Thursday, May 21, 2009

Math, biology and the city

Moral of the story: While I usually stick to the content I say I cover, I found this article to be sufficiently interesting to warrant its only marginal appropriateness. Studying mathematics may be boring in my opinion, but the results they come up with surely are not. The laws described in this New York Times article describe how similar cities are to mammalian bodies. The same natural principles governing life in our bodies holds sway over the structure and content of cities across the globe. I'm sorry, but you will have to read the whole article to get the full benefit this time.

May 19, 2009, 8:26 pm

Guest Column: Math and the City

Thanks again to Leon Kreitzman for four fascinating articles about biological clocks in everything from peonies to people. My sabbatical is rapidly drawing to a close — but it isn’t over yet! My guest for the next three weeks is Steven Strogatz, a professor of applied mathematics at Cornell University and the author of “The Calculus of Friendship: What a Teacher and a Student Learned about Life While Corresponding about Math,” to be published in August.
Please welcome him.
— Olivia

By Steven Strogatz

As one of Olivia Judson’s biggest fans, I feel honored and a bit giddy to be filling in for her. But maybe I should confess up front that, unlike Olivia and the previous guest writers, I’m not a biologist, evolutionary or otherwise. In fact, I’m (gasp!) a mathematician.

One of the pleasures of looking at the world through mathematical eyes is that you can see certain patterns that would otherwise be hidden. This week’s column is about one such pattern. It’s a beautiful law of collective organization that links urban studies to zoology. It reveals Manhattan and a mouse to be variations on a single structural theme.

The mathematics of cities was launched in 1949 when George Zipf, a linguist working at Harvard, reported a striking regularity in the size distribution of cities. He noticed that if you tabulate the biggest cities in a given country and rank them according to their populations, the largest city is always about twice as big as the second largest, and three times as big as the third largest, and so on. In other words, the population of a city is, to a good approximation, inversely proportional to its rank. Why this should be true, no one knows.

Even more amazingly, Zipf’s law has apparently held for at least 100 years. Given the different social conditions from country to country, the different patterns of migration a century ago and many other variables that you’d think would make a difference, the generality of Zipf’s law is astonishing.

Keep in mind that this pattern emerged on its own. No city planner imposed it, and no citizens conspired to make it happen. Something is enforcing this invisible law, but we’re still in the dark about what that something might be.

Many inventive theorists working in disciplines ranging from economics to physics have taken a whack at explaining Zipf’s law, but no one has completely solved it. Paul Krugman, who has tackled the problem himself, wryly noted that “the usual complaint about economic theory is that our models are oversimplified — that they offer excessively neat views of complex, messy reality. [In the case of Zipf’s law] the reverse is true: we have complex, messy models, yet reality is startlingly neat and simple.”

After being stuck for a long time, the mathematics of cities has suddenly begun to take off again. Around 2006, scientists started discovering new mathematical laws about cities that are nearly as stunning as Zipf’s. But instead of focusing on the sizes of cities themselves, the new questions have to do with how city size affects other things we care about, like the amount of infrastructure needed to keep a city going.

For instance, if one city is 10 times as populous as another one, does it need 10 times as many gas stations? No. Bigger cities have more gas stations than smaller ones (of course), but not nearly in direct proportion to their size. The number of gas stations grows only in proportion to the 0.77 power of population. The crucial thing is that 0.77 is less than 1. This implies that the bigger a city is, the fewer gas stations it has per person. Put simply, bigger cities enjoy economies of scale. In this sense, bigger is greener.

The same pattern holds for other measures of infrastructure. Whether you measure miles of roadway or length of electrical cables, you find that all of these also decrease, per person, as city size increases. And all show an exponent between 0.7 and 0.9.

Now comes the spooky part. The same law is true for living things. That is, if you mentally replace cities by organisms and city size by body weight, the mathematical pattern remains the same.

For example, suppose you measure how many calories a mouse burns per day, compared to an elephant. Both are mammals, so at the cellular level you might expect they shouldn’t be too different. And indeed, when the cells of 10 different mammalian species were grown outside their host organisms, in a laboratory tissue culture, they all displayed the same metabolic rate. It was as if they didn’t know where they’d come from; they had no genetic memory of how big their donor was.

But now consider the elephant or the mouse as an intact animal, a functioning agglomeration of billions of cells. Then, on a pound for pound basis, the cells of an elephant consume far less energy than those of a mouse. The relevant law of metabolism, called Kleiber’s law, states that the metabolic needs of a mammal grow in proportion to its body weight raised to the 0.74 power.

This 0.74 power is uncannily close to the 0.77 observed for the law governing gas stations in cities. Coincidence? Maybe, but probably not. There are theoretical grounds to expect a power close to 3/4. Geoffrey West of the Santa Fe Institute and his colleagues Jim Brown and Brian Enquist have argued that a 3/4-power law is exactly what you’d expect if natural selection has evolved a transport system for conveying energy and nutrients as efficiently and rapidly as possible to all points of a three-dimensional body, using a fractal network built from a series of branching tubes — precisely the architecture seen in the circulatory system and the airways of the lung, and not too different from the roads and cables and pipes that keep a city alive.

These numerical coincidences seem to be telling us something profound. It appears that Aristotle’s metaphor of a city as a living thing is more than merely poetic. There may be deep laws of collective organization at work here, the same laws for aggregates of people and cells.

The numerology above would seem totally fortuitous if we hadn’t viewed cities and organisms through the lens of mathematics. By abstracting away nearly all the details involved in powering a mouse or a city, math exposes their underlying unity. In that way (and with apologies to Picasso), math is the lie that makes us realize the truth.

Wednesday, May 20, 2009

Study finds volunteering decreases mortality risk among retired

Moral of the story: Start volunteering, it may save your life. This study looks at retirees and found volunteering has bidirectional affects with health. Not only is volunteering a sign of good health, it also improves health. Get yourself, your parents or your grandparents out there volunteering.

Study finds volunteering decreases mortality risk among retired

The Advisory Board Company
05/19/2009

Retirees older than age 65 who volunteer have a lower mortality risk than their non-volunteering peers, according to a study presented earlier this month at the American Geriatrics Society’s annual meeting in Chicago. Although previous research identified a link between volunteering and lower mortality rates, such studies involved individuals born before 1920 and failed to adjust the results for possible confounders, such as socioeconomic status and chronic health conditions. To assess the relationship when accounting for those variables, researchers from the University of California-San Francisco and Montefiore Medical Center examined 6,360 retired men and women older than age 65 who were enrolled in the Health and Retirement Study—considered representative of all U.S. adults—in 2002. Study subjects had an average age of 78, and 60% were female. Examining participants’ volunteerism patterns, the researchers found that 12% of participants who volunteered died, compared with 26% of non-volunteers. After adjusting the data for participants’ demographics, socioeconomic status, chronic health conditions, geriatric syndromes, functional limitations, self-rated health, depression, and cognition, the researchers found that the link “wasn’t as strong, but still existed.” Commenting on the study, one researcher notes that volunteering may be associated with self-efficacy—a belief in one’s own abilities to accomplish tasks—which helps individuals remain engaged in a healthy and active lifestyle (Gordon, HealthDay, 5/8).

Wednesday, May 13, 2009

Cancer Patients Challenge the Patenting of a Gene

Moral of the story: Patents on genes are creating controversy and in the name of free speech and medical necessity need to be restricted. They are creating undue burden for patients because of the lack of market forces preventing innovating and driving up costs. As the article states, my genes can no more ethically be patented than my left arm or my brain. The laws need to change and reflect this reality. At the same time, genetically modified foods need to be revisited as the ethics of genetic patents are reviewed. It may be time to stop bowing to argibusiness and start fighting for every American.

http://www.nytimes.com/2009/05/13/health/13patent.html?em

Cancer Patients Challenge the Patenting of a Gene

Published: May 12, 2009

When Genae Girard received a diagnosis of breast cancer in 2006, she knew she would be facing medical challenges and high expenses. But she did not expect to run into patent problems.

Benjamin Sklar for The New York Times

Genae Girard, 39, is suing Myriad Genetics and the Patent Office over the granting of a patent on a gene. Myriad also has patented the only test that measures the risk of breast and ovarian cancer.

Ms. Girard took a genetic test to see if her genes also put her at increased risk for ovarian cancer, which might require the removal of her ovaries. The test came back positive, so she wanted a second opinion from another test. But there can be no second opinion. A decision by the government more than 10 years ago allowed a single company, Myriad Genetics, to own the patent on two genes that are closely associated with increased risk for breast cancer and ovarian cancer, and on the testing that measures that risk.

On Tuesday, Ms. Girard, 39, who lives in the Austin, Tex., area, filed a lawsuit against Myriad and the Patent Office, challenging the decision to grant a patent on a gene to Myriad and companies like it. She was joined by four other cancer patients, by professional organizations of pathologists with more than 100,000 members and by several individual pathologists and genetic researchers.

The lawsuit, believed to be the first of its kind, was organized by the American Civil Liberties Union and filed in federal court in New York. It blends patent law, medical science, breast cancer activism and an unusual civil liberties argument in ways that could make it a landmark case.

Companies like Myriad, based in Salt Lake City, have argued that the patent system promotes innovation by giving companies the temporary monopoly that rewards their substantial investment in research and development.

Richard Marsh, Myriad’s general counsel, said company officials would not be able to comment on the lawsuit until they had fully reviewed the complaint.

The coalition of plaintiffs argues that gene patents actually restrict the practice of medicine and new research.

“With a sole provider, there’s mediocrity,” said Wendy K. Chung, the director of clinical genetics at Columbia University and a plaintiff in the case.

Dr. Chung and others involved with the suit do not accuse Myriad of being a poor steward of the information concerning the two genes at issue in the suit, known as BRCA1 and BRCA2, but they argue that BRCA testing would improve if market forces were allowed to work.

Harry Ostrer, director of the human genetics program at the New York University School of Medicine and a plaintiff in the case, said that many laboratories could perform the BRCA tests faster than Myriad, and for less money than the more than $3,000 the company charged.

Laboratories like his, he said, could focus on the mysteries still unsolved in gene variants. But if he tried to offer such services today, he said, he would be risking a patent infringement lawsuit from Myriad.

Christopher A. Hansen, senior national staff counsel for the civil liberties union, said the problem was with the patent office, not the company. He recalled that when he first heard that the office had granted a patent for a gene, “I said that can’t be true.”

As the A.C.L.U. explored the restrictions on competition that companies like Myriad had put in place — blocking alternatives to the patented tests, and even the practice of interpreting or comparing gene sequences that involved those genes — the restrictions started to look like not just a question of patent law, Mr. Hansen said, but of the First Amendment’s guarantee of free speech as well.

“What they have really patented,” he said, “is knowledge.”

A patent was also granted to a single company for genetic testing on long QT syndrome, which can lead to heart arrhythmias and sudden death, and to the HFE gene, linked to hereditary hemochromatosis, a condition in which iron accumulates in the blood and can cause organ damage. Doctors and scientists have complained about both patents.

On the other hand, the company that owns the patent to the gene CFTR, which has been linked to cystic fibrosis, has licensed the testing to dozens of laboratories, drawing praise from the medical world.

The decision to allow gene patents was controversial from the start; patents are normally not granted for products of nature or laws of nature. The companies successfully argued that they had done something that made the genes more than nature’s work: they had isolated and purified the DNA, and thus had patented something they had created — even though it corresponded to the sequence of an actual gene.

The argument may have convinced patent examiners, but it has long been a sore point for many scientists. “You can’t patent my DNA, any more than you can patent my right arm, or patent my blood,” said Jan A. Nowak, president of the Association for Molecular Pathology, a plaintiff in the case.

So far, however, two panels of government experts who have looked at the issue have not found significant impediments to research or medical care caused by gene patents. A 2006 report from the National Research Council found that patented biomedical research “rarely imposes a significant burden for biomedical researchers.”

That report and others, however, warn that the patent landscape “could become considerably more complex and burdensome over time.”

In the future, genetic tests are likely to involve the analysis of many genes at once, or even of a person’s full set of genes. Some 20 percent of the human genome is already included in patent claims, amounting to thousands of individual genes, says a draft report from the National Institutes of Health. The report warns that “it may be difficult for any one developer to obtain all the needed licenses” to develop the next generations of tests.

For Lisbeth Ceriani, a single mother from Newton, Mass., and a plaintiff in the case against Myriad, the biggest obstacle that gene patents present is one of cost. She has had breast cancer and a double mastectomy, but wants to have BRCA testing to determine her risk of ovarian cancer and help her decide whether to have her ovaries removed. But Myriad has refused to work with her insurance plan, Mass Health, and paying for the test herself is beyond her means.

She is reluctant to have surgery that might prove unnecessary, she said, but she also worries about her 8-year-old daughter and the inherited risk she might face. Which is why, Ms. Ceriani said, she wants to “find out if I have the mutation, so I can take the necessary steps to stay on the planet.”

“I want to be here,” she said, “to make sure she does her screening by the time she’s 30.”

Tuesday, May 12, 2009

One Fish, Two Fish, Fish You Want to Buy, Fish You Never Want to Die

Moral of the story: We all know we are supposed to eat more fish. It is a diet rich is omega-3 fatty acids and low in more harmful fats. Yet at the same time we are constantly reminded of the terrible overfishing going on around the world. This website will help you select the most eco-friendly fish to help keep you healthy.

http://www.edf.org/page.cfm?tagID=1521

The website is easy to use, has recipes and health information along with lists of what fish to eat and which ones to avoid. Highly recommended.