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.”

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?

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.”