of the avian band. An ancient sound; Sandhill Cranes have flown across North America for at least ten million years.

In this recording, made on my phone, you’ll hear the cranes overhead, and the ack-ack artillery of photographers shooting their pixel flak skyward:

2015-01-16 Sandhills 028“…not quite the world’s” William Stafford, Watching Sandhill Cranes

“…so stears the prudent Crane/Her annual Voiage, born on Windes;/the Aire
Floats, as they pass, fann’d with unnumber’d plumes…” John Milton, Paradise Lost

“The crane’s legs/have gotten shorter/in the spring rain” Basho (Matsuo Kinsaku)

2015-01-16 Sandhills 022

Posted in Archosaurs, Bioacoustic revelry | Tagged , | 21 Comments

Je suis Charlie?

Charlie Hebdo is back in circulation. But freedom of expression is of course massively restricted in many parts of the world. Je suis Charlie? Unfortunately the answer is too often, no.

For a couple of practical steps that you can take to help one writer experiencing egregious punishment for setting up a blog in Saudi Arabia, see these pages at PEN America and Amnesty International.

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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?


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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!

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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.

Posted in Travels, Water | Tagged , | 13 Comments

All Saints’ Day

Rembering the Communion of all Saints:

and the nameless multitude of Pre-Cambrian microbes.

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