## Monday, July 28, 2008

### DNA and birthdays: fun with math

While I was reading up for my last blog entry, I became enraged that the FBI is doing so little to inform the public that our DNA fingerprints aren’t as unique as originally believed, since DNA profiling has become so important as evidence in court trials. But then my husband reminded me of the birthday problem, and it became clear that there is no real reason to be upset.

Originally, it seemed unfair to me that juries are told that if the DNA profile of a sample from the crime scene matches that of the defendant, the odds of the match being a false-positive—in other words, the odds that the sample didn’t really stem from the defendant—are less than one in a billion.

Recently, database searches have shown that the odds of two people sharing identical DNA profiles may be much higher—as many as 3 pairs of individuals in a database of 30,000 (see
previous blog entry). At first glance, it appears that jurors are being duped into thinking that DNA evidence is more solid than it really is.

But they’re not, and a look at the birthday problem shows why.

What is the birthday problem? Stanford professor Keith Devlin
explained it on NPR as follows:

"The birthday problem asks how many people you need to have at a party so that there is a better-than-even chance that two of them will share the same birthday. Most people think the answer is 183, the smallest whole number larger than 365/2. In fact, you need just 23. The answer 183 is the correct answer to a very different question: How many people do you need to have at a party so that there is a better-than-even chance that one of them will share YOUR birthday? If there is no restriction on which two people will share a birthday, it makes an enormous difference. With 23 people in a room, there are 253 different ways of pairing two people together, and that gives a lot of possibilities of finding a pair with the same birthday."

The point is, that as soon as you start comparing random pairs of people instead of specific individuals, the odds of a match increase dramatically.

Which means that it is entirely possible that the odds of a match between the defendant and someone else in the database are less than 1 in a billion, even while the odds of any two random matches are much higher.

So my anger at the FBI for trying to hush up the story has now been replaced with frustration with the press and myself for not thinking the story through before judging the FBI’s decision.

Any objections to this application of the birthday problem?

## Thursday, July 24, 2008

### What to keep in mind if you are on the jury

How reliable is DNA evidence really? The FBI is working hard to keep a lid on an increasing number of cases that show that DNA fingerprinting isn’t as credible as we’re supposed to believe, write Jason Felch and Maura Dolan of the LA Times (July 20, 2008).

DNA profiles are commonly admitted as evidence in court cases, and are often sufficient to convict a suspect even when there is no other evidence. The DNA profile of the suspect is compared to that of a sample found at the crime scene.

The vast majority of our DNA is identical from person to person, but there are some stretches, called Variable Number Tandem Repeats, which vary in length between individuals. Humans have two copies of DNA—one from mom and one from dad—so we have two versions of each of these repeat segments.

In DNA fingerprinting, investigators look at the length of these repeat segments on both sets of DNA. The Combined DNA Index System (CODIS), the FBI-funded computer system that searches DNA profiles, uses 13 of these repeat segments.

As recently as 2001, a match of 9 loci was sufficient for conviction in many states, though most states now try to compare all 13 loci. Juries are often told that the odds of two unrelated people sharing 9 of these markers are less than one in a billion.

But a search of Arizona’s DNA database by Kathryn Troyer in 2001 revealed two unrelated men who matched at 9 of the 13 loci.

Instead of trying to get to the bottom of things, the FBI responded to these findings with skepticism, and even tried to block future searches. Thomas Callaghan, head of the FBI's CODIS unit, called Troyer’s findings “misleading,” and reprimanded her laboratory for releasing the search results to a California court.

Despite threats from Callaghan to be cut off from the national database, similar searches followed in California, Illinois, and Maryland.

A Maryland judge wrote, “The court will not accept the notion that the extent of a person's due process rights hinges solely on whether some employee of the FBI chooses to authorize the use of the [database] software.”

The database search in Maryland turned up 32 pairs of individuals which matched at 9 loci, in a database of 30,000. Three of these pairs matched at all 13 loci, though it is not clear whether these individuals were related.

The Illinois search revealed 903 pairs of individuals, in a database of 220,000, whose DNA fingerprints matched at 9 loci.

DNA has become a strong weapon in courtroom battles, so it is easy to see why the FBI and prosecutors would panic at these findings. But it does kind of make you wonder whose interests they are serving by hushing up the truth.

## Tuesday, June 10, 2008

### Be nice to your plants—you never know what they are planning

Kin recognition is important for the social behavior of most animals. Animals tend to behave in ways that benefit their relatives, often at a loss to themselves. Some common examples are honeybees, who work to promote the reproduction of their queen, or prairie dogs, who call out to warn nearby relatives of danger, at the same time drawing attention to themselves and risking attack.

Recognizing relatives is also helpful for avoiding inbreeding.

Until recently, the ability to recognize kin has been attributed exclusively to animals. But last year, Susan Dudley, at McMaster University in Hamilton, Ontario, reported on the “secret social life” of the American sea rocket, a dune-dwelling plant with little purple flowers, found on the beaches of the Great Lakes.

Dr. Dudley and her graduate student Amanda File found that sea rockets grow more roots when they share a pot with strangers than when they are potted with relatives.

By growing more roots, plants increase their competitive ability underground. Plants with more roots are better at soaking up water and nutrients.

So sea rockets purposely leave more space in the pot for their relatives, giving them a better chance to access water and nutrients. But when a stranger is nearby, they have no inhibitions about hogging all the resources.

Sea rockets seem to recognize their neighbors based on some cue in the roots, since plants potted individually do not change their root-growing behavior when non-relatives are placed in nearby pots.

Since Dr. Dudley published her findings, kin recognition has been demonstrated in several other plant species.

Plants have several different ways of sensing their neighbors. They can detect changes in light, caused by absorption of particular wavelengths by neighboring plants. They can also detect chemicals released by other plants into the soil or air.

One parasitic weed, the dodder, which thrives on nutrients extracted from other plants, actually grows towards its victims, a behavior startlingly similar to hunting.

Plants may be more aware of their surroundings than we’d like to admit. Scientists have known for 100 years that plants send electrical signals from one part of the plant to another. But nobody knows what these signals are for.

Sensory plant biology has blossomed into a hot topic, with a deep rift separating scientists who believe that plants have some sort of sensory-nervous system, and those who maintain that intelligence is limited to animals.

Attributing intelligent or planned behavior to plants may seem a stretch, but maybe plants are smarter than we think. We just haven’t noticed, because they move orders of magnitude slower than we do.

(photo from Harold Davis on flickr.com)

## Sunday, June 8, 2008

### When modern technology catches up with science fiction

As with most of biology’s wonders, we take our coordination for granted. We see something we want; we reach out and grab it. Even if the desired object is moving, like a glass of champagne on the tray of a passing waiter. How do our brains do it?

Our brains analyze the visual target (the approaching glass), make an estimate of its velocity, and send a signal to the arm and hand to reach out and grasp. The grasping has to be timed precisely, and the hand has to open the right amount. We use a different grasping motion for a wine glass than for a beer mug.

Amazingly, scientists now know enough about these brain signals to tap into them and use them to control artificial limbs.

A team of scientists headed by Andrew Schwartz at the University of Pittsburgh trained monkeys to use their brain activity to control a prosthetic arm (Nature, May 28, 2008).

The monkeys were first trained to control the prosthetic arm using a joystick. The arm had 6 degrees of freedom; three at the shoulder, one at the elbow, and one at the hand.

Once they got the feel for the arm, the monkeys were implanted with electrode arrays situated on the part of the brain that controls arm and hand movement. The prosthetic arm was hooked up to the monkey and controlled by the signals recorded from the electrodes.

After several weeks of training, the monkeys were able to grasp bits of food held out to them by a researcher, and put the food into their mouths. The monkeys’ arms were restrained to keep them from grabbing the food with their own hands.

The monkeys got very comfortable eating with the prosthetic limb. They even licked their prosthetic fingers when bits of marshmallow stuck to them. There are some nice videos of the monkeys in action here.

Prosthetics which are controlled by nerve signals already exist for humans, but they intercept the nerve signals at the shoulder. They’re great for patients with amputated arms, and they’ve made remarkable progress, allowing users to grasp objects and move individual fingers.

Brain-computer interfaces exist for patients with locked-in syndrome, which is a syndrome in which patients are awake and aware, but cannot move or communicate. Generally, these interfaces allow patients to move a cursor on a computer screen, and thus communicate with the outside world.

Tapping brain signals to control prosthetic limbs will someday help paralyzed patients to regain movement.

## Friday, May 30, 2008

### The miracle of biology

Huge progress has been made in restoring normal hearing to the deaf: within the last 40 years, scientists have developed prosthetic devices, called cochlear implants, which allow deaf people to communicate without lip reading or signing, and even to talk on the phone.

So why isn’t there something like this for the eye, to restore vision to the blind?

The most common causes of blindness arise from degeneration of the retinal cells that detect light, the photoreceptor cells. When these cells die, the remaining nerve cells in the retina survive for a while before they too die.

Several labs are building chips that can be inserted behind the retina, where the photoreceptor cells are in the normal eye (TÃ¼bingen, Tokyo Institute of Technology). These implants stimulate the surviving nerve cells, mimicking the photoreceptor cells.

Other labs want to tack (yes, tack) their implants onto the front of the retina (Harvard & MIT, John Hopkins & USC).

The visual scene is captured either by a camera attached to a pair of glasses, which transmits the signals to the implant in the eye, or by photocells on the chip itself.

Retinal implants are being tested in patients, with moderate success. Patients who were completely blind are able to make out bright light sources and some movement.

Great, right? Seeing vaguely is better than not seeing at all, and certainly makes daily life easier. But retinal implants may never advance to the level of the cochlear implants.

This is because the retina is far more complex than the cochlea. The cochlea pretty much just encodes frequency (pitch) and intensity (loudness). All the rest, including the location of a sound source, is processed in the brain. The retina, on the other hand, does a huge amount of processing before sending its signals to the brain.

Object location, brightness, orientation, motion, and color are all encoded in the retina. So the electrical signals that the retinal implant produces need to include all of this information. But retinal scientists are only just beginning to understand how all this works.

These problems may be solved eventually, and in the meantime, people with implants are happy to have 16-pixel vision.

But this month, Botond Roska, of the Institute for Biomedical Research in Basel, presented a brilliant new idea for restoring vision to the blind (Nature Neuroscience 11:667-675).

His idea was to confer the ability to detect light onto the nerve cells which survive after the photoreceptor cells die. His team did this by introducing the gene for a light-sensitive protein into a specific group of nerve cells in the retina.

This protein builds channels in the membrane of the cell. When the channel is stimulated by light, it opens, allowing charged particles to flow into and out of the cell. This flow of charges is an electrical signal, and it is the same as the signal that these cells produce in the normal retina when they are stimulated by photoreceptor cells.

Dr. Roska’s team tested their idea in blind mice. When these mice were treated with the gene for the light-sensitive channel protein, their vision was restored with relatively high acuity.

This project is in its infancy, and there are a lot of problems to be worked through. For example, normal room lighting is too dim to stimulate the channels, so some sort of amplifying system will have to be worked out.

It may be another 50 years before scientists are able to restore vision of reasonable quality to blind people, but I’d be willing to bet that when it does happen, it’ll be by gene targeting and not by retinal implantation.

## Monday, May 26, 2008

### Finally, a pill to treat crankiness

How many people do you know who eat a balanced, healthy diet? I mean the kind with 5+ servings of fruits and veggies per day.

To massage our bad consciences, we swallow multi-vitamin pills, hoping this will make up for skipping the salad. But how much do these vitamin supplements really help?

One recent study, which flew through the media, claimed that vitamins A and E increase the risk of death. That study didn’t actually involve any experiments or subjects; it was a statistical analysis of data from other people’s experiments, all of which had already shown that vitamin supplements have either no or negative effects on life expectancy. So the study didn’t actually present anything new.

Nevertheless, if you are taking vitamins hoping they will make you live longer, you can stop now. But if you are worried that taking vitamins will kill you, just keep in mind that vitamin supplements are intended to supplement the diet. If you eat a balanced diet, you don’t need them. And too much of the fat-based kind (A, D, E, and K) can be toxic.

So, vitamins won’t make us live longer, but can they make our short stay on Earth healthier and happier?

How can these benefits be measured scientifically? Ideally, the effects of vitamins would be studied by monitoring two large groups of people: one group gets vitamins every day, and the second group placebos. The catch is, all members of both groups need to eat the same foods and get the same amount of exercise.

Where to find hundreds of people whose diet and activities are the same every day? Prisons!

One of the first studies to examine the effects of vitamin supplements came out in 2002. A team of researchers headed by C. Bernard Gesch, of the University of Oxford, recruited 231 prisoner volunteers to act as subjects in their study.

Neither the subjects nor the prison guards who distributed the pills knew who was receiving the supplements and who got placebos. The study was also randomized, to eliminate effects of ethnic or social factors.

Daily intake of vitamin supplements reduced antisocial behavior, including violence, by 35%. These improvements showed up after just two weeks.

A new 3-year study is starting in the UK this month to reproduce these findings. The scientists plan to evaluate 1000 prisoners over the course of 12 months.

Professor John Stein of Oxford University, said that the prison food was not lacking in nutrition, but the inmates generally chose not to eat the fruits and vegetables. (He didn’t say how fresh the prison veggies were.) The scientists are hoping that their findings will encourage schools to provide dietary education and vitamin supplements.

What does this mean for us? Vitamin supplements won’t extend our lives, but they may make life more pleasant for those around us.

## Monday, May 19, 2008

### Today’s tricorders

Olga Kharif, in Tech News World (May 5), gives us one more reason to love the iPhone. As if we needed another reason!

The software company Life Record is developing ways to let physicians view medical records, including electrocardiograms and brain scans, using the iPhone. Their software also lets doctors send and receive patient records by SMS, and order prescriptions.

For those of us who are not doctors but want an excuse to buy an iPhone, the company is also developing software for patients. For \$50 a year (which is nothing compared to the cost of the 2-year contract you have to sign when you buy the phone) patients can have access to their own records via iPhone. This could be handy when visiting a new doctor or specialist.

iPhone users aren’t the only ones who will benefit from new medical technologies. Kharif reports that 17 of the 30+ health care projects funded by Microsoft Research involve cell phones. And sales of phone applications for medical professionals are expected to more than double by 2011.

Researchers hope that mobile phones will help reduce the frequency of medical errors. Gentag is developing wireless disposable skin patches which store the patient’s medical records. The patches are equipped with a chip that transmit to a mobile phone. If the patient is about to receive medication, the patch can warn of any allergies. The patch will also allow patients’ blood glucose and temperature to be monitored by phone.

Another life-saving idea, being developed at the University of Pittsburgh, connects a heart monitor with a cell phone: the cell phone analyzes the readings, and calls an ambulance if the heart starts behaving dangerously. The phone provides the EMTs with the patient’s location, and the EMTs know what to expect when they arrive.

A similar application has been introduced in California by BeWell Mobile. Patients with asthma or diabetes can send their home test results to their doctors by mobile phone. The software can make dietary suggestions based on glucose levels. This sort of program can cut down on emergency room visits.

## Wednesday, May 14, 2008

### The probiotic trend

Today’s marketing experts are so savvy, they can get us to want to eat bacteria, just by dropping buzz words like “numerous health benefits,” “clinically proven,” and my personal favorite, “boost the immune system.”

We don’t mind eating what we would normally call germs when they are given the scientific-sounding name “probiotics.”

Whether the stuff actually works, or consumers are being duped, is hard to say, but sales of food products containing probiotics have taken off in the last 2 years. One market leader, Activia by Dannon, had a 48% increase in sales in 2007, according to Brendan Borrell in the LA Times (May 12, 2008).

What are probiotics? The Food and Agriculture Organization of the United Nations defines probiotics as "live microorganisms that when administered in adequate amounts confer a health benefit on the host." This leaves very little room for skepticism, since by definition, probiotics are good for you.

A common source of probiotics is yogurt. Companies are winning over consumers by promising that their yogurt regulates the digestive system (Activia) and helps “strengthen your body's defenses” (DanActive).

Can probiotic products really deliver these benefits? Companies that sell these products conduct research to support their promises, and surprise, surprise! Company-funded research shows positive effects on the immune (Culturelle) and digestive systems (Procter & Gamble and Dannon).

Consumers should be aware that there are many different strains of bacteria. Different strains can have different effects. Lactobacillus reuteri RC-14, for example, can fight vaginal infections; Lactobacillus casei, found in DanActive, has been shown to reduce diarrhea in children; and Bifidobacterium animalis, used in Activia, reduces constipation.

Some companies boast benefits which were demonstrated in a completely different strain. To make it even harder for consumers to inform themselves, companies often use scientific-sounding trademark names for their products.

Another thing the companies don’t print on the labels is that you have to eat a LOT of yogurt to get the promised benefits. Dannon’s 2002 report claimed that women who ate 3 cups of Activia yogurt per day exhibited more frequent bowel movements than when they ate the same amount of yogurt without the probiotic.

Three cups per day!

Huge amounts of probiotic yogurt are probably necessary because plain yogurt itself, without probiotics, helps to regulate the digestive system.

In order to be called yogurt in the United States, it must contain certain strains of bacteria. These bacteria help prevent indigestion that many people suffer while taking antibiotics.

Normal yogurt is also good for people with lactose intolerance, since the bacteria produce the enzyme that breaks down lactose.

## Thursday, May 8, 2008

### Obsessive cleaning can be hazardous to your health

Having twice been the victim of other people’s careless bleach use, I’m not a fan of bleach. Most people don’t seem to know that you are supposed to dilute it before use. Clorox recommends using 3/4 cup in 1 gallon of water.

Even diluted, bleach is not as harmless as many people think. More than 85% of American households use it, according to the American Chemistry Council.

One major use of bleach is for laundry. Quite handy for removing stains, but regular use should not be necessary if you have a good detergent.

Bleach is also commonly used for disinfection in the kitchen or bathroom. But many users don’t know that prolonged exposure is required to kill germs. Clorox recommends soaking for 5 minutes. Just splashing bleach on the cutting board isn’t going to do it. But it could make you sick.

Bleach is toxic. It causes skin and eye irritation, breathing problems, and asthma.

Studies have shown that children whose parents frequently use bleach are much more likely to develop persistent wheezing, which can lead to asthma. It’s not clear whether the bleach itself causes the wheezing, or whether extreme cleanliness is at fault. Children who grow up without being exposed to germs end up with weak immune systems, which can lead to asthma or allergies.

When combined with other common, household substances, such as ammonia, toilet bowl cleaners, or vinegar, bleach produces a poisonous gas. The Washington State Department of Health warns that prolonged exposure to this gas can damage the lung tissue, causing severe breathing difficulties, pneumonia, or even death. If you use bleach to clean your toilet, don’t pour any other cleaners in until you’ve flushed the bleach out.

According to the American Association of Poison Control Centers, more than 20,000 children were reported to have been exposed to bleach in 2006 (http://www.aapcc.org/annual.htm). In comparison, approximately 40,000 cases of salmonella infection are reported each year, according to the Center for Disease Control.

If you do use bleach, be smart about it. Make sure it is clearly labeled and kept out of the reach of small children. Dilute it, rinse with lots of water afterwards, and either let it air dry, or dry with a clean towel.

It doesn’t make sense to splash bleach on the utensils, then dry them with the towel that’s been hanging there all week. And my favorite: people who bleach their cooking utensils, but use their dish sponge on the floor.

If you’re worried about germs, (or if you swear by bleach but order your burgers rare) then check out the Center for Disease Control and Prevention’s guidelines for preventing salmonella infection: http://www.cdc.gov/nczved/dfbmd/disease_listing/salmonellosis_gi.html.

## Monday, May 5, 2008

### Mixed meds

We all want to live long, healthy lives, but most of us accept that those two adjectives generally don’t go hand in hand. The longer we live, the more likely we are to develop one sickness or another. Or several simultaneously. Which means lots of physic.

But what if those incontinence pills react badly with the dementia therapy? A team of doctors headed by Kaycee Sink at the Wake Forest University in North Carolina sifted through data from over 3,500 nursing home patients to find the answer to this question. Their study appeared in the May edition of the Journal of the American Geriatrics Society.

Dementia patients are often prescribed cholinesterase inhibitors to slow down the decline in cognitive function and their ability to perform daily tasks. These drugs work by increasing the amount of a substance called acetylcholine, which is underproduced in the brains of dementia patients.

Patients with dementia often also suffer from urinary incontinence, and the drugs typically given for this condition do the opposite of what cholinesterase inhibitors do: incontinence drugs are anticholinergics, which reduce the amount of acetylcholine. So in theory, the drugs for incontinence should counteract the dementia treatment.

Prescribing these two opposing medications is common practice, even though nobody really knows how the two drugs interact: Dr. Sink and her colleagues found that at least one in ten nursing home residents receive both cholinesterase inhibitors and anticholinergics.

The researchers examined the medical data from patients who had been taking either the two drugs together, or just the cholinesterase inhibitors alone, for at least two years. For both groups, they looked at the patients’ ability to perform normal activities of daily living.

Both groups showed a decline in mobility, as expected for dementia patients. Perhaps not surprisingly, the decline in mobility was 50% faster in patients taking both drugs together than in those that didn’t take the anticholinergics. This translates to a change from requiring limited assistance for daily activities to being completely dependent on care givers within one year.

This poses a difficult dilemma for nursing home doctors: treat the dementia symptoms or the incontinence? And surely these aren’t the only two ailments with conflicting treatments.

## Thursday, May 1, 2008

### Another green scheme from the land of ideas

We’ve all been stuck behind them, those dirty, noisy trucks. And we’ve probably all asked ourselves why everyone is pushing for hybrid cars, when those smoke-belching monsters are still on the road. Over sixty percent of goods are transported solely by truck in the United States, according to the Federal Highway Administration, and that’s not counting the goods that are flown or shipped into the country and driven by truck to their final destination. The fact is, when you buy something at the store, it probably got to that store by truck. No wonder the streets are congested.

Wouldn’t it be nice to get the trucks off the streets? Dr. Dietrich Stein, at the Ruhr University of Bochum, Germany, has come up with a clever solution. It’s called CargoCap, and it’s an innovative system for transporting goods in high-traffic downtown areas by underground pipelines. Goods are loaded into the Caps, which are independent, computer-operated vehicles. A Cap can hold two euro-pallets, which are the common cargo transport units in Europe. This means the Caps are small enough to be transported through tunnels with a diameter of 1.6m, or about 5 feet three inches.

The advantages of this system are obvious: reductions in traffic, pollution, noise, accidents, and road expansion. The founders have even come up with a way to build the system without disturbing everyday life aboveground. They plan to use an underground, computer-controlled pipe jacking system to precisely drive the pipes into place. Displaced earth is automatically returned to the surface by way of the pipes. The pipe jacking system and small diameter of the pipes allows CargoCap to be implemented near existing infrastructure, and the system can easily be expanded to meet increases in demand.

So far, CargoCap only exists as a model. Dr. Stein and his team are planning to start a company to build the Caps, but realization of the CargoCap system in a German city will take many years, as the political machinery stands in the way.

Intrigued? See www.cargocap.com.