Thursday, April 2, 2009

New Blog Address

I've finally moved my blog to my new website

Friday, March 6, 2009

This Month’s Curious Critter: the Sloth

The remarkable adaptation of this mammal to its lofty environment is perhaps unfairly reflected in its name. Whereas in some circles, slothful behavior is regarded as a moral sin, for the sloth, it is a neatly refined way of conserving energy and avoiding the attention of potential predators.

Last year, a study came out in the Royal Society journal Biology Letters showing that sloths are not the lazy creatures they’d been held for. In the first study ever to investigate sleep in wild animals, Niels Rattenborg of the Max Planck Institute for Ornithology in Starnberg, Germany, discovered that sloths actually sleep less than 10 hours a day, instead of 16, as observed in captivity.

However, while sloths may not sleep any more than the average human teenager, they earn their name by holding the record as the slowest land mammals. The sloth can sprint short distances at 5 yards per minute, but its average ground speed is closer to 2-3 yards per minute.

Sloths are so slow and inconspicuous that a new species went undiscovered until less than a decade ago.

This remarkable lethargy is one of many tricks that help the sloth maximize the energy that it gets from the energy-poor leaves that make up its diet. Sloths also have large, specialized stomachs similar to those of cows, in which food is digested for up to a month. The contents of the sloth’s stomach contribute up to 30% of the animal’s body weight.

To further conserve energy, sloths have less than half the energy-burning muscle mass of mammals of comparable size. When it is cold, sloths don’t shiver; they roll up in a ball, and their specialized blood vessel systems keep the vital organs warm. Sloths have extremely low metabolic rates, and, although warm-blooded, their body temperature falls when they are inactive.

The sloth spends most of its life hanging upside-down. Eating and sleeping are done in this position. Females give birth in this position. The sloths’ long arms and claws enable them to hang effortlessly from tree branches—so effortlessly, in fact, that they often remain hanging after they die.

Sloths rarely venture from their home trees, except to urinate and defecate. It is during these weekly trips to the forest floor that the sloth’s slowness can prove dangerous.

Because sloths spend most of their time upside-down, their hair parts on their belly, allowing water to run off efficiently. Symbiotic algae growing in their hair causes it to appear greenish. In exchange for a warm place to grow, the algae supply the sloth with camouflage against predators.

This just shows that names can be deceiving. Sloths are not lazy; they are shrewdly tailored to life in the tropical treetops of South America’s rainforests.

Intrigued? Browse these links for more info:

A review of sloth biology
Rattenborg's article on sloth sleep
Speed of a sloth
Sloth fanpage
Video of the newly discovered pygmy sloth

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

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 (Tübingen, 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.