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.”

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.”

Ever wonder why the calendar requires us to retool a schedule every year? Ever question why your birthday will fall on a different day of the week next year? Do you grit your teeth trying to remember to insert a leap day every four years, except on the century, except you do add a leap day on the fourth century?

Any rule that requires a double-exception to the exception, friend, is a rule that has overstayed its welcome.

Our calendar must account for the fact that Earth rotates 365.2422 times during one full orbit of the sun, so any calendar will require some shimming.

Two questions: How many shims are too many? And how many people would be willing to swap out the clunky calendar for a better one? Remember, no matter how smart the invention, inertia always gives an undeserved advantage to tried-and-true kludges like the QWERTY keyboard, invented to slow your typing speed.

Shims and arrows of outrageous calendar

The modern calendar dates to 46 B.C., when Julius Caesar (or more likely a lackey) built a calendar on the assumption that the year contains 365.24 days.

For a while, that was close enough, but by the 16th century, the tiny error was adding up, and the actual seasons no longer jibed with the calendar. In 1582, Pope Gregory (or was it his flunkeys?) pruned 11 days from October and produced the modern calendar.

The Gregorian calendar, sadly, still relies on that jury-rigged leap day, and it also forces any given date, whether holiday or not, to rotate around the seven days of the week like a weather vane in a tornado.

All those encumbrances bothered Richard Conn Henry, a professor of astronomy at Johns Hopkins University. “It’s disjointed, hideously inefficient and there’s no value added,” he told us.

Hideously inefficient?

Rather than kvetch ’til the end of days, however, Henry worked with Steve H. Hanke, an economist also at Hopkins, to build the logical, “permanent” calendar seen in the rollover, above.

Henry studies an obscure type of background radiation in the universe. We mentioned that astronomers are obsessed with time, date and Earth’s position, but Henry says, “I got into this calendar as a complete sideline. Some years ago, I was putting together a schedule for my course, and I thought, ‘Why do I have to put together a schedule? I just taught the same identical course.’ The reason is the stupid calendar changes each year in a pattern that is completely irregular.”

Nor was he the only person with this problem, he realized. “Every school, team, club, everybody has to go through this. But it’s not necessary at all. We can make a simple adjustment, preserve religious sensibilities, and come up with a stable calendar.”

Calling clever calendars

The Hanke-Henry Permanent Calendar has 12 months: four have 31 days, and eight have 30. Each quarter of the year is 91 days long, with two 30-day months and one 31-day month. Each year starts on Sunday, meaning Christmas is also Sunday.

Every year.

If you’ve been pecking keys on your calculator, you’ve already objected: I’ve been short-changed! The year has only 364 days! Right, and to compensate, every five or six years, we get an added seven-day week.

The freebie week, while not part of a month, allows the calendar to jibe with the seasons.

Beyond simplicity, the new calendar would help the money-changers, Hanke observes. Financial institutions calculate interest on a daily basis, but months have different numbers of days, and calculations require a lot of software tweaks. “Our calendar would simplify financial calculations and eliminate what we call the ‘rip off’ factor,” explains Hanke. “To determine how much interest accrues on mortgages, bonds, forward-rate agreements, swaps and others, day counts are required. Our current calendar is full of anomalies that have led to the establishment of a wide range of conventions that attempt to simplify interest calculations.”

Can the new calendar fly? The Gregorian calendar won acceptance because the Pope backed it, Henry notes, but he’s not sure he can get papal participation this time around. But without widespread acceptance, an “improved” calendar would really make things even worse.

Image: eliazar

Here’s a great idea that flopped: Part of a lesson in Esperanto, a simplified language invented in 1887 that, sadly, never caught on and brought international peace despite its many practical advantages.

One time fits all?

We’ve been saving the best for last. Doesn’t a stable calendar deserve a universal system of time? That’s right: one time, one date, worldwide. If it’s midnight in London (already hour zero on universal time), it’s midnight in San Francisco — where the sun is shining.

For people who do lots of traveling, or arrange international meetings, the advantages are obvious. Although this sounds awkward to The Why Files, Henry notes that, “In every single country, with zero exceptions,” airplane pilots already use coordinated universal time (UTC) rather than local time.

UTC helps fight confusion in the air, but even Henry recognizes that one-time-fits-all could be a tougher harder sell than the permanent calendar. The new calendar, he says, can stand on its own. “There are 365.2422 days in the year, there is nothing you can do about that. Our calendar must reflect that length. We have to take that magic number that nature has given us by accident and see what kind of calendar we can make.”

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.”

With little notice until recently, a shortage of medicine is starting to impair treatment at America’s hospitals. Common, cheap and necessary drugs needed to fight bacteria or cancer, to ease pain or to nourish premature infants are running out.

Many of these meds are injectables, which must be made under sterile conditions. All are generics, which sell for pennies compared to the buck-buster drugs that feed the bottom lines at the big-name drug companies.

Most shortages are unnanounced until a wholesaler’s shipment arrives lacking an ordered drug. “It’s unbelievable,” says Sara Shull, manager of the drug policy program at the University of Wisconsin Hospitals and Clinics in Madison. “Today I was trying figure out alternatives to papaverin,” an old drug used to prevent spasm in the many surgeries that involve grafting a blood vessel. “We have identified some alternatives, and I am now I working with the surgeon to figure out how to dose them, how to apply them. Is it bathed on? Sprayed on? He’s busy, we’re all busy, and sorting this all out takes a lot of time. The continual need to find replacements gives me a headache.”

Shortage-induced substitution played a role in Alabama, where nine hospital patients were killed by intravenous nutrients this summer, says Allen Vaida, executive vice president of the Institute for Safe Medication Practices, a non-profit that targets medicine hazards. “Because of a shortage, this compounding pharmacy was making a product from raw material, and it got a bacterial contamination.” (The maker of the nutrient solution, Meds IV pharmacy in Birmingham, Ala., is apparently out of business.)

Medications on this rack will restock a robot that fills individual patient envelopes that will be sent tomorrow to nurses’ stations in the hospital. Actually, the robot restocks itself in its 24/7 delivery of thousands of prescription drugs.

Photo: The Why Files

ENLARGE

Source: U.S. House of Representatives

Shortages are growing, especially for injectable medicines.

Running long on shortages

Pharmacists have always had to find substitute medicines, as patients keep coming through the door, but Vaida cites Food and Drug Administration numbers to argue that shortages are now at “crisis” proportions. “The FDA shows 70 shortages in 2006, 129 in 2007 and last year, there were 211. So far this year, we are already above 200 shortages, and the year isn’t done. Shortages have been around forever, but they have never reached this number.”

Some drugs can be substituted, says Vaida, but “especially with chemotherapy and nutritional products, it’s not like are three alternatives for some medications, as there are with blood-pressure drugs. Some chemotherapies are specific for certain cancers, and if they are not available, you may have no alternative or [you] may have to use a third-line alternative.”

The pharmaceutical situation has never been more complicated, with more than 45,000 prescription drug products on the market, from about 1,400 manufacturers. Although we could not easily find numbers, drug shortages are also rising in the United Kingdom, where the supply situation is complicated by the restriction on exports within the European Union.

Shortages have many possible causes, but because manufacturers tend to be closed-mouthed, it’s not clear which problems are most momentous or easiest to solve:

How short is short?

A drug is considered “short” if a specific dosage and formulation is unavailable, and in some cases, a similar item can be substituted. But Shull says that’s still a problem in a big hospital. If a product that is normally purchased in a pre-loaded syringe is only available in a vial, University of Wisconsin Hospitals and Clinics can no longer send a “unit of dose” to the nurse, and “that’s what the nurses are expecting,” Shull says.

Changing procedures complicate care and raise costs, Shull adds. “All our people are working in a complex system, with lives on the line. These shortages can be a recipe for increased errors.” Her hospital must dedicate one staffer to securing supplies of the common blood-thinner heparin, she says. Searching for alternate sources is less rewarding than studying the efficacy of various medication treatments, she adds. “It’s not what I was taught in pharmacy school, but when your back is up against the wall, you have no other options.”

Beyond impairing patient care, shortages have also become a major burden in medical research. Tests of new medicines, often set up to run at several hospitals nationwide, must give standardized meds to the treatment and control groups, and chaos can result when the drugs become unavailable. “These shortages are now affecting clinical trial options for patients with cancer,” Robert DiPaola, director of the Cancer Institute of New Jersey, told the House Energy and Commerce Subcommittee on Health on Sept. 23. “Due to the uncertainty of being able to obtain many of these drugs, enrollment of patients on clinical trials has been delayed or stopped in several of our trials.”

Howard Koh, assistant secretary of health and human services, reinforced that message to the committee: “Many of the cancer drugs in short supply … are mainstays of the anti-cancer arsenal, and were largely developed through federally funded research begun 20, 30, even 40 years ago. They are still essential to treatment and research,” he said. The National Cancer Institute is currently sponsoring 349 clinical trials that require these drugs, Koh added. “Taken together, these studies represent thousands of patients, as well as a significant federal investment in clinical trials research.”

At the same hearing, Mike Alkire, chief operating officer of Premier healthcare alliance, told Congress how widespread the shortages have become. In a recent Premier survey, 53 percent of hospital pharmacists said they had faced at least six shortages “that had the potential to cause a medication safety issue or an error in patient care.” And 34 percent of respondents said at least six shortages had “resulted in a delay or cancellation of a patient-care intervention.”

Premier estimates that the 2,500-plus non-profit U.S. hospitals in its membership pay an extra $66 million per year due to these shortages — which translates to $415 million at all U.S. hospitals.

Market going gray?

When the usual sources run dry, hospital pharmacists often get emails, faxes and phone calls from the “gray market,” sources outside the usual supply chain. In the summer of 2011, the Institute for Safe Medication Practices surveyed 549 hospitals and found that:

Alkire, of the Premier alliance, told Congress that the gray market is “appalling,” with an average markup of 650 percent. Forty-five percent of the offers were marked up at least 1,000 percent above normal price, and drugs for leukemia and non-Hodgkin’s lymphoma were marked up 4,000 percent. “We saw similar markups for medicines for sedation during surgeries; to dilate veins and prevent brain or heart spasms; and to prevent damage during a heart attack,” Alkire said.

For these reasons, University Hospital at UW-Madison does not buy gray, says Shull, although it does buy from a wholesaler that seems to have supplies of drugs when nobody else does.

The gray market arouses suspicion: How do some firms know about shortages before anybody else? How do they obtain drugs when normal sources are short?

“There is speculation going on,” says Vaida. “Some secondary wholesalers may try to buy up some available drugs and sell them for higher prices. Often times, they are looking for people who need the product, and try to obtain it from whatever sources. Some are playing it almost like Wall Street, anticipating what may go on shortage — if two manufacturers have just consolidated, and there’s a generic product that is only going to be made by one of them.”

Cures for missing meds

Many measures have been proposed to ease the medication shortage:

Photo: Armin Kübelbeck

Generic, injectable drugs comprise the majority of shortages.

The FDA seems to be getting the message. In testimony to the subcommittee on Sept. 23, Koh claimed that the agency had already headed off 99 looming shortages in 2011, compared to 38 for all of 2010. But Koh added that today’s shortages “include standard therapies for the treatment of lung, breast, ovarian, testicular and colorectal cancers, as well as several types of lymphomas and leukemias.”

Sometimes, Koh said, common-sense, proven measures can sidestep shortages. “… the FDA was able to mitigate a shortage by allowing the use of a filter to safely remove foreign particles contained within vials of injectable drugs, averting the obvious risk to patients of having metal shavings or other particulate matter injected into their veins.”

A pessimist, of course, could say the higher number of averted shortages simply reflects the greater number of shortages overall.

At any rate, organizations concerned with shortages say they are in a vise. “From our members’ perspective, it’s become [a] crisis,” says Hill. “We are seeing shortages nationwide. We have been tracking this for about 10 years, but in the last few years, we’ve seen a spike in the numbers.”

Given the problem’s multiple and sometimes obscure, roots, Hill sees “no single solution, and that’s the troublesome part. Unfortunately we will be dealing with this for a while. But there are some things we can do. We’d like to establish a mandatory early-warning system, so a manufacturer that has a problem has to notify the FDA. The FDA says it has avoided 99 shortages in the past year when it had that information. When there are multiple sources, the FDA can reach out to other manufacturers and urge them to ramp up production.”

David J. Tenenbaum

Japan, a world leader in earthquake engineering, has been paralyzed by a series of giant waves that followed one of the most violent earthquakes in a century.

Although the magnitude 9.0 quake on Mar. 11, 2011, apparently did not collapse high-rise buildings, the ensuing tsunamis flattened vast areas along the northeast coast. The death toll is swelling steadily as bodies wash in on the surf, and citizens and Japan’s Self Defense Forces scour a landscape turned upside down by inconceivably powerful waves.

The news recalls the estimated 250,000 people who perished, mainly on the Indonesian island of Sumatra, in the 2004 “Christmas tsunami” that followed a huge, offshore quake. (Both Japan and Indonesia are volcanic lands in the Ring of Fire, which partly surrounds the Pacific Ocean in a giant series of subduction zones and volcanoes.)

Shortly after Japan stopped shaking at 2:46 pm local time on Friday, March 11, we began hearing about troubles at a series of nuclear plants. After the reactors automatically shut down during the quake, emergency systems for removing heat still being generated in the reactors were routinely switched on.

But because the electric grid was down and the standby generators were damaged — perhaps by seawater — the emergency cooling failed. By Tuesday, March 15, three reactors had exploded, a fourth was burning, radioactive material was airborne, reactor workers were being evacuated, electricity was growing short in Tokyo, and the crucial containment vessels were under severe threat if not already breached.

With the first nuclear meltdowns since Chernobyl, in 1986, under way, global stock markets were crashing.

What causes tsunamis?

As Japan licks its wounds, The Why Files wants to know what causes tsunamis. How do they travel across the ocean? How they have impacted coastal people through history? Can we reduce our vulnerability to nature at its most cataclysmic?

Graphic: Anthony Liekens

Movement of the sea floor translates into waves at the surface.

Tsunamis — once slangily called tidal waves — are extremely powerful waves caused by large undersea disturbances. (“Tsunami” derives from Japanese for “harbor wave,” reflecting the fact that harbors can concentrate their energy. True tidal waves are the slow oscillations that drive ocean tides in response to solar and lunar gravity.)

Although landslides and volcanoes cause some tsunamis, probably 95 percent result from underwater earthquakes that contain a strong vertical motion. Such quakes often occur where one of Earth’s tectonic plates dives, or “subducts,” beneath another.

Like the Sunda trench near Sumatra, the subduction zone in the Japan trench is notorious for large earthquakes, says Timothy Masterlark, an associate professor of geological science at the University of Alabama. Although the timing is always uncertain, he says, “The history was known, big earthquakes were known, and even though the people and government went to great lengths to prepare, at some level … there is simply nothing they can do.”

Lessons from Sumatra

Masterlark, who has studied the giant, 2004 earthquake and tsunami in Sumatra, says the magnitude 9.0 earthquake in Japan likely broke a fault stretching at a shallow angle from the sea floor roughly 150 kilometers beneath Japan, along a trench several hundred kilometers in length.

We asked Masterlark how, if the slip was mainly horizontal, the rocks had enough vertical movement to cause a tsunami. “In Sumatra, we found a shallow slip created some vertical movement because the rock at the surface was softer, so the fault became more vertical, which changed the slip from mostly horizontal to mostly vertical.”

To imagine how vertical movement of the seafloor causes a tsunami, imagine making waves by throwing a stone in a pond. Even though earthquakes disturb the bottom of the water, the analogy works: just as a larger stone, thrown faster, makes a larger wave, the size of the tsunami depends on extent and speed of the ocean-floor movement.

The tsunami is usually most intense close to the earthquake: as waves spread from the epicenter in a typical arc-shaped pattern, their energy also spreads out.

Spread out, but still powerful

One factor that distinguishes tsunamis from more familiar waves is their extreme wavelength. On the open ocean, the peaks of waves may be 300 kilometers apart, and they may travel at 500 to 600 miles per hour. Even though they can keep pace with a jetliner, you wouldn’t see a tsunami from the cockpit of a jet. A killer tsunami may be only 2 feet tall in mid-ocean — far too small to be noticed from an airplane or even a ship, yet it can carry huge amounts of energy across the Pacific.

All that kinetic energy can hide in waves we can barely see because long-wavelength waves are extremely deep, and the massive amount of water moving beneath the surface contains enormous energy.

In deep water, boats can ride the worst tsunamis without noticing them; but when they reach shallow water and “run aground,” these waves become dangerous.

Like all waves, tsunamis slow when the lower part of the wave encounters the upward-sloping ocean floor. But while the front of the wave slows, the wave behind is still moving faster, causing a giant pile-up at the front, and the kinetic energy that was spread through the ocean depth concentrates in a towering wave at the surface.

Wild waves

It is these surface waves — which can be 10 meters high or taller as they cross the beach — that cause the utter destruction of tsunamis. Like all waves, tsunamis have both a rising and a falling motion, says Masterlark. “Depending on where you are with respect to the earthquake, you may first see a wall of water, or the opposite, the sea retreating.” In 2005, during a research cruise to Sumatra, “We were told that the tourists had heard that the ocean was retreating, and saw this as a great holiday, ‘Let’s walk on the seashore,” and this wall of water came in and killed them. This was a great warning, when they saw the water retreat, they should have headed away from the shore.”

Tsunamis have other quirks. They can be spaced as much as one hour apart, so subsequent waves can kill those who return to help victims of earlier waves.

In 1998, Harry Yeh, a civil engineering professor now at the University of Oregon, told us that tsunamis can have decidedly unconventional behavior. In one case, he said, a tsunami destroyed houses in a cove without damaging a house on an unprotected headland: “It’s the exact opposite of what a storm wave would do.”

A warning

Modified from original image by NASA

Location of foreshocks, aftershocks and the March 11 Japan earthquake (M 9.0). Circle size represents quake magnitude. Dotted lines = foreshocks; solid lines = aftershocks

The Pacific Tsunami Warning Center, established in Hawaii in the wake of the deadly 1946 tsunami, is a nexus in the global warning network. Since almost all tsunamis originate in earthquakes, the warning centers rely on data from seismographs, many of them located on the unstable ring of fire.

Tsunami warnings are now triggered automatically, says Masterlark, based on measurements of earth movement. “Seismographs are excellent because in seconds they can tell that a quake of some magnitude, big enough to trigger a tsunami, has occurred. This information can automatically trigger a warning in seconds.”

In tsunamis, seconds saved can translate into lives saved.

Researchers are working to use global positioning system (GPS) data to refine size estimates, Masterlark adds, to give “a more refined view of the potential risk, but this takes a little longer and is still in a research mode.”

Further confirmation of the size of the wave may come from special purpose ocean buoys, if they are in the right place, Masterlark says. “But they only work once the tsunami has already arrived, so they can only confirm or help refine the warning.”

Tricks of the tsunami trade

In terms of generating tsunamis, not all underwater earthquakes are created equal, says Andrew Newman, assistant professor of earth and atmospheric sciences at Georgia Tech. “A few times a decade, we have what we call ‘tsunami earthquakes’ that create a tsunami that’s much larger than would be expected for the magnitude of the earthquake,” largely due to a shallow rupture. “Usually a magnitude 7.8 earthquake would create a tsunami that might rise only 20 centimeters to 1 meter [when it reaches land], but one in Sumatra last year created a 17-meter tsunami.”

These large tsunamis come from a smaller break in the ocean floor, and so contain relatively little energy and do not travel well across the ocean, Newman says. But they also offer less warning because local people do not feel the massive shaking associated with a major tsunami.

Newman and colleagues have developed software to detect the peculiar signature of the tsunami earthquake, and are now running it on a research basis. “We get an earthquake or tsunami warning within four or five minutes, our algorithm starts processing, and a few minutes after that, the system sends email to the Pacific Tsunami Warning Center and the U.S.G.S. [Geological Survey],” Newman says.

Although the Japanese had little time between the earthquake and the tsunami, Newman says the national warning system did work. “In some ways, you have to look at real success in Japan. They have developed a substantial tsunami warning system, and it worked in as quickly as three minutes. People did evacuate, for the large part. Much of the video you see is from helicopters, or people watching from two or three stories up in buildings. There is only so much you can do with these events; this is a massive force.”

But the rising casualty counts highlights the deadly role of proximity to the quake, says Masterlark. “The very sad part is that because the quake was so close to the coast, they had very little warning; the time between the earthquake and the tsunami was minutes.”

More distant regions had adequate warning, Masterlark adds. “We had several hours before the wave reached Hawaii, and so were prepared. But Japan, unfortunately, even if you knew it was coming, you had only minutes, and that’s not enough time for many people to get to higher ground.”

Photo: Sarah Ruth

Basic tsunami safety

Public education and quick personal action remain the only ways to reduce the tsunami death toll:

1. Be on guard for strong earthquakes, which can spark a tsunami. If you feel one near the water, run inland.

2. Heed the warnings, and stay tuned to emergency radio stations.

3. Never go down to the beach to watch for tsunamis — they move much faster than you can run. People die doing this.

4. Most structures in the danger zone provide no protection. However, the upper stories of tall, reinforced concrete hotels can provide refuge if you have no time to move inland or to higher ground.

5. A tsunami is a series of waves. Don’t go near the water until you hear the all-clear from emergency authorities.

Following fatal footsteps?

Seismologists are loathe to predict earthquakes, but in the past decade or two, they have recognized that earthquakes occur in series along major faults in Turkey and Sumatra, as big quakes place extra stress on the adjacent fault. In Sumatra, a violent series of quakes began in 2004 with a magnitude 9.1, a magnitude 8.7 in 2005, a magnitude 7.6 in 2009, and a magnitude 7.7 in 2010.

The large quake in 2005 did not cause a major tsunami, but its timing, just three months after the Dec. 26 monster, suggests a compelling reason to focus intensively on the earthquake zone in the Japan trench, says Masterlark. “I am not trying to be alarmist, but I’m trying to look at where earthquakes have occurred along nearby faults to identify faults at risk. We’ll bring in numerical modeling and try to predict this as fast as possible. Time is of the essence, as we saw in Sumatra.”

As deadly American drones work the skies over Afghanistan and Pakistan, we got to wondering how similar remote-control approaches are contributing to science. In science, as in war, leaving the staff behind can slash costs and allow sustained exploration of no-go zones.

Part of the story is propulsion: New science vehicles can travel long distances through the ocean and atmosphere with minimum energy. Brains-on-board also matter: Computers enable these super-sensors to make decisions and work long stretches with little or no back-seat driving.

The result is a lot of science per gallon.

Although the vehicles we’ll look at have scientific purposes, they get major financial and technical support from the Department of Defense, proving that military and peaceful pursuits are inextricably linked in extreme environments.

If you dig the deep ocean, WHOI — the Woods Hole Oceanographic Institution on Cape Cod — is a good place to be. The renowned saltwater scientific outfit has a new, deep-water explorer that works without a lifeline.

Meet Sentry, which can take photos and make chemical and geophysical measurements down to 4,500 meters depth, and has worked two high-profile environmental issues: global warming through methane release, and BP’s Deepwater disaster.

Sentry has been used to look for “cold seeps,” regions of the seafloor that release large amounts of methane, says Chris German, WHOI’s chief scientist for deep submergence. “Cold seeps are like the overlooked younger sisters of hydrothermal vents,” the “black smokers” that release superheated fluids and anchor unique ecosystems at the sea floor, usually in mid-ocean.

Cold seeps are located closer to the continents, and “are not as spectacular thermally or geologically, but they do have some of the same chemistry,” says German, “and a lot of the same kinds of animals, even the exact same species.” Cold seeps may explain the distribution of deep-sea organisms around the ocean, he adds. “We want to understand … whether animals are using these locations as stepping stones.”

Most cold seeps were found by accident, but German thought Sentry could detect subtle chemical clues, and last October, he got to test that idea at an underwater landslide off the coast of Norway. The landslide had released pressure on a material called methane hydrate, and a large amount of methane was bubbling from the seafloor mud, creating a “mud volcano.”

Methane is a much more powerful greenhouse gas than carbon dioxide, and given the staggering amount of methane held in methane hydrates, such releases could create a nightmare feedback: warming releases methane, which traps more heat, causing more warming that releases more methane.

Getting engulfed

By prowling around the known cold seep near Norway, German confirmed the detection hypothesis.

Then, the day after Sentry returned to Woods Hole, a real-world opportunity appeared for the new technique.

Biologist Charles Fisher at Penn State was about to embark on a mission into the aftermath of BP’s blowout in the Gulf of Mexico, and he wanted help locating a coral patch to compare to another he’d already located 1,200 meters deep, 11 kilometers southwest of the blowout.

That coral was coated with a brown goop that looked suspiciously like crude oil. Could Sentry locate, for long-term comparison purposes, a similar coral outside the oil plume?

Fisher was part of a National Science Foundation-sponsored “rapid response” cruise to the Gulf, but German was still unpacking. “We’d have two weeks to turn around and get going, and I went to our guys Monday morning and asked, ‘Can you do this?’”

The maintenance crew figured out who would miss what weekend, and they agreed to do it, German says.

Cold seeps and deepwater coral in the Gulf of Mexico are linked, German explains, because the coral live on bare rock, which is often carbonate, and carbonate rock forms at cold seeps when methane is oxidized into carbon dioxide. “So beneath every healthy deep coral, is an active or historic cold seep.”

Suddenly, a theoretically interesting search technique became relevant to the biggest American oil spill in a century.

“Flying” with a map

Based on oil-industry data about the sea bottom, Sentry visited one location southeast of the Macondo well and found no coral. But at the second location, German says, “We hit pay dirt. We flew backward and forward, and found an active cold seep and evidence for tube worms, mussels and coral.”

Ocean-floor research seldom moves so fast, German says, and within hours, he was one of three people to visit the spot in Alvin. “In 36 hours, we went from nothing other than a hunch, to having a topographic map and photos,” German says. “We dove to the sea floor, and there was no mysterious driving around in the dark. Within 15 minutes, we drove to the site because we had a perfect map of where to go.”

In fact, German was holding a fresh, glossy photo of the target, taken less than two days previously.

Sub-terra cognita? Not!

And so is the ocean bottom, as people often say, still less familiar than the far side of the moon? German insists that it still is, despite years of research and an increasingly capable flotilla of deep-sea ships. “In December, in the Gulf, I could see at least 10 to 20 oil rigs… but I’m pretty sure, driving across that seafloor a couple of hours offshore from the United States, that nobody ever laid eyes on it before.”

A recent survey of marine biodiversity shows a chain of ignorance stretching across the Pacific, located near regions of extremely high biodiversity near the Philippines and Australia, German says. “In many of those locations, they’re 300 miles square, there have been fewer than 50 biological measurements in the history of the ocean. This is a chain across the South Pacific ocean, the single biggest contiguous ecosystem on the planet, and it has not been studied.”

And that’s the rule, not the exception, German says. “Close to one-half of the planet is at least 3,000 meters deep, and it’s much further away [and deeper] than the Gulf. From satellite altimetry we have an idea where the bumps are on the seabed, but we don’t know what’s going on; we have a vanishingly small idea.”

Deep water may be the sexiest place in oceanography, but long-term studies are also difficult and expensive in shallow waters, especially if they are remote, icy, stormy, or all three. Propellers, the standard way of moving through water, require a lot of energy and quickly drain batteries on artificial fish.

Gliding — think of soaring like a hawk as opposed to flapping like a sparrow — is a much more conservative approach.

And gliding is the MO of Seaglider, a project built by the University of Washington with money from the Office of Naval Research and the National Science Foundation. Using battery power, the glider alters its buoyancy, causing it to rise or fall through the water. By altering its center of gravity and adjusting its fins, the metal fish moves horizontally with minimal amounts of electric current.

How minimal? In 2009, a Seaglider traveled a record 3,050 miles through the North Pacific during a 9-month journey, without the caress of a human hand or an electric transfusion.

Costing “only” about $100,000 apiece, about 60 gliders are working around the globe, says Craig Lee, a principal oceanographer at UW’s Applied Physics Laboratory, recording basics like temperature, salinity, dissolved oxygen and optical characteristics of its surroundings.

In 2008, south of Iceland, gliders and floats studied carbon uptake by phytoplankton — floating plants that bloom in spring and play a major role in the global carbon cycle. The goal was to follow “parcels” of water during the entire bloom — which ends after some weeks when plankton are eaten or sink in the water. Both processes can remove carbon dioxide from the atmosphere for long-term storage, and therefore have implications for global warming.

“We were trying to learn what drives the carbon flow,” says Lee. “Nobody had done this before: the Seagliders and the buoys had the persistence, the ability to be there for the entire duration of the bloom. You would have to schedule a ship one year ahead, and … if you got there on time, it would be too expensive to keep the ship out there for the whole bloom.”

If ice is nice, under ice is nicer!

In 2009, a Seaglider spent 51 days in Davis Strait, the frigid water separating Greenland and Baffin Island, traveling more than 450 miles under the ice. The Strait is a chief source of melt-water from the frozen Arctic Ocean.

Climatologists worry that a rush of cold, fresh water through the Strait could alter the warm Gulf Stream and freeze Northern Europe.

Getting measurements from Davis Strait is expensive and dangerous, especially considering how much of it is under ice. But the Seaglider did just fine, says Lee. “This was very exciting, that ability to stay out there for a long time, and the ability to get to places that otherwise would be difficult. In winter in the North Atlantic, nobody wants to be there…”

The fish navigated under the ice using five anchored sonar beacons that created an undersea version of GPS, Lee says. Ten times, using its software, the glider found holes in the ice, poked its nose through them, and phoned home via satellite telephone. “It tries to sense ice by looking at the temperature of the water,” says Lee. “It emits a ping and tries determine whether ice is overhead, and it has a climate map that tells it, for a given position at a given time, is ice likely to be overhead? Using all that information, it decides whether to surface.”

During those famous North Atlantic storms, “It just keeps working, it does just fine, continues to navigate, continues to report. We’ve been in 40-foot seas, with 60- to 80-knot winds, and everybody’s happy, although it takes a little longer to get a phone call through.”

The glider carries a quarter for the phone call, but no Dramamine…

A fruit of the military’s desire to see everything from a safe vantage, Global Hawk is a secretive, high-flying, pilot-free jet that can fly at 60,000 feet for 30 hours, non-stop.

For its occasional forays into peaceful work, Global Hawk carries a large cargo of scientific instruments that can monitor light, pollution, ozone, water vapor, weather, clouds, incoming and outgoing radiation, even particles smaller than 1 millionth of a meter across.

The Hawk, which flew scientific missions from NASA’s Dryden Flight Research Center in California in April, 2010, can also be used for earth observation, such as tracking algal blooms in the ocean, vegetation on land, and various resource issues.

Hawk has tracked pollution from Asia above the North Pacific as it moves toward North America and looked at large-scale atmospheric circulation, which influences weather and the distribution of radiation-blocking high-altitude ozone.

We could not get through to a source at the National Oceanic and Atmospheric Administration, which plays a role in Hawk’s science, but we grabbed a press release issued after Hawk’s first environmental flight.

According to Paul Newman, an atmospheric scientist from NASA, “The Global Hawk is a revolutionary aircraft for science because of its enormous range and endurance. No other science platform provides this much range and time to sample rapidly evolving atmospheric phenomena. This mission is our first opportunity to demonstrate the unique capabilities of this plane, while gathering atmospheric data in a region that is poorly sampled.”

In their quest for data on the deep, scientists have gotten a trickle of info from sensors attached to deep-diving marine mammals. In November, 2009, the Scripps Institution of Oceanography launched SOLO TREC (Sounding Oceanographic Lagrangrian Observer Thermal RECharging vehicles; glad you asked?), a bobber that can sink 500 meters into the ocean, then return to the surface to report via satellite to scientists who may prefer sipping lattes at a Java Joint to crowding the rail on a topsy-turvy research ship.

Let’s call this Solo, and let’s agree that it’s a strange vessel. Solo can adjust its buoyancy, but lacks propellers and cannot drive laterally, so its location is at the mercy of the currents.

Solo records basic ocean conditions, but the real accomplishment is proving that its power system needs no recharging and could, theoretically, operate more or less forever – or at least until it breaks or barnacles or plants foul the fish up and slow it down.

Solo had already completed 300 dives by March, 2010, and although it sounds like a perpetual motion machine, it actually sucks its energy from the ocean as it rises toward the surface:

According to Yi Chao of the Jet Propulsion Lab, a Solo principal investigator, “This technology to harvest energy from the ocean will have huge implications for how we can measure and monitor the ocean and its influence on climate.”

Funded by NASA and the U.S. Navy, Solo’s technology is also obviously useful for monitoring animals and the movement of ships and submarines.

When Deepwater Horizon blew up and melted down in April, the wound it tore in the Earth’s crust released a gusher of crude oil, estimated at 4.2 million barrels, into the Gulf of Mexico.

The massive microbial munching of methane during the BP spill may be the only good news from the Deepwater Horizon disaster.

The blowout also released about 160,000 tons of methane. If you counted molecules in BP’s blowout, methane (CH₄), the simple hydrocarbon that fuels stoves, furnaces and electric generators, was the single most abundant one.

But a report published in today’s Science shows that BP’s methane was totally devoured by microbes in the Gulf of Mexico, leaving less than .01 percent of the methane to enter the atmosphere. “We measured the sea-to-air flux of methane and found it was completely negligible,” says first author John Kessler, an assistant professor of oceanography at Texas A&M University.

Within four months of the April 20, 2010, blowout, a population explosion among methane-eating bacteria native to the Gulf decomposed virtually all of the methane, mainly in deep water, says Kessler.

Study author John Kessler extracts a water sample from a device that detects changes in water conductivity and temperature with depth.
NOAA Pisces.

The study offered three lines of evidence that bacteria were “eating” the released methane:

• Methane levels in the Gulf fell up to 10,000 times between June and October.
• Methane-munching microorganisms became extremely abundant downstream of the blowout. “Over the summer, the methane degraders were higher than we have ever seen at any other place in the world,” says Kessler.
• Dissolved oxygen in the water dropped as methane and oxygen reacted to form carbon dioxide and water, Kessler says. “Once we summed up all the lost oxygen in the area of the methane plume, we saw that it could only be explained by a complete [microbial] consumption of this methane.”

Although oxygen depletion is already a concern in the Gulf’s “Dead Zone,” the average loss was only 3 percent, Kessler says.

In a previous study, ethane and propane, two other natural gases that BP also released, decomposed even faster than methane, and were no higher than background levels by early fall. In both studies, Kessler collaborated with David Valentine of the University of California at Santa Barbara.

Cool news for your atmosphere

In the short term, spilled methane is less environmentally dangerous than crude oil, but it can pose a global warming problem in the long term, since a molecule of methane stores much more heat than a molecule of carbon dioxide.
Methane seeps are frequently found at ocean floors, where methane from decomposition enters the ocean. And unfathomable quantities of frozen methane are stored beneath the seabed.

So inquiring minds want to know: If and when this methane enters the ocean, could it reach the atmosphere and accelerate global warming?

Pisces, a research ship of the National Oceanic and Atmospheric Administration, was a floating laboratory to study Deepwater Horizon's aftershocks.
Photo: John D. Kessler/TAMU

The giant Deepwater spill contained too little methane to affect atmospheric levels, says Kessler, “but it does simulate a very energetic release from a seep or a methane hydrate, and so we were interested in using it as an analog for understanding how a massive submarine release of methane might behave.”

Although the microbes-eat-methane story provides a rare bright spot in BP’s ecological disaster, it’s not clear what would happen in shallow water, and in places lacking natural methane and a ready supply of methane eaters.

“The Gulf of Mexico has many natural methane seeps,” says Kessler, “that probably account for why Gulf waters are populated with these microorganisms, which are ready to degrade methane once there is a massive restocking of their ‘buffet.’ How this may play out at another place, without the natural seeps, I’m not sure.”

Within four months, bacteria had spawned enough offspring to devour essentially all of the added methane in the Gulf. “But if the bacteria are at lower abundance, would this take five months or two years? We don’t know.”

– David J. Tenenbaum