To sleep, perchance to dream

I’ve written a fair amount about sleep in the past. But there’s one thing that I haven’t yet written about as far as sleep is concerned – dreams. I dream a lot. Most mornings, I wake up with a memory of at least 1 of my dreams, if not pieces of many of them. It is an integral part of sleeping, therefore it is probably pretty important. I started looking into how and why we dream to answer a few of my questions about what makes it so important.

Let’s first deal with how we dream. Dreams occur during REM sleep, the part of your sleep cycle when your body is inactive and your brain is active. (To refresh your memory on the sleep cycle, you can read my entry “Zzzzz…” from September 21.) Dreaming seems to be based in very specific regions of your brain. Using a variety of technologies, scientists have found that the limbic system is the most active part of your brain during REM sleep.

The limbic system is a set of brain structures deep within your brain that has a broad effect. Overall, it regulates both the endocrine system and the autonomic nervous system. The endocrine system is responsible for the production of all the hormones in your body, and regulates metabolism, growth and development, tissue function and emotions. The autonomic nervous system is a master control system for your body, regulating body temperature, heart beat, digestion, breathing, and pupil dilation. The limbic system contains numerous brain structures to help it do all of these things, including the hippocampus (which regulates long-term memories), hypothalamus (which affects heart rate, blood pressure, thirst, hunger and the sleep/wake cycle), thalamus (which communicates with the cerebral cortex) and amygdala (which is involved in motivational stimuli such as fear and pleasure). It is also closely connected to the nucleus accumbens, which is the brain’s pleasure center.

During REM sleep, our brains are active. So why don’t our bodies respond by moving, like when we are awake? That’s because REM sleep involves not only the activation of the limbic system, but also the inactivation of the cells in the brain that control muscles. REM sleep also inactivates the part of the brain that handles judgment. This happens in the frontal lobe, one of the 4 hemispheres of the cerebrum. Inactivation of this judgment process means that we accept the bizarre and illogical features of our dreams as they happen, and easily forget them upon waking.

Okay, so we know at least a little of how we dream. Our brains activate the limbic system and inactivate our muscles and our judgment. But why do we do it? While there is no clear-cut answer, scientists have many different theories. Because the limbic system is involved in both sensory processing and emotions, many people have suggested that dreaming is a way for us to connect our emotions and our thoughts. This is the psychological school of thought, in which dreams are believed to help us deal with emotions and complicated thoughts that we can’t handle while conscious. Some, however, believe that there is a physiological basis for dreaming. This argument says that dreaming exercises the synapses in our brains while we are resting. When we are awake, our brains are processing billions of messages through our brain cells. Dreams would allow this continual flow of messages, even as our bodies and brains get the benefit of being asleep.

So let’s review. How do we dream? The answer lies in the regions of our brains that are active and inactive during REM sleep. Why do we dream? Who knows.

On a final note, here’s one interesting fact that I cam across in my research for this entry –the percent of our sleep that allows for dreaming decreases as we get older. Babies spend around 16 hours a day sleeping, and half of that is REM sleep. That’s 480 minutes a day. Adults (those over 50, anyways) only sleep around 6 hours per day. And only 15% of that time is spent in REM sleep. That’s only 54 minutes. What a difference age makes!

Funny things about humans

There are a number of funny things about our bodies that make me curious. So I have decided to devote an entry to a few miscellaneous things about the human anatomy that particularly intrigue me. For example, have you ever thought about why we have kneecaps? Or wondered why we have clumps of junk in the corners of our eyes when we wake up? Or how about earwax - what is that for?

First in my list of funny things about humans are kneecaps, also known as patella. The patella is a thick, triangular piece of bone that sits on top of your knee, covering and protecting it. It’s 1 of 4 bones in your knee, including the tibia (shin bone), the fibula (parallel to the tibia) and the femur (thigh bone). The kneecap is connected to the rest of your knee through tendons, ligaments and cartilage. The quadriceps tendon connects it to your thigh muscles, multiple ligaments connect it to the bones of the lower leg, and cartilage surrounds the whole thing. The patella is a sesamoid bone, which means it is a bone embedded within a tendon. (Do you remember my entry on the funny bone? The patellar tendon is the one that gets tapped in a knee jerk reflex test.) Sesamoid bones function to increase the mechanical effect of a particular tendon; that’s why they are mostly found in the hands, feet and knees. So the kneecap increases the leverage of the knee joint – actually, it increases the extension strength of your knee by about 30%.

Knees are complicated joints, and they have many things that can go wrong. There are several problems associated with kneecaps. Runner’s knee (or Chondrolmalacia) occurs when the cartilage directly underneath the kneecap becomes irritated. This is because the patella is directly rubbing against one side of the knee joint. Another problem is housemaid’s knee (or Prepatellar bursitis). There is a small lubricating sac between your skin and the surface of your kneecap called the bursa. People who spend a lot of time on their knees often have their patellar bursa become inflamed, causing swelling over the knee and limiting movement. Still another common problem is patellar dislocation. Your kneecap slides in a grove along your thigh bone as your knee extends. In some people, the patella moves out of that groove, and becomes dislocated. Kneecap dislocation is a fairly painful problem, underscoring how important it is for our knees for our kneecaps to be positioned properly. All in all, I’d say that kneecaps are really an underappreciated piece of our bodies.

Now on to another funny piece of our anatomies – eye gunk. Perhaps you call it crusts, sleepy eyes, or (here’s a truly unscientific name) eye goobers. Whatever it’s name, I’m talking about the clumps that accumulate in the corners of our eyes when we wake up in the morning. This junk is what’s left over from our tears once the water has gone away. Tears have 3 components – salt water, protein and fat. The salt water is produced by the tear gland, which sits behind the upper outer corner of the eyes. Protein is secreted by the conjunctiva, the clear film over the surface of the eye. And the fat comes from ducts in the eyelids. All 3 of these things serve very important functions. They clean the eye, help correct for imperfections in the cornea, and deliver nutrients to the eye. When you sleep, however, most of these things aren’t needed. We don’t get dirt in our eyes and we don’t need have the imperfections in the cornea corrected because we’re not looking at anything. So we don’t make tears. The liquid already on the surface of your eye seeps out as you sleep, and the water dries up. This leaves behind clumps of fat and protein. We don’t get this when we’re awake, because our eyes are always producing new liquid. So, tomorrow morning, if you find crusts in your eyes, you can tell yourself – look, it’s protein and fat!

Today’s final topic is earwax. Earwax is more properly known as cerumen (pronounced suh-ROO-mun). It is a yellow, waxy substance secreted by glands in the ear canal of many mammals, including humans. In humans, 2 types of glands in the outer ear canal produce the wax – the ceruminous glands (which are modified sweat glands) and sebaceous glands. It’s made up of over 40 different components, including wax and oils. The most abundant component is keratin, an extremely important protein found in all the outermost layers of our skin. Everyone’s earwax is unique, with a specific composition, color and consistency. Color can range from golden yellow to black – though no one knows what pigment is responsible for this coloration. Consistency can be either dry or wet – and that seems to be genetically determined, as dry earwax is common in Asians and Native Americans, while wet earwax is common in African-Americans and Caucasians.

Earwax is actually very important for your ears. It protects and moisturizes the inner ear canal. It helps prevent both bacterial and fungal infections within the ear canal. It keeps dirt, dust, and other unsavory things from accessing the inner portions of your ears. And it helps move dead skin cells out from the inside of the ear to be shed away. On your skin, dead cells are sloughed off through friction. Within the ear canal, the movement of your ears through talking, chewing and swallowing cause the earwax to rub against the cells, picking them up. Small hairs called cilia then move the earwax and dead cells towards the outside just like a conveyor belt. Without this, we would have no way of shedding dead cells from within our ear canals. All in all, while this is certainly something I’ve never really fully appreciated before, we should really be grateful for our earwax!

These are just a few of the intriguing questions I have about the human body. I have many others – but I’ll have to save those for another time. How about you? What about the human body makes you sit back and think, “Why on earth do we have that?”

The image of the kneecap was taken from:
http://orthopedics.about.com/cs/patelladisorders/a/kneecap.htm

Purrrrrr…..

I love watching my 2 cats, especially when my older cat decides to sneak up on the younger one. She crouches down, her ears held low, the tip of her tail twitching. She stealthily prowls over (hiding behind the furniture, of course), until she is close enough. Then – pounce! – out she leaps. (Of course, my younger cat is very used to this game, so she isn’t often caught unawares!) She also does this to stalk the occasional insect that makes its way into the house. From everything that I’ve seen, a wild cat stalking its prey acts in a very similar fashion. With ears down and crouched low, they slink closer to the target, tail twitching - then they attack.

I love to think about ways in which domesticated cats are like their wild cousins. Stalking prey, cleaning themselves with their tongues, perching in high places to look over their territory, roughhousing with each other – wild and tame cats all do these things. But there’s one thing that tame cats do that I was unfamiliar with in their wild counterparts – purring. My cats purr a lot. But do wild cats do the same? Do lions purr on the African savannah, or tigers when they are relaxing in the jungle? For that matter, what is purring, anyways? And why do housecats do it?

Many people who’ve spent time around cats know that they purr when they are content, such as when they are cuddling on the lap of their favorite person. However, this isn’t the only time that they purr. It also happens when a mother cat is giving birth, when kittens are nursing, or when a cat is severely frightened or injured; cats will even purr as they are dying. An obvious question, therefore, is why?

It is possible that purring serves a mental purpose in cats. For example, a mother cat could be trying to soothe her newborn kittens. The kittens could telling their mother that they are okay. A gravely injured cat could be trying to comfort itself. A stressed cat could be trying to keep itself calm. It is also likely, however, that purring also serves a physiological role, as well. Scientists have shown that the measurable frequency range of a cat’s purr is consistently between 25 and 150 Hertz. This range of sound has been demonstrated to promote physical health, including bone growth and repair, pain relief and decreased inflammation. Apparently there used to be an old adage often repeated in veterinary school – “If you put a cat and a bunch of broken bones in the same room, the bones will heal.” It is highly likely that cats actually purr to help themselves get better – consistent with the observation of purring by injured or dying cats. In fact, here’s something very interesting – comparing cats and dogs, cats heal from injuries such as broken bones or even surgery better, faster, and with fewer complications than dogs.

So that’s what purring does. But how do cats do it? Actually, no one knows for sure. It could be from the hyoid bone, a small flexible bone in the neck. When a cat pushes air through its voicebox, the bone can rattle, possible causing the distinctive rumble of a purr. Alternatively, purring could be caused by false vocal cords, located slightly behind the real vocal cords. Yet another possibility is that it is caused by something called the “neural oscillator” stimulating the vibration of the vocal cords themselves.

This confusion over what makes a cat purr actually makes it difficult to say whether big cats purr or not. I’ve come across multiple references to the purring ability (or lack thereof) of lions, tigers, cheetahs, leopards and jaguars. Here’s what I believe to be the most reliable information. According to a paper published in 2002 in the journal Mammal Review, cats in the Pantherinae subfamily (this includes lions, tigers, leopards and jaguars) can make some snuffling, purr-like sounds as they exhale, but it is not true purring. Only cats in the Felinae subfamily (that is, bobcats, cheetahs, Eurasian lynxes, and pumas) have the ability to truly purr. One possible explanation for this is that Pantherinae cats have a rigid hyoid bone that cannot vibrate as well as the hyoid bone in the Felinae cats.

Don’t feel badly for those lions, tigers, leopards and jaguars, though. The construction of their hyoid bones give them the distinct ability to let out a ferocious roar. That’s something that their purring cousins cannot do. So it seems that there are really 2 kinds of cats in the world – those that can purr, and those that can roar.

Personally, I’m glad my cats are the purring kind.

That’s not very funny!

Today’s topic is one that, if you have an elbow, I’m sure you are familiar with. I’m confident that, at some point, you’ve managed to whack your elbow in such a way that pins and needles shot through your arm, funny tingling went through your hands, or just downright pain reverberated through your elbow. I’ve done it more times than I can count. And, of course, whenever I do, I know exactly what to blame.

My funny bone.

But hitting your funny bone isn’t really very funny, is it? In fact, it hurts! I want to know – what is the funny bone? Is it really a bone? Why do we have one? And why is it called the funny bone, anyways? Shouldn’t it be called the hurts-a-lot bone?

Actually, the funny bone is not really a bone. It’s a nerve – specifically, the ulnar nerve, which connects your fourth and fifth fingers to your nervous system and helps control the movement of your hands. The ulnar nerve goes from your hand to your shoulder, passing around the back of your elbow. There, it sits directly on top of the humerus, the bone of your upper arm. Because of its position on top of the bone, the only protection this nerve has is the skin of your elbow. It has no other fatty cushion to serve as a shield. In fact, the ulnar nerve is the only exposed nerve in the human body. All the rest of your nerves are deeply embedded in deep tissue, ligaments or muscles. But because this nerve has no such protection, it can come into direct contact with your humerus. So when you bang your elbow just wrong, the ulnar nerve bumps into the bone, and it sends pain signals through the nerve. Because this nerve is the main connector for your ring and pinkie fingers, in fact, the most common pain associated with hitting your funny bone is tingling in those fingers. Some lucky people, however, don’t feel any real pain when they hit their funny bones, just a funny tingling feeling. And that’s probably why it’s called the funny bone.

So why do we have this exposed nerve in our bodies? It seems like a strange place to put it, doesn’t it? Unfortunately, there isn’t a lot of choice when it comes to the nerves in our elbows. Elbows are, by nature, a lot of bone and not much else. To connect our forearms to our upper arms, the ulnar nerve has to run up the backs of our elbows. This is unlike the joint on our legs that is analogous to our elbows – the knees. Knees have a lot more connective tissue surrounding them than elbows, and thus the nerves are much better protected.

Speaking of comparing knees and funny bones – is the funny bone comparable at all to the reflex kick you have when the doctor taps your knees with that little hammer? Actually, not really. That kick reaction is called the knee jerk, and it is caused by an impact on a tendon. The patellar tendon runs down from your quadriceps muscles (in the front of your thigh), over your kneecap, and down to the lower leg. When the knee is held loosely at a 90 degree angle, with your lower leg hanging freely, and the patellar tendon is tapped, it sends a message to your nervous system that the tendon and the attached muscles have been stretched. The nervous system then sends a rapid message back to the muscle to contract, causing your thigh muscles to tighten. And this tightening makes your lower leg kick out.

So the funny bone and the knee jerk are 2 different physiological reactions. Personally, I much prefer the knee jerk reflex to hitting my funny bone. The knee jerk reaction is interesting. The funny bone reaction – well, I think it’s just painful.

Ayumu, the amazing chimpanzee

A well-written headline can really catch your eye. Like this one, from an article on National Geographic Online: “Young Chimp Outscores College Students in Memory Test.” I saw that and, of course, had to read the article!

This story is about a study done recently in Japan to test the short-term memory abilities of humans and chimpanzees, and published in the December volume of Current Biology. This test involved 3 chimpanzees (who know the numbers 1 through 9) and 12 human volunteers. The subjects were placed in front of a touch computer screen that displayed 9 numbers in various places around the screen. The task was to touch the numbers in numerical order from 1 to 9. Sounds pretty easy, right? Sure, until you add the last tricky part. Once the number 1 was pressed, the rest of the numbers were covered by white squares. The challenge, therefore, was to remember where each number had been, and still be able to touch them in the proper sequence. Of the subject tested, both the chimps and the humans were about the same in accuracy. But the chimps did it faster.

A second test was done, this time pitting the fastest chimp (named Ayumu) against 9 college students. This time, 5 numbers were flashed briefly on the screen, then covered up with white squares. Again, the subjects had to touch the numbers in order. When the subjects saw the numbers for a long period of time – almost 1 second – both humans and Ayumu performed equally well. However, when the numbers were shown only very briefly – 2 to 4 tenths of a second – Ayumu performed much better than the humans. He was correct approximately 80% of the time, while the human scores dropped by half, to 40%. Ayumu was much better at taking in the whole picture extremely rapidly, and remembering the positions of the numbers, than were his human competitors. I looked at the videos of Ayumu performing the test, and it was pretty incredible. The numbers would flash on the screen and then disappear so quickly that I could hardly even find the first one! But Ayumu consistently touched the numbers in the right order. I was really impressed.

Now, before we start bemoaning the poor intellectual abilities of the humans studied here, one very important caveat must be mentioned. Ayumu is only 5 years old. Chimpanzees can live to be 50 or 60 years old, so he’s still several years away from adulthood. The humans he competed with were in their early 20s, past the age of adolescence. The test uses the ability to handle "eidetic imagery," also known as photographic memory or total recall. This is the ability to remember complex spatial arrangements or sounds with extreme accuracy. Eidetic imagery is known to decrease with age; children perform much better on tests of eidatic imagery than do adults. Perhaps what was really shown in this test was eidatic imagery in chimpanzees? Quite possibly, actually, since Ayumu performed much better on the memory tests than did the older chimps in the study, including Ayumu’s mother, Ai. In fact, Ai actually performed worse on the tests than did the human subjects. So perhaps a better comparison to understand how good Ayumu’s memory is would be to compare him to a human 8-year-old.

The study in question was performed by researcher Tetsuro Matsuzawa of Kyoto University. Dr. Matsuzawa is a leading figure in the field of chimpanzee intelligence. Most of his work is known as the “Ai-project,” which studies the language and number skills of Ai (who is, if you remember, the mother of Ayumu). Ai is 29 years old, and is part of an established colony of chimpanzees in Kyoto, a group that has been studied for intelligence since 1978. That makes this paper one of many from the longest-running study on chimpanzee intelligence in the world.

Which way is up?

Let’s engage in a little thought experiment for a minute.

Imagine that you are a cell on the inner surface of your intestine. Your job is to transfer food (or rather, the nutrients resulting from food’s digestion) from the interior of the intestine to the bloodstream. It’s really important, therefore, that you know which side of you faces the intestine and which side faces the bloodstream. But how do you know which side is which?

Now imagine that you are a plant; specifically, you are a part of the plant that is about to bud into a leaf. It’s really important, therefore, that you develop as a leaf, and not as a flower or a root or an extension of the stem. But how do you know that which end of you is the part that connects back to the stem, and which part is supposed to flatten out into the leaf tip?

Finally, imagine that you are a developing fly. (Gross, perhaps, but bear with me.) As you go from embryo to larva, your body must pattern itself in such a way that you wind up with a head at one end, wings in the middle, and a tail at the other. It’s really important your body gets oriented correctly, or else you won’t hatch. But how do you know which end is supposed to be the head?

If you look at the world from a human perspective, it’s easy to know how to orient yourself for any task – can I walk on my feet, could I sit on a chair, or do I have to stand on my head? From the perspective of a cell, however, the task of orienting yourself is a little trickier. But it’s extremely important. If a cell gets its orientation wrong, the consequences could be dire – nutrients won’t get sent into the bloodstream, neurons will not send the right messages to the right places, entire pieces of anatomy could develop incorrectly, even entire organisms could die. This question of how cells orient themselves properly is quite a large topic. Every single cell in the world has “directionality” – top and bottom, left and right, front and back. How they do this is vast and complicated, and I’m not going to go into all of the ways it is done today. I just want to highlight a specific example: how does a developing fly know which end is the head and which is the tail?

A fly’s life begins with the fertilization of an egg. This single cell will then divide over and over to produce thousands of cells needed to make the final fly. And this single cell already contains the information to determine which end is the head and which end is the tail. The information is crucial from the very start of the fly’s life, because the early cells that are produced build on that information to reinforce the body plan. This all happens through the use of protein gradients.

Take a look at the diagram below. I’ve drawn an example of the protein gradients that help determine a fly’s head and tail. The single egg contains a gradient of proteins, which are called maternal-effect proteins. In this picture, there are 2 such proteins – blue and pink. There is a lot of blue at what will be the head, and a lot of pink at what will be the tail. In the middle, there is a mixture of both. Cell that are surrounded by a lot of blue protein know that they are in the head, cells surrounded by a lot of pink protein know that they are in the tail, and cells with some of both know that they are somewhere in the middle. These maternal-effect proteins cause each cell to produce different proteins themselves, based on where they are. First come the gap proteins, which subdivide the body plan. The gap proteins then specify production of the pair-rule proteins, which make segments along the body. Finally, the pair-rule proteins specify which segment polarity proteins get made, which tell each segment which end points to the head and which to the tail. The combined action of all of these proteins tell each cell where it is in relation to the overall body. And that information helps each cell develop properly – so that the fly gets wings on his back, legs from his belly and eyes on his head.

This model of using protein gradients to specify orientation is commonly used in developing multicellular organisms, including mammals. Of course, as the animal gets more complex (with limbs, organs, and highly developed brains), the system of patterning gets more complex, too. It’s a topic that is being intensely studied among developmental biologists to this day. And it will probably continue to be studied for many years to come.

A super-sized bug

I’m not a big fan of insects. They have entirely too many legs for me to be comfortable with. Granted, there are exceptions. I like butterflies, big fuzzy bumblebees, dragonflies and grasshoppers. I don’t even mind certain kinds of ants (though not if they’re in my home). Oh, and of course I like the Katydid. But there are some bugs that I just cannot stand. Spiders, earwigs, centipedes, beetles, flies, mosquitoes, wasps, silverfish, termites, cockroaches, mites, ticks, weevils, scorpions, fleas… you get the idea. They make my skin crawl. Of course, I know it’s somewhat irrational. Even though some insects are poisonous, most have more reason to be scared of me than I do of them. And I’m easily many orders of magnitude larger than them – so it’s easy enough for me to squish them.

It’s this size difference that I want to talk about today – specifically in light of an article that I found which made me realize that bugs were not always the size they are today.

Paleontologists from the University of Bristol have recently discovered a fossil of the world’s largest bug – at a whopping 2.5 meters long. That’s 8 feet. That’s over 2 feet longer than I am tall! Whoa.
(To see a diagram comparing this insect to a human, you can see one at: http://www.msnbc.msn.com/id/21906979/)

The bug in question is an Eurypterid, or ancient sea scorpion. Eurypterids are believed to be aquatic ancestors of modern-day arachnids (which includes scorpions, spiders, and horseshoe crabs). They were predators of the ancient seas, from the Cambrian to the Permian periods (500 to 250 million years ago). Eurypterids had segmented bodies, a long, tapering, flexible tail, and claws protruding from their heads. They were ubiquitous in their day, and their fossils have been discovered all around the world. Most of the fossils are of small specimens – 1 to 15 inches long. However, the fossil announced this year was 18 inches long – and that was just one of its claws!

The finding was just published in the November edition of the Royal Society's Biology letters. However, the fossil itself was discovered several years ago in Germany by paleobiologist Dr. Markus Poschmann. Since then, Dr. Poschmann has worked with Dr. Simon Braddy to determine how big an animal would have to be to have a claw of that size. It turns out that sea scorpions have a constant ratio between claw size and body length. With that ratio, they calculated that a sea scorpion with an 18 inch claw would have a body 8 feet long – 11 feet if you include the reach of the claws.

Exactly how and why this creature grew so large is unknown. Scientists have long known that giant land-based bugs existed during the Carboniferous period, around 300 million years ago. At that time, there was a boost in atmospheric oxygen, which might have allowed creatures that use breathing systems that diffuse oxygen into tissues (like insects) to get bigger and bigger. However, two things argue against this being the reason for the giant sea scorpion. First, it predates this increase in atmospheric oxygen. And second, this beast was too big to come onto land, so it wouldn’t have even used atmospheric oxygen. So it is unlikely that this atmospheric oxygen boost is the cause of this giant bug. Dr. Braddy speculates that eurypterids grew increasingly large to be better able to prey on armoured fish. Moreover, there was not much competition from vertebrates at that time, and the sea scorpions themselves had no predators. So they could get as large as they wanted. However, eventually these giant bugs had to downsize due to competition from large fish with jaws and teeth. They eventually disappeared from the fossil record during the Permian extinction approximately 250 million years ago, which wiped out 95% of marine species.

Personally, I’m glad that we don’t have insects this large around anymore. If I get the creepy-crawlies from a spider less than an inch in diameter, imagine what I’d do if faced with a scorpion 8 feet long! (On second thought, let's not imagine that. It's too creepy.)

Mirror Images and Molecules

In my last entry on turkey, I mentioned that the proper name for the amino acid tryptophan is really L-tryptophan. Though we usually leave the L out, it is actually very important, at least as far as the chemistry is concerned. The L designates a characteristic of the molecule that is called chirality (pronounced k-EYE-ral-it-ee).

Chirality comes from the Greek word meaning “hand,” and is a property of asymmetry. To understand chirality, take a look at your hands. To a certain extent, your hands are identical – 4 fingers and 1 thumb, all of comparable sizes and arranged the same way around palms of equal size. However, your hands are different in one important respect – you cannot overlay them. If you put your right and left hands in the same orientation (say, palm down), and then put your right hand on top of your left, they don’t match. Your thumbs are on opposite sides. That’s because your hands are really mirror images of each other. Hold them palm-to-palm, and they match up.

An object is chiral if it cannot be superimposed on its mirror image. I’ve given you an example in the diagram below. There are a few important notes that you need to know to understand a picture like this. First, it is a 2-dimensional image of a 3-dimensional object, so you’ll have to use your imagination a little. Second, each letter represents a different atom. Third, the lines connecting the atoms are bonds – chemical links that hold the 2 atoms together. You can’t break the bonds, or shuffle the orientation of the atoms relative to each other. A bond designated by a solid triangle points out of the picture at you, while an empty triangle points into the picture away from you. A single line represents a bond flat in the plane of the picture.

In this diagram, the central atom (N) is bonded to 3 other atoms (X, Y, and Z). In the diagram on the left, N and X are in the plane of the picture (flat), Y points out of the picture at you, and Z is behind the picture away from you. In the center panel is the mirror image. Its mirror image is the same (N and X in the plane, Y pointing out, and Z pointing back). However, if I now flip the image on the left to try and superimpose back on the original (that's on the right), all of a sudden it doesn’t work. Though N and X are still in the plane, now Z points out at you and Y points back. These molecules have the same chemical composition, the same type and number of atoms, and the bonds connect the atoms in the same way in both. But the 2 molecules are mirror images of each other, and they cannot be overlaid. That makes them chiral.

But who cares if you can superimpose them or not? They’re still the same molecule, right? Actually, no, they’re not. So let’s go back to L-tryptophan. Tryptophan is a chiral molecule, which means that it is not the same as its mirror image. The 2 mirror image versions of tryptophan (called isomers) are L-tryptophan and D-tryptophan. Your body cannot use D-tryptophan at all. It can only use L-tryptophan - as a building block for proteins, as a precursor for serotonin, or for any other metabolic process. In fact, almost all of the amino acids in your body are L. (The exception is glycine, which is so simple a molecule that it doesn’t have chirality.) The only organisms to use D amino acids are some bacteria and a few exotic sea creatures. Even if you were to eat D-amino acids, you can’t use them. Your body would just get rid of them.

I find it fascinating that a molecule - like an amino acid – can be chemically identical to another (as in its mirror image), and yet the 2 have totally different properties in your body. Our body chemistries are really exquisitely specific!

Don’t blame the turkey!

In honor of the upcoming Thanksgiving holiday, I wanted to write about a scientific topic that I’m sure will be brought up in many households across the country. Sometime after dinner, you may find yourself sitting on the couch, trying to stay awake. And you just might think:

The tryptophan in the turkey I just ate is making me sleepy.

A Newsweek article that I came across today definitely bolsters this idea: “Four Reasons Thanksgiving Makes Us Sleepy.” Reason #1? The turkey and the trimmings.

But is it true? Does eating a tryptophan-rich food like turkey really make you sleepy? If yes, why? If not, why does everyone think it does? For that matter, what is tryptophan, anyways?

Tryptophan is an amino acid, one of 20 standard amino acids used as building blocks to make proteins. (Actually, its proper name is really L-tryptophan, but hardly anybody uses the L.) Tryptophan is a pretty complex amino acid, considered hydrophobic (which means it doesn’t like water) and aromatic (which refers to its chemical structure). It is actually one of the essential amino acids, which means that our bodies cannot make it ourselves. We have to get it from our diet. (Nine of the twenty standard amino acids are essential; we can produce the other eleven.) Tryptophan is found from several food sources, including poultry (both chicken and turkey), pork, cheese, beef, fish, peanuts and soybeans. (Basically, foods rich in protein are also rich in tryptophan.) In addition to being used as a building block for proteins, tryptophan is also used by our bodies to make hormones. For example, tryptophan is used to make niacin (a B-vitamin). Niacin, in turn, is used to make serotonin. And serotonin is a remarkable hormone that exerts a calming effect on your brain, and plays a key role in making you sleepy. Tryptophan is also used in the production of melatonin, another hormone that regulates sleep.

With all that, it makes sense to think that eating a tryptophan-rich meal would result in increased levels of serotonin in your brain, which would then make you drowsy, right? In fact, in the 1980s, many people took L-tryptophan supplements to help combat insomnia. It’s not taken in the US anymore, as the FDA has banned it due to problems with production. But L-tryptophan supplements are still used to treat insomnia in Canada – though it’s only available by prescription.

Unfortunately, while the idea sounds good in theory, it doesn’t really work that way. In order for tryptophan to cause sleepiness, it must get to the brain. To do that, it must be eaten on an empty stomach, with no other protein source. If eaten with other proteins, all of the amino acids are trying to go to the brain at once. And since they all use the same transport system to get there, too many amino acids at once make it slower for all of them. (Just like driving during rush hour.)

So why do we get sleepy after Thanksgiving dinner? One of the biggest factors is that we simply eat a lot. To digest food, your body diverts blood away from your brain and down to your digestive system. The more food that has to be digested, the more blood has to be diverted to your stomach. This is especially true if you ingest a lot of fats in the meal. Fats (for example, in the meat, gravy, butter and desserts) take a longer time to digest than other components of your meal. So not only does your body need to use a lot of blood to digest the quantity of food, it needs extra time to digest the quality of food. And all that blood diverted from your brain to your stomach means sleepiness.

Another big food culprit is the carbohydrates (found in potatoes, bread, yams, stuffing and dessert). A carbohydrate-rich meal causes your pancreas to secrete insulin. When the insulin hits your blood stream, it causes your muscle cells to absorb glucose out of the blood. Since glucose is essentially energy, reducing your blood glucose level results in a feeling of low energy. Have you ever eaten a lot of sugar? You probably got a big boost of energy that quickly wore away, leaving you feeling very tired. That’s because sugar causes a rise in blood glucose, which gives you energy. But your body compensates by producing insulin, which pulls that glucose out of your bloodstream, leaving you tired.

I do want to address an issue raised in the Newsweek article I mentioned above. This article cites research published in the Canadian Journal of Physiology and Pharmacology in 2007. The research report, entitled “Protein-source tryptophan as an efficacious treatment for social anxiety disorder: a pilot study,” argues that tryptophan reaches the brain better when eaten in combination with carbohydrates than when eaten by itself. That’s because insulin causes specific absorption of some amino acids into your muscle cells, but not tryptophan. These other amino acids can no longer compete with tryptophan for delivery to the brain. The authors of the research say that serotonin increases in the brain, as measured by an anxiety test. (Remember, serotonin helps calm you down.) Two big problems with this study, though are (a) they didn’t test sleepiness, and (b) they tested pure components – deoiled gourd seed (a tryptophan source) and pure glucose (a carbohydrate). So it’s a stretch to say that this proves that turkey makes you sleepy on Thanksgiving. Relative to the other 2 factors mentioned above (blood diversion and insulin production), sleepiness induced by serotonin in your brain from ingested tryptophan is going to be small. You’re going to fall asleep because of the amount of food you ate much sooner than you would from the tryptophan in your turkey.

So while you may feel sleepy after dinner on Thursday, don’t blame the turkey. It gets a bad reputation for keeping us prone on the couch, when we should probably be helping with the dishes!

Language and Sound – A Baby’s Sophisticated Brain

I recently had the pleasure of listening to a seminar entitled “Learning Language,” which was about many different aspects of how babies and children acquire language skills. It was given by Dr. Patricia Kuhl, Professor of Speech and Hearing Sciences at the University of Washington’s Institute for Brain and Learning Sciences. Dr. Kuhl is internationally renowned for her research on brain development and language acquisition in infants and young children, and is one of the leading experts in the world. This was one of the more interesting seminars I’ve ever sat through – and believe me, I’ve sat through many seminars during my years as a scientist! Before this seminar, I had never really thought about the science behind how we learn language. But now that I know a little bit about it, it’s a fascinating topic.

To begin, let me tell you a story. I had a Chinese-American roommate fluent in both English and Mandarin. She once told me a popular Chinese children’s rhyme, which was in Mandarin. It was the strangest sounding children’s rhyme I’d ever heard! To me, it sounded like the same word, repeated over and over. To her, however, the words were different – distinguished by tonal differences in each word that her ears could detect. (If you’ve ever had experience with Asian languages, this may sound familiar to you!) The reverse is also true. Native Japanese speakers, for example, often cannot hear sound differences in the English language, such as the difference between “ra” and “la.”

Have you ever wondered why this is? I mean, it’s just sounds, right? I can hear pretty well – so why can’t I hear the tonal differences associated with Mandarin Chinese? Why can’t a native Japanese speaker distinguish an “L” from an “R?” It’s not just that we can’t pronounce them right – we can’t even hear them.

One possible answer is something called the “Native Language Magnet/Neural Commitment Theory.” Babies are born with the ability to recognize a vast range of differences in sounds, and studies have shown that they can distinguish differences in sounds from languages all over the world. However, once they’ve reached a year of age, their ability to distinguish sounds from foreign languages is greatly diminished. An example showed by Dr. Kuhl concerns the ability of Japanese and American babies to distinguish “ra” from “la.” Both sets of babies can distinguish “ra” from “la” very efficiently at 6-8 months of age. However, at 12 months, Japanese babies are only half as likely the be able to hear the difference as American babies; their discernment gets worse as they get older.

According to the Native Language Magnet/Neural Commitment Theory, the brains of babies are constantly listening to the world around them. And the sounds that they hear most often are the ones that their brains hone in on. An American baby, for example, will hear “ra” and “la” quite often in the speech of those around her. So her brain recognizes that the difference must be important! Therefore, it puts special effort into remembering the difference between the sounds. A Japanese baby, on the other hand, will likely never hear the sound “ra” - it doesn’t exist in the Japanese language. His brain will therefore have no reason to make an effort to remember the difference between the sounds. Instead, his brain will focus on important tonal sounds in the Japanese language.

In this theory, the infant brain passes through 4 phases. Phase 1 is the initial state, in which infants can discern phonetic differences of a wide variety. Phase 2 is the neural commitment state. Auditory processing results in the classification of vowels and consonants into “bins,” or distinguishable groups. When 2 different sounds are put into the same bin, the brain loses the ability to distinguish between them. A Japanese infant will group “la” and “ra” in the same bin – and thus, to them, it becomes the same sound. Phase 3 is really an enhancement of phase 2, in which these phonetic groupings get reinforced. And in phase 4, this neural commitment is stable. The infant brain has now developed in such a way that it can distinguish between the sounds of its native language, but not of other languages.

One interesting ramification of this work is that the sounds a baby hears is really important! He may not know the words you use, but he can use the sounds you make to build his foundation for understanding the language as a whole. It’s the sounds that matter. This means that baby talk is actually really, really important.

In baby talk (also known as “mother-ese” or “infant directed language”), adults exaggerate the phonetic sounds they make. The vowels are stretched, the pitch changes are exaggerated, and the words are slowed down. The end result is to make the sounds even easier for babies to hear and distinguish. Babies find this kind of talk immensely appealing – studies have repeatedly shown that baby talk holds an infant’s attention better and longer than does regular speech. And in terms of the neural commitment theory, baby talk makes it clear to infants what sounds are important for their native language. So evidence indicates that baby talk actually helps infants in the early stages of language acquisition.

There are vast reams of research on language acquisition and skills that I haven’t even hinted at here. It’s an immensely complicated subject, studied by neurobiologists, behavioral psychologists, and linguists, to name a few. But once again, I am amazed at how well our brains handle such an enormously complex thing – especially when we’re as young as 6 months old.

Planning for the future

Take a look around you one day and you will see a pattern in human thinking. Each Friday, grocery shoppers take lists to the store to buy food for their families to eat the next week. Each month, paychecks in America are taxed by the Social Security Administration for the money to be returned to those who are retired. Each year, Christmas decorations are put into storage for millions of households to be reused the following holiday season.

Every day of our lives, we plan for the future in some way or another. We save food, money, or supplies. We plan careers, houses and vacations. Do we eat dinner early to watch our favorite TV show, do we hire a babysitter this weekend to go see a movie, or do we really want to go for a jog to reap health benefits years from now? Planning is so common in our lives that it might surprise you to realize that knowing how to plan for the future has always been believed to be an ability exclusive to humans. Animals can exhibit saving behavior. Any city dweller sees how squirrels hide acorns every fall, and dog owners know how their pets bury their bones to be dug up later. However, these behaviors fall short of the true scientific definition of “planning ahead.”

Let’s talk about what qualifies a behavior as “planning ahead.” To non-scientists, planning ahead is a state of mind where you think beyond the present, anticipating a need and doing something ahead of time to fill it. To biologists, however, the definition of planning ahead is more rigorous and based in the animal’s behavior, not their state of mind. After all, we can’t ask squirrels why they bury acorns in the forest.

Two things determine whether an animal is really planning ahead. First, the behavior must be a novel action or actions, something new that the animal has not done before. Second, it must be appropriate to a motivational state, rather than a current condition. In other words, it has to be something the animal will anticipate needing, rather than something it currently needs. Thus a bear fattening up for hibernation cannot be said to be planning ahead for the winter, since it fails both criteria. The bear does it every year after learning from watching their mothers, so it is not a novel action. Moreover, metabolic changes in the bear’s body result in the addition of layers of fat to its anatomy. Biologically speaking, then, it is not a planned response to future hunger but to a current condition of hunger.

Proving whether an animal can plan ahead is very tricky, so it has never been done before. Until recently, that is. Early this year, researchers working with Dr. Nicholas Clayton at the University of Cambridge found a way to test the planning skills of a small, unassuming bird.

Western scrub jays are native to western north America. These birds, which live in oak woodlands in the wild, are well adapted to suburban environments. They are omnivores, and will eat just about anything, including a variety of seed. Importantly for Dr. Clayton, they are known to store their seed. But does that mean that they are planning ahead? Or are they acting on instinct?

Dr. Clayton tested the jays in a variety of caged environments with differing availability of food. In one experiment, the birds were allowed access to three cages. The first evening, the middle cage contained a supply of powdered pine nuts. Jays can’t carry this, thus they can’t save it. The next morning, they were contained for two hours into one of the other two cages, one that contained breakfast and one that did not. After several days of this, the birds were given whole pine nuts for dinner instead of ground pine nuts. The next morning, the scientists discovered a supply of whole pine nuts in the “no breakfast” room, but not the “breakfast” room. The jays knew which cage would not have food in the morning, so at their first chance, they stored food there. All the data for this experiment came from one test, so the birds could not have learned over time how their actions would determine whether or not they would have whole pine nuts to eat the next morning. The conclusion: the jays were planning ahead for their next breakfast.

A second experiment expanded the results. This time, the birds were confined to one of the two side cages for breakfast, where they were given one of two kinds of food. In one room they were fed whole pine nuts, and in the other, they were fed dog kibble. After several mornings of this, they were given both kinds of food in the central room. At this one and only opportunity, the birds stored the type of food that each room was lacking for the next morning (dog kibble in the pine nuts cage and vice versa). Again, the conclusion was clear: this behavior fit the definition of planning ahead.

This story, published earlier this year in the journal Nature, was the first generally accepted scientific proof of a non-human animal planning ahead. And I hope that you get a few things out of this story. First, I think the results are fascinating. Who would have thought that blue jays could think abstractly about the future? But in addition, it really shows how complex living systems are. We can observe a behavior in an animal, but that does not mean we know why they do it. That’s extremely difficult to test. But along with that difficulty comes one of the fun things about being a scientist. We have to be extremely creative sometimes to find a solution to an incredibly complex problem!

Cats, cats cats!

Today’s topic is one near and dear to my heart – cats. I think cats are among the most fascinating animals on earth. Whether they are domesticated or wild, whether they are big or small, whether they are cute or ferocious, there is something about all of them that I find irresistible.

The list of wild cats is vast and varied. You probably already know about the most famous of the wild cats, such as lions, tigers, cheetahs and leopards. But I thought I’d take some time to tell you about a few wild cats that you might not have heard of before.

For example, take the caracal. The caracal, also known as the African Lynx or the Desert Lynx, is found in northern Africa, the Arabian peninsula, and southwestern Asia. They are one of the largest “small” wild cats, and their relatively small bodies are very stocky. Males are about 2 feet long (plus another foot for their tails), and they weigh in at an average of 28-50 pounds. Caracals look somewhat like a cougar - their bodies are usually reddish-brown, and they have white chins, throats, and underbellies. By far their most distinctive feature is their ears. A caracal’s ears are long, tufted and tinged with black. (The name Caracal actually comes from the Turkish word for “black ear” – karakulak.) These ears are one of their most important assets for hunting – each one is controlled by 20 muscles, allowing them to pivot and pinpoint prey. Like all cats, caracals are strict carnivores, subsisting on rodents, birds and small deer. They are nocturnal and highly territorial, which means that they are very difficult to find in the wild. However, they are relatively easy to tame, and there are numerous examples of pet caracals that have been raised from kittenhood by humans.

Another relatively obscure wild cat is the serval. Servals are considered medium-sized wild cats; though their weight is comparable with the caracal (20-45 pounds), their bodies are significantly longer (3 feet in length, plus a foot and a half for the tail). This makes them very slender animals, an image assisted by the fact that they have one of the longest legs in the cat family. (That, though, is due to really long feet rather than legs). Like leopards, servals have tawny-gold bodies marked with round, black spots. In general, these spots tend to be large, and merge into stripes on their necks and backs. Servals are excellent hunters, especially of rodents. Small mammals, in fact, make up approximately 90% of their diets. This includes squirrels, hares, and mole rats, though they will also eat lizards, snakes, frogs and birds. When a serval is hunting, it prowls slowly through grasslands, pausing for as long as 15 minutes at a time to listen for prey. When they find something, they leap high with all four feet off the ground, then pounce on their victim, stunning it with a blow from their forefeet. If they miss, they will repeat the process (at the risk of looking somewhat like a wind-up toy). They don’t miss very often, though. One of every two pounces by a serval results in the capture of prey – making it one of the most effective feline hunters.

A wild cat that I particularly like is called the Fishing Cat. Fishing cats are native to Indochina, Pakistan, India, and southeast Asia, including the islands of Java and Sumatra. They live in densely vegetated areas near water, such as marshes, mangroves, rivers and streams. This is a fairly small cat, weighing 15-25 pounds and measuring 2 to 3 feet long, with short tails. Their legs are very short and their heads very broad, giving them a very stocky appearance. They tend to be olive-gray in color, and have dark spots roughly arranged in stripes along their bodies. Fishing cats, as you might have guessed, eat mostly fish. Because of that, they do not have the same dread of water that most cats do – in fact, they dive into water to catch them! A fishing cat will tap their paws on the surface of the water, mimicking insect movement. When a fish comes close, the fishing cat will then dive in after it. They will also eat other aquatic animals, like frogs, snakes, and crustaceans. When a fishing cat is swimming, it can use its short tail like a rudder, helping it turn suddenly to catch their prey. In addition, their webbed paws can act like oars, or also give them extra traction in the mud. They are probably one of the few cats I have seen who don’t look completely bedraggled when wet!

The final wild cat of the day is the Margay. Margays are also known as tree ocelots or long tailed spotted cats, and are native to Central and South America. Their fur is patterned much like an ocelot: a yellow-brown body covered with black spots and whorls, as well as white underbellies. They are one of the smallest cats in the cat family, only weighing 4-6 pounds and measuring 1.5 to 2.5 feet long (with an extra foot for the tails). These are also the most accomplished climbers of all cats, too. Their light bodies and strong paws help in that, as do their specially adapted claws and ankle joints. These can rotate 180 degrees, which allows them to move almost like monkeys through tree branches – including running down trunks head first, crawling along the underside of branches, or hanging from a branch with 1 leg!

I think it’s fun to compare traits of wild cats with my 2 housecats. Like caracals and servals, both of my cats like to stalk their “prey” (though, since they are indoor cats, their prey consists mostly of catnip-stuffed mice). They have also been known to pounce with a wild, all-4-feet-in-the-air jump. However, unlike fishing cats, they absolutely hate being wet (baths are a particularly unpleasant time for them). And they are nowhere near as coordinated as a margay. In fact, they have been known to fall off the couch from time to time, so I definitely would not trust them in a tree!

The pictures I posted here are from the following websites:
Caracal: http://wildfeline.tripod.com/african_cats.htm
Serval: http://www.vulkaner.no/n/africa/somaliwildlife-n.html
Fishing Cat: http://www.bigcatrescue.org/fishing_cat_photos.htm
Margay: http://www.guyana.org/Guyana_Photo_Gallery/animals/animals2.html

Now that’s an old clam!

Well, I’ve written about animals that live a long time, and I’ve written about clams. So I guess now would be a good time for an entry on clams that live a really long time!

Scientists at Bangor University in the United Kingdom have found a quahog clam that holds the title of oldest animal in the world – at a whopping 405 years. Now that’s old.

So what are quahogs? Quahogs (pronounced “KO-hogs”) are hard shell clams. If you picture a clam on the menu in a seafood restaurant, you’re thinking of a quahog. They, along with soft-shell clams, oysters, scallops and mussels, are known as bivalve mollusks. That’s because their shelves are made of two halves, or valves. The valves connect at a joint called the hinge, which contains the oldest part of the clam’s shell. That part is known as the beak. The hinge will be in an open position and the valves ajar if possible, but if water conditions are bad or there are predators around, the clam can snap its valves shut, and hold itself tightly closed for as long as necessary.

Quahogs have several muscles that are important for their physiology. Their adductor muscles control the opening and closing of the hinge. They also have a foot for burrowing in the sand, which is controlled by the foot retractor muscles. One other important feature of their bodies is their necks. A quahog’s neck can stick upwards through the sediment and into the water above. Through the incurrent siphons in their necks, they filter water over their gills, collecting algae, plankton and diatoms to eat. The filtered water then gets spit back out through their excurrent siphons.

There are actually 2 different species of quahogs in the world. The clam that we eat in North America is called Mercenaria mercenaria. These clams are also known as Northern quahogs, round clams, chowder clams, littlenecks, topnecks and cherrystones. You might wonder at their scientific name, which is related to the Latin word for money (“mercenaria” means “something of value”). Apparently, Native American tribes in New England used to use quahog shells to make valuable beads for barter. In addition to the Northern quahog, however, there is another species native to the North Atlantic ocean. This species is called Arctica islandica, and it is this variety of quahog that was found to be over 400 years old. It was collected from water over 250 feet deep off the coast of Iceland, and it beats the previous record holder for longest-lived clam by several decades.

So how do the scientists know how old these clams are? Remember, the oldest part of the clam’s shell is the beak, which is found near the hinge. Every year a quahog is alive, its shell grows outwards from its beak. And every year, the growth creates a ring in the shell. Scientists can simply count the number of rings to see how many years of growth the shell has undergone. This is very similar to the way that trees are dated.

How do these clams live so long? No one really knows, though the finders of this old quahog speculate that it may be due to slow cell division. Scientists think that geoducks, another kind of clam, can live 100+ years because they have a low-stress lifestyle (you can read my entry “What do you call that?” if you missed it before). So an alternate theory could be that perhaps quahogs in the waters off Iceland live even easier lives than geoducks in the Puget Sound!

I don’t know if the same could be said for the North American quahog, though. There is a large and active clamming industry in American and Canada, which harvests quahogs for consumption around the world. So it’s a safe bet that they do not live as long as their Icelandic cousins.

You can find an article describing this clam on National Geographic Online:
http://news.nationalgeographic.com/news/2007/10/071029-oldest-clam.html.

A Medical Use for Capsaicin

A few weeks ago, I wrote about a molecule called capsaicin, which is the ingredient that makes peppers spicy (‘Those red hot chili peppers”). Apparently, capsaicin is not only used in cooking – it also has medicinal value. Scientists are testing whether capsaicin can be used as a painkiller.

This may sound a bit odd. After all, capsaicin causes pain, doesn’t it? (Try pouring some tabasco sauce straight into your mouth and see how you feel.) It does, but here’s the catch. If you apply enough capsaicin to a nerve cell, it will stimulate so much pain that the nerve will become numb. And numb nerves can no longer signal pain. So a brief pain associated with the capsaicin treatment can result in a long time of no pain at all.

This idea is being used to treat long-term or throbbing pain, which is caused by a very specific set of nerve endings. Called C fibers, they are a type of sensory fiber associated with chronic pain and warmth. C fibers possess a protein that bridges the membrane of the nerve ending. This protein, called TRPV1, acts like a gate, which is usually closed. However, when capsaicin comes along, it binds TRPV1 and opens the gate. As a result, calcium ions flood the cell, and if there’s enough calcium ions, the nerve goes numb. A high enough dose of capsaicin can result in numbness that can last several weeks, in fact.

Capsaicin works only on the C fiber nerve endings, not those that work in other kinds of pain or for movement. That means that numbness associated with capsaicin treatment would only block this pain signal. It would not interfere with any other kind of nerve process. If you’ve ever had your mouth numbed by the dentist, you may be able to appreciate the distinction. When you are treated with Novocaine, all the nerves in your mouth go numb, including those for sensation and movement. That’s why you lose feeling across your entire mouth (and perhaps your tongue and nose). A capsaicin-based anesthesia would be much more selective in its ability to block pain. So a dental filling would not only be pain-free, you would also be free of that awkward drooling that results from an immobile mouth.

Doctors are using this treatment in patients undergoing extremely painful surgery. They treat the nerves exposed during the operation with an ultra-pure form of capsaicin - since the patients are anesthetized, it doesn’t hurt any more than the surgery does. However, once they recover from the anesthesia, doctors hope that their nerves will be numbed enough to allow for better, less painful recovery. And early indications suggest that it works as predicted. In small tests of those recovering from either open hernia repair or knee replacement, those who received the capsaicin treatment reported less pain than their untreated counterparts.

For an article discussing this work, you can check out:
http://www.baltimoresun.com/news/health/bal-te.peppers30oct30,0,1228065.story

Protein Folding - a Group Effort

In my last column (“The Problem with Proteins”), I described the problem with protein folding. Today I wanted to describe one of the major efforts underway to solve this problem. And believe me, this really is a group effort. This effort uses a process called Distributed Computing.

Labs at Stanford University, the University of Pittsburg, the University of California at San Francisco, Notre Dame, California State University Long Beach, and the Mediterranean Institute for Life Sciences in Croatia use computers around the world to model and predict protein folding. It is a method of computer processing that runs different parts of a program, or different sets of data for the same part of the program, simultaneously on more than one computer. These individual computers, working at the same time on different parts of the same project, then share their results. This results in much greater computing power than any individual computer can provide.

Okay, so these labs use computers around the world to do the work. What work? What are these computers solving?

Computers are often used to model possible ways for a protein to fold. They can run through the innumerable possible folds and configurations for a given stretch of amino acids in a step-by-step process. At each step, it can analyze how likely it is that the protein folds in that way, based on biophysical and biochemical criteria. Step-by-step, the computer can work its way through from the raw amino acids to what is the most physically likely structure for that sequence. This takes a lot of computing power.

One standard modern computer can simulate how a protein will fold in a nanosecond (that’s 1 billionth of a second) in one day. That’s 1 billionth of a second of folding done in 1 day of work. Unfortunately, proteins fold on an average of around 10,000 nanoseconds. That would take 10,000 days for one computer to analyze a protein from start to finish. Alternatively, if you could link 10,000 computers and have them all run different parts of the prediction, you could finish in 1 day! (I know which method I’d prefer.)

Okay, so by coordinating all of these computers around the world, we can dramatically speed up the predictions and modeling of protein folding. Why is this helpful? Scientists hope that this will allow them to discover the "first principles" of protein folding. Knowing these first principles will allow them to (a) predict what final shape any given protein sequence will ultimately form, (b) make artificial proteins that form a certain shape and thus perform a certain task, and (c) determine why some proteins in our bodies dramatically misfold with dire consequences. There are numerous examples of how misfolding proteins cause human disease, including Huntington's diseases, Alzheimer's disease, and the prion disease Creutzfeldt-Jakob. Figuring out why these diseases are associated with dramatically misfolded proteins is one of the major goals of many protein folding scientists in the world.

If you are interested in checking out the software involved in this project, or even adding your computer to their work, you can read more about them at:
http://folding.stanford.edu/

The Problem with Proteins

Proteins are one of the basic building blocks of life. They are the workhorses that accomplish most of the physiology of every cell, including DNA replication, cell division, energy production, metabolism, and degradation of cellular waste, to name a few examples. There are multiple thousands of different proteins in each cell, and each one is distinct from every other by virtue of its shape.

Wait, what do you mean, a protein’s shape? Well, proteins are much like keys. They have a very specific 3-dimensional structure, which must be maintained for them to do their jobs. A protein shaped for one job will not work for another job, just as a key for one lock will not open a different one. And if a protein gets warped out of shape, it will no longer work properly, much as a bent key will no longer open its lock. We know how keys get their shape – go to any home improvement store and you can see the key-making machine. But how do proteins get their shape?

Would it surprise you to learn that this simple sounding question is actually one of the biggest unsolved questions plaguing biologists today? How proteins achieve their final shape is referred in science circles to the problem of protein folding. And it is a thorny problem indeed.

To understand why this is such a tough question, let’s talk first about how proteins are made. Imagine that you have lots of different beads that you can string together to make a necklace. These beads are connected together end-to-end, and each necklace that you make will look different from each other depending on which beads you choose. Proteins are the same way. The beads are called amino acids; there are 20 standard amino acids in your cells that can be strung together to make thousands of different proteins. The standard amino acids are all different from each other by several biochemical criteria. Some are large, others are small. Some have positive charges, and others have no charge at all. Some are really simple, and others are very complex. Whatever their characteristics, these amino acids are strung together by a “machine” in the cell called the ribosome. Once the amino acids are connected together, though, the process of making the protein is only halfway done .

Now that the protein is in its raw form, it must fold itself into the final 3-dimensional shape. The final shape is enormously complex, usually comprised of different substructures within the overall shape. The final shape directly depends on the linear string of amino acids. But the big question is this: how does the protein know how to do this? How does it know how to take this end-to-end string of different amino acids and twist, turn, fold and bond to itself in such a way as to form the final, complex structure?

Here’s what we know about protein folding:

1. We know that the folding of a protein will depend largely on its amino acids. Let me give you a few examples. Amino acids can be hydrophobic (“water-fearing”) or polar (“water-loving”). Hydrophobic amino acids do not like contact with water, while polar ones prefer a watery environment. Hydrophobic amino acids, therefore, like to be tucked away into the inside of the protein, where there is no water. Polar amino acids like to be on the surface of the protein, where they will encounter water a lot. Another example depends on the size of the amino acids. Some are extremely bulky, and simply cannot fit into tight pockets. They must be folded in a place with lots of room. Thus the structure of a protein is limited by the physical properties of its amino acids.

2. We know that there are several kinds of folds, or substructures, that proteins can adopt in their overall structure. To understand this, imagine the engine of a car. It has an overall structure. But the individual parts of the engine (the transmission, the cooling system, the fuel injection) have their own shapes, as a subset of that larger structure. The same is true with proteins. Proteins can have some part of themselves fold into an alpha helix (kind of like a slinky), while others fold into a beta sheet (like an accordion fan). These smaller bits then fold together in larger structures to form the overall protein shape.

3. We know the structures of many different kinds of proteins. These have been determined experimentally (and this is actually a problem that I will talk about below).

4. We know that proteins can fold extremely quickly (sometimes as fast as a millionth of a second).


That sounds great, right? Yes, but there are also lots of things we don't know about protein folding. Here are some examples:

1. We cannot predict what the final shape will be of a given stretch of amino acids. So far, the only way we can know the structure of a protein is to solve it biophysically. This is done mostly with x-ray crystallography. But this is difficult, expensive, and doesn’t always work. As a result, we do not know the structure of the majority of the innumerable proteins in the world.

2. We do not know what steps most proteins take to form the final shape. It is a multi-step process, and requires the help of lots of other cellular machinery. But most of those steps are a mystery.

3. We don’t know why some proteins fail to fold properly. In fact, sometimes they misfold so badly that the only thing that cell can do is destroy them and start over.

4. We don’t know how to take a predetermined shape and artificially produce a protein to fold into that shape. This is really the converse of problem number 1. We cannot predict a structure based on certain amino acids, nor can we predict amino acids to give a certain structure.

5. We don't know how on earth proteins fold so fast.

The biggest problem facing protein folding experts right now is problem #1. We simply are unable to predict what a protein will look like, even if we know its sequence of amino acids. This is actually a pretty big problem for molecular biologists. We know lots of protein sequences. But we'd be able to conduct much better research if we knew what shape that protein adopted. Again, imagine a protein to be like the engine of a car. If a mechanic needs to fix the engine, simply having a list of the parts that engine contains won't be much help. He needs to know what the engine looks like to have any success.

Okay, I’ve given you the problems we have with protein folding. The good news is that there are lots of scientists working to solve these very problems. And now that I ’ve laid the groundwork for the problem, I’ll come back to this in another post and discuss how some scientists are trying to solve these problems.

The best time for sleeping

I just spent an interesting few days at the annual meeting of the National Association of Science Writers. At the meeting, we learned a lot about a wide range of topics, not the least of which was science. I was fortunate enough to have lunch one day with a sleep researcher from Washington State University. And, if you recall from some of my previous posts, I think that sleep is a really fascinating scientific topic! One thing I learned from this sleep scientist is that everyone has an optimal time of the day in which to fall asleep. This depends largely on your circadian rhythms.

I bet that you've heard of circadian rhythms before - but do you know what they really are?

Circadian rhythms are 24-hour (roughly) cycles that occur in the physiology of all living beings - animals, plants, and even bacteria. Human circadian rhythms are those cyclical changes that occur in our bodies during a 24 hour period. The rhythms are controlled by something called the superchiasmatic nucleus (or SCN), which is a pair of structures in your brain about the size of a pinhead. The SCN, containing around 20,000 neurons, sits in the brain just above where your optic nerves cross. Different levels of light that hit your eyes are translated into a signal for the SCN, which then regulates multiple physiological processes. These processes mostly relate to the sleep/wake cycle - body temperature, blood pressure, brain activity and hormone secretion. In particular, when it gets dark, our brains signal the secretion of melatonin, a hormone that makes us feel sleepy.

Now, while our circadian rhythms are regulated by the light/dark cycle around us, they do not absolutely require it! Animals kept in total darkness for an extended period of time will have what is called a "free running" rhythm - the rhythm is still there, it's just not dependent on light levels. In fact, blind subterranean mammals (such as blind mole rats) maintain their endogenous clocks without any external stimulus. (That's good news for those of us who live far enough north that the winter months have significantly more darkness than daylight.)

Even for blind rodents living in the dark, circadian rhythms help determine the optimal time for an organism to go to sleep. And since everyone's circadian rhythm is different from everyone else, so is their best sleep time. How do you determine what your ideal bedtime is? The answer is called a sleep latency test.

A sleep latency test is based on the premise that, as you get sleepier, the amount of time it takes you fall asleep decreases. If you were to lay down in a dark room with nothing to do, eventually you will fall asleep. How long it takes you to do so is called your sleep latency. If you are wide awake, it will take you a long time; if you are sleepy, it won't take very long at all. Your ideal bed time is that time of day when you have the shortest sleep latency. If you try to fall asleep before then, it will take you a longer time. Interestingly enough, if you stay awake past that point, it will also take you longer!

If you want to find out your ideal time to sleep, this sleep scientist said that conducting a sleep latency test is very easy to do (though you need someone to help you). For a few nights, go to bed at different times (8:00pm, 9:00pm, 10:00pm and 11:00pm, for example). Have someone monitor you to see how long it takes you to fall asleep. Whenever you fall asleep the fastest is the closest optimal bed time for your circadian rhythm. Of course, this test must be done when you are not sleep deprived, or that will skew the results. (If you're tired enough, it may not matter what time you lie down, you might go right to sleep regardless!)

I believe that I know roughly my optimal bed time, but I would be interested to try this to see whether I'm right or not. Does anyone else want to try it?

Those red hot chili peppers (no, not the band)

Are you a fan of spicy food, or do you steer clear of anything with spicy zest to it? I used to be reluctant to order anything remotely spicy in Thai restaurants, I would not cook with any peppers other than bell peppers, and merely the thought of deliberately adding cayenne pepper to my chili made my eyes water! However, over the last several years, my tolerance for spicy food has increased significantly. In that time, I’ve grown more familiar with a variety of peppers, many of which are now used regularly in my cooking. Ranging from jalapenos to habaneros, pepperocinis to scotch bonnets, and chilis to cayennes, peppers are arguably the biggest source of spiciness in the food that we eat.

So here’s a question for you - do you know why peppers are spicy?

The main culprit in the spiciness of peppers is a compound called capsaicin (pronounced kap-say-sin). Actually, capsaicin is a type of capsaicinoid. There are several capsaicinoids in pepper plants (which, incidentally, belong to the genus Capsicum). Capsaicin is the most abundant (accounting for about 70% of the total capsaicinoids), followed by dihydrocapsaicin (which makes up around 20%). There are also three minor related compounds (with fairly complex names), which total approximately 10% of the capsaicinoid load. Both capsaicin and dihydrocapsaicin are about twice as potent as the 3 minor compounds in terms of irritation. They are particularly strong against mucous membranes, including your mouth, nose and eyes. That means that, when you eat a pepper and your mouth burns, your eyes water, and your nose runs – you have mostly capsaicin to thank.

Capsaicin is produced by pepper plants at glands located at the junction of the placenta and the pod wall. (That’s the white “ribs” that run down the inside of a pepper.) As the peppers develop, it gets dispersed unevenly throughout the pepper, becoming heavily concentrated in the seeds. The seeds themselves do not produce capsaicin, but they are a major storage point for it. (So if you ever want to eat a pepper but don’t want all the spice, simply remove the seeds and the white ribs. That won’t get rid of all the spice, but it will eliminate most of it.) Capsaicin itself is not used as a metabolite for the plants, but it is theorized to be useful as a defense mechanism. Mammals generally will not eat peppers, presumably because they don’t like it when their mouths hurt! The peppers are eaten mostly by birds. For birds, capsaicin is an analgesic rather than an irritant - in other words, it acts as a pain killer, not a pain producer. It does them no harm, allowing them to pass the seeds through and deposit them for plant dispersal.

Capsaicin is an interesting molecule. For one thing, it is incredibly stable. It is unaffected by either cold or heat, and retains its spicy potency despite cooking or freezing. That means that you cannot cook the spiciness out of peppers. Another interesting fact is that capsaicin is not very soluble in water, but it is soluble in oils, fats and alcohols. Have you ever eaten something really spicy, then tried to quench the burning by drinking water? I bet it didn’t work. That’s because capsaicin does not dissolve well in water, so drinking water will not wash it off your tongue. You’d be better off drinking a glass of milk, which contains casein, a fat-loving compound that dissolves capsaicin much like soap dissolves grease.

Pure capsaicin is an incredibly powerful compound. At a cellular level, an exposure to capsaicin triggers calcium ions to flood into the affected cell, ultimately triggering a pain signal to the next cell. This is very similar to what happens during a thermal burn. A single milligram (which weighs 1/1000th as much as a paperclip) would be enough to blister the skin on your hand. When pure, it can only be handled by chemists wearing full body protection, including a closed hood to prevent the inhalation of the powder. Lloyd Matheson, a pharmaceutical chemist from the University of Iowa was reported to have once inhaled pure capsaicin accidentally; according to him, “It’s not toxic, but you wish you were dead if you inhale it.” Capsaicin also features prominently in pepper spray, which is a strong irritant for all of the mucous membranes on your face (eyes, nose, mouth, and respiratory system.)

But don’t worry. There isn’t enough capsaicin in peppers to be dangerous – only spicy! The spiciness of peppers is measured in terms of Scoville Heat Units, which is parts per million of capsaicinoid content. At the extremes of the scale are pure capsaicin and bell peppers. Pure capsaicin has a Scoville Heat Unit score of 16 million, while bell peppers have a score of 0. Here are the scores of other common peppers:
Habaneros: 100,000 – 300,000
Scotch Bonnets: 100,000 – 250,000
Thai Peppers: 50,000 – 100,000
Cayenne Peppers: 10,000 – 30,000
Jalapenos: 2,500 – 5,000
Pepperocinis: 100 – 500

As I said, I’ve gradually been increasing my tolerance for spiciness. Of course, I’m not munching on habanero peppers for an afternoon snack, but I can handle jalapenos, cayenne peppers, and even very small levels of Thai peppers. Of course, now that I know how potent Scotch Bonnet peppers are, I may have just reached my limit on the peppers I’m willing to try!

The useless parts of human bodies

Have you ever had your wisdom teeth removed? I have – all 4 of them. I was 18, and my dentist was concerned that my jaw was too small to handle these extra teeth butting their way in, so – bam! – out they came. It was not a pleasant experience. I’m glad that I had them all out at the same time, so that I don’t ever have to go through it again! Of course, the reason I could have them pulled out like that is that wisdom teeth don’t seem to have a purpose. For modern humans, all indications are that they are totally useless. Of course, they may have been a useful part of our jaws thousands of years ago, but that usefulness is (apparently) long gone.

Interestingly enough, wisdom teeth are not the only seemingly useless parts of our bodies. There are 2 other well-known pieces of anatomy that fall into this category of uselessness – the tonsils and the appendix. In fact, not only are all 3 of these body parts apparently pointless, they can be a lot of trouble. Tonsils are often infected and inflamed. When wisdom teeth become impacted, they can damage other teeth or cause gum infection or bone damage. And appendices can become inflamed, requiring rapid removal by surgery to reduce the risk of the infection turning lethal. So surgeons remove these things routinely. And people live just fine without them. So, they’re useless, right?

Maybe not. It turns out the appendix may have a purpose after all. In October, scientists at Duke University’s medical school announced a theory about the possible job of the appendix. They suggest that the appendix is a back-up storage system for intestinal bacteria.

It turns out that our intestines are chocked full of bacteria – in fact, your body contains more bacteria cells than your own body cells! Most of these bacteria (which are also referred to as “bugs”) are helpful, and in fact are essential for you to digest your food. However, there are certain diseases that can wipe out the flora from your digestive system – diseases such as cholera and amoebic dysentery. These diseases are characterized by severe diarrhea, which quickly flushes out the friendly bugs residing in your gut. If that happens, your digestive tract needs a way to rapidly recover those helpful bacteria. Enter the appendix. The authors of the report argue that the appendix serves as a safe-house for intestinal bugs, allowing them to survive in an offshoot of the intestines that would be protected from the intestinal ravages of severe diarrheal diseases. (The location of the appendix is consistent with this hypothesis. It is a small, finger-shaped structure located near the beginning of the large intestine.)

In the western world characterized by dense populations, we don’t have much of a need for this function of the appendix. Cholera and amoebic dysentery are rarely (if ever) encountered in western society anymore. But even if we were to contract some disease that wiped out our intestinal flora, we could rapidly pick them up again from the people we encounter every day. (Yes, the bugs can be shared.) However, in areas of the world where cholera could devastate entire regions of people, this job of the appendix could be very relevant. In fact, here is a curious fact – in less developed societies in the world, the rate of appendicitis is much lower than in first-world countries. That would be consistent with the fact that people in regions exposed to severe diarrheal diseases must rely more on their appendix than do those who live elsewhere.

On a related note, I found some interesting facts about appendices in other animals. It turns out that appendices are large and very functional in animals whose diets consist mainly of vegetative matter. This includes koala bears (who have perhaps the longest appendix of any animal in the world), opposums, kangaroos, rabbits and zebra. The diet of these animals is very dense in cellulose. Cellulose is the main component of the cell walls of plants, and it is very difficult to digest. Our digestive systems cannot make the enzyme needed to break cellulose apart, so we are actually unable to digest cellulose at all. (It simply goes through our systems.) The appendices of animals that eat a lot of plant matter house a specialized set of bacteria that secrete the enzyme to digest the cellulose that they eat. Without this bacteria, these animals would simply be unable to digest most of what they've taken in.

I guess that means it would be pretty serious for a koala bear to get a case of appendicitis!

What do you call that?

The geoduck. Large. Long-lived. Tasty. Weird. And native to where I live.

Odds are, unless you live in the Pacific Northwest somewhere, you’ve probably never heard of a geoduck. I’d never heard of them, until I moved to the Puget Sound! Geoducks are native to the Pacific coast of the northern US and Canada, primarily concentrated in Washington State and British Columbia. In fact, there are an estimated 109 million of them in the Puget Sound area! That makes this creature the single most abundant organism in the region. So you’re probably wondering – what on earth is a geoduck?

“Geoduck” is, in my opinion, one of the most confusing words in the English language. It is properly pronounced “gooey-duck.” And these things aren’t ducks at all! They are large saltwater clams, which are also known as king clams or elephant trunk clams. Geoducks are actually the largest saltwater burrowing clam in the world. If you were to go dig a geoduck out of the sand, you would probably find one weighing somewhere between 1 and 3 pounds. However, there are tales of geoducks reaching upwards of 20 pounds. (That’s a lot of clam.)

Geoducks are burrowing clams, and you will find them buried in sandy areas around bodies of salt water. (They are also buried beneath the sediment underneath the surface of the water, too. In fact, they have been observed at depths of 360 feet in the Puget Sound.) About 50 days after they begin their lives, they begin digging down into the sediment at a rate of 1 foot per year. Once they reach about 3 feet below the ground, they generally stop digging, and remain at that level for the rest of their lives. They eat and breathe through their siphons, which protrude up through the sediment to the surface. Through one hole in the siphon, they suck in water (from which they extract plankton and oxygen), then spit the remaining water back out through a different hole in the siphon.

Interestingly enough, the geoduck is one of the longest-living creatures in the region. It has an average life span of 146 years, and the oldest geoduck on record was around 160 years old! In a previous column (“the small animal, short life phenomenon”), I discussed how the average longevity of mammals correlates with body size. For the most part, small mammals live short lives, while large mammals live long ones. For reasons that scientists do not understand, that correlation only holds true for mammals. Reptiles, amphibians, birds and insects all play by their own rules when it comes to average lifespan.

For example, here are the average size and lifespan of a few non-mammals:
Oriental Fire-bellied toad: <0.1 pounds / 11-14 years
American Alligator: 1300 pounds / 50-65 years
African Grey Parrot: 1-1.5 pounds / 50-70 years
Ostrich: 250 pounds / 50-70 years
Alligator Snapping Turtle: 200 pounds / 50 years
Tarantula: 0.1 pounds / 10-30 years

If you notice, there is really no correlation between how big these animals are and how long they live, and that is certainly true for the geoduck. Their lifespan is roughly comparable to that of a blue whale, which is hundreds of times larger. Scientist speculate that the reason for the geoduck’s long lifespan is because they live a very low-stress, easy lifestyle. They have relatively few predators, though sea otters, dogfish, and starfish will sometimes attack them. And, of course, humans love them.

Washington state is home to a large and growing industry of geoduck aquaculture (worth 80 million dollars a year), primarily because the large meaty siphon can be sold for upwards of $30 a pound in Asia. It is extremely popular in Hong Kong and Japan, where it is eaten either raw (sashimi style) or cooked in a fondue-style hot pot.

Of course, given what they look like, I don’t know if I’d ever be brave enough to eat one raw.

Boo!

In my last column (“when sleep goes awry”), I wrote about a sleep disorder called narcolepsy. I mentioned that there are several well-known videos of narcoleptic dogs collapsing without warning in the middle of playtime. Watching those videos made my mind think back to another kind of animal that I’ve heard sometimes collapses without warning, and I wanted to investigate it further. The animal? The fainting goat.

Fainting goats have gone by many names over the years, including Tennessee goats, nervous goats, stiff-leg goats, wooden-leg goats, and Tennessee scare goats. All of these names are reflective of the fact that these guys (a) originate from Tennessee and (b) have the unfortunate tendency to fall over when startled. When spooked or surprised, the muscles in their legs become as stiff as a board, resulting in the goat falling on its side, as if in a dead faint. (In animals less severely affected, though, they don’t actually fall over. They just stand there on unbending legs, looking really awkward.) Mind you, the goat has not really fainted, since it is fully conscious - it just can’t move its muscles! After 10-15 seconds, the muscles will relax enough to let the goat walk, albeit stiffly at first. Once the stiffness has worn off, though, they walk and run just like any other goat. (To see a picture of what they look like when they’ve fallen over, check out: http://agonline.com/runningbird/goats.asp. It’s a good illustration of a goat that has fainted in the midst of ones that haven’t.)

This may sound similar to what I described for a narcoleptic/cataplectic attack, but it is actually something different. Fainting goats suffer from a muscle condition called myotonia congenita. Myotonia congenita occurs in many animal species, including humans. It is a disease of the cells in skeletal muscles, preventing normal muscle contraction and expansion. Let’s take a look at how muscle cells work to understand what’s going wrong in these poor goats.

When muscles expand and contract, they do so in a coordinated fashion, regulated by the flow of ions in and out of the muscle cells. Ions are electrically charged atoms due to the fact that they have unequal numbers of protons (conferring positive charge) and electrons (conferring negative charge). Ions are essential for life – there are literally thousands of cellular processes regulated by them. Ions used by your cells include sodium, potassium, calcium, magnesium, zinc and chloride; because they are so important, their movement and levels are carefully controlled. Muscle contraction and expansion requires a tightly regulated flow of chloride and calcium ions through dedicated ion channels that sit in the membranes of the muscle cells. These channels act like tunnels through the barriers of the cell, letting only their designated ions through. There are many such barriers in a cell, including the outer membrane (separating cell from non-cell) and organelle membranes (enclosing numerous compartments within the cell). One important compartment in muscle cells is called the sarcoplasmic reticulum. The sarcoplasmic reticulum is a major storage compartment of intracellular calcium (a positively charged ion).

When your skeletal muscles receive a signal to contract (the signal coming from the nervous system), calcium channels in the membrane of the sarcoplasmic reticulum allow a rush of calcium to flow from the sarcoplasmic reticulum to the interior of the cell (the cytoplasm). The calcium allows the proteins that control muscle contraction to work. When the contraction is finished, the cells must have some way of balancing out the positive charge in the cytoplasm – if they don’t, the contraction would not end! There are 2 ways to achieve this balance. First, a different set of channels pump the calcium back into the sarcoplasmic reticulum. And second, there is a counterbalancing inrush of chloride ions. Chloride, being negatively charged, cancels out the remaining positive charge conferred by the calcium. This balance of electrical charge in the cell keeps the muscles from contracting abnormally.

(It’s important to emphasize that what I’m talking about here is skeletal muscle. There are actually 3 different kinds of muscles in your body – skeletal, cardiac and smooth. Both cardiac and smooth muscles contract and relax involuntarily, while skeletal muscle function can be both voluntary and involuntary. The muscles differ in their organization and mechanism of action, and what I’ve written above is specific for skeletal muscle.)

Okay, back to the goats. Fainting goats have a genetic defect in the chloride channel in their skeletal muscles. This mutation - in a gene called CLCN1 - results in chloride channels with an abnormal shape – as a result, they cannot properly control the flow of chloride in or out of the muscle cells. If the goat is startled, it will contract its muscles to run or jump away. Once the muscles are contracted, though, they cannot be relaxed as normal because the chloride ions are not flowing properly. The result - their muscles remain contracted abnormally long. And tightly contracted leg muscles equates to falling over. Eventually, the calcium ions causing the contraction get pumped back into the sarcoplasmic reticulum in the goat’s muscle cells, which is why they are able to move again after a while.

I do want to emphasize that this condition is painless and harmless to the goats. While it makes them easier prey for goat-eating predators like coyotes, if properly protected, they suffer no ill effects from their condition. The only muscles affected are the skeletal muscles, not their hearts or digestive muscles. In fact, if anything, these goats tend to be slightly more muscular than their unaffected counterparts.

Of course, only a goat could tell you whether being buff would make up for the embarrassment of falling over every time you were startled.