Crumb Trail
     an impermanent travelogue
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Tuesday, January 31, 2006

Why do you think that?

Most bioweapons research has focused on traditional biological agents, such as anthrax and smallpox. But that focus is dangerously narrow, the report says; emerging technologies in biotechnology and the life sciences could be hijacked to take control of genes, immune systems, and even brains. . .

Scientists who drafted the report were also particularly concerned about the potential of bioregulators -- small, biologically active organic compounds that can regulate different systems in the body. Newer technologies such as targeted delivery methods that zero in on the immune or neuroendocrine systems could make it easier to use bioregulators in insidious ways.

Terrorists could also co-opt relatively new technologies, such as synthetic biology, which aims to build organisms that can detect or produce chemicals or perform other functions; and RNA interference, a technique that allows scientists to easily control gene expression.

Terrorists are a drag and all, but they aren't the most likely users and abusers of these technologies. Governments top that list, since politicians already use every trick they can to delude voters, government institutions seek to control society, governments seek to control one another, and there is no shortage of rule-the-world nutters pointing to one doomsday scenario or another to justify draconian acts to save us from ourselves with tight global governance.

Business and entertainment will find the technologies tempting too. Kids will be prime targets from not just marketing attacks but also their parents and teachers. Everybody thinks they have a right and a duty to manipulate kids.

In a sense we have always had this threat from cults and ideologies. The 60s did happen after all. But it seems poised to accelerate. This is an old SF trope. You might find some of the novels interesting if this is a new concept for you.

Monday, January 30, 2006

Prometheus notes that the IPCC has a fully functional cognitive kaleidoscope.

. . . the following passage from Dr. Pachauri’s chapter provides a telling indication of how a narrow focus on human-GHG-caused climate change tends to warp the thinking of otherwise smart people about issues that involve much more than just human caused climate change:
In Mauritius, a couple of weeks ago, there was the major UN conference involving the small island developing states. In discussions with several people there, I heard an expression of fear based on the question: suppose a tsunami such as that of December 26 were to take place in 2080 and suppose the sea level was a foot higher, can you estimate what the extent of damage would be under those circumstances? Hence, I think when we talk about dangerous it is not merely dangers that are posed by climate change per se, but the overlay of climate change impacts on the possibility of natural disasters that could take place in any event.
So by 2080 society is going to experience changes probably far greater than from 1930 to 2005 and he is talking about the difference in impacts between a 25 foot and 26 foot wall of water? In this case, he probably would have been on solid ground by saying that patterns of coastal development over the next 75 years are far, far more important than an extra 12 inches of sea level rise, rather than trying to link climate change to tsunami impacts. But as we've argued ad repeatium here, this is the kind of thinking that necessarily results from Article 2 of the FCCC.
"A narrow focus . . . tends to warp the thinking of otherwise smart people". Perhaps it isn't only a narrow focus, it is also ideological blindness and confirmation bias too. They twirl the cognitive kaleidoscope until any bit of information can be made to fit into their preconception of how things are supposed to look.

This isn't just an intellectual or aesthetic failing, however human, it is also a character defect since the impulse is given free reign and exploited for political purposes, to the detriment of society.

Sunday, January 29, 2006


There is a lot of good advice to help us avoid becoming obese, such as "Eat less," and "Exercise." But here's a new and surprising piece of advice based on a promising area of obesity research: "Wash your hands."

There is accumulating evidence that certain viruses may cause obesity, in essence making obesity contagious . . .

The study, by Whigham, Barbara A. Israel and Richard L. Atkinson, of the University of Wisconsin, Madison, found that the human adenovirus Ad-37 causes obesity in chickens. This finding builds on studies that two related viruses, Ad-36 and Ad-5, also cause obesity in animals.

Moreover, Ad-36 has been associated with human obesity, leading researchers to suspect that Ad-37 also may be implicated in human obesity. Whigham said more research is needed to find out if Ad-37 causes obesity in humans. One study was inconclusive, because only a handful of people showed evidence of infection with Ad-37 ? not enough people to draw any conclusions, she said. Ad-37, Ad-36 and Ad-5 are part of a family of approximately 50 viruses known as human adenoviruses. . .

The notion that viruses can cause obesity has been a contentious one among scientists, Whigham said. And yet, there is evidence that factors other than poor diet or lack of exercise may be at work in the obesity epidemic. "The prevalence of obesity has doubled in adults in the United States in the last 30 years and has tripled in children," the study noted. "With the exception of infectious diseases, no other chronic disease in history has spread so rapidly, and the etiological factors producing this epidemic have not been clearly identified."

"It makes people feel more comfortable to think that obesity stems from lack of control," Whigham said. "It's a big mental leap to think you can catch obesity." However, other diseases once thought to be the product of environmental factors are now known to stem from infectious agents. For example, ulcers were once thought to be the result of stress, but researchers eventually implicated bacteria, H. pylori, as a cause.

"The nearly simultaneous increase in the prevalence of obesity in most countries of the world is difficult to explain by changes in food intake and exercise alone, and suggest that adenoviruses could have contributed," the study said. . .

There is still much to learn about how these viruses work, Whigham said. "There are people and animals that get infected and don't get fat. We don't know why," she said. Among the possibilities: the virus hasn't been in the body long enough to produce the additional fat; or the virus creates a tendency to obesity that must be triggered by overeating, she said.

Obesity may be "triggered by overeating". I suspect this is true.

Wednesday, January 25, 2006

And someone is home.

[L]ittle is known about the comparative performance of inhabited and uninhabited reserves in slowing the most extreme form of forest disturbance: conversion to agriculture. In a paper recently published in Conservation Biology (2006, Vol 20, pages 65-73), an international team of scientists, led by Daniel Nepstad of the Woods Hole Research Center and the Instituto de Pesquisa Ambiental da Amazonia, use satellite data to demonstrate, for the first time, that rainforest parks and indigenous territories halt deforestation and forest fires.

According to Nepstad, "Protecting indigenous and traditional peoples' lands and natural areas in the Amazon works to stop deforestation. The idea that many parks in the tropics only exist 'on paper' must be re-examined as must the notion that indigenous reserves are less effective than parks in protecting nature." . . .

The group used satellite-based maps of land cover and fire occurrence between 1997 and 2000 to compare parks and indigenous lands. Deforestation was 1.7 to 20 times higher along the outside versus the inside perimeter of reserves, while fires were 4 to 9 times higher. Indigenous lands clearly stopped clearing in high-deforestation frontier regions: 33 of 38 indigenous territories with annual deforestation greater than 1.5 percent outside their borders had inner deforestation rates of 0.75 percent or less. Few parks are located in active frontier areas (4 of 15 in the sample) than indigenous lands (33 of 38). But parks' and indigenous lands' ability to inhibit deforestation appear similar.

Indigenous lands occupy one-fifth of the Brazilian Amazon - five times the area under protection in parks ? and are currently the most important barrier to Amazon deforestation. Some conservationists argue that with acculturation to market society, indigenous peoples will cease to protect forests. But the authors found that virtually all indigenous lands substantially inhibit deforestation up to 400 years after contact with the national society. There was no correlation between population density in indigenous areas and inhibition of deforestation. In much of the Amazon, not only can protecting nature be reconciled with human habitation - it wouldn't happen without the people.

My emphasis. I think it's an important point, one that has implications for developed countries too. There is no better defense for resources than ownership and occupation, property rights if you insist, since those who depend on those resources for life and livelihood are motivated and ever vigilant.


Mental exercise. It's not just for kids.

Research from the University of New South Wales (UNSW) provides the most convincing evidence to date that complex mental activity across people's lives significantly reduces the risk of dementia. The researchers found that such activity almost halves the incidence of dementia. . .

"Until now there have been mixed messages about the role of education, occupation, IQ and mentally stimulating leisure activities, in preventing cognitive decline. Now the results are much clearer," said the lead author, Dr Michael Valenzuela, from the School of Psychiatry at UNSW. "It is a case of 'use it or lose it'. If you increase your brain reserve over your lifetime, you lessen the risk of Alzheimer's and other neurodegenerative diseases."

The key conclusion is that individuals with high brain reserve have a 46 percent decreased risk of dementia, compared to those with low brain reserve. All the studies assessed agreed that mentally stimulating leisure activities, even in late life, are associated with a protective effect.

We all need stimulating environments.

Tuesday, January 24, 2006

Politics is stupid.

The investigators used functional neuroimaging (fMRI) to study a sample of committed Democrats and Republicans during the three months prior to the U.S. Presidential election of 2004. The Democrats and Republicans were given a reasoning task in which they had to evaluate threatening information about their own candidate. During the task, the subjects underwent fMRI to see what parts of their brain were active. What the researchers found was striking.

"We did not see any increased activation of the parts of the brain normally engaged during reasoning," says Drew Westen, director of clinical psychology at Emory who led the study. "What we saw instead was a network of emotion circuits lighting up, including circuits hypothesized to be involved in regulating emotion, and circuits known to be involved in resolving conflicts." Westen and his colleagues will present their findings at the Annual Conference of the Society for Personality and Social Psychology Jan. 28.

Once partisans had come to completely biased conclusions -- essentially finding ways to ignore information that could not be rationally discounted -- not only did circuits that mediate negative emotions like sadness and disgust turn off, but subjects got a blast of activation in circuits involved in reward -- similar to what addicts receive when they get their fix, Westen explains.

"None of the circuits involved in conscious reasoning were particularly engaged," says Westen. "Essentially, it appears as if partisans twirl the cognitive kaleidoscope until they get the conclusions they want, and then they get massively reinforced for it, with the elimination of negative emotional states and activation of positive ones."

"Twirl the cognitive kaleidoscope".

Thursday, January 19, 2006

. . . that's very unusual, but it may be less so in near future.

By using a laser foot scanner to create a 3D computer model of a person’s feet, the ERGOSHOE system bridges the design gap between shoe manufacturers and customers, allowing shoe comfort to be improved efficiently and at relatively low cost in the mass market, and in niche markets such as healthcare and worker footwear. . .

“Traditional shoe manufacturing business models are not designed for personalised treatment but rather mass production,” notes ERGOSHOE coordinator Enrique Montiel at INESCOP in Spain. “With our system to create digital foot models, we have made personalised treatment more feasible.”

In the mass market, the system would primarily help manufacturers better adapt their designs to their customers at large while vendors could use the scanner and 3D model analysis to direct customers to shoes that best fit their feet. It would also allow customised shoes to be produced for individual clients, which Montiel estimates would only cost around 10 to 20 per cent more than a mass produced pair. The hardware and software costs between 6,000 and 15,000 euros to implement.

I wear out several pairs of boots a year in my field work. I'm amazed that I still have feet after all the miles I've put on them, especially since boots never actually fit, you just break them in - a process that uses my poor feet to subtly reshape the boot. If these were available I'd buy several pair at once and hopefully get a volume discount. I often get two pair at a time since two pairs wear like three when you alternate them, allowing more time for the boots to properly rest and dry out.


There's a lot of confusion about fertilizer.

Then, in 1909, German physical chemist Fritz Haber developed a high-temperature, high-pressure process to fix atmospheric nitrogen in his lab. Another German chemist, Carl Bosch, soon expanded Haber's process to a factory scale. Known as the Haber-Bosch process, industrial fixation of nitrogen combines atmospheric nitrogen and hydrogen into ammonia, the basis for all synthetic nitrogen fertilizers. Natural gas is most often the source of the hydrogen.

Imagine the power now vested in humankind. With the ability to fix our own nitrogen we could free ourselves from dependence upon lightning and microbial masses and ramp up agricultural productivity to feed a hungry world. Perhaps the human species could yet outwit the Malthusian math that predicted that population growth would always outstrip our ability to increase food production. Indeed, so marvelous was this alchemy that both Haber and Bosch were awarded the Nobel Prize for chemistry.

Human kind had already outwitted Malthusian math before Malthus did his work, but Malthus was unaware of it. Huge deposits of sea bird and bat dung were mined and shipped around the world, and huge deposits of Chilean nitrate, a.k.a saltpeter, were used for everything from fertilizer to gunpowder.

It may help to remember that natural gas is methane, plus a few contaminants, and that methane is not just a fossil fuel, it is continuously produced.

Imagine now, just a little less than 100 years later and as world hunger continues to rise, asking farmers to stop using industrially fixed nitrogen. It's a wonder that the organic movement ever got off the ground.

The National Organics Program, which regulates the use of the organic label in the United States, prohibits the use of synthetic substances unless their use is specifically allowed via exemption, an exemption not granted for synthetic nitrogen fertilizer.

The reasons why are of such import that they alone should set off a stampede to the nearest organic farmer's market.

Reason No. 1 is that synthetic nitrogen fertilizers are not sustainable. Building an agricultural system based upon industrially fixed nitrogen makes our ability to feed ourselves dependent upon a non-renewable fossil fuel and upon the wisdom, benevolence and cooperation of heads of state and multinational petroleum companies.

No, it doesn't. Every farmer can make his own methane and could have home made nitrogen fertilizer if he also had a solar powered Haber-Bosch type system. That fertilizer is currently made from fossil methane as a centralized industrial practice is due to economics and habit. Both can change.
Synthetic nitrogen fertilizers also fail to pass muster because of the environmental damage done when we pump enormous quantities of nitrates into the natural atmospheric and biological cycling of nitrogen. Overuse of nitrogen fertilizers are a primary cause of "dead zones" in coastal waters because nitrates are highly soluble; any nitrates not taken up by plant roots move quickly down through the root zone and enter ground water. When nitrate-laden rivers enter bays and estuaries, the excess nitrogen can cause larger than normal algae blooms.
This is a symptom of agronomic practice, one that is rapidly being resolved. Nitrogen is expensive and farmers can't afford to waste it. Applying nitrogen fertilizer to fields is expensive too. It usually takes labor and machinery though there are "fertigation" systems that mix fertilizer with irrigation water. The trade off is nitrogen loss before uptake by plants vs. extra costs to apply it in small quantities as plants need it. When many small applications are made there is no leeching from the field.
Nitrates may create a dead zone of sorts on the land as well.
Well, so does water when there is too much for too long. This is a nonsense claim made for instrumental reasons. When nitrogen is applied properly there are no dead zones, it's the exact opposite, everything flourishes.
Finally, nitrogen oxides also contribute to acid rain, reacting with water in the atmosphere to form acidic compounds. When the compounds rain on or wash into lakes and rivers, they jeopardize fish, plant and bacteria populations that are sensitive to changes in water pH. As it percolates through the soil, acid rain leaches nutrients such as calcium, magnesium and potassium out of the root zone and mobilizes aluminum, which inhibits root growth.
Most things you do to soil make acids. Plants themselves make acid as they take up cations such as calcium through their roots and exude anions (acidic) to maintain internal electroneutrality. Sometimes all of this is wonderful, such as on farms with calcareous soils that need acids to become more neutral, and sometimes the soil is neutral or acidic naturally, such as with granitic soils weathered from rock, so farmers add lime, calcium carbonate from limestone, to both lower acidity and provide calcium to plants.

Organic agriculture is based on ignorance, and that's a shame because an informed agriculture that avoids truly dangerous chemicals and cultivation techniques that degrade land is not that difficult or expensive. With population expected to reach half again as many people as there are today we don't have enough land to humor quasi-religious superstitions about agriculture. If some of the energies and resources being squandered on organic systems were spent instead to develop solar powered farm scale fertilizer production systems then something closer to a closed system could be used. Crops wastes and dung could be turned into methane and compost in bioreactors by anaerobic bacteria, and the methane could be turned into nitrogen fertilizer by the heat of the sun in solar furnaces that can produce the heat and pressure needed for the Haber process.

Still, it may be cheaper to have centralized facilities with larger solar furnaces so long as the methane is available. The problem is transporting the feedstocks, the organic materials, to a central site. Feedlots, mills and urban waste disposal sites are natural candidates since they already have lots of organics available to decompose into methane. Farm scale systems might be limited to just making methane to power machinery, and generate heat and electricity. And compost, of course.


You can run but . . .

Antibiotic resistance has become an increasing public health concern because the organisms that cause infections in humans and animals are becoming less receptive to the healing aspect of antibiotic drugs. . .

Approximately two-thirds of all known antibiotics are produced by bacteria called actinomycetes, commonly found in soils, compost, and other environmental sources.

"By evolving in an environment of antibiotic production, incredibly resilient bacteria must develop diverse ways to survive or resist the toxic antimicrobial compounds produced by their neighbors," said Wright. "Their coping tactics may be able to give us a glimpse into the future of clinical resistance to antibiotics." . .

Researchers screened 480 strains of soil bacteria isolated from diverse locations for resistance to 21 clinically relevant antibiotics. At high drug concentrations, the soil-dwelling bacteria displayed a stunning level of resistance. Not only were the bacteria resistant to an average of seven to eight antibiotics, but every strain was found to be multi-drug resistant.

The bacteria showed resistance to all major classes of antibiotics, regardless of whether the compounds were naturally produced, semi-synthetic, or completely synthetic.

Researchers also found that the way bacteria was resistant to vancomycin, one of the most commonly prescribed antibiotics for drug resistant staphylococcal infections, was identical to resistance found in clinics.

Furthermore, the researchers' uncovered bacteria that produced enzymes capable of breaking down or modifying or rendering inactive two recently U.S. FDA-approved antibiotics, a situation which has yet to emerge clinically for these drugs.

"The link between clinical and soil-associated resistance to vancomycin illustrates the value of studying resistance in the soil to rationally anticipate future clinical resistance," said Wright. "It suggests that the soil serves as an under-recognized source of resistance, resistance that has the potential to reach clinics.

"This work could prove to be extremely valuable to the drug development process, complementing traditional laboratory studies of clinical situations. By screening newly developed drugs for resistance in soil bacteria, not only can pharmaceutical companies can gain a better understanding of what may emerge in the future as clinical problems, but sufficient warning can be given to hospital microbiology laboratories, physicians and the drug discovery sector to allow for the development of diagnostic techniques and alternative therapies.

"Furthermore, studying enzymes that inactivate antibiotics can serve as a foundation for the development of new combination therapies for resistant bacterial strains. Studying antibiotic resistance from an evolutionary perspective is one way that researchers are attempting to stay one step ahead of resistant bacteria."

. . . you can't hide. It's interesting that soil bacteria seem even more antibiotic resistant than those infecting people, but it makes sense as they live in an environment where antibiotics are produced as part of the ancient struggle for survival, the weapons of choice.


One of the key issues in ag is growing locally adapted cultivars, those that grow well in local conditions with local agronomic practices. The timing of maturity - switching from vegetative growth to flowering and setting seed - is an important part of that. It needs to happen at the right time to match temperature and moisture conditions, and it needs to happen uniformly across the field in most cases to facilitate efficient harvest.

Local adaptation is primarily genetic. New capabilities for identifying desired genes speeds up the development of cultivars since new crosses can be evaluated without needing to grow them out. Researchers have found the "maturity gene" for barley.

Researchers funded by the Biotechnology and Biological Sciences Research Council (BBSRC) at the John Innes Centre in Norwich have identified the gene in barley that controls how the plant responds to seasonal changes in the length of the day. This is key to understanding how plants have adapted their flowering behaviour to different environments.

The John Innes Centre researchers have discovered that the Ppd-H1 gene in barley controls the timing of the activity of another gene called CO. When the length of the day is long enough CO activates one of the key genes that triggers flowering. Naturally occurring variation in Ppd-H1 affects the time of day when CO is activated. This shifts the time of year that the plant flowers.

The most interesting and useful consequence of deep knowledge about the genetics of crop plants is an improved ability to develop cultivars for different parts of the world that combine good yield, disease resistance and uniform development with maturity timing suited to localities. The developing world with its growing population and consequent need for increased production using fewer inputs and less land needs these cultivars. But that's not the spin we hear these days.
Dr David Laurie, the research leader at the John Innes Centre, said, "Growing crops will become more difficult as the global climate changes. The varieties of crops grown in the UK are suited to the soil, seasons and traditional cool, wet summers. Later flowering in barley means it has a longer growing period to amass yield. If British summers get hotter and drier we will need types of wheat, barley and other crops that flower earlier, like Mediterranean varieties, to beat summer droughts. However, new varieties will need to be adapted in all other ways to UK conditions. "

With the new knowledge about the workings of barley researchers and plant breeders will find it easier to select variations that will thrive in the UK environment but will also flower earlier, coping with hotter summers.

The climate change bogey seems to have dulled the social mind.

Sunday, January 15, 2006

The Alaska Volcano Observatory page tracking the recent activity of the Augustine volcano is fascinating. Observations are updated hourly and there is a webcam. Text includes current information, background and history, and informed guesses about the likelihood of an eruption. The "useful links" section includes everything from How to collect an ash sample for AVO to the tsunami warning center.

Saturday, January 14, 2006

No, not that Bush, the bush.

Animal-rights activists and many environmentalists are up in arms about the bushmeat business. As part of their propaganda war against the hunters, they send out gruesome images of gorilla corpses and monkeys strung from poles, illustrating literature on “the slaughter of the apes.” A particularly unsettling image caught by the anti-bushmeat campaigner Karl Ammann shows a fresh-cut gorilla head in a kitchen bowl on a sideboard next to a bunch of bananas. Such reports concentrate entirely on the burgeoning bushmeat business as a crisis for wildlife and Africa’s biodiversity. And there is no question that some of the world’s most endangered wild animals are, quite literally, being eaten to death.

But, asks Fa, is our Western squeamishness getting in the way of a sensible appraisal of the importance of bushmeat? Are we in danger of caring more about the survival of a few rare rain forest species than the survival of their hunters? If we condemn all hunting for bushmeat, then how do we propose that Africans eat? And equally, if we do not take the trouble to find out why bushmeat hunting is still so prevalent in Africa, how can we hope to stop it? . . .

Fa’s research has led him to come out against the conventional environmental response to the slaughter of wildlife—demands for bans on hunting and trade. He says that environmentalists are in danger of behaving like Marie Antoinette, who, on being told the French peasants had no bread, replied, “Let them eat cake.” Pork and chicken are no more available in Central African supermarkets than cake was in prerevolutionary Paris. Right now, the majority of poor Africans have no alternative to hunting and eating bushmeat. Many countries across the continent are going backward economically. They have deteriorating infrastructures, near-constant civil wars, and virtually no governments. Food production on farms in Central Africa has not risen since the 1960s, and in many areas it has fallen back sharply. Their economies are going “back to the bush.” How can their diets do other than follow? And of course, the one thing that the civil wars do provide them with is guns and other weapons with which to go hunting.

“We are understandably horrified by wild animals, especially primates, being killed for food,” Fa says. “But we must remember that bushmeat is a cheap source of protein for many malnourished people in Africa.” Until now, the bushmeat crisis has been portrayed as an animal-rights and environmental issue. But it is also a human rights issue. To solve it, he says, biologists must turn into social scientists. Rather than concentrating on the biology of the animals, Fa says, the outside world has to first understand the social and economic problems of the hunters. Only that way, he believes, can the animals of the African forests—and the people—be saved. And only by saving both can the forest be saved.

No fair. He's being a sensible and honest humanitarian. Clearly he doesn't understand what environmental activism is all about, especially the sort that goes on in developing countries.


. . . them Uzbek Kochia (pronounced KO-chuh).

K. prostrata is native to central Eurasian countries such as Russia, Kazakhstan, and Uzbekistan, where Waldron has journeyed on plant-collecting expeditions. He has brought back hundreds of superior specimens from these treks and is now testing them in greenhouse and outdoor experiments. . .

K. prostrata is a distant relative of an annual weed, K. scoparia, that can be poisonous to cattle and sheep. This annual kochia is popular with home gardeners who know it as “firebush” because of its red fall foliage. Fortunately, the annual weed and the promising perennial can’t interbreed, according to ARS plant geneticist Richard R.-C. Wang at Logan.

Understandably, forage kochia is sometimes confused with the garden ornamental. “This mix-up sometimes makes it hard to convince people that forage kochia is really a good-guy plant,” says Waldron.

But a good guy it certainly is. Forage kochia tolerates drought, flourishes on salty or alkaline soils that make life hard for many other plants, and survives with as little as 5 inches of rain or other precipitation a year. It also offers shelter and tasty seeds for upland songbirds and game birds such as sage grouse; helps control erosion; serves as a greenstrip or firebreak in fire-prone ecosystems; and seems to thrive on poor-quality sites that have been damaged by overgrazing, wildfire, or off-road vehicles. . .

“From these observations, we determined that forage kochia does not crowd out native perennials,” Waldron notes. “It thrives in elevations from 1,600 to 7,000 feet and can actually grow better on inhospitable sites, such as dry areas with gravelly soils, than many other rangeland plants.”

I suppose it makes sense that plants from the "stans" might fit well in the American west. It's interesting that this cross fertilization - so to speak - is happening now. I suppose it would have been awkward in the soviet days.


. . . them Kazak apples.

Forsline explains that central Asia—Kazakhstan and Kyrgyzstan in particular—is likely the ancestral home of familiar domestic apples (Malus x domestica) such as Red Delicious, Golden Delicious, and McIntosh.

“We tapped millions of years of adaptations to improve today’s apple,” he says.

Forsline went on seven of the trips, including four to central Asia, to collect apple material, conserve it, and, after evaluation, distribute it to breeders and geneticists worldwide. Other trips were to Sichuan, Russian, and Turkish sectors of the Caucasus region, and Germany. . .

He says the trips resulted in “at least a doubling of the known genetic diversity of apples. It turns out that this gene pool is much more diverse than we had originally thought. And what we’ve found may help make the trees stand up better to diseases.”

Among all this material, it is the Kazak samples that have become the apple of Forsline’s eye, so to speak. Especially noteworthy are accessions collected there of M. sieversii, an important forerunner of the domestic apple. (See Forum in this issue of the magazine.) . .

“Silk Road traders and their predecessors started the spread of apples from there to other parts of the world,” he says. “But the seeds they carried likely represented a narrow genetic sampling. That’s probably why today’s American domestic apples have a fairly narrow genetic base that makes them susceptible to many diseases.”

Forsline says that many of the Kazak apples lack the size and flavor needed for commercial success. “But it’s the trees’ ability to resist diseases that sets them apart. Breeders will be able to cross them with palatable varieties.” . .

Forsline says the Kazak trees showed significant resistance to apple scab, the most important fungal disease of apples, whose outbreaks blemish fruit and defoliate trees. “Twenty-seven percent of the Kazak accessions were resistant to it,” he says. “This makes sense, because the tree co-evolved with the disease, through natural selection.”

In addition, he led a project in which the popular Gala apple variety was crossbred with seven Kazak accessions. “This produced 7 populations of 250 seedlings each,” he says. “In one of these populations, we achieved a 67-percent resistance rate against apple scab. . .

“Also, about 30 percent of samples inoculated with fire blight resisted that disease,” he adds. Fire blight destroys apples, pears, and woody ornamentals in the Rosaceae family. . .

And it is in rootstocks that Fazio, director of PGRU’s apple rootstock breeding project, also sees great potential—especially with crosses between Kazak apples and elite American material. “This is the future of the apple industry,” he says. “Give it 5 to 7 years.”

hmmm, I guess Johnny Appleseed didn't have a lot of variety, but he continued a very old tradition.

Monday, January 09, 2006

Fear. People die from it sometimes and have ruined lives even when they don't die.

But most troubling of all, according to the UN report in 2005, is that "the largest public health problem created by the accident" is the "damaging psychological impact [due] to a lack of accurate information…[manifesting] as negative self-assessments of health, belief in a shortened life expectancy, lack of initiative, and dependency on assistance from the state."

In other words, the greatest damage to the people of Chernobyl was caused by bad information. These people weren’t blighted by radiation so much as by terrifying but false information. We ought to ponder, for a minute, exactly what that implies. We demand strict controls on radiation because it is such a health hazard. But Chernobyl suggests that false information can be a health hazard as damaging as radiation. I am not saying radiation is not a threat. I am not saying Chernobyl was not a genuinely serious event.

But thousands of Ukrainians who didn’t die were made invalids out of fear. They were told to be afraid. They were told they were going to die when they weren’t. They were told their children would be deformed when they weren’t. They were told they couldn’t have children when they could. They were authoritatively promised a future of cancer, deformities, pain and decay. It’s no wonder they responded as they did.

In fact, we need to recognize that this kind of human response is well-documented. Authoritatively telling people they are going to die can in itself be fatal.

Kinda makes you want to stab an environmentalist. Bad idea, but the thought lingers.

Sunday, January 08, 2006

Or, the loneliness of the honest skeptic. Philip points to this essay by Hendrik Tennekes, retired Director of Research, Royal Netherlands Meteorological Institute, and offers some tea - Earl Grey, hot - to enjoy while we consider this thoughtful meditation on the problems of being skeptical and the necessity of doing so.

Tennekes seems to be what Cosma Shalizi calls a Left Popperian in that he requires some rigor in predictions and simulations. As Tennekes puts it:

His [Popper] claim that scientists should be held accountable for the accuracy of their predictions boils down to the requirement that they have to compute in advance the reliability of their computations. For complex models, Popper wrote, this demand leads to "infinite regress": computations of forecast skill are much harder than the forecasts themselves, and the next level, forecasting the skill of the skill forecast, is insurmountable when a complex system such as the climate is involved. Popper concluded that the positivist claims of science are in general unwarranted.
This is similar to the assertions of Trout & Bishop.
It is time for epistemology to take its rightful place alongside ethics as a discipline that offers practical, real-world recommendations for living. In our society, the powerful are at least sometimes asked to provide a moral justification for their actions. And there is at least sometimes a heavy price to be paid when a person, particularly an elected official, is caught engaging in immoral actions or defending clearly immoral policies. But our society hands out few sanctions to those who promote and defend policies supported by appallingly weak reasoning. Too often, condemnation is meted out only after the policies have been implemented and have led to horrible results: irresponsible war and spilt blood or the needless ruin of people’s prospects and opportunities. Epistemology is a serious business for at least two reasons. First, epistemology guides reasoning, and we reason about everything. If one embraces a defective morality, one’s ability to act ethically is compromised. But if one embraces a defective epistemology, one’s ability to act effectively in all areas of life is compromised. Second, people don’t fully appreciate the risks and dangers of poor reasoning. Everyone knows the danger of intentional evil; but few fully appreciate the real risks and untold damage wrought by apparently upstanding folk who embrace and act on bad epistemological principles. Such people don’t look dangerous. But they are.
Tennekes applies this kind of thinking to climate models and finds them to be dodgy in the extreme, even when they are bolstered by "Ensemble Forecasting, which in fact is a poor man's version of producing a guess at the probability density function of a deterministic forecast."
. . . ensemble forecasting and multi-model forecasting have become common in climate research, too. But fundamental questions concerning the prediction horizon are being avoided like the plague. There exists no sound theoretical framework for climate predictability studies. As a turbulence specialist, I am aware that such a framework would require the development of a statistical-dynamic theory of the general circulation, a theory that deals with eddy fluxes and the like. But the very thought is anathema to the mainstream of dynamical meteorology.

Climate models are quasi-deterministic and have to simulate daily circulation patterns for tens of years on end before average values can be found. The much more challenging problem of producing a theory of climate forecast skill is left by the wayside. In IPCC-documents one finds phrases like "climate surprises", showing that the IPCC-staff is unaware of the ignorance it reveals by that choice of words, or unwilling to state forcefully that climate predictability research deserves much more attention than it has received so far.

This is no minor matter. . .

I protest against overwhelming pressure to adhere to the climate change dogma promoted by the adherents of IPCC. I was brought up in a fundamentalist protestant environment, and have become very sensitive to everything that smells like an orthodox belief system.

The advantages of accepting a dogma or paradigm are only too clear. One no longer has to query the foundations of one's convictions, one enjoys the many advantages of belonging to a group that enjoys political power, one can participate in the benefits that the group provides, and one can delegate questions of responsibility and accountability to the leadership. In brief, the moment one accepts a dogma, one stops being an independent scientist.

The issues here aren't just the arcane calculations of climate scientists, they are also how those results bear on policy. That's what brings to mind Shalizi's ideas about Popper.
Popper was a democrat, an egalitarian and a humanitarian, but with a decided and very characteristic twist. Usually democracy is justified on some such grounds as "the sovereignty of the people" or the like, but Popper rejected that altogether. The problem of politics is not Who should rule? but How can we correct mistakes of policy without violence?; not How can we make people good or happy? but How can we minimize avoidable suffering?; not What is the best state? but What can we do now to make things better? The virtues of democracy is that, of all known systems, it is the one where policy can be reformed most peacefully and most rationally, and the one which is least likely to inflict or condone needless or unequal suffering. As for the virtues of piece-meal social engineering and reform over the construction of Utopias and revolutions, one would think they'd speak for themselves after the twentieth century; but no. Popper is often, with Hayek, associated with a return to classical liberalism, or rather a certain caricature of it which sees no role for any social institutions but markets and a minimal nightwatchman state to enforce property rights. I think this is a gross misunderstanding, and that his actual, sound, political theory is quite compatible with the best traditions of social democracy; I would be happy to call myself a Left Popperian, if I thought anyone would get it.
Tennekes applies this style to climate modelling issues.
I cannot bring myself to accept any type of prediction paradigm, and choose a adaptation paradigm instead. This brings me in the vicinity of Roger Pielke Sr.'s emphasis on land-use changes and Ronald Brunner's modest bottom-up alternatives. It goes without saying that I abhor such dogmas as various claims to Manage The Planet or Greenpeace's belief in Saving the Earth. These ideologies presuppose that the intelligence of Homo sapiens is capable of such feats. However, I know of no evidence to support such claims.
What makes this more than a fussy debate among specialists, more than an academic noogie war, is that the true believers propose massive socio-economic change in response to the threats they see from those predictions. And if they are wrong, as seems quite possible when we examine the scientific details? Worse, they can't even promise that their draconian alterations of society will avoid the threatened melt down. At best the inevitable may be delayed by a very small amount of time. We would be far wiser to choose a democratic, piece-meal approach that seeks to minimize harm and is sufficiently responsive and agile to usefully react to improved assessments of the situation as events unfold.

Friday, January 06, 2006

Discussion of an article in Ecology and Society

Some rural areas are depopulating and going fallow. Consequences for ecosystem services are imagined in a couple of scenarios.

Marcelino sees no problem.

Too bad that my lack of concern for the environment may lead to more native forests and cleaner rivers.

Read more at biopolitical.blogspot.c...

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