Thursday, March 29, 2012

Social Medicine

A new Facebook-like Web portal turns doctors and patients into research collaborators

Despite medical advances, the treatment of many chronic diseases remains haphazard and
inconsistent. Teenagers with Crohn’s disease, a painful digestive disorder often diagnosed in adolescence, for example, sometimes get conflicting information regarding medications, diet modifications and alternative therapies. To help improve the care these patients receive, a team of pediatricians and computer scientists is developing a new type of social network that turns doctors and patients into research collaborators.

Here is how it works: With each therapy or treatment modification, doctor and patient participate in a mini clinical trial. The patient records symptoms through daily reports, filed via text message or the Internet. The doctor uses that information to make immediate decisions. Should the dosage of medication be changed? Is the new diet helping to alleviate symptoms? And the data from those individual experiments are then deposited in a Web bank, where they can be aggregated with other patient data, from similar experiments, to further the understanding of the condition in question. In early tests of this process, doctors were able to increase the rate of remission from 55 to 78 percent without adding any new medications to their arsenal. “The idea is to make care continuous and to collect real-time data that will change our understanding and treatment of [Crohn’s],” says Peter Margolis of Cincinnati Children’s Hospital Medical Center, a co-founder of the new portal, the Collaborative Chronic Care Network.

The network, known as C3N, launched earlier this year at some 30 institutions around the country. For now it focuses on pediatric Crohn’s, but it could grow to include other conditions, such as diabetes, heart disease, psoriasis and some cancers. The site’s founders believe C3N will also provide a new platform for clinical research, one that is significantly less profit-driven. “Because largescale clinical trials are so expensive, we only ever really test the treatments that promise a big payoff,” says Ian Eslick, a Ph.D. candidate at the M.I.T. Media Lab and C3N’s chief Web architect. “With C3N, we can scientifically test all the other things—probiotics, gluten-free diets, changes in iron intake—that people are already trying at home and that seem promising, even if they aren’t profitable.”

Source of Information : Scientific American Magazine

Monday, March 26, 2012

Zombie Insects

A bug expert discusses a sinister virus that causes gypsy moth caterpillars to self-destruct

You recently identified a gene known as egt that allows a specific group of viruses to control the behavior of caterpillars. Tell me what it does.
Gypsy moth caterpillars have a normal behavior they do every day. They climb out onto the leaves to feed at night. During the day they climb back onto the branches or bark to hide from predators because they’re very obvious when they’re on the leaves. But once caterpillars are infected with these viruses, known as baculoviruses, their levels of the EGT protein become elevated. Once that happens, you find them on leaves in the middle of the day. It’s like: “What are you doing here?”

And how does that harm the caterpillars?
Eventually they climb to the tops of trees, where they get converted into a sac of virus that liquefies and rains virus particles down on the foliage below so that new hosts can be infected by eating the virus on the leaves. Egt is manipulating the insect to die in the right location to transmit the virus to new hosts. What is the mechanism by which the gene does that? In short, we don’t know, but we have a couple of ideas. It was already known that egt blocks molting in caterpillars. What happens when the insects molt is they stop feeding for quite some time; if they’re kept from molting, they’re kept in a feeding state. It’s possible that because they’re being stimulated to keep feeding, they’re staying up in the tree when everybody else is climbing down.

What are some other viruses that can change host behavior?
If you think about rabies, rabies causes the infected animals to come out during the day when they’re normally nocturnal, and their behavior becomes more aggressive. There’s also a really cool virus that is sexually transmitted in moths. It causes the female moth to keep calling for mates by sending out pheromones, even though she already just mated. That way she infects more and more males. Finally, in toxoplasmosis, cats are the primary host, but mice get infected. When mice are infected, they lose their fear of cats, and they’re more likely to get eaten, which allows the pathogen to be transmitted to cats.

What does this mean for humans?
It certainly does suggest that other pathogens may contain genes that influence behavior, even in humans. When you have the flu, you cough a lot, which can help transmit the virus to other people. Is that a symptom, or is it the virus making us do that? And has that been selected for through evolution? Who knows?

Source of Information : Scientific American Magazine

Friday, March 23, 2012

Olympians of the Sky

Researchers unravel some long-standing mysteries of bar-headed geese, the world’s highest-flying birds

Climbers struggling the last few steps to the peak of Makalu in the Himalayas have long marveled at the sight of bar-headed geese flying high above to their winter refuge in India. The birds cruise at an altitude of 29,500 feet, nearly as high as commercial aircraft.

For years scientists believed that strong tailwinds and updrafts aided the geese on their journey. A team of researchers led by Charles Bishop of Bangor University in North Wales tested this theory by tracking more than a dozen bar-headed geese harnessed with small backpacks containing satellite transmitters that established their location, speed and altitude.

To their surprise, the researchers discovered that instead of flying in the early afternoon, when heat from the earth can create 12-mile-per-hour updrafts, bar-headed geese consistently fly at night or during early-morning hours, when there is actually a slight downdraft. In a paper published recently in the Proceedings of the National Academy of Sciences USA, the team theorizes that because air is cooler and denser at these times, it allows the geese to generate greater lift. Cooler air also helps to regulate body heat and contains more oxygen, enabling geese to fly even as the air thins at higher levels.

Bishop and his colleagues also were amazed to find that the geese cross the Himalayas in a single day, traveling 20,000 feet in seven to eight hours. To fly so far at such a great height, the barheaded geese must sustain a 10- to 20- fold increase in oxygen consumption. By comparison, lower-altitude birds such as the Canada goose cannot sustain resting levels of metabolism at 30,000 feet. Bigger wings, bigger lungs, a dense network of capillaries surrounding the flight muscle, and hemoglobin that more tightly binds oxygen to the lungs work together to sustain oxygen flow throughout the bird’s circulatory system, including its flight muscle. Improving the understanding of why tissues in bar-headed geese are so adept at taking up oxygen might elucidate human respiration as well.

Source of Information : Scientific American Magazine

Tuesday, March 20, 2012

Bigger Plates, More Food— Or Is It the Other Way Around?

When the same set of data yields opposite conclusions

A recent study by researchers at the University of Utah suggested that the amount of food diners in a restaurant consumed was influenced by fork size. I haven’t seen details of the study, but it does remind me that people can draw diametrically opposite conclusions from the same raw data by altering definitions ever so slightly. If only such contradictory results were contrived and isolated phenomena, but they’re not.

When dealing with weakly correlated quantities, we often can come up with spurious trends and associations by artfully defining the size of the categories we use. This has been done recently in studies of violent crime to show that certain categories of crime were changing in the desired direction, and I intend to illustrate the point here with a similar story.

Using the fork study for inspiration only, let’s see how small variations in definitions can make all the difference. Imagine 10 diners at a buffet and consider the possible influence of plate size on how much they consume. Three diners were provided with plates that were deemed small, say, less than 8 inches in diameter, and they consumed 9, 11 and 10 ounces of food, for an average of 10 ounces. Now further assume that four diners were provided with medium-size plates, say, between 8 and 11 inches in diameter, and they consumed 18, 7, 15 and 4 ounces of food, for an average of 11 ounces.

Finally, we’ll assume that the remaining three diners were provided with plates deemed large, say, larger than 11 inches in diameter, and they consumed 13, 11 and 12 ounces, for an average of 12 ounces.

Spot the trend? As the plate sizes increased from small to medium to large, the average amount consumed increased from 10 to 11 to 12 ounces. Aha, a nice result! But wait. What if the medium-size plates were very slightly redefined to be between
8.2 and 10.8 inches, and the small and large plates were redefined accordingly? And what if this redefinition resulted in the misclassification of two diners? The diner who ate 18 ounces of food was actually provided with a small plate (say, 8.1 inches in diameter), and the diner who ate only 4 ounces was actually provided with a large plate (say, 10.9 inches in diameter).

Let’s do the numbers once again under this assumption. Four (rather than three) diners were provided with small plates, and they consumed 9, 11, 10 and 18 ounces of food, for an average of 12 ounces. Two (rather than four) diners were provided with medium-size plates, and they consumed 7 and 15 ounces of food, for an average of 11 ounces. Four (rather than two) were provided with large plates, and they consumed 4, 13, 11 and 12 ounces of food, for an average of 10 ounces.

Spot the trend? As the plate sizes increased from small to medium to large, the average
amount consumed decreased from 12 to 11 to 10 ounces. Aha, a nice result! Moreover, small samples are not the problem here. A large number of data points make this sleight of hand even easier because it provides more opportunity to fiddle with the categories. Anyone for sunspot intensity or Super Bowl outcomes?

Source of Information : Scientific American Magazine

Friday, March 16, 2012

A Cybersecurity Nightmare

We can’t keep malware out of our computers if we can’t find it

The world of cybersecurity is starting to resemble a paranoid thriller. Shadowy figures plant malicious software, or “malware,” in our computers. They slip it into e-mails. They transmit it over the Internet. They infect us with it through corrupted Web sites. They plant it in other programs. They design it to migrate from device to device—laptops, flash drives, smartphones, servers, copy machines, iPods, gaming consoles—until it’s inside our critical systems. As even the most isolated systems periodically need new instructions, new data or some kind of maintenance, any system can be infected.

The effect could be devastating. After lying dormant for months or years, malware could switch on without any action on the part of those who launched it. It could disable emergency services, cause factories to make defective products, blow up refineries and pipelines, poison drinking water, make medical treatments lethal, wreck electric generators, discredit the banking system, ground airplanes, cause trains to collide, and turn our own military equipment against us.

Many public officials are now aware that something needs to be done. Putting aside worries about privacy and civil liberties, they propose giant government programs to search our critical computer systems and scan everything that goes into them.

But here’s where the plot thickens. We don’t actually know how to scan for malware. We can’t stop it, because we can’t find it. We can’t always recognize it even if we are looking right at it.

Like a thriller character who discovers he doesn’t know whom to trust, cybersecurity experts start running through the options. Can we recognize malware by its identifying characteristics? No, because each piece of malware can be different, and it can keep changing its appearance. Can we recognize it by the tools it needs to spread? No, because the malware might be a payload inserted by someone or something else.

Can we find malware by looking in likely hiding places? No, because it could be in a hiding place we didn’t know was there— an area of memory we can’t see or some component we didn’t even realize had a memory. It could be moving around even as we’re looking for it. It could copy itself into the place we just looked and erase itself from the place we’re about to look.

Can we create a safe area, bit by bit, reading every line of code in each program to make sure it’s innocent? The problem is that we can look directly at a line of malware and not recognize it. Sometimes a tiny modification in a line of code can cause a malicious effect. Malware doesn’t need to be in the individual lines of code. The malicious part of the malware might be the sequence of operations that causes a normal instruction to be carried out at exactly the wrong time.

If all else fails, can we recognize malware by what it does? This won’t work either. Malware can take control of every display, message box, graphic or reading. It can make sure you see only what it wants you to see. If you do manage to catch it doing something bad, it might be too late. If the first time a malicious program operates it turns your missiles back at you, fries your electric generators or blows up your refineries, it won’t do much good to recognize it by that behavior.

We truly can’t trust anything. The very computers we are using to search for malware might be the vehicles delivering it. Our authentication systems could be authenticating programs infected with malware. Our encryption systems could be encrypting malware. Even if we manage to come up with an effective barrier, we will not know which side the malware is on.

This is the world many cybersecurity professionals are currently living in. We are stopping most malware, most of the time. But we don’t have a reliable solution for the cases where it might matter most. America and its allies have always been good at coming up with timely breakthroughs when they are most needed. We need one now.

Source of Information : Scientific American Magazine

Tuesday, March 13, 2012

Safety First, Fracking Second

Drilling for natural gas has gotten ahead of the science needed to prove it safe

A decade ago layers of shale lying deep underground supplied only 1 percent of America’s natural gas. Today they provide 30 percent. Drillers are rushing to hydraulically fracture, or “frack,” shales in a growing list of U.S. states. That is good news for national energy security, as well as for the global climate, because burning gas emits less carbon dioxide than burning coal. The benefits come with risks, however, that state and federal governments have yet to grapple with.

Public fears are growing about contamination of drinkingwater supplies from the chemicals used in fracking and from the methane gas itself. Field tests show that those worries are not unfounded. A Duke University study published in May found that methane levels in dozens of drinking-water wells within a kilometer (3,280 feet) of new fracking sites were 17 times higher than in wells farther away. Yet states have let companies proceed without adequate regulations. They must begin to provide more effective oversight, and the federal government should step in, too.

Nowhere is the rush to frack, or the uproar, greater than in New York. In July, Governor Andrew Cuomo lifted a ban on fracking. The State Department of Environmental Conservation released an environmental impact statement and was to propose regulations in October. After a public comment period, which will end in early December, the department plans to issue regulations, and drilling most likely will begin. Fracking is already widespread in Wyoming, Colorado, Texas and Pennsylvania.

All these states are flying blind. A long list of technical questions remains unanswered about the ways the practice could contaminate drinking water, the extent to which it already has, and what the industry could do to reduce the risks. To fill this gap, the
U.S. Environmental Protection Agency is now conducting comprehensive field research. Preliminary results are due in late 2012. Until then, states should put the brakes on the drillers. In New Jersey, Governor Chris Christie set an example in August when he vetoed a bill that would permanently ban fracking, then approved a one-year moratorium so his state could consider the results of federal studies. The EPA, for its part, could speed up its work.

In addition to bringing some rigor to the debate over fracking, the federal government needs to establish common standards. Many in the gas industry say they are already sufficiently regulated by states, but this assurance is inadequate. For example, Pennsylvania regulators propose to extend a well operator’s liability for water quality out to 2,500 feet from a well, even though horizontal bores from the central well can stretch as far as 5,000 feet.

Scientific advisory panels at the Department of Energy and the EPA have enumerated ways the industry could improve and have called for modest steps, such as establishing maximum contaminant levels allowed in water for all the chemicals used in fracking. Unfortunately, these recommendations do not address the biggest loophole of all. In 2005 Congress—at the behest of then Vice President Dick Cheney, a former CEO of gas driller Halliburton—exempted fracking from regulation under the Safe Drinking Water Act. Congress needs to close this so-called Halliburton loophole, as a bill co-sponsored by New York State Representative Maurice Hinchey would do. The FRAC Act would also mandate public disclosure of all chemicals used in fracking across the nation.

Even the incomplete data we now have suggest specific safety measures. First, the weakest link in preventing groundwater contamination is the concrete casing inside well bores. Inspection of casings should be legally required. Second, the toxic fluid that is a major by-product of fracking is routinely stored in open pits, which can overflow or leach into the soil. It should be stored in tanks instead. Third, gas companies should inject tracers with the fracking fluid so inspectors can easily see whether any of the fluid ends up in the water streaming from residents’ faucets. Finally, companies or municipalities should have to test aquifers and drinking-water wells for chemicals before drilling begins and then as long as gas extraction continues, so changes in groundwater are obvious.

It is in the industry’s interest to accept improved oversight. Public opinion is turning against fracking. That is unfortunate, because more natural gas could benefit everyone. With basic precautions, we can enjoy both cleaner energy and clean water.

Source of Information : Scientific American.Magazine

Saturday, March 10, 2012

Living in a Bacterial World

Invisible bacteria are everywhere. Trying to find their many hiding places is like counting poppy seeds in a bagel factory. And while having bacteria on your skin is a healthy fact of life, the bacteria that fill the world around you aren’t always as well behaved.

In a sense, we have no one to blame but ourselves. Bacteria mostly stay put, until a person like you arrives to move them around. All day long, while we think we’re cooking, cleaning, looking after our kids, or working at the office, we’re also busy transferring bacteria from one place to another. To find the favorite living spaces for bacteria, you simply need to look at the places we touch most.

For example, in a public restroom the amount of bacteria on the muchfeared toilet seat is minimal. It certainly can’t compare to the thriving colonies on the sink taps and door handles. And in many popular restaurants, the bacteria in the ice machine top what you can extract from toilet-bowl water—a fact originally discovered in a 7th-grader’s science project. (The toilet has the advantage of frequent cleaning and fast-running fresh water to rinse it out. The ice machine has the disadvantage of coming into contact
with countless people’s grubby fingers and a much less frequent cleaning schedule.)

Your own home has similar surprises in store. The places you come into contact with when you touch and prepare food—such as kitchen sponges and rags, cutting boards, and countertops—as well as doorknobs and toothbrushes, are the most bacteria-laden. In fact, if an alien being were to arrive in your home, it would have to be excused for using the kitchen sink as a washroom and preparing a cheese plate on the toilet seat. From a microbiologist’s point of view, this arrangement would be safer for everybody.

So with all this bacteria on the loose, what’s a paranoid person to do?

• Sanitize sponges and cutting boards. These are not only hotspots of bacterial life, they’re also the primary vehicles for spreading bacteria around. To sterilize a sponge, you can boil it in hot water for a few minutes, run it through a dishwasher drying cycle, or soak it lightly and then pop it in the microwave. To clean your cutting board, scrub it with a light bleach solution (1 tablespoon of bleach to a quart of water). To be extra safe, use a separate cutting board for meat duties, and replace your cutting board when it becomes heavily scored, because bacteria love to pile into the grooves.

• Treat the sink with caution. Give it a thorough, regular cleaning. And once you clean the sink, make sure you dry it thoroughly. That’s because a moist environment encourages the last, lingering bacteria to reproduce. And whatever you do, don’t eat something you’ve dropped into your sink unless you cook it first.

• Prepare food properly. Proper cleaning is important for foods that you plan to eat raw, like fruits and veggies. To prevent crosscontamination, rinse all fruits and vegetables, even those that you plan to peel (like oranges, cantaloupes, and potatoes). Rinse with ordinary water—soap may leave a residue you shouldn’t ingest, and fancy food-cleaning systems don’t make much of a difference in serious tests. Lastly, don’t wash chicken or raw meat before you cook it. Your oven destroys all the bacteria it contains. Washing the meat simply gives you an opportunity to spread tiny droplets of bacteria-laden water throughout your kitchen.

• Wash your hands properly. With a world of bacteria around you, it’s safe to assume that your hands harbor some unwanted guests. Clean your hands before you handle food and before you sit down to eat. Soap and warm water does the trick. Scalding hot water still won’t be hot enough to kill bacteria, so don’t torture yourself. Antibacterial soap isn’t much help, either. The active germ-killing ingredient, triclosan, works only if you leave the soap on your hands for several minutes before rinsing, which virtually no one does.

Before you panic, remind yourself that bacteria can’t cause any trouble until it breaches your body’s defenses. So that means it’s probably safe to touch virtually anything in the filthiest restroom, as long as you give your hands a thorough washing before you poke a finger in your eye, mouth, nose, or bacon sandwich.

One study found that bachelors have the cleanest kitchens. That’s because they’re less likely to use the kitchen to prepare food, and even less likely to pick up a rag to clean off a countertop (which often simply smears the bacteria around).

Studies show that ordinary soap does a perfectly good job of removing dangerous pathogens from your hands. Antibacterial soap can do the same job, but it has a potential side effect. By rinsing antibacterial chemicals down the drain, you increase the odds that they’ll encounter a colony of bacteria on the way down and cause it to evolve into a more dangerous, resistant strain. If you use antibacterial products, choose the ones that actually have proven benefits—for example, toothpaste. And skip the antibacterial soap, which offers nothing more than a dose of false comfort.

Source of Information : Oreilly - Your Body Missing Manual

Wednesday, March 7, 2012

Skin Bacteria

If you don’t want to come into contact with bacteria, your first step is to avoid touching yourself. That’s because healthy human skin is teeming with dozens of different types of bacteria that are all competing for a plot of prime skin real estate. Some help you, some hurt you, but most just hitch a harmless ride that lasts your entire life.

So what do we know about the bacteria that call our bodies home? Surprisingly little—in fact, scientists spend most of their time concentrating on species of bacteria that cause disease. But if you’re really intent on making yourself unpopular at parties, here are a few things you should know about your bacterial cohabitants:

• They’re unique. Each of us has a different blend of bacterial species living on our skin. In fact, studies show that only about 13 percent of the bacterial species on your left hand are shared with your right hand. Based on this principle, some forward thinkers imagine a day where microbiologists can examine objects and determine who touched what by sampling the bacteria they’ve left behind.

• They have preferences. Specialized bacteria live in different ecosystems on your body. For example, your inner elbow has its own thriving bacterial communities that are quite different from those on your inner forearm, only a few inches away.

• Women’s hands have more germs. No one’s sure why women carry around more hand bacteria, despite the fact that they wash their hands more frequently. Possible explanations are the lower acidity of female skin or differences in sweat and skin oil.

• Washing won’t remove your permanent settlers. It may cut down their numbers (particularly if your soap includes an antibacterial compound that stays on the skin), but they’ll soon reestablish themselves in their normal proportions. In fact, bacteria may spread more aggressively immediately after a deep cleaning—which is good, because you need some bacteria to keep your skin healthy, as described in the next point.

• Competition is good. The bacteria on your body protect you from more dangerous, disease-causing strains. That’s because the benign bacteria that’s packed onto your skin doesn’t leave much room for anyone else to get established.

Source of Information : Oreilly - Your Body Missing Manual

Saturday, March 3, 2012

You Are Bacteria

We’re used to thinking of bacteria as unwelcome hitchhikers. But in many cases, the boundary between the human body and bacteria is surprisingly blurred. First, your microbial partners have a hand in many of the functions that we consider a normal part of human life. Without beneficial bacteria, you’d lose valuable vitamins and give up your unique, lifelong body odor. You’d also have no defense against the attack of far more dangerous strains of bacteria and, as a result, you’d probably suffer from nearly constant diarrhea, skin rashes, and bladder infections. It’s even possible that without friendly bacteria to continuously prod your immune system, its careful calibration would slip, leaving you at a greater risk for allergies and asthma.

But bacteria are more than the permanent residents of your body. There’s solid scientific evidence that the relationship between humankind and bacteria is older and far more complex than most people realize. Many scientists now believe that mitochondria, the biological power plants that fuel the work of every human cell, were once free-floating bacteria that somehow became incorporated into the bodies of our most ancient, primitive ancestors. And almost all scientists agree that the tree of life leads back through time to a simple, single-celled creature that was at least a bit like a modern-day bacteria, which means that the stomach bug that makes you ill today might bear more than a passing resemblance to your great-great-great-great- (and so on) grandfather. Thank goodness no one had invented antibacterial soap back then.

Source of Information : Oreilly - Your Body Missing Manual