Mar 16, 2013

beautiful defiance

A couple weeks ago I pruned the saucer magnolia in the front yard. The pruned branches now bear defiant flowers. Life is powerful and spirited.

Though doomed, these branches retain water and even draw some in when humid air sits over these hills. Death can be sudden, but only after taking its time. We all get a fair allotment of life to use wisely. I can not keep the spirit down when I see a cut branch make a few final blossoms, laughing a pink punchline. What a wonderful world.

Feb 9, 2013

painful interpretation

National Geographic News asks, "Did your seafood feel pain?" It is an interesting question that really can not be answered. "No" is not a legitimate answer, mostly because you can not prove a negative. Animals, even invertebrates, have the types of neurons that signal tissue damage, nociceptors, so the null hypothesis has to be that they can feel pain. From there, the question only gets more complicated.
In terms of animal welfare and dietary choices, it's not really pain that we are concerned with so much as suffering. That implies higher-order cognition and all the baggage that comes along when contemplating awareness and consciousness in animals. Pain and suffering are not equivalents. At times we seek pain, as evidence that exercise is generating desired effects, for example, and most pain is more annoying than traumatic. Fright can be exhilarating, and many modes of play simulate danger, so even when we observe behaviors in animals that imply pain and panic, we can not conclusively declare that the animal is suffering.
Even if we grant animals a considerable allotment of consciousness and intellect, they don't become doctors or philosophers. Most animals likely have no conception of death, so injury and danger would not trigger abstract pangs of loss and longing. Those are burdens we bear.
In a classic ethological observation by French entomologist Jean-Henri Fabre, a wasp consuming food was captured by a praying mantis. Fabre watched the mantis devour the wasp's abdomen while the wasp continued to consume its own meal. With invertebrates at least, there is evidence that even lethal injuries do not result in significant pain.
It is quite possible that confining animals results in more psychological distress than killing them. You have to assume that animals experience some degree of pain. The real question is how much should you care? Me, I care more about the quality of life than the manner of death.

To appreciate how complicated this question is, read the National Geographic article and pay close attention to the crab experiment. Researchers concluded that crabs can feel pain because electrical shocks serve as training cues. But in their experiment, one out of every nine crabs "cast off" the leg with electric wires attached. Some crabs severed two of their own legs, so the experimenters excluded them from the results.
That's a convenient move if you are hoping to conclude that crabs feel pain. Otherwise, how do you explain that some crabs prefer self-mutilation to mild shocks or the simple discomfort of constrained leg motion? It's utterly routine to find spiders and other arthropods with missing legs, and if you've ever witnessed an incident where a leg is lost, you know that there is no writhing or other signs of major pain.
I find it painfully amusing that an experiment which revealed how readily a crab will amputate its own leg is offered as a reason to concern ourselves with a crab's pain. Is an experiment where we deliberately inflict pain so we can decide whether the subject feels it really about animals, or is it a dissection of our own morality?

Aug 10, 2012

prison science

According to this article in Nature News, University of Utah researcher Nalini Nadkarni has been devising and carrying out conservation projects that put prisoners to work. At one women's prison, inmates have released 800 endangered butterflies and are rearing 3600 caterpillars for next year's release. They also conducted egg-laying experiments and determined what science had not yet learned: the native host plant of the endangered Taylor's checkerspot, which turned out to be a threatened plant, the golden paintbrush.
At an Oregon prison, inmates are rearing tadpoles of the endangered Oregon spotted frog, and their experimentation with rearing conditions have resulted in a protocol that yields bigger, healthier frogs than professionals in zoos and laboratories had been able to manage. Similarly, inmates in a prison greenhouse discovered that smoke-infused water provides nutrients that increase germination rates in several declining prairie plants. Prairie ecosystems are often fire-dependent.
Rates of recidivism and violence have dropped while knowledge and conservation have advanced. There is an immense supply of such projects that could involve not just prisoners, but homeless or unemployed individuals, giving them new skills and a new sense of purpose. Behind the tiresome barrage of negativity and obstructionism poisoning the airwaves there are solutions large and small to many challenges. Conservation organizations should take note.

Aug 6, 2012

connecting the rails

Several recent sightings in Costa Rica have firmed up the likelihood that clapper rails are residents in mangrove swamps along the Pacific coast. First documented in 1998, the birds are now being seen often enough to make residency likely, as opposed to clapper rails being transients or stray birds. The country's ornithological union has just added the rail to its list of residents.

It is always good to add new territory for birds that have lost as much habitat as rails, prime victims of our centuries-old tendency to drain or fill wetlands. The clapper rail's preference for saltwater has shielded it from development compared to smaller cousins like Virginia rail and yellow rail, who use what is left of eastern, interior marshes as breeding grounds. Still, the clapper rail is not immune. Gulf coast mangroves and Atlantic coast salt marshes have all shrunk as we have encroached. The San Francisco Bay population of clapper rail is considered endangered because so little of its habitat remains.

Clapper rails are found throughout the Americas, and there are multiple described subspecies that vary in size and coloration. With so little known about them, it is unclear which subspecies the Costa Rican rails might be.

When you get right down to it, we do not know enough about rails to say for sure whether what we call Rallus longirostris is one species or two or more. We are not sure how much they wander for food or mates or how likely they are to fly inland to cross from one coast to another.

Costa Rican birds could be part of a Baja population or part of an Ecuadoran population, or Gulf coast birds that crossed the Central American isthmus to establish a population on the Pacific coast. Connecting Costa Rica with the Baja population is tempting, but Costa Rican birds have little red in their breast feathers. Baja birds have the reddest breasts of any clapper rail variant.

Costa Rica is an intriguing new dot in an empty area of the clapper rail range map.

Mar 12, 2012

on coal

To understand the coal industry, you must understand a bit of history. Part of that history goes back millions of years to the time when the Mississippi River Basin was an inland sea bordered by vast swamps. Those swamp beds compacted and petrified into layers of coal, some thick, some thin. As the North American plate lifted above sea level, much of this coal eroded away.
In Tennessee, coal seams tend to be thin, often too thin to be practically nor economically worth extracting. Only 22 of Tennessee's 95 counties have coal deposits, and only six counties have active mines. Most coal production in the state happens in Claiborne and Campbell counties. Coal played an important role in the history of Chattanooga and Sequatchie Valley, fueling iron production, but no active mines remain in that region. Seams were just a couple feet thick, so miners had to dig in a prone position. Work was slow and dangerous, and mines were abandoned as soon as it was feasible to bring in coal by rail.
Presently, Tennessee accounts for just one percent of Central Appalachian coal production, and virtually all Tennessee coal is consumed out of state. Our coal is high in sulfur, giving it an emissions profile that electricity generators shy away from, so it remains a specialty fuel used primarily in making steel or in other industrial processes requiring high temperatures. Tennessee imports 30 million tons of coal per year and produces 2 million tons.
In 2008, coal mining employed 558 workers, with demand and production on a steep decline. Surface mining accounts for 66 percent of production and 54 percent of jobs. Mountaintop removal mining offers the fewest jobs of any extraction method, relying more on explosives and heavy machinery than laborers. Since 1985, four out of five Tennessee coal-industry jobs have gone away due to the low quality and inaccessibility of remaining coal deposits.
Short of slavery, few industries have a more profound history of worker exploitation than coal. In West Virginia and Kentucky, there is an inverse relationship between the amount of coal in a county and the rate of poverty. Mining jobs carry high risks of fatality, injury and respiratory illness, and salaries simply do not match the health and social costs. Furthermore, mines often contaminate streams and land, making farming more difficult. The net result is tremendous wealth for mine owners, with little opportunity for workers to claim a fair share.
The industry created and sustained this wealth gap through political influence. The laws in big coal-mining states make it easy for mine operators to walk away from tragedy and pollution by using shell companies, and where the law itself has not been rigged, coal titans have simply paid off judges. The conglomerates that sit above the maze of shell companies and contractors are insulated from the risks and long-term costs of coal extraction.
Costs borne by taxpayers include repair of haul roads, monitoring of active and abandoned mines, reclamation and control of persistent pollution sources, water treatment or replacement where drinking supplies have been contaminated and diminished recreational, aesthetic and agricultural value of land. Much as with wages and poverty in coal communities, government expenses exceed revenues collected from the coal industry.
In Tennessee, coal companies have gotten themselves exempted from most sales taxes, to the point where the industry paid only $1.1 million in taxes on $114 million production in 2008. Severance taxes, kept by local governments, are 20 cents per ton, with the average price of coal in 2008 being $45 per ton. In 2009, the state legislature raised the severance tax to one dollar per ton, but delayed the increase until 2013.
While coal supplies were critical to manufacturing a century ago, coal mining now plays a vanishingly small role in the Tennessee economy. Moving into the future, coal will mainly be known by the legacy of pollution and destruction it has left behind. Nonetheless, the industry remains significant in other states, and Tennessee is an important political battleground. The industry lobbies heavily in Tennessee and gives generously to campaigns so they can fend off changes here that other states could imitate. Analysis by NewsChannel5 in Nashville showed that Lt. Gov. Ron Ramsey's 2010 gubernatorial campaign took $195,000 from coal interests. That is $20,000 more than the industry paid to the top coal-producing county in severance taxes.
This evening in Nashville, we will see whether this declining industry's political giving pays off. The state Senate is considering the Scenic Vistas Protection Act, which as originally written would end mining that alters any ridgeline over 2,000 feet elevation. Already the industry has interfered by convincing Cleveland Senator Mike Bell to entirely rewrite the bill so it is redundant with federal guidelines already enforced in the state. Still, this got the bill out of committee and onto the Senate floor, where it could be restored to original form or otherwise amended.
A Knoxville-based coalition of churches has been pushing to end mountaintop removal mining since 2009. Part of the Creation Care movement, Tennessee LEAF views mountains as God's handiwork and the scriptural appointment of man as stewards of Creation as a command to protect those mountains from destruction. To promote their bill, LEAF sponsored 40 Days of Prayer for the Mountains in December and January.
That effort must have had an impact on Pastor Michael McLaughlin of First Presbyterian in Manchester who, despite being unaffiliated with LEAF, concluded his March 1 invocation to the General Assembly with these words:

"Lord, for the sake of Tennessee’s health, economic prosperity, our environment, and our communities, keep in all our hearts and minds the truth that Tennessee is better than blowing the tops off of our mountains. Grant that we may continue to grow in our grateful enjoyment of your abundant creation, to the honor and glory of your name, now and forever through your Son, Jesus Christ our Lord. Amen"

Feb 16, 2012

porcine foam

Once someone asked me what the next form of life to evolve would be. I said a bacteria that can live in landfills and feed on plastic. I was close.

Midwestern pig farms have begun to explode. Mysterious foams have started forming atop waste pits, and with poor ventilation, gases can accumulate. In several barns these gases have ignited, killing thousands of pigs and injuring farm workers.

Hog farms have always been bacterial breeding grounds. It is not pig shit that stinks so much as the bacteria breaking it down. The stench of a pig operation is proportional to the vigor of its microfauna, but a bacteria that farts foam may be new to the mix. The foam might be evolution in action.

Foams were first observed in 2009 and have formed in many hog barns, but only a few have exploded. Experts in agricultural gas production at the University of Minnesota have been studying the foam, and they believe it may be associated with distillery offal. Spent grains are mostly cellulose, depleted of nutritional worth, but some anaerobic strains of bacteria can break it down. Hosting such bacteria in their guts is what gives ungulates the ability to survive on a grass diet, and dinosaurs surely used the same trick.

A new anaerobic species of cellular life may have evolved in industrial hog waste, or an existing species of gut bacteria could be exploiting new opportunities in the outside world. Either way, some cellular critter in hog shit is generating copious quantities of gas, enough to create up to 4 feet of gray foam on the surface of hog slurry. Experts recommend knocking down the foam with water, but dry manure generates less odor. Controlling runoff is a major expense for farms, so they prefer to use less water, not more. Water is also a temporary solution, and outbreaks or rising temperatures can catch operators off guard, resulting in explosions.

Manure scientists are hard at work on the mystery foam. You may think I'm being facetious, but manure science really exists. Industrial hog and chicken farms require waste processing systems, pollution permits, and sophisticated emissions management. Hog farms have neighbors and odors that carry miles downwind.

Jacek Koziel at Iowa State use chemical methods and his own nose to measure and identify "compounds in the swine manure headspace." Advanced techniques allowed Dr. Koziel and his team to identify 295 airborne compounds in a 2010 study, 71 considered odorous and 16 regulated pollutants. They were able to expand the library of known swine manure gases by 44 molecules, but no one has yet determined the culprit behind the foam. Methane likely powers the explosions, but the filmy substance trapping the methane appears to be new.

Quoted in campus newspaper the Minnesota Daily, professor Charles J. Clanton said, "you have two identical buildings sitting next to each other with same management, genetics, diets, etc. One foams, and the other does not." That suggests differences in microfauna and the possibility that a new species of bacteria has evolved but is still spreading from barn to barn and farm to farm.

Dec 19, 2011

hooded crane hubbub

Birdwatchers at the crane refuge on the Hiwassee River spotted a black crane with a white head among thousands of grey sandhill cranes December 13. Soon it was identified as a hooded crane, an Asian species rarely found in North America. In fact, the Tennessee sighting is only the third known occurrence in the U.S. The second was this spring in Nebraska, and the first the prior spring in Idaho (the bird in the photo).

Hooded cranes have escaped from captivity in the U.S., including a 2006 escape from an Idaho aviary. Three hooded cranes escaped in 2001, also in Idaho. Cranes can live long lives, spanning several decades. If one or more escapee survived, it is likely trying to find a flock and a mate among sandhill cranes it encounters, but it may be having trouble on one or both counts due to its appearance. This could account for the pattern of sightings.

North America has three crane flyways, an eastern route between Florida wintering grounds and breeding grounds near the Great Lakes, a Great Plains route between Texas and the northern plains and tundra, and west-of-the-Rockies flyway between Mexican wintering grounds and northern Alaska. If the Idaho, Nebraska and Tennessee sightings are the same bird, it has switched from the western to central to eastern flyway in the span of four migrations.

In winter, cranes are opportunistic, nomadic, and travel in flocks. On their breeding grounds, they break into pairs or small family groups, and individual birds return to the same nesting area year after year. Unless a crane has no family and no mate, it will be geographically loyal. Unmated birds are subjected to harassment, especially on breeding territory, and an unmated bird that looks different likely gets double trouble. This social pressure could explain how one bird could show up on three migratory routes in close succession.

It does not explain whether the hooded crane originally strayed from a Siberian flock on its own or with human assistance. An initial sighting in Idaho would be expected either way. The retreat of Arctic ice in recent summers has created more opportunities for Siberian flocks to come in contact with Yukon flocks. The wings of a captive bird would be clipped, so it would struggle to fly and keep up with other cranes until molting in a new set of feathers. It should also have leg bands, and the observed bird does not.

Is it the same bird? Is it a wild bird? No one knows for sure.

Nov 30, 2011

watching a fritillary evolve

The most abundant butterfly on Caribbean islands is likely the gulf fritillary. Its wings from above are rich orange with black spots, from below a dirty orange mottled with white spots that glimmer silver in sunlight. Medium-sized, these butterflies reproduce all year long on Caribbean islands and along the gulf coast. Each year they spread northward as spring warms into summer, each generation expanding their range, but the gulf fritillary can not survive a hard freeze in any form, egg, caterpillar, pupa or adult. When winter comes, the species range collapses back to its coastal core.

Most years, gulf fritillaries make an appearance in East Tennessee, and they may hatch a generation or two before winter sets in. This year they did well. I witnessed at least three generations, including an adult that hatched in November in my kitchen from a chrysalis on a plant brought in from the porch a few days prior. I don't know whether it would have emerged had it remained outside. I don't know whether it headed south after I released it, whether a bird gobbled it up before it got anywhere or what, but the day after it hatched, in good flying weather I set it free.

In early November, I saw a pair mating. The female surely had trouble finding a passionflower vine to lay eggs on, and her offspring likely starved or froze if they even hatched. They were this year's doomed generation of gulf fritillary.

These November butterflies were the last of 2011, but they were not the first. The fritillary that emerged in my kitchen was born in late August, part of a hatching that reduced a prolific, porchrail passionflower to bare vines as September progressed. At the height of the feast, black-spined, red caterpillars in all stages of growth covered the plant. The biggest eaters hatched in late September. Most faced a dwindling supply of leaves and cold nights, pupating later in the year if at all. Though at best a quarter of the caterpillars survived to form a chrysalis, we still ended up with a good dozen pupa hanging under the eave above the porch.

The first generation to reach Tennessee in 2011 arrived as July turned to August. They hatched a generation of fritillaries that fatted themselves on Tennessee leaves before laying eggs of their own. If the first generation's grandchildren had the good sense to fly south, their genes may have blended back into the core population in and around the Gulf of Mexico.

Is the gulf fritillary evolving an overwintering strategy? Is their range expanding due to climate change? Was their success in Tennessee this year merely stochastic? Yes to all three. Any traits that favor range expansion are likely to perpetuate and rise toward dominance, and stochasticity is always present because it is entropy. A yearly excursion northward is an overwintering strategy, even if a clumsy one. The gulf fritillary is evolving right before our eyes.

Aug 18, 2011

not a bird no more

A trove of fossils in China from around the time birds were evolving continues to yield insights into how feathers and flight evolved. Science still does not have a good story for the evolution of birds, but the cast of characters has gotten bigger. With so many new clues, Archaeopteryx has now been dethroned as 'oldest bird'. Birds came off the dinosaur family tree near Archaeopteryx, but not from its branch.

Recently National Geographic ran an article on feathers that summarizes much of the known fossil record, how it relates to the chain of ancestry and what it tells us about the evolution of flight.

At the time of Archaeopteryx, numerous dinosaur species had feathers or protofeathers, and evolutionary pressure was diversifying and selecting feather traits. Many animals clearly unable to fly possessed feathers, so they did not originate to enhance flight. Flight originated once feathers already existed.

The better story emerging from the fossils is this: flight evolved from swimming and diving. In their squabbles over whether birds flew from the ground up or down from the trees, scientists neglected this third option. Dinosaurs started entering water for prey, gradually evolving specialized scales with thermal properties and spending more time in the water. Their aquatic habits eventually included true swimming, which lead to the gradual evolution of larger and more powerful muscles and aerodynamic feathers. Swimming set the stage for aerial flight.

The origin of flight in birds is the story of the evolution of the breastplate to which a bird's wing muscles attach. This bone shows specializations seen only in birds, and flight muscles attach in a way that is essentially an inversion of forelimb musculature as it appears in every other four-limbed vertebrate including humans. We know that flying reptiles like Pterodactyls are unrelated to birds because they lacked an inverted musculature and large breastplate.

Birds have a muscle configuration all their own, and the wishbone is part of their unique skeleton. It is found only in birds and in dinosaurs like Archaeopteryx, Sapeornis and few others. While those fossils have wishbones, they lack large muscle-attachment sites on the breastbone and show no indication of significant strength in their forelimbs. So inverted musculature evolved prior to the origin of birds. It is not an adapatation to flight but a precursor.

Aerial flight requires strength, even just to glide. The power demand makes transitions from terrestrial to aerial locomotion unlikely, and the major retooling of the breastplate in birds is the sort of change that happens gradually, on geological time scales rather than generational scales. It is simply not reasonable to expect the evolution of flight to be as simple as the tales science has been exploring.

To understand the origin of flight, we need to think of a process taking many steps and millions of years, and the story should take place in water. Water is far more buoyant than air, so flying in water requires less power. We call that swimming. Gliding in water we call diving. An aquatic origin provides the time and opportunity for big changes in power and musculature. Diving lizards become swimming lizards, and shorelines become open waters. Eventually a master swimmer makes transition to aerial flight.

The oldest fossils that possess a bird's breastplate are the Hesperornithes, which resemble diving birds like loons. There are numerous marine varieties of birds, including albatrosses, ducks, gulls, pelicans and sandpipers, and they are deeply rooted in bird phylogeny. Terrestrial and forest birds arose later in avian history: fowl, hawks, songbirds, woodpeckers, these are younger varieties of bird.

Science has overlooked an aquatic phase in bird evolution, but it is staring us right in the face.

Jun 12, 2011

blackberry season

Right about now, your tomato vines need you to pick their first fruit so they will grow a dozen more. It is tempting to wait for the first red fruit, but foolish. A green tomato harvest is a must for a bountiful year. Do not succumb to red's seduction.

Instead, harvest a handful or two of the ripest blackberries you can find, toss them in oil with a chopped onion or leek, salt and a dose of dry spices. Cook to submission, then toss a layer of basil and other fresh herbs onto the pile and smother with green tomato chunks. Cook it down to a sauce. When the blackberry seeds are cooked, your sauce is done. They like it if you share your wine.

Serve the resulting sauce over pasta, fish, rice, tofu, tempeh, vegetables or meat, which you can toss into the pan if the sauce refuses to thicken. Happy green tomato season!

Jun 2, 2011

nest update

This morning the blue-headed vireos were vigorously defending their territory from a blue jay. Though it was much higher up in the trees than their nest, the pair was scolding and dive-bombing the jay, hoping to drive it off.

Unfortunately they may be protecting a young cowbird. The noise overhead roused a hungry nestling, just one, its eyes still closed. It seems too large already. Cowbird nestlings eject their nestmates, so seeing just one head is a bad sign. I checked the ground beneath the nest for evidence and found nothing, but such a morsel probably would have been found by a possum or raccoon on its nightly prowl. I fear my guests may be raising a chick that is not their own.

May 31, 2011

science for the fishies

If you've read anything about commercial fishing in the past decade or two, you know that industrial fishing practices range from irresponsible to appalling. The worst practices cause major seafloor destruction and grotesque slaughter of "by-catch," marine life ranging from rough fish to sea turtles. Over the past century, countless fisheries have collapsed under the strain of unsustainable harvest, leaving regional economies in ruins while the global industry trudges blithely to its next victim.

The anonymous fish flesh that you buy frozen and breaded in the supermarket or fast-food restaurant is the product of a shadowy industry where breaches of treaties, boundaries and quotas are routine. Even when a seller makes promises about the origin of a fish, their claims are unreliable and unverifiable, until now.

The Economist reports that a European consortium has developed a DNA-sampling procedure that can ascertain not only which species of fish a fillet came from, but which ocean and population. Right now the technology only covers four major commercial species: cod, hake, herring and sole, but its scope will expand.

The device is not intended for consumers at the end of the supply chain, but for those who buy in quantity. As a consumer, you can help by being curious about fish you buy and responsive to labeling or the lack thereof. This new technology is a welcome development that should bring some honesty to a market that has thrived on obscuring links between products and the sometimes horrendous practices used in harvest.

May 22, 2011

new yard nester

Red-eyed vireos nest in my yard every year. They are wonderful birds and welcome guests, but this year a different vireo seemed to be settling in the yard. I had heard it singing for a week, longer than migrants stick around, but I still did not tell anyone for fear of jinxing it. I thought a blue-headed vireo might be taking up residence!

Both species are common in the eastern U.S., but red-eyed vireos are more widely distributed. Blue-headed vireos prefer higher elevations and deeper forests. When I first came to the South, it was to study neotropical migrants in Nantahala National Forest, and blue-headed vireos were abundant in that rare place.

Aside from reminding me of a special time and place, they are charming in their own right. They used to be called solitary vireos, a terrible misnomer since they almost always occur in pairs, chattering at each other like an old married couple. The only reason I can imagine for their former name is the melancholy tone of their song. That same endearing expressiveness comes through in all their vocalizations.

Also, they look like they are wearing spectacles.

Today I saw their nest just a few yards from my front porch in the lowest limb of a white oak.