Science is the best way to dig out the truth of the natural world, but that doesn’t prevent many people from denying truths that are inconvenient or contrary to their preconceptions or faith.

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U.S. 30, east of Blair, Neb. June, 2011, Iowa DOT

The stunning floods, tornadoes, droughts and heat waves in 2011 caused more Americans to accept global warming — even if climate whizzes are chary of attributing individual weather events to the warming trend.

In the last month, denial of global warming has subsided in the wake of a string of floods, droughts and heat waves, culminating in the “summer in March,” 2012. Although Americans’ attitudes toward warming ebb and flow, on April 17, a Yale University poll reported that 69 percent think global warming is affecting the weather in the United States.

In the same month, however, a Discovery Channel series called “Frozen Planet” attracted ire when scientists noted that it documented massive melting at the poles, but ignored the “why?” question. Scientists have said for decades that polar warming would be an early sign of global warming.

In the recent past, this phenomenon of “denialism” has also appeared in doubts about issues that have long been settled in the scientific community, such as whether:

An April conference at the University of Wisconsin-Madison delved into the origin and development of denialism. Is a refusal to face facts growing more common? Are there better ways to explain how the world works?

Denial in the brain

Scientists, by training, are professional skeptics, but if after decades of debate 97 percent of them accept the link between greenhouse gases and global warming, why are so many unconvinced? “The theory is that if we tell people what we know, they will change,” says Arthur Lupia, a professor of political science at the University of Michigan, but that ignores how people really listen and make decisions.

Speaking to a high-level gathering of science journalists in Madison, Lupia said the problem does not reside with the audience. “The problem is us. Our expectations aren’t consistent with how humans react to information, what they will listen to, or what they will remember. People don’t pay attention, or they don’t remember what we said or what we intend them to remember.”

To change an opinion, you must first attract and then hold the audience’s attention, but attention wanders all the time. No matter how important you think your message is, Lupia says, “Biology does not change its rules … about when people will think about things that challenge them. … If I am saying something abstract, that does not connect to your core aspirations,” you may be more interested in counting tiles on the ceiling.

Can you hear me now?

To communicate with a general audience, Lupia says, “You have to make it close, concrete, immediate. I understand the joy of telling the whole story about climate, but there are some audiences that can’t handle it; in their reality, it’s not the most immediate thing. They might be more receptive if you make the conversation about pollution, energy security or energy costs.”

Information is filtered by attention and ideology, Lupia concludes. “Learning is always an away game. All the real action occurs in the audience’s heads,” he says.

Reasoning: Logical or “motivated”?

Ideally, science adheres to logical reasoning: the conclusion must be true if the premises are true.

But psychologists say it’s common to see “motivated reasoning,” the tendency to fit new information into existing attitudes.

Making a judgment or decision can often involve a “fundamental tension between believing what you want and believing what you have to believe based on the information in front of you,” says Peter Ditto, professor of psychology and social behavior at the University of California-Irvine.

“There is overwhelming evidence” that hopes, fears and social connections affect our judgments, Ditto adds, “but it’s not just that we believe whatever we want. I want to be taller, but I don’t believe that because the data won’t let me.”

Since processing information and making judgments have major emotional components, the standards for evidence are skewed in favor of reinforcing our preconceptions. We are more skeptical about ideas that are new, or that conflict with our thoughts and opinions, Ditto contends.

Over the course of evolution, bad events — but not beneficial ones — forced our ancestors to focus on whether to fight or flee. “People are the same way about information,” says Ditto.

The social element in motivated reasoning surfaced in a 1950s experiment, when six people convinced a seventh, the only real subject, that two lines were equally long. One line was clearly shorter than the other, Ditto says, “But six of them are confederates, and a substantial number of [subjects] go with the obviously wrong answer. That’s the power of having other people who believe as you do. It’s much easier to believe something that does not comport with reality if a whole bunch of others” hold the same erroneous belief.

History of denialism

Although denial of global warming and the erroneous link between vaccines and autism both originated in the 1990s, the organized rejection of evolution dates to the 1920s, when some American Christian fundamentalists promoted creationism — a Biblical explanation for the diversity of life on Earth.

In a 2009 survey, 87 percent of scientists, but only 32 percent of all Americans, agreed that organisms have evolved over time through natural processes. Thirty-one percent of Americans thought humans and other living things “have existed in the present form since the beginning of time.”

Scientists and other Americans certainly have a different understanding of how organisms change through time!

Scientist data and general public data from Pew Research Center for the People & the Press surveys, May-June 2009. For question wording, see survey toplines. Numbers may not sum to 100 due to rounding. Reprinted from Pew Research Center’s Forum on Religion & Public Life.

Much of the attention to the issue comes from battles over teaching of evolution or creationism in public schools, but there is “a lot of misunderstanding,” about the anti-evolution movement in the United States, says Ronald Numbers, a professor of the history of science at the University of Wisconsin-Madison, and longtime student of the movement.

Although creationism is commonly considered a backlash against science, “Virtually nobody in the movement [in the 1920s] thought of themselves as anti-scientific,” Numbers says. “They were denying the scientific status of evolution.”

The dictionary defines science as “organized, certain knowledge about nature, and they said, ‘Nothing is certain about evolution, nobody has seen it.’”

During the 1970s, primarily in response to court decisions, creationism morphed into “creation science” or “scientific creationism,” Numbers says. “The anti-evolutionists realized that evolution had a great deal of scientific support … so their approach was that they, too, were scientific.”

Unlike most anti-evolutionists in the 1920s, the new creationists used a literal interpretation of the Bible to date creation to less than 10,000 years ago. But this created a problem, Numbers says, since according to the Bible, on the sixth day, “God created the animals and Adam named them all.”

No way Adam could rattle off the more than 1 million names of the modern species so quickly, but Numbers notes that the Bible refers to “kinds,” not “species.” If those “kinds” — created in Eden and saved on Noah’s ark — were equivalent to taxonomic families, they could have evolved into the profusion modern species.

“So creationists can accept evolution within the family, and all the evidence for speciation is welcome, because in only about 4,300 years since the flood, they have to have evolution of all the species,” says Numbers. “It’s evolution in fast-forward,” but only among closely related species.”

Even if “kind” equals family, anti-evolutionists exempt humans from this reasoning, allowing them to reject human descent from apes — our fellow hominids.

“It’s strange, I know,” says Numbers. “They are anti-evolution, but most of the evidence evolutionists use against them, they are happy to embrace! One thing that has not been true for 50 years, but lingers in the popular mind, is that creationists deny all forms of evolution.”

The manual of denialism?

Evolutionary biologists regard evolution through natural selection as the organizing principle of biology. Yet for 30 or 40 years, surveys have shown a substantial fraction of Americans, even a majority, who do not “believe in” evolution, Sean Carroll, vice-president for science education at the Howard Hughes Medical Institute, told the denial conference.

Carroll, who like many biologists is aghast at the effort to squeeze evolution into a biblical straitjacket, says, “The denial of evolution was my introduction to denialism.”

ENLARGE

American Museum of National History

In 1954, children got a “Polio Pioneer” card, and a piece of candy after getting a jab of polio vaccine.

Typically, biologists have approached the evolution debate by amassing evidence, but “it’s never been about the data,” maintains Carroll, who is also a professor of genetics at the University of Wisconsin-Madison. “And if it’s not about the data, what are we talking about?”

An earlier example of denialism occurred in the 1950s, after Jonas Salk developed the polio vaccine, a breakthrough that halted a dreaded, paralyzing disease.

Many chiropractors, Carroll found, opposed vaccines since they negated the central premise of chiropractic — that all disease results from misalignment of the vertebrae. “It shocked me. They actively opposed, disputed the efficacy of the polio vaccine. The opposed the March of Dimes, and federal and state efforts to get everybody vaccinated.”

Five hallmarks of denialism

The opposition continued — even after the polio epidemic tapered off as a result of the mass vaccination that started in 1955, says Carroll. And he identifies the tactics used then as a “playbook” of science denial that is echoed in more recent struggles over evolution, vaccines and global warming:

We just don’t agree!

Add it up, and the theme is this: The science must not be allowed to endanger a key philosophy, Carroll says.

But the cost of denialism is high, Carroll maintains. “It’s difficult, as an evolutionary biologist, to realize that half the county is deaf to anything you have to say, especially if the story you have to tell is about a magnificent achievement, understanding the complex relationship of living things on the planet, the deep history of our species.”

To reach young people, Howard Hughes has begun producing and giving away a series of videos on evolution called The making of the fittest.

Go to links for videos

Howard Hughes Medical Institute

To bring science to the masses, Hughes has produced videos on evolution; this one describes how cold-water fish evolved “anti-freeze” genes.

The idea is to engage in storytelling — to help people understand and remember facts by putting them into a narrative framework, Carroll says. As a professor, he’s seen the power of a story. “When I got lost, off-topic, and students see me years later, they say they still remember some of those stories, and I know they don’t remember any of the genetics. Stories count.”

Time (dis)honored tactics

Naomi Oreskes, a professor of history and science studies at the University of California at San Diego, has written about the “merchants of doubt.”

The message, she says, is simple: The facts are not all in. We need to hold judgment until the scientists agree.

This kind of corrosive doubt — in the face of scientific certainty — is “very depressing” if you “believe that knowledge is power,” Oreskes says. “Knowledge is not powerful enough — an ideology is more powerful still. It’s about ideas, not facts.”

During the last half-century, she says, “Political powers are willing to attack rational truths, and those who deliver them.”

There is also money at stake in many of the issues, especially in the case of climate change, which threatens the fossil-fuel industry.

Car exhaust from eutrophication&hypoxia; smoky butt from Raul Lieberwirth

What do these have in common? Many companies in the oil and tobacco industries have sown seeds of doubt about the long-term effects of their products.

The model for such campaigns, Oreskes said, came from the tobacco industry in the 1960s. Facing growing evidence linking their profitable product to lung cancer, the industry settled on a strategy of promoting “Questions, manifested in a memorable maxim: “Doubt is our product.”

And for decades, doubt helped big tobacco deride and deny a tidal wave of evidence that cigarettes cause lung and heart disease.

December, 2011, Pew Research Center for the People & the Press.

After the crazy weather of the past year, pollsters have seen a bump in the number of Americans seeing “solid evidence” for global warming.

The same strategy, Oreskes says, was adapted to undermine “nuclear winter” (the discovery that huge clouds of ash and dust released during nuclear war could freeze and starve the planet), the dangers of the insecticide DDT, acid rain caused by power-plant pollution, the ozone hole, and global warming.

The tactics were to “challenge the evidence, claim the science is not settled, cherry-pick the data, to demand balance from journalists and threaten to sue if they don’t,” says Oreskes.

Changing the climate change story

The basic physics of global warming have been known for 100 years, Oreskes said. Scientists started exploring the subject with early computerized climate models in the 1980s.

In 1992, Oreskes said, the first President George Bush, “Called for concrete action to protect the planet. We had political leadership that committed us to doing something, yet we never did take the concrete steps that Bush called for. It’s a story about political challenges, selling uncertainty, about science in the age of denial.”

The doubters, funded by the oil industry, included some prominent Cold-War physicists who had been advocates for Ronald Reagan’s anti-missile defense system. “They said the science was unsettled, that it would be premature to act,” says Oreskes, who was intrigued to find that one of those physicists, Frederick Seitz, had been a consultant to the R.J. Reynolds tobacco company.

In 1998, Seitz organized a petition against the Kyoto Protocol, the first international agreement to control greenhouse gases.

Seitz and his fellow doubters, Oreskes says, “Found a new enemy: environmental extremism. You see anxiety about environmentalists as socialists, using climate change as a lever to effect social or economic change.”

What began with a handful of people with roots in the Cold War has since spread to “a range of free-market think tanks, including the Cato Institute and the American Enterprise Institute,” Oreskes says.

The arguments against the settled scientific debate over warming, she adds, “are not just different interpretation of the data; that’s a normal part of scientific life. This is not about normal scientific claims. These are the scientific equivalent of saying Belgium invaded Germany during World War I.”

Why deny? Because it works, Oreskes implies. Almost 25 years after the scorching summer of 1988 brought global warming into the public sphere, the United States has yet to get serious about controlling greenhouse gases.

“We ignore the facts of nature at our peril,” says Oreskes. “Ignoring them is not going to make them go away.”

Microsoft’s April 9 deal to spend $1.3 million apiece on 800 patents from AOL was another skirmish in the patent wars that have engaged the technosphere. Just last summer, we watched a blizzard of headlines, lawsuits, and billion-dollar bills:

We wonder: Is this a situation that only a patent lawyer could love, or are these purchases and lawsuits the inevitable price of progress in our high-tech world? Are they the inevitable outgrowth of a venerable system that, for all its flaws, is still better than nothing?

Patents are licenses to exclusively make and market an invention that are inscribed in the U.S. Constitution. The concept is simple — and ridden with inherent conflict. If you invent a small device (a “midget widget”) that is new, useful, and “not obvious” to people skilled in the art of widgetry — your widget can be protected by a U.S. patent.

If I make or sell a widget that uses your invention (that “infringes on your patent”), you can sue me for damages, and a court may order me to close my widget-works.

So far, my invention has benefited me, my employees and customers, but when the patent (which must explain the inner workings of my midget widget) expires after 20 years, it becomes available to anybody.
And so (in theory) patents stimulate innovation and progress by conferring a short-term monopoly in return for short- and long-term social and economic benefits.

But what sounds good on paper can hide complexities that only a patent lawyer could love:

“Greasing the wheels of innovation” or “throwing sand in the gearbox”?

It’s not hard to find claims that the patent system is “broken,” and nobody disputes that “bad patents” have been issued for innovations that are obvious, inane or unworkable.

Patent battles are nearly as old as the U.S. patent system: Eli Whitney spent years in court trying to enforce his patent against infringers who cobbled together homemade cotton gins. His “victory” came just one year before the patent expired.

Lawyer-letters about patent infringement are a dreaded fact of life in technology industries, but no matter who wins, patent battles transfer money from the buyers of phones and computers to patent lawyers.

The pace of U.S. patent awards has picked up to about 200,000 per year, and some with a dog in the fight say the system does protect the rights of inventors.

The sentiment is not universal.

Adam Jaffe, an economist at Brandeis University, co-wrote a book on the patent system² that refers to a “broken patent system” in the subtitle. Jaffe says patents cut both ways. “Patents are important in fostering innovation, because 99.9 percent of the time, inventing something is just the first step. You require a significant investment … to get something from the invention stage to actual production, and unless you are independently wealthy, you need someone who is hoping to make money to take you through the development stage.”

And that “someone” may view a strong patent as your most valuable asset.

Software and high-tech patents?

Innovation “is a very complicated process,” Jaffe adds. “In most cases multiple ideas are interacting. In the extreme case, in software and high technology, people say a product might invoke 100,000 patents. It can get very messy.”

When the United States started issuing large numbers of software patents in the 1990s, the inexperienced patent examiners issued many dubious patents. Although the examinations have gotten more stringent, some still think software should be exempt, or patented under different standards.

Searching for competing inventions in software, for example, is comparatively difficult, and the search is the basis of the patent examination.

In most cases, says Tim Berners-Lee, a commentator on tech issues, software developers don’t bother doing thorough patent searches, which, he maintains, could require more patent lawyers than exist on earth.

Trolling for profits?

Although patent disputes are nothing new, they have been systematized by “patent trolls” — companies that own, defend and license a library of patents. Depending on your point of view, trolls are:

NPR covered a prominent case of trolling, complete with shadowy, unoccupied offices.

But even if trolls can be a barricade to innovation, “in practice it will be very difficult to change the rules in such a way as to prevent that,” says Jaffe. Would you allow infringement suits only from those who are moving a patented idea toward the market? “Say I’ve got an invention and am looking for a company that has the resources to bring it to market… and someone else comes along and steals the idea. Are you saying I can’t sue because I am not on the market?”

As with many parts of the patent system, finding faults is easier than fixing flaws, he indicates. “I don’t disagree that in a sense people are abusing the system by amassing piles of patents, but it’s naïve to think you can tweak the system to shut that down.”

First-to-file, or first to invent?

The America Invents Act, signed into law September, 2011, made what former commissioner of the Patents and Trademark Office Robert Stoll calls “the most revolutionary change in patent law in 60 years.”
The changes start with the basis for obtaining a U.S. patent. Previously, you had to prove that you were the first to invent something; now you must be the first inventor to file.

“First-to-file” will make life simpler, Stoll told an audience at the University of Wisconsin-Madison in April, by deleting disputes about who made the invention first. “First-to-file provides more certainty to the system, and reduces the ugly interference cases that don’t provide much benefit to the United States.” (An interference proceeding now determines whether someone made the invention before the patent applicant.)

“First-to-file really favors large companies that have sufficient resources to get to the patent office first,” argues Carl Gulbrandsen, managing director of the Wisconsin Alumni Research Foundation (WARF), the private, not-for-profit technology transfer arm of the University of Wisconsin-Madison, “and it disadvantages independent inventors and universities. I expect filing costs will go up.”

Got an app for that patent?

Here’s the snag: When you invent a molecule that could make a tire last forever, you may not know right away if it’s worth filing a patent application. Under first-to-invent, you could wait as much as one year to file.

Filing a patent can cost tens of thousands of dollars, which is money you could better spend on research that might show that your invention is solid — or as evanescent as a rainbow.

But under first-to-file, you lose if an inventor in Berlin or Tokyo files an app before you have time to decide. “AIA has weakened the grace period and the ability of independent inventors to test out the invention, and appropriately get financing to help with filing,” says Gulbrandsen.

Gulbrandsen also charges that the new law contains, “So many undefined terms that they will be litigating it for 15 years. They have essentially thrown out 100 years of case law; it’s a full employment act for lawyers.”

Winnowing the chaff — or weakening the patent system?

Although interference proceedings are now history, Gulbrandsen says AIA contains too many new ways to challenge patents. “There used to be two principal ways to attack a U.S. patent, and that made them strong. Now there are literally nine ways, and that weakens them overall. For a university, this will mean increased expense [for defending existing patents], and many of them won’t be able to bear that.”

Since its founding in 1925, WARF has contributed $1.24 billion to UW-Madison as royalties from more than 2,300 patents for inventions by university researchers. It has become a significant source of income to the university’s researchers and a model for other university patent offices.

A strong patent system has benefited the United States, says Gulbrandsen. “It’s necessary for innovation, and the last thing you want to do, if you want to create jobs, is to weaken the patent system, and that is exactly what we have done” with AIA.

But Jaffe, although no fan of the patent system, sees a benefit in these after-the-fact challenges, since “the vast majority” of the 200,000 U.S. patents granted each year are trivial (like that baling-wire-and-chewing-gum flying machine). Because the patent office must judge a flood of applications with limited resources, “It cannot do an exhaustive analysis, and it would be crazy to invest the resources to get it right every time.”

Under the new system, after the initial patent examination culls the obvious chaff, Jaffe says, competing inventors could contest a wobbly patent. Now, he says, “You have the opportunity, at least in theory, to go to the patent office and say, ‘This wasn’t really novel.’”

Although it’s easy to criticize the patent office, Jaffe says it has more expertise than the federal courts, the final resting place for most patent disputes.

Who benefits, who gets hurt?

In the ideal world — where patents are perfectly drawn — innovation wins. “I equate patents and innovation,” says Gulbrandsen. But despite its promising moniker, the America Invents Act “makes it more difficult for the inventor to raise the funds necessary to bring the invention to market. One of the best tools an entrepreneur or a startup has to raise money is a patent. It gives some assurance to investors that if they provide the funding, they will be able to recover it and get a return. The patent gives you the right to exclude others. Weakening the patent system increases the risk for investors, and that’s bad for inventors.”

University technology-transfer offices are going to suffer, says Gulbrandsen, who directs one of the oldest and largest in the nation, since many of them must wait to file a patent until they have found a business that wants to pay for filing and license the patent. “Although WARF is an exception, under first-to-file, you don’t have time to find a licensee, and so most universities tech-transfer offices will drop out.”

Individual inventors, Gulbrandsen notes, seldom have a patent lawyer on retainer.

Still, too much protection stifles innovation, says Jaffe, who says the system requires balance. “I don’t think first-to-file changes a lot. The rest of the world has been on that for a long time. There are going to be impacts in both directions, but in most cases, first-to-invent is just a source of conflict, because it’s harder to establish. This just simplifies things and reduces controversy, which is a very good thing.”

As farmers north of the equator get ready to plant their seeds, we’ve started wondering about agriculture before Columbus. Conventional wisdom says Native Americans were mostly hunters and gatherers. When they did farm, their slash-and-burn techniques exhausted the soil, forcing them to clear new fields.

Although Native Americans domesticated corn, tomatoes and potatoes, their farms were generally unproductive, and most of their plant food came from gathering tubers, greens, berries and shoots.

But as we learned at a series of talks at the University of Wisconsin-Madison, this picture needs editing:

The provision of permaculture

Until the 1960s, the government of Canada enforced assimilation of First Nation children at boarding schools that banned ancestral languages and practices. The goal was to homogenize Canada’s population, but suppressing culture also squelched knowledge of the traditional methods for raising and gathering food.

When the police boats arrived in British Columbia in the 1930s, to take children to boarding schools, Adam Dick (tribal name Kwaxsistalla) escaped, and went to live in secluded locations with his grandparents for about a decade.

Dick, a member of the Kwakwaka’wakw (formerly Kwakiutl) tribe, has become a link to a vanishing past. “His people have learned from him, they all benefit from his teaching,” says Nancy Turner, in the School of Environmental Studies at the University of Victoria (Canada).

Turner, who has spent a career studying indigenous agriculture, says knowing what to look for is key to understanding native agriculture on the coast of British Columbia. “They used perennial cultivation. ‘Keep it living’ was part of their philosophy, and it shows the way they value other life. A lot of perennial plants were being cultivated, but outsiders saw this as random plucking.”

People in the First Nations of British Columbia ate 35 species of roots, 25 greens, berries, even the inner bark of some trees, Turner says.

Overall, coastal people used 250 species of plants for food, tea, fuel, construction, fiber, canoes, dye and glue, Turner says.

When the natives harvested bark and wood from a living tree, they took what they needed without killing the tree. “They believed trees have sentient life, and called these ‘begged from’ trees,” Turner says. “‘We have come to beg a piece of you today.’”

“Gardens” in the water

The same attitude of “stewardship and caring” also applied to aquatic food, Turner says, especially the all-important salmon. “The salmon streams were carefully tended, and even cleaned. If the stream changed course, Adam and the others were taught by the elders to transplant [salmon] eggs to the new stream channel.”

Similarly, she says, people moved rocks to “create the most productive clam beds on the coast.”

Courtesy Nancy Turner.

Small plots of springbank clover (Trifolium wormskioldii), about to blossom in British Columbia produced “immense quantities” of roots that were “regarded as indispensable to good health,” says Turner. In this permaculture, the harvesters replanted segments of the roots for another crop.

This was more like farming and harvesting than hunting-and-gathering, Turner insists. But the colonists, more interested in survival and profit than the people they were displacing, “were blind to these practices. They had in mind Mr. McGregor’s garden, with a fence and rows you can harvest. They looked at these things, but they did not see them.”

Restoring the foods

Most cultures give a central role to the production, preparation and consumption of food. What happens when the land that grew traditional foods is drowned by dams?

That’s the conundrum facing Linda Different Cloud Jones, an activist and student from the Lakota Sioux Nation. “The loss of biodiversity is the greatest challenge on traditional lands,” she told an audience in March at the University of Wisconsin-Madison, “and the loss of one culturally important species has significant impact.”

The Lakota people “are stereotyped as the people of the plains,” says Jones, “but we are also people of the river, or were a people of the river, until, in the 1950s and ’60s, when dams built in the Pick-Sloan project changed the way of life for the Lakota forever.”

Standing Rock, the Lakota reservation, is sandwiched between the Dakotas, and borders the Missouri River. “Overnight, hundreds of thousands of acres of native land was underwater,” said Jones. “All the plant and animal species in the riparian cottonwood forest were gone.”

The underground seedpods of the hog peanut (AKA mouse bean), were collected by prairie voles. These small mammals, which the Lakota called “mice,” cached the big seeds underground.

Lakota women found the caches with a stick and removed the seeds, Jones said, but “They always left a gift, dry berries, animal fat or corn. They would sing, ‘You have helped sustain my children during this coming winter, and we will not let your children go hungry.’ Their song echoed from the trees, and it seriously breaks my heart that my young children will never see that.”

A sustainable yield?

The song revealed that “an entire world view and behavior went along with this one plant species,” Jones said, and both suffered when dams flooded the forest. “We haven’t eaten these for 50 or 60 years. With the death of this one plant was the death of a little piece of our culture.”

The hog peanut was part of a larger cycle, Jones says. In spring, “We would tap box elder maples for syrup, then collect biscuit root, wild strawberries, currants, juneberries, cattail shoots, and acorns in December. Nothing was ripe at exactly the same time. When the plants are no longer there, the cycle is broken.”

Jones, a Ph.D. student at Montana State University, is attempting to grow the hog peanut as a form of “ecocultural restoration.” “Research for the sake of research was not what I wanted to do,” she says. “I wanted to change the world for my people, to make their lives better.”

Millions of people made a living for thousands of years in the New World, she says. “Everyone always thought that when European people colonized the Americas, they were coming into a pristine place, but we were managing the landscape for thousands of years.”

Iroquois corn

Corn is an indisputable triumph of Native American agriculture. The plant, domesticated thousands of years ago in Mexico and Central America, was a staple of the American diet and is now the largest crop in the world (global production in 2009 was 819 million metric tons).

Although natives also invented the highly productive “three sisters” companion-cropping technique, their agricultural prowess has been underestimated, says Jane Mt. Pleasant, an associate professor of horticulture at Cornell University.

Although the Native Americans had transformed a weed into the phenomenally productive crop maize, “There are claims by scholars, archeologists, geographers and historians that native agriculture was predominantly shifting cultivation… largely marginal, not too productive,” Mt. Pleasant says.

In “shifting cultivation” (a politically correct locution for “slash and burn”), farmers move to new plots as they exhaust their soil. According to this logic, native farmers in North America “sowed the seeds of their own destruction through environmental degradation,” says Mt. Pleasant, who directs the American Indian Program at Cornell.

But Mt. Pleasant says this is bunk. Rather, she contends that:

The soil should be the starting point for understanding agriculture, says Mt. Pleasant. While many soils on the Eastern Seaboard are not great, large parts of upstate New York had good soil that still supports productive farms.

About 300 years ago, the Iroquois Confederacy, a union of five (later six) tribes, lived in the area, and evidence for their farm productivity comes, ironically, from armies that sought to destroy them. “The quantity of corn which we found in store in this place, and destroyed by fire is incredible,” wrote the governor of New France in 1687.²

The French attacked the Iroquois, who were allied with France’s great enemy, Great Britain.

Slash ‘n burn, or sustainable agriculture?

Then in 1779, a soldier sent by General George Washington reported that his unit had destroyed at least 200 acres of Iroquois corn and beans that was “the best I ever saw.”

“This was not backyard gardening, not primitive farming,” Mt. Pleasant says. “They were dynamic, producing farmers on really good soils.”

In modern tests of corn varieties believed to resemble those grown by the Senecas, one of the Iroquois tribes, Mt. Pleasant got yields of 2,500 to 3,000 pounds per acre (45 to 54 bushels per acre or 2,800 to 3,400 kilograms per hectare).

This was far above the 500 kilograms per hectare of wheat grown in Europe.

Turner calculated that the Iroquois could support roughly three times as many people on an acre as contemporaneous Europeans could with their wheat crops.

Part of the advantage, she says, comes from maize’s inherent productivity. But observers have long wondered how this production could have occurred with neither plow nor draft animals, usually deemed the hallmarks of agricultural progress.

Plows, however, are now viewed as mixed blessing by many soil scientists. Although they prepare a good seedbed and bury weeds, they expose soil to the air, which encourages oxidation of humus, the organic content that supports essential microorganisms.

Although, after plowing, the humus briefly releases a burst of nitrogen, the depletion of organic matter and increased erosion continue for decades.

And thus on balance, Mt. Pleasant says the lack of the plow was an advantage, because planting with hand tools saves soil organic matter.

“If you are not tilling, and start with good soil, you are not going to lose fertility,” Mt. Pleasant says. “The system is stable as long as the crop yields are moderate and there is no plowing.”

But without plowing, there was no need for slash and burn.

Overall, Mt. Pleasant says, the new data provide a “quite different” perspective on agriculture. “Who were the primitive farmers? This is sustainable agriculture at its highest level.”

Rethinking agriculture

This type of revelation changes our view of the origin of agriculture, says Eve Emshwiller, an assistant professor of botany at UW-Madison who organized the seminar on native agriculture and who studies oca, a root crop grown in the Andes. “We have always talked about hunter-gatherers as if one day they were gathering food and noticed a plant growing from seed and thought, ‘We could gather seeds and start farming,’ as if this brilliant idea happened all of a sudden.”

Aside from historical curiosity, why worry about how native Americans grew their crops? One reason is the growing interest in sustainable agriculture, says Emshwiller. As agriculture faces the challenge of feeding more people without further damaging soil and water, older traditions could contribute.

Looking at other ways to grow and gather food will broaden our perspective, Emshwiller says. “There were a lot of people who were not considered agriculturalists, who were [supposedly] just gathering from the wild. But if you really understand what they were doing, there is not a sharp line between gathering and farming. There is a huge continuum of ways that people manage resources and get more from them.”

Should an artificial waterway in Chicago be closed to block two highly destructive fish from entering Lake Michigan and then the other four Great Lakes?

On Feb. 27, the Supreme Court said ‘no’ when it declined to revisit an appeal by the State of Michigan, which wanted to compel closure of the Chicago Ship and Sanitary Canal. The canal, created to drain stormwater and wastewater from Chicago, could allow silver and bighead carp from the nearby Des Plaines River to enter Lake Michigan.

Since the two carp, native to Asia, escaped from fish ponds in the South in the 1970s, they have occupied much of the Mississippi River system, and have become extremely abundant in rivers near the Canal. Biologists, state agencies and the Great Lakes Commission warn that once the fish reach Lake Michigan, they will likely spread through the five lakes, then into the St. Lawrence River.

The Great Lakes hold almost 20 percent of the world’s fresh water and border eight states and two Canadian Provinces. Given the silver carp’s fearful jumping habits, and the potential for both species to steal food from the mouths of sport fish, the invasion could threaten recreational boating and commercial, sport and tribal fishing that gross $16.4 billion per year.¹

Although the Great Lakes already house at least 180 invasive species, ecologists warn about irreparable harm from Asian carp. They say prevention is cheaper and easier than eradication — which may be a practical impossibility.

Originally, the watersheds of the Great Lakes and Mississippi River were separate. The two were united by the Chicago Sanitary and Ship Canal, which drains stormwater and treated wastewater into the Mississippi River system.

Don’t fence me out!

Although three electric “fences” across the canal have apparently managed to block the fish from entering Lake Michigan, many scientists view the barriers as stopgaps at best, and Asian carp DNA has been found several times beyond the fences.

While that DNA suggests that the carp are already in Lake Michigan, the fish have not been found there. Still, ecologists, accustomed to studying the disastrous aftermath of invasives on land and in water, would love to protect the Great Lakes from the carp by closing the canal. That would also protect the Mississippi River from invasion from the Lakes.

“The Asian carp situation is analogous to medicine, where an ounce of prevention is worth a pound of cure,” says Jake Vander Zanden, a professor of zoology at University of Wisconsin-Madison, and an expert on freshwater invasive species. “It makes so much more sense to keep them out, rather that let them in and deal with the consequences forever.”

The shipping industry, reliant on these waterways, wants to keep the Chicago waterways open, said Mark Biel, chairman of UnLock Our Jobs by email. “Nobody wants to see the Asian carp get into the Great Lakes… This is, however, a manageable issue that requires a long-term, comprehensive plan, and separation is simply not a solution. Given the size, scope and complexity of separating the two bodies of water, it’s clear that the costs would be enormous and the timeline — if it’s possible at all — would do nothing to address the immediate threat of Asian carp.”

Invasions can be expensive. The Environmental Protection Agency figured that just the invasives delivered in ballast water cut commercial fish landings by 13 percent to 33 percent in the U.S. Great Lakes, at an annual cost of $200 million. The estimate did not cover Canada’s part of the lakes, or species that arrived by other means.

What’s the problem with carp? What can be done to prevent their entry into the Great Lakes and beyond? Are invasive species always so damaging to ecosystems?

What’s the beef about carp?

Asian carp are heavy-bodied fish native to Asia that have occupied large parts of the Mississippi River watershed, where their rapid reproduction, voracious feeding (up to two or three times their body weight in plant and animal plankton per day), and made-for-home-video jumps are making life miserable for native fish and fishing people alike. The two carp considered most threatening to the Great Lakes — silver and bighead — originated in Southern fish ponds, where they were placed as natural vacuum cleaners to suck plankton from dirty ponds.

Since at least 1980, when the escape of the silver and bighead was detected, that voracious appetite was transformed from selling point to sticking point.

You might observe — correctly — that species have been moving since life began. It’s true that invasions are an old story, but it’s only half the story: the process has been force-fed by commerce and technology. “This is a natural process; it was once a trickle, but the rate at which it happens now is so devastating,” says Vander Zanden. “With globalization, trade, travel, things are moving so fast, it’s a fundamentally different process, and the implications are huge.”

It’s impossible to predict exactly how well Asian carp would fare in the Great Lakes; their abundance will depend on temperature, food supply, the emergence of diseases and predators, and factors that we can’t predict. But the lakes have a wide variety of habitats, and inevitably some would be conducive to the invaders.

The fundamental reason why invasive species reach nuisance levels resides in the predators, diseases or competitors they leave behind in their homeland. In the new habitat, the traveling species often gets an unfair advantage, enabling it to grow to astonishing abundance and crowd out native species.

Asian carp provide a perfect example of the process. They were deliberately imported to work on Southern fish ponds, and their ability to outcompete native fish for food and habitat “has led to the widespread establishment of Asian carp in the Mississippi River, impacting the natural balance of the aquatic ecosystem,”².

Can we keep carp from the greatest lakes?

On January 31, 2012, the Great Lakes Commission, an international body charged with maintaining the environmental and economic vitality of Earth’s largest lakes, issued a report describing three options for physically separating the two giant drainages to block invasions in both directions. The report was greeted by a number of officials from the region, including Michigan Senator Debbie Stabenow and Chicago mayor Rahm Emanuel.

The Obama Administration opposes closure of the Chicago canal, and in February it proposed to spend $51.5 million on Asian carp research. The money will buy more trapping and netting, to assess whether the fish have reached Lake Michigan, research on fish trapping with chemical attractants, and noisemakers to scare carp from entrances to the lake.

The focus on Chicago is misleading, according to Biel, who notes that the Great Lakes and Mississippi River Interbasin Study, from the Army Corps of Engineers, found “18 aquatic pathways throughout the region (not just Chicago alone) by which the Asian carp could get into the Great Lakes. The existence of these other pathways, which cannot simply be closed, demonstrates the importance of a regional solution to control Asian carp populations. That’s why we have to expand our sights beyond Chicago to determine a comprehensive control plan that implements measures in all of the pathways… .”

Philip Moy is a senior scientist at the Aquatic Sciences Center at UW-Madison who previously worked on the issue for the Corps of Engineers. “Electric barriers buy us time, and we need to do two things,” Moy says. “We should look into additional barrier technologies that can be added to augment the electrical approach… . We need to look pretty hard at the Great Lake Commission report suggesting that the lake and river can be re-separated. It would cost a lot of money, a century of infrastructure has built up there, but what’s the logic of waiting another 10 years to get started on a project that can take a generation to complete?”

The “mid-system separation alternative” proposed by the Great Lakes Commission was estimated to cost $3.26 to $4.27 billion. The latest federal appropriation for monitoring and research related to Asian carp will bring the three-year cost for controlling Asian carp in the area to $156.5 million.

Separation, Biel wrote, “would effectively end waterborne commerce through the Chicago Area Waterway System. The Great Lakes Commission report mischaracterizes how vessels could move containers around the Chicago rail gridlock, giving the impression that there would be a way to facilitate both separation and continued cargo movement.”

Muscling in on the mussels

There are good reasons why zebra and quagga mussels are often mentioned in discussions about invasives in the Great Lakes. Since the zebra entered the lakes in ballast water used to stabilize ships a couple of decades ago, it has clogged water intakes at power plants and water utilities.

Along with a later arrival, the quagga mussel, the zebra has eaten enough plankton to change the ecology of the lakes, and the zebra is now spreading to smaller lakes and rivers.

To prevent further hitchhikers in ballast water, ships now must replace their ballast water in the ocean with salt water, which carries organisms that are unlikely to survive in the freshwater lakes. “Every ship coming in is inspected by the Coast Guard before it reaches the Great Lakes,” Moy says, “and we haven’t discovered another ballast-related species since 2006. In the lakes, there is a growing spirit of cooperation between the companies that operate ships and the states.”

p. 74, “Aquatic invasive species in the Rio Bravo/Laguna Madre Ecological Region”

Salt-water invaders are carried in ballast water and through the pet and fishery trades.

Species invasions also plague smaller lakes, which explains the growing push to prevent the movement of invasive fish, mollusks and plants, by requiring boaters to clean and dry their boats and trailers as they leave a lake.

In Wisconsin, at least, that effort seems to be succeeding, even though not every boater complies, Moy says. “Some people say, ‘If this guy didn’t do it, it’s not the end of the world if I don’t also,’ but it usually takes multiple introductions over time to establish a population. If we reduce the number of introductions per year, we reduce the potential for establishment. Every person makes a difference.”

Buying time, but could time be on our side?

As ecologists pursue the science of invasives, what to do about the carp now knocking on the door of the Great Lakes? Biel, of the shipping industry, says, “Despite the uptick in hysteria on this issue, Asian carp populations in Illinois haven’t actually moved up river in six years. That said, we fully support funding the existing electric control barriers because their effectiveness has been demonstrated over and over again.”

Despite “substantial strides” in controlling Asian carp in Illinois and Indiana, including a third electric barrier and physical barriers along the Des Plaines River and the Illinois and Michigan Canal, “there’s simply not enough being done by other Great Lakes states,” Biel says. “Continued calls for lock closure remain a higher priority for our neighbors and other like-minded groups than actually implementing tactics for prevention.”

During the years it would take to seal the Chicago waterways, control technology may improve, says Moy, who points to fresh ideas from the U.S. Geological Survey. Instead of using the pesticide rotenone as a “big hammer” to kill all fish, he says, the Survey is testing a coating for rotenone that would make a deadly fish feed. Once sprinkled in the water, carp and other filter feeders would eat the feed, but only Asian carp have the enzyme that can dissolve the coating to release the rotenone. “It’s much more specific; an elegant application that takes advantage of the fish’s feeding behavior and internal physiology, using an existing, certified” chemical agent, Moy says.

There are benefits to working several angles at once, Moy adds. “These invasions are not inevitable. We can reduce the rate of invasions and the number of introductions per year, and that reduces the likelihood of establishment, and each year we delay introduction to a lake gives research time to come up with a solution.”

Four genomes for ants have just been decoded. The genetic information gives us a better picture of why ants are so successful, and helps us understand why leaf-cutter ants live in a close, mutually beneficial relationship (symbiosis) with fungus. Some argue that leaf-cutters are the most industrious farmers on Earth.

Graphic: The Why Files

Find the article:

Discussion Questions

1. Discuss: How does the leaf-cutter ant “make a living”?
2. What are some reasons why ants are such a successful group of organisms?
3. Discuss: How does the new leaf-cutter genome flesh out the picture of its symbiosis with fungus?
4. How does long-term interaction enhance cooperation in a symbiotic relationship?
5. What are two reasons to believe that the leaf-cutter’s symbiosis with fungus is a successful arrangement?

Lesson Plans/Activities

1. Amazing Ants! Match ant species to their unique behaviors through this interactive game. What does this diversity of behavior tell you about the evolution of ants?
2. Making sense of symbiosis. Guide your students through this in-depth lesson on symbiosis. Recommended for grades 9-12.
3. Critical thinking. Decoding genomes has opened new possibilities, as well as posed new questions. Have students explore the Human Genome Project to learn how genome deciphering is done and what the completed project means. Then, ask students to read these articles and write an essay on one of the topics, incorporating all sides of the issue. Recommended for grades 9-12.

In hot, dry places, water recycling has joined water conservation as a weapon against water shortages. After being treated at a sewage plant, wastewater is increasingly used for irrigation, industrial purposes, restoring groundwater, and after further purification, for drinking.

Photo: gingerpig2000

He thinks it’s pure water, but could this thirsty hiker be guzzling recycled filtered, treated, oxidized, and disinfected, sewage water?  Could that be safe?

About 0.1 percent of the municipal wastewater treated in the United States is reused for potable (drinking) water, according to a new National Research Council report. That may sound trivial, but “reclaimed water can account for the majority of the drinking water supply in some areas,” the report said.

In general, those areas have taken every reasonable measure to clamp down on water waste before embarking on the more dicey path of reuse. Drinking water is a small part of the growing movement toward reuse; far more common is the recycling of water for irrigating farms and landscapes, recharging groundwater, and for cooling generators and other industrial equipment.

But recycling for potable water is a growing trend in the Middle East, Australia, California and Florida. Miami-Dade County, Florida is about 80 percent through a project at a sewage plant that will use microfiltration, reverse osmosis, advanced oxidation and ultraviolet disinfection to disinfect partially treated wastewater. Each day, 21 million gallons of water “whose quality will be near that of distilled water” will be piped from a moat at the Miami Metrozoo. From there, the water will percolate into the ground to recharge groundwater.

The interest in reuse coincides with a need to update potable water-treatment plants, to the tune of $200 to $300-billion over the next 20 to 25 years.

In 2002, Florida was recycling the most wastewater, followed by California, Texas and Arizona.

The 2004 Guidelines for Water Reuse from the Environmental Protection Agency (EPA) estimated total U.S. water reuse at 1.7 billion gallons per day, with a growth rate of 15 percent per year.

But that’s just an estimate; the comprehensive Research Council report could not find solid numbers on current water recycling in the United States. “In 30 years we have not made a concerted effort in the United States to even figure out how much water we are reusing,” says Anders Andren, a professor of environmental chemistry and technology at the University of Wisconsin-Madison, and director of its Sea Grant Institute.

Globally, the estimate on total (not just potable) water reuse was 5.5 billion gallons per day.

Drink in the irony

If you’re gagging at the idea of guzzling highly treated wastewater, you may already be doing so, courtesy of “de-facto reuse.” The treated effluent discharged by wastewater plants often winds up in rivers, streams and lakes, and can easily enter intakes at downstream water utilities.

“Nobody has tried to figure out where we are in the United States by doing a quantitative survey of de facto reuse,” says Andren, meaning an unknown number of water utilities are delivering drinking water containing an unknown amount of treated wastewater.

If drinking water meets federal water-purity standards, it’s safe, but the issue of de facto reuse does merit further study. “This is the kind of thing every water system ought to be looking at, where the source water is coming from, and what is its quality,” says Henry Anderson, adjunct professor of population health science at the University of Wisconsin-Madison. In most cases, he says, the quality of the intake water is already a factor in deciding how to treat potable water.

On a per-capita basis, Israel, Singapore and Australia are leaders in water reuse. In every case, the local culture, economy, environment and demand for water affect how water is treated and used.

Here, we’ll concentrate on drinking water — the most demanding aspect of water reuse. Because it’s not legal to connect a drinking-water system directly to a sewage plant outfall in the United States, the treated effluent must reside in groundwater, surface water or a container for a while before it is piped to the water-treatment plant.

This delay provides a second layer of protection called “environmental attenuation,” says Anderson, who helped write the recent Research Council report. “The concern of the committee is that no system works with 100 percent efficiency all the time. If you are using a membrane to treat wastewater and it tears … we want multiple layers of protection.”

During attenuation, the treated wastewater can be mixed with surface water or groundwater, and then the water will go through the complete process for treating potable water, Anderson says.

How clean is safe?

Science and technology play dual roles in the adoption of water recycling. Improving water purification technology is offering an increasing number of choices. But technology costs money, and drinking water that comes from ground- or surface water is almost always cheaper than reclaimed drinking water.

But science is also able to detect an increasing number of contaminants in drinking water, and at ever-lower doses. In recent years, this analytical equipment has raised worries about hormones and pharmaceuticals in wastewater that have added to traditional worries about pathogens.

However, these highly accurate chemical-detection methods can raise spurious warnings, says Andren, an expert in water purification techniques. “Analytical capacities are such now that you can find literally everything, but they may pose no health hazard at those concentrations. It’s getting to the point that we can detect a thousand molecules in a liter of water, but this does not necessarily mean there’s anything wrong with the water.”

How it’s done

Water treatment plants come in two varieties. Some treat sewage, and others treat drinking water. In essence, water recycling creates a loose connection between these two plants, although federal law requires that treated wastewater be mixed and stored before it enters a plant treating potable water.

Both types of water plant already use multiple steps for treating water, but recycling has entailed an increase in the amount and intensity of treatment.

The specific treatment methods depend on the nature of the incoming water stream, which could come from sewage treatment plants, street runoff or industry. “The incoming streams can vary so much, in composition, type, quality and quantity,” he says.

Technologies must be chosen to deal with the situation, says Andren. “In certain instances, the main problem is getting rid of salt, in others it’s getting rid of bacteria, or pharmaceuticals, or organic chemicals or metals. It depends on the source water.”

Many challenges

Even though per-capita use in the United States is declining, recycling makes a lot of sense in water-short regions, says Andren. In the United States, “about 12 billion gallons a day [of 32 billion gallons treated per day] is shot into estuaries and oceans. In areas with generally high populations we are shooting away this water and will never have our hands on it again. If just a part of that could be reused, that would be good.”

But due to cost, recycling will only interest places with significant water shortages, Andren says. “We can do a great job at a cost, we can do anything at a cost.”

Ramping up reuse depends on introducing new technology, but that is a natural outgrowth of the steady introduction of sophisticated ways to clean wastewater and drinking water.

Andren, who reviewed the recent National Research Council report, says, “One of the major recommendations is that we basically have the treatment technology, and the approach to assess the hazards through risk assessment. Now we have to formalize that and work together on federal guidelines on how to start using more reclaimed water in daily life.”

Although a water shortage is not healthy, recycling, even if it increases supply, must still overcome the obvious “ecch” factor. “A lot of people ask, ‘If you have effluent from a sewage plant, and it goes through treatment, would you drink that?’” Anders says. “Absolutely, the technology is there, it’s being done all over the world. Our treatment technology and our ability to determine the quality of the water are such that it can be absolutely safe; it can be better than what you presently get out of the tap.”

Running short of worries? Then ponder the super-volcanoes — earth-bombs that can vomit 10 or 100 or 1,000 cubic kilometers of molten rock. Super-volcanoes can change history by creating rivers of red-hot ash moving at highway speed, spreading dust across hundreds of kilometers and spewing vapors that block the sun, destroy crops and start famines.

A volcano may go dormant for thousands of years after such a huge eruption, so they may be even harder to predict than smaller ones — which are also unpredictable at this point…

But this week, Nature published a new analysis of Santorini, a Mediterranean monster, that shows the movement of molten rock that preceded the eruption.

Santorini’s sudden release of 40 to 60 cubic kilometers of rock and ash was followed by a giant collapse that left a characteristic ring of hills called a caldera. Thousands may have died in the eruption, which laid down a 60-meter layer of ash and rock.

Eruptions of this general size happen about every 300 years, says Timothy Druitt, a volcanologist at the Université Blaise Pascal in France, who lead the current study. The most recent was in 1815 at Tambora, in Indonesia.

Druitt’s new analysis of crystals within the frozen magma offers a rough schedule for the entry of molten magma into a holding tank — the magma chamber — below the volcano, which is a precursor to eruption.

Caldera-forming eruptions rival earthquakes and tsunamis as the deadliest natural disasters. “People who work in the field know these volcanoes are not rare, even on a human time scale,” says Druitt, but “we have never been able to monitor one of these big eruptions during the long buildup phase, so we are not really sure how that happens.”

The crystal analysis detects microscopic changes in chemical composition, offering a unique, after-the-fact picture of the gestation of eruption.

In the crystals

As crystals grow in the cooling magma, atoms of trace elements diffuse within them, and both growth and diffusion are affected by conditions within the hot magma, says Druitt. “These crystals grow progressively, and as they do, their chemical composition changes according to the composition of the magma around them, and the temperature and amount of water in the magma.”

The crystals revealed that a big gob of magma — perhaps 10 percent of the magma chamber’s total contents — entered in the decades before the eruption. “Looking at the crystals in this magma, we were able to reconstruct very crudely events taking place in the last few decades prior to the eruption,” Druitt says.

That final addition probably made the magma chamber unstable, leading to the eruption, Druitt explains.

If such a late, large magma movement proves typical of super-volcanoes, that could contribute to a distant early warning system for mega-eruptions, based on more conventional methods, such as seismic monitoring.

Distant early warning

But the findings also carried a caution, Druitt says, since Santorini was apparently dormant for about 18,000 years before the last apoplectic outburst. “That is a slightly alarming result. There are lot of these big caldera systems, but most are in a stage of repose.”

The upshot is more proof that a dormant volcano can still be a dangerous one, he adds. “We can imagine that a big caldera in a remote region of the world, such as the Andes, which is not monitored very well, could reawaken pretty quickly on a human time scale.”

The crystal method gives after-the-fact data on an eruption. Current attempts to anticipate eruptions rely on data about earth shaking, deformation of the crust, and release of gases.

“It’s a very timely topic, and solid science in terms of the measurements and observations,” says Bradley Singer, a volcanologist and professor of geoscience at University of Wisconsin-Madison. “They admit that there are issues about the time scales,” largely because the diffusion of strontium and titanium is imperfectly understood in the hot magma.

The study’s title, however, specifies that the final growth of the magma chamber occurs on “Decadal to monthly timescales,” Singer notes. “It could be centuries or even longer, which implies that we’d have a longer time prior to the eruption” to worry about the effects of the rising magma.

Singer concurs on the importance of understanding the relationship of magma flows, instability and eruption, and says the crystal analysis is gaining traction in volcanology.

That’s just as well, since giant caldera-forming volcanoes may be frighteningly common. The one at Yellowstone, for example, released 1,000 cubic kilometers of rock 640,000 years ago. Wouldn’t you want to know if something like that was building on your continent?

2010 marked the completion of a bizarre telescope composed mainly of ancient ice. One billion tons of ice.

Buried a mile deep in the ice at the South Pole, IceCube is the world’s strangest telescope. Composed of water, it’s looking for the neutrino, nature’s most unusual particle. Eighty years after the neutrino was “invented” to balance a physics equation, it remains ultra-difficult to detect, measure and understand.

IceCube is focused mainly on particles that come all the way through the Earth. In other words, this telescope looks down.

Scientists say neutrinos can pass unscathed through a long bar of lead. How long? Say, one light year long — about 10 trillion kilometers. Because neutrinos can slip through everything in their path, including stars, galaxies and vast clouds of dust, they are unrivaled tattle-tales of ancient explosions in the deep universe.

The bad news is that the same property makes neutrinos extremely difficult to see.

But if you can somehow observe the neutrino’s insanely rare interaction with matter, you could learn something about the universe, and the gargantuan energy released by exploding stars.

Roots of a frozen telescope

That is the promise and the premise of IceCube, a $271-million project intended to solve a problem posed in 1930, when physicist Wolfgang Pauli proposed a new and rather odd particle. Tiny, energetic, with no electric charge and not necessarily any mass, it would be virtually undetectable.

Pauli himself admitted “I have done a terrible thing. I have postulated a particle that cannot be detected.”¹

The “now-you-don’t-see-it-and-you-never-will” neutrino was tailor-made for controversy; scientists detest what they can’t detect. Pauli’s idea was mocked² as “simply wrong” or “crazy.”

Today, scientists are sure nature is full of these shadowy characters: Rough calculations say a hundred trillion neutrinos whistle through your body every second.

Why make a big deal about neutrinos, which are, after all, less offensive than campaign ads? Because that ability to pass through all manner of interstellar crud allows neutrinos to carry messages from the far reaches of the universe.

Moreover, some neutrinos carry more punch than the wildest gamma ray. And just as you can’t pull a hot coal from a cold fire, you shouldn’t get “hot” neutrinos from “cool” sources like ordinary stars. These neutrinos, in other words, may deliver signals of some hip, blazingly hot stuff — neutron stars, active galactic centers, and exploding stars.

Finally, according to some scenarios, lower-energy neutrinos may comprise a small proportion of the mass — the stuff — of the universe, but they played a key role in the evolution of the universe.

In astronomy, as in love and antiques, “hard-to-get” translates into “most-wanted.” “The hope is that the particle that is almost nothing will tell us almost everything about the universe,” says Francis Halzen, a theoretical physicist at University of Wisconsin-Madison. Halzen directs IceCube, and did the same at IceCube’s predecessor, AMANDA, the Antarctic Muon and Neutrino Detector Array.

Search strategy for an elusive character

Neutrinos may be shy, but once in a great while, they actually hit an atom and produce a subatomic particle called a muon, which is easier to see.

Because the odds of a neutrino hitting anything are so dismal, physicists require bigger targets. It’s the same principle that lottery players use to “beat” the tiny odds of winning by buying hundreds of tickets.

Previous neutrino targets have included tubs of oil or dry-cleaning fluid and 5,000 tons of steel plates salvaged from battleships. To block spurious signals due to cosmic rays rather than neutrinos, these detectors have been sunk in the ocean or placed inside deep mines.

IceCube relies on a two-step detection sequence: First, the tiny percentage of neutrinos that interact with atomic nuclei in the ice produce muons. Second, these muons create Cherenkov light when they interact with matter.

When the detectors see Cherenkov light, they digitize the data and send it through electric cables to the surface for analysis. The detectors are housed inside 5,160 crush-proof glass spheres placed in holes drilled through the ice, and located 1450 to 2450 meters deep.

Another 324 detectors at the surface detect muons made by cosmic rays arriving from the Southern sky.

The Antarctic ice also has little radiation, and the detectors are so deep that air bubbles have been squeezed out, ensuring great optical clarity. Yet while the detectors are shielded from damage, they are under crushing pressure, and if they go bad, they will be busted forever.

IceCube will only look at muons that trigger at least eight detectors, says Halzen, and is most interested in muons moving upward — coming from the Northern Hemisphere. Downward signals can be confusing, as most of them are due to cosmic rays or lower-energy neutrinos, which Earth blocks.

Data from IceCube should suggest where the neutrinos originated and what sort of cosmic engine started them on their journey.

This desire to concentrate on neutrinos rather than cosmic rays explains why this frozen telescope, oddly but logically, looks downward.

What can these neutrinos tell us?

Neutrinos, “invented” to balance a physics equation, have grown to fascinate astrophysicists, galactic voyeurs seeking signals from astonishingly energetic structures and events in the deep universe. The direction and energy of neutrinos from each source should offer clues about the origin:

Image: NASA/JPL-Caltech/STScI/CXC/SAO

Located 10,000 light-years away in the constellation Cassiopeia, Cassiopeia A is the remnant of a massive star that died in a violent supernova 325 years ago. The dead star (turquoise dot in center) became a neutron star surrounded by a shell of junk blasted away in the explosion. Image is a composite from three orbital telescopes: Infrared data from the Spitzer Space Telescope is red; Visible light from the Hubble Space Telescope is yellow; Chandra X-ray Observatory data is green and blue.

Although supernova neutrinos have low energy and are hard to detect, a nearby supernova could light up IceCube enough to overwhelm the system. To prep for a supernova, Reina Maruyama, an assistant professor of physics at University of Wisconsin-Madison, is working to ensure that IceCube can handle this once-in-a-lifetime chance to get good data on a stellar explosion.

If something like the 1987 supernova exploded nearby in our galaxy, Maruyama says, “there would be so many neutrinos, the whole ice would glow. We expect that a few supernovas will occur each century in the galaxy, if one goes off, IceCube has to be ready. We stand to learn a whole lot about how they explode, and about the particle nature of neutrinos.”

Dark matters

Even weirder than neutrinos, IceCube may explore dark matter, a type of, well, something, that comprises 23 percent of the overall universe. A measly 4 percent of matter, including the galaxies, stars and planets, is visible. The balance is an even stranger quantity called dark energy.

The first inkling that some matter is invisible came in the 1930s, when a physicist noticed that galaxies rotate too fast: their visible mass would create too little gravity, and thus they should spin themselves into oblivion.

The explanation for that increased gravity is now called dark matter, and the race is on to detect it.

Since dark matter affects gravity, Maruyama says it must gather in the sun and the galaxies. When dark matter particles collide, they are expected to release a type of neutrino called muon neutrinos. But IceCube found no muon neutrinos coming from the sun and the Milky Way, using a technique that was 1,000 times more sensitive than previous ones.

Does absence make the heart grow fonder?

It depends on your perspective whether that’s good or bad, says Halzen. “There was a big celebration when we published, because we placed limits on that particular type of dark matter, but I looked at it another way: We had gone 1,000 times deeper, and it was very disappointing not to see dark matter.”

However, an experiment in Italy may have seen dark matter interacting with a hunk of sodium iodide, based on an annual variation in the signal. If Earth indeed orbits through a cloud of dark matter, the detector would register alternating downstream and upstream motions that could account for that annual cycle.

The cycle could, however, be due to something unrelated to dark matter.

To answer that riddle, Maruyama wants to place a similar detector deep in the Antarctic ice, and has already piggybacked two prototypes onto IceCube strings. The prototypes are working well enough to justify a larger, more expensive detector, Maruyama says.

If and when the experiment is replicated in Antarctic Ice, Maruyama says, “A positive result would be interesting, and a negative result would be interesting. If we can see a signal with the same timing, that confirms the [Italian] results. If we don’t see a signal, the source must be something aside from dark matter.”

Lurking behind the IceCube project is the tantalizing prospect of learning more about the bizarre particle it detects — the neutrino. We already know that neutrinos have a tiny amount of mass, and that they range in energy through at least 30 orders of magnitude — an unimaginable range of energies. There have been recent — and controversial — reports that neutrinos can travel faster than light — breaking a basic law of physics.

Why so weird?

That’s another indication that neutrinos exist at the edge of the standard model that attempts to explain everything by gravity, electromagnetism, and two nuclear forces, Halzen says. “We are measuring the properties of neutrinos any way we can, and extrapolating to see what the standard model predicts, and looking for variations. The simple way to describe the experiment is that we collect muons and neutrinos, and everything you don’t understand is a discovery, either it’s physics beyond the standard model, or it’s new astrophysics.”

Halzen anticipates spotting an extremely high-energy particle called the GZK neutrino. “These are predicted by theory, and if one hits the detector, we won’t have to do any analysis, we will be able to look at the event display and know that we have made the discovery.” GZK neutrinos are, according to theory, made by cosmic rays that strike photons in the microwave background, Halzen says, and thus could finally reveal the origin of the cosmic rays, one century after their discovery.

Neutrinos are slippery characters; shy, coming in incomprehensible numbers, being emitted by sources we cannot pinpoint. Maruyama notes that neutrinos seemingly change to a different “flavor” without any apparent cause, and says this “oscillation” from one state to another is the strangest part of the neutrino story. “Oscillation could have implications on how the universe evolved to have matter, and not anti-matter,” she says. “These tiny particles could have such an influence on the universe.”

So what?

Why should non-scientists worry about neutrinos? Halzen, who has answered this question many times, says “I have a personal answer. The reason we know our place in the universe is not because of French philosophers, it’s because of physicists. With dark matter and dark energy, we know most of the universe is not made of the same material we are made of. … Is that important to know? I think so.”

IceCube is not intended to produce technology or solve today’s problems, Halzen acknowledges. “This is total curiosity-driven science, and you are allowed not to care. But if you don’t do fundamental research, we’re going to be a developing country, that is clear.”

Particle physics proves that theoretical pursuits can have results that are unpredictable, yet practical and profitable, Halzen says. “My previous job was at CERN [the European particle-physics lab], where people discovered the Web in 1989, to enable collaboration among remote scientists. I think we have paid for all theoretical physics with that one discovery.”

Astronomers have just discovered two Earth-size, rocky planets around a nearby star. Though the planets are way too broilsome for life, they suggest that steady improvements in telescope technology has made the discovery of habitable planets just a matter of time.

But as astrobiologists continue to search for life in space, geo-biologists (ok, we coined that) continue to find bizarre life in strange places on Earth: in the dark ocean depths, between grains of sand, and at roasty-toasty temperatures once considered deadly.

Hot, humid, and totally alive!

Fifty years ago, nobody believed organisms could survive near the boiling point of water. When Thomas Brock started probing the hot springs in Yellowstone in the 1960s, he was not looking to overthrow a ground rule of biology. Instead, the University of Wisconsin-Madison professor, then at Indiana University, sought to study bacteria in a simplified, real-world environment.

At the time, and even today, precious little was known about how bacteria live their lives — unless they cause disease.

As Brock sampled his way up a hot stream, he approached its source in a hot spring, and the water temperature rose steadily.

At the time, biologists thought life would not tolerate temperatures near 80° C. But Brock kept finding bacteria, so he kept looking. Eventually, he found some that could live and reproduce near the temperature of boiling water — 100° C.

The prize of his collection was a bacterium he named Thermus aquaticus (for its hot-water habitat) and placed in a public repository for study by other scientists.

Over the years, T. aquaticus proved interesting indeed. For one thing, it was the first of more than 50 species of thermophilic bacteria known to tolerate or require temperatures near water’s boiling point.

For another, it was the first of the Archaea (ancient ones), primitive microorganisms that scientists now regard as a separate and highly primitive kingdom of life.

Deep roots indeed

Because thermophiles are Archaeans, and prefer the steamy conditions typical of early Earth, many scientists think they may tell us about the origin of life itself.

To any basic scientist, those contributions would be enough. But because their enzymes work in high temperatures, where chemical reactions are faster, the thermophiles have proven to be extraordinarily useful.

Today, enzymes derived from thermophiles are used to convert millions of pounds of corn (maize) into sugar to sweeten soft drinks.

But more important, at least to scientists who don’t guzzle fizzy pop at the lab bench, T. aquaticus supplied TAQ polymerase, the essential enzyme for polymerase chain reaction, AKA PCR.

PCR is an artificial technique that does what living critters do every day — replicate DNA. But PCR is the rocket ship of replication, since it allows you to multiply a piece of DNA a billion times in a few hours. That produces enough DNA to analyze to your heart’s content — for genetic engineering, biotechnology and forensic purposes.

PCR depends on TAQ polymerase.

Aware that PCR and soda pop are both billion-dollar industries, corporations and scientists around the world have frantically searched for other thermophiles that may have equally useful enzymes. They’re looking in odd places — not just hot springs and volcanoes, but also deep-sea vents, hot petroleum-bearing rock, the outflow of geothermal power plants, and smoldering piles of garbage.

Prowling for glow-in-the-dark squid

Call me Bob.

Short for bobtail squid. (Did I mention that I’m a 3-4 centimeter cephalopod, formally Euprymna Scolopes?)

Anyway, I hang out in shallow waters around Hawaii. Save your crocodile tears — somebody’s got to live in the sunny, tropical ocean. Anyway, here’s my problem: Even though I have 10 tentacles, I don’t have spines, poisons, or any other decent defense.

So I spend my days burrowed in sand at the ocean bottom, trying to keep out of mischief. Still, a fellow’s got to eat, don’tcha know, so I cruise at night, looking to grab a bite.

Here’s the snag: All sorts of nocturnal predators seem to have this thing about calamari sushi.

Light before flashlights

A long time ago, my ancestors evolved a nifty defense against their big teeth: stealth. Even their tiny squid brains figured out that predators could see them from below, as tasty dark blobs against the bright ocean surface.

Since this was before flashlights, my relatives had to improvise. So they press-ganged billions of luminescent bacteria into making light for them. The idea was to make us just as bright as the ocean surface — and hence invisible.

At least, this is how my great-aunt Tentacla tells it. To tell the truth, I think it had more to do with the evolutionary advantage of being hard to see.

Anyway, my ancestors fed the bacteria, and gave them a home in two specialized light-emitting organs. These “photophores” have a reflective membrane to shine all their light down, toward the hungry predators. They use a diaphragm to control brightness, and even have a lens to spread the light.

The photophore reminds me of a backwards eye — one that makes light rather than detects it.

My folks even figured out how to switch the bacteria “on” when needed.

In return, the bacteria got room and board, in the biological deal they call “symbiosis” or “mutualism.” Sometimes I think people could learn from this cooperative spirit….

But that’s enough thinking for today. My squid brain is squashed.

As I burrow into the sand for another daytime nap, permit me to introduce somebody who considers me almost as fascinating as I do.

Seriously speaking…

Margaret McFall-Ngai, a biologist at University of Wisconsin-Madison, says the bobtail squid may pretend it’s cooperating in a symbiosis with those light-making bacteria, but the reality is more ominous.

She says there’s evidence that this may be slavery, not symbiosis, since the squid, “inhibits the growth of the bacteria to enhance their luminescence.” The bacteria, Vibrio fischeri, could make a better living drifting in the ocean, or in the gut of another marine animal, McFall-Ngai observes.

The concept of bacterial enslavement broadens our perspective on the many possible relationships in the living world.

Most people, if they think about bacteria at all, conjure up disease and decay, but people would be dead without bacteria, since the little critters play essential roles in producing vitamins and preventing disease.

Since the bacteria in our guts vastly outnumber the cells in our bodies, it helps that they’re helpful!

Nevertheless, and for understandable reasons, bacteriologists have traditionally focused on disease-causing organisms, and, for simplicity, on one species at a time. But that skews our view of how bacteria actually live, says McFall-Ngai.

Three cheers for complexity!

Complexity and subtlety may be the hallmarks of these interactions, and the complexity begins by recognizing that V. fischeri is closely related to V. cholerae, which causes the human intestinal disease, cholera.

Cholera is caused by a V. cholera toxin similar to a toxin produced by the light-emitting bacterium. But far from harming the poor little bobtail, that toxin signals it to secrete food for V. fischeri, so the toxin is really a chemical “dinner bell.”

And this raises the intriguing notion that a cholera bug secretes toxins not to kill its host but to discuss its menu. If so, our whole notion of pathogenesis may need rewriting, McFall-Ngai suggests. “Maybe when we’ve been studying cholera pathogenesis we’ve been studying an aspect of a normal conversation that’s gone wrong.”

Indeed, the traditional bacteriological view of bacteria as pathogens to be studied in pure culture may be “like trying to understand the complexity of all the cultures that lived in Paris by studying the activity of the Nazi occupiers,” McFall-Ngai suggests. “You are studying groups that don’t belong there, and have disrupted the normal activities.”

Want more on how the flashlight squid bullies its bacterial brethren?

Between the grains

(1996 story, only photos have been updated)

To zoologist Robert Higgins, small is beautiful. His infatuation with small creatures — “meiofauna” — dates to a student job in a biology lab that paid 35 cents an hour. Instead of quitting for more lucrative work, Higgins was intrigued.

He’d heard about tiny, amazingly diverse creatures, and put grains of sand and muck through a fine mesh, and used a microscope to find hundreds of organisms.

Forty-four years later, Higgins has retired from the Smithsonian Institution, but he’s still goggling at meiofauna — a complex group of animals found in most Earthly environments.

Indeed, a handful of wet sand could contain more biological diversity than a whole rain forest, Higgins says.

In the course of peering through countless microscopes, Higgins has discovered hundreds of species. With Danish biologist Reinhardt Kristensen, he found an entire phylum, called Loricifera.

Phyla are the broadest categories of organisms, based on structure, and according to the International Association of Meiobenthologists, “The majority of recognized phyla have meiofaunal representatives. Currently, 20 phyla considered to be meiofaunal from the 34 recognized phyla of the Kingdom Animalia. Out of these 20 phyla, five are exclusively meiofaunal in size.”

Photo: Giulio Melone, department of biology, Milan University.

A bdelloid (a type of meiofauna) shrinks when it undergoes anhydrobiosis. The dormant, dehydrated bdelloid has greater resistance to environmental stress but is ready to spring back to the active form in conducive conditions.

Meiofauna living between grains of sand have made some fancy adaptations to their harsh environment. Some have hooks on their feet, used to grab the sand. Others have hooked mouthparts, also useful for locomotion.

Beyond freeze-dried

To survive a difficult environment, meiofauna called tartigrades have evolved an amazing adaptation called “anhydrobiosis.” In this form of suspended animation, the animals replace water in their cell membranes with sugar, protecting the membrane from destruction through radiation and freezing. Microorganisms die when their cell membrane ruptures.

During anhydrobiosis, organisms are rather like plant seeds or bacterial spores, Higgins explains. “They can dry up for 100 years, and be rewetted, and come right back to active metabolism.”

Fun is fun. But what is the practical importance of studying stuff that can hardly be seen, doesn’t seem to cause disease, and is — at least to some — utterly ugly?

In other word, who cares about microscopic beach crud?

Meet the beach-cleaning crew

Anybody who likes to hang on the sand should be interested, Higgins says. “This is the system that helps keep our beaches clean.” Plankton, bacteria, all sorts of dead material is continually washing ashore, and a lot of people love to sit on beaches.

There’s a public-health angle here. Hookworms occur on beaches where dogs defecate, but meiofauna may consume hookworms, along with other nematodes. “So if we upset that, we could upset beach cleanliness,” Higgins says.

Higgins notes that meiofauna comprise a basic part of the food web, and disturbing them could have unforeseen consequences for the entire system.

Still, it’s hard to escape the notion that most of the motivation here is the pure scientific urge to discover, to classify, to understand. Meiofauna, Higgins notes, were seen under the microscope Anton van Leeuwenhoek invented in 1683.

The key to finding these things, Higgins indicates, in patience, technology, curiosity — and institutional support. “If you stare through a microscope for hour after hour, you have a chance of finding these things, but if you need to get out a certain number of papers each year, you have to take shortcuts and you won’t find as much.”

Fantastic freak show

If you’ve hung around a big-city park, you may think that pigeons are countless — or uncountable. But according to scientists from New Zealand, pigeons now join the short list of animals that can count — or at least, can places images containing two countable items in numerical order.

It’s blue news for those who think only humans deserve human capacities. From empathy and altruism to murder and war, animals seem to have caught on to some of our best — and worst — tricks.

Now Damian Scarf, a post-doctoral researcher at the University of Otago, with his colleagues, has taught three pigeons to order pairs of numbers in the range from one through nine.

This is not exactly counting, but it certainly is a sign of numerical awareness in birds.

More important, the researchers have taught these retired racing pigeons the concept of smaller-to-larger, Scarf says. “Previously, this number abstraction was only known in primates, and now we have shown that it is not unique to primates.”

Serious screen-time serves science

The experiment began with a year-long training period, during which the birds were shown pairs of images, each containing one, two or three countable items. If the birds pecked at both images, smaller number first, they were rewarded with some wheat. (Although the images never contained a numeral, we refer to the “number” they contain for brevity.)

To prevent the birds from focusing on color, shape or other non-numerical details, the images showed a range of items, so that the only correct answer would reflect their number rather than other distinctions.

“The training time reflects how difficult it is for them to abstract,” Scarf says. “It’s such a foreign situation, number is not the first port of call when presented with a stimulus to discriminate. That’s why we had so many shapes, colors, surface areas.”

Even if the birds originally made their judgments based on color, “we pushed them to use a different strategy, to break away from that. Number is not the default discrimination mechanism” for pigeons, says Scarf, who worked under advisor Michael Colombo of Otago.

A genius for abstraction?

This does not mean that the birds are counting, says Scarf. “It’s more a fuzzy representation in the brain of what ‘three’ is. We can apply this verbal label to three, but they cannot. Pigeons, and animals in general, don’t have a definite idea of a number, that’s why they don’t perform perfectly, and why we see the distance effect.”

When the numbers on the test pair are further apart, Scarf found, “the fuzziness overlaps a little less.”

A greater distance between the numbers produced a quicker response and greater accuracy. For adjacent numbers, like four and five, the birds scored about 66 percent accuracy, compared to more than 95 percent for numbers separated by at least six. Once the difference rose to at least three, the pigeons did as well as monkeys in a path-breaking 1998 study that opened the field of numerical “thinking” in animals.

Scarf stresses that the birds were not just regurgitating what they had learned, but were learning numerical rules. “The goal was to find out whether they could acquire an abstract rule. We were just training for one through three, but they learned some flexibility, an abstract, ascending rule for ordering numbers” that would apply to other numbers on the screen.

Rooted in evolution, but where?

Being able to recognize that one thing is more numerous than another could help an animal survive, Scarf says. “When food is available in multiple places, an animal has to develop an optimal strategy for figuring out where the most food is, and I think we have subverted that capacity for this task.”

Where this capacity arose is anybody’s guess at this point. The evolutionary lineage of mammals and birds divided about 300 million year ago, Scarf says. “If this derived from a common ancestor, it’s very old. It’s also possible that primates and birds have evolved this independently.”

“I do think it’s important, just as our study of mirror self-recognition in monkeys, from the fundamental standpoint of how these abilities come about,” says Luis Populin, a professor of anatomy at the University of Wisconsin-Madison, who has found that, under certain conditions, monkeys can recognize themselves in a mirror. “It’s very nice and is yet another step toward understanding how our cognitive functions develop.”

You have to hand it to these birds, which have set a new standard for avian aptitude. “The new part is the idea that this abstraction of numbers is not tied to training,” says Scarf. “Most numerical tests with animals involve training and testing with the same numbers, but we were training with a limited set of numbers and testing them with numbers outside the range. They learned an abstract rule, and that’s what makes this study unique.”