The Wonders of Science

The wonderpus and the mimic

2009-01-22T10:02:00.001-08:00

Did you know that there is a kind of octopus called a wonderpus?

Sounds like a Dr. Seuss creation, doesn't it? But no, it's a real animal! The wonderpus octopus (Wonderpus photogenica) is a beautiful creature, with dark red skin marked by bold, white stripes on the arms and spots on the mantle. These spots are extremely distinctive, and vary for each individual octopus - so much so that they allow for the identification of specific animals. In fact, the wonderpus's distinctive appearance is what enabled its discovery. They are close relatives of another type of octopus called a mimic octopus (Thaumoctopus mimicus). In fact, it is highly likely that people have observed wonderpus for many years, but didn't realize it because it is very similar to the mimic. The mimic, however, has much more muted colors than the wonderpus. It was only in 2006 that scientists realized that mimics and wonderpus were 2 different creatures.

The mimic octopus is, in an of itself, pretty interesting, too. Found in the seas off southeast Asia, the mimic shows an amazing ability to hide itself in plain sight simply by looking like something else. It has been observed disguising itself as more than a dozen different species, including sea snakes, crabs, stingrays, jellyfish and sea anemones. It accomplishes this amazing feat of deception by altering the color and texture of its skin, as well as contorting its arms with a high degree of flexibility. While all octopus are able to hide themselves with camouflage, the mimic is unique in its ability to not just blend in to the environment, but to actively disguise itself to look like something else. While that makes it difficult for predators to find the mimic, it also makes it difficult for scientists to find them!

Deep sea creatures

2009-01-12T13:34:00.000-08:00

The other night I was watching one of the episodes of the Discovery channel's documentary "Planet Earth." In case you haven't seen any of these shows, they are truly amazing. They captured some of the most amazing video of creatures in places all over the globe - from the topics of mountains to the depths of the sea, from the lushest jungles to the most barren stretches of desert, from the poles to the equator - and everything in between. In the episode "Deep Ocean," the viewer is introduced to the largest habitat on the planet - the sea.

Deep ocean is considered anything away from the coasts and beyond the continental shelves. Out in these areas, the water can reach several miles deep. Historically, water this deep has been impossible for man to reach - the crushing pressure associated with it has been too much to overcome. But while it is too deep for man, it is not too deep for machine. In recent years, the use of remote underwater submersibles has allowed scientists to see just what is down there in the deepest parts of the world. And it turns out that this region, once considered barren and devoid of life, is not quite the wasteland we once believed. In fact, the deepest oceans in the world contain some amazing life. Amazing - and quite bizarre!

Here are a few examples of what lives in the depths of the world. (Some of these creatures are very poorly understood, given how hard it is to even find them.)
Vampire squid: The Vampire squid lives at depths of 2000 feet or more in what is called the OMZ, the oxygen minimum zone. At this depth, the amount of oxygen in the water is too low to sustain life in most oxygen-utilizing higher organisms. However, the vampire squid survives - and even thrives - in water with as little oxygen as 3%. (It is the only known cephalopod capable of this.) Interestingly, the vampire squid uses light as a defense mechanism. While shallower-dwelling squid squirt ink when startled, the vampire squid instead squirts a bioluminscent mucus that can glow for up to 10 minutes. This presumably blinds would-be predators in the inky darkness of the deep sea, allowing the squid to escape.

Sawtooth eels: These eels are so named for their inward-slanted teeth, arranged in a saw-like pattern. There are 11 known species of sawtooth eel, and they live in waters up to 2000 feet deep.

Tube worms: Tube worms are arguably some of the most well-understood deep water creature. Tube worms live around deep sea hydrothermal vents. The giant tube worm is the easiest to recognize - they can reach up to 4 feet tall, and grow more than 33 inches a year. Giant tube worms are only found in the Pacific ocean; other oceans contain tube worms such as Jericho worms, benthic worms and palm worms. These worms have a symbiotic relationship with deep see vent bacteria, which colonize the worms and provide them with energy as a byproduct of bacterial metabolism.

There are no doubt countless deep sea creatures that we know nothing of, given how difficult it is to get down there. But what little we do know about the creatures who make this region home makes me really appreciate how amazingly diverse a planet we live on.

All things baby and science-y

2009-01-08T15:17:00.000-08:00

Hi everyone! I'm starting to get back into the swing of things after the birth of our daughter, which means I'm hopefully going to be able to start blogging again! Over the last 3 months, my brain has been all-consumed with all things baby-related, so I thought I'd start off with the list of baby-related science thoughts.

1. Cradle cap: Our daughter had a pretty severe case of it. For those of you unfamiliar with it, this is a skin condition characterized by thick, scaly flakes on the scalp, forehead and eyebrows. Some babies get it, some do not. But we really don't know what causes it. It seems to have something to do with the same reason why many adults get dandruff. Who knew - apparently it's not just a case of dry skin!

2. Hearing tests: Newborns are given hearing tests these days before they even leave the hospital. It's pretty neat how it's done, too, considering that a newborn can't tell you whether she's heard a noise or not. Sensors are attached to their foreheads, and then a tone is played in their ears. If they hear it, the sensors detect the neuronal signals passing through their brains, and output a signal to the detection machine. From a parenting standpoint, it was a relief to know that our daughter's hearing was normal. From a science standpoint, the process was really neat.

3. Colic: We were extremely fortunate to have a non-colicky baby. Many parents are not so fortunate. Despite it's prevalence, however, colic is poorly understood. Some believe that many cases of colic are actually undiagnosed cases of acid reflux (otherwise known as heartburn). But what about those colicky babies who do not have reflux? No one really knows why they have such a fussy time during their first 3 months of life.

4. Speaking of reflux: Did you know that the sphincter that closes the stomach off from the esophagus actually weakens from birth until about 4 months of age? Only after that does it begin to get stronger. That's what babies do most of their spitting-up between the ages of 2 and 4 months.

5. Baby fingernails: These are really amazing. Baby fingernails are so soft and pliable - and yet incredibly sharp! If you don't keep them trimmed, a baby can give herself or you some strong scratches. I wonder when they start to become harder, like adult fingernails?

6. Baby blue eyes: Like many Caucasian babies, our daughter has started life with blue eyes. We strongly suspect that they will change color as she ages - many babies develop their adult eye color at around 6 months. But here's a question - why would a baby's eye color change from blue to something else? Why aren't they born with their final eye color?

7. SIDS: That dreaded fear of all parents - sudden infant death syndrome. A small percentage of babies suddenly stop breathing while sleeping, and thus they die. It's been known about for centuries, and the reasons for it are still a mystery. Here's some good news, however. The risk of a baby dying of SIDS has been drastically reduced in recent years due to current recommendations that babies sleep on their backs. While we may not know why this reduces the risk of SIDS so much, I'm grateful for it!

These are just a few of the science type thoughts I've had in the last few months related to parenthood. I'm sure I'll come up with many others, and I strongly suspect that my posts for a while will all relate to baby topics. Hopefully you'll all find this as interesting as I do these days!

An update

2008-10-19T14:45:00.000-07:00

For those of you who've been wondering where I've been, my family has been a little busy with the recent birth of our daughter. Please be patient! I will start posting entries again in the near future.

More than just bed-head: UHS

2008-09-05T08:57:00.000-07:00

I came across an article on a news website today that I read and thought, "this has got to be a joke." The article was entitled "The tangled truth about uncombable hair," and it began with the following sentence:
"If ever there were a disease designed to vex a mother, it’s uncombable hair syndrome (UHS)."

You're joking, right? Uncombable Hair Syndrome? They came up with a disease name for when someone has messy hair? As I read on, I became more disbelieving; my disbelief was not helped by the statement that it was first described 35 years ago in a French medical study, which called it "cheveux incoiffables." Okay, now I know you're pulling my leg, right?

Actually, much to my surprise, no! This story is legit. This syndrome is legit. It may sound wacky, but it's for real. Some people have messy hair. Some people have hair that is easily tangled. Some people have truly horrible cases of bed-head when they get up in the morning. But others have truly uncontrollable hair.

Uncombable Hair Syndrome is also known as Pili trianguli at canaliculi, or Spun Glass Hair. This syndrome can manifest itself in children anytime between the ages of 3 months and 12 years old. While these kids start out with hair that looks thin and glassy (though still relatively normal), the hair begins to become drier, curlier and lighter in color. Eventually, it stands straight out from the scalp and is literally impossible to comb flat.

The reason for this disorder lies in an abnormality in the hair shafts of the affected individual. When examined under high magnification, these hair shafts have 2 unique qualities. First, their cross-section is shaped like a kidney bean (instead of a circle). And second, there is a deep groove or canal that runs down the entire length of the hair. This makes the hair unable to bend like normal hair without such a groove. So it stands straight out from the scalp. But here's the good news. Kids with UHS usually outgrow it. So while their hair may be unmanageable now, it'll get better as they get older.

But in case you're wondering whether your messy hairdo could be the result of UHS, the odds are quite strong that it's not - UHS is an incredible rare syndrome. In the last 35 years, barely 100 cases have been reported in the medical literature.

It's far more likely that you just have easily tangled hair.

In honor of the start of school

2008-09-03T09:14:00.000-07:00

I thought I’d write an entry in honor of all of the children, teachers and administrators in our country who are just starting up another year of school. The start of the school year brings lots of exciting opportunities, does it not? New books, new subjects, new friends, new challenges – oh, and of course, the possibility of new illnesses. Sometimes school seems the perfect place for the propagation of viruses, bacteria and other assorted bugs. And it’s one of these bugs I want to discuss today – the ever-popular, ever-fun, and ever-exciting pediculosis. Otherwise known as head lice.

What are head lice? A head louse (singular, as opposed to the plural form lice) is a small, wingless insect that lives among human hairs and feeds off small amounts of human blood. How small are they? Lice go through three stages during their life cycle. They start out as eggs, otherwise known as nits. These are very small, about the size of a flake of dandruff. About 7 days after the nits are laid by a female, the lice hatch into the nymph stage. Nymphs look like adult lice, but they’re much smaller. At this point, they need human blood to survive to adult. If they feed enough, after about 7 days as a nymph, they will mature into adult lice, capable of laying their own nits. Adult head lice are tan to grayish-white and about the size of a sesame seed, easily visible to the naked eye; so if you’re going to spot an infestation, it’s the adults you want to be on the lookout for. And adult louse can survive for around 30 days as long as it keeps feeding; if it falls off its human’s head, however, it will die within about 2 days.

Here’s a few facts about head lice that I did not know before I started looking into them:
Head lice cannot survive on any animal besides a human. That means you cannot catch head lice from your pets – cat or dog blood will not sustain a louse.
Head lice cannot jump or fly from head to head. The only way to pass head lice among people is for them to come into direct contact with hair that has a nymph or an adult louse clinging to it. Once that contact is made, the louse can transfer itself to the new person’s head and begin feeding.
Head lice have very strong claws that allow them to hang on very tightly to a strand of hair.
Dessicated head lice and head lice nits have been found on the hair and scalps of Egyptian mummies.
It is believed that 1 in 10 kids in America will come down with head lice at some point during their lives.

Okay, now that I’ve given myself the creeps over imagining all these little bugs crawling over my scalp…

An update from MESSENGER

2008-08-12T10:36:00.000-07:00

In February of this year, I wrote an entry about the MESSENGER spacecraft, NASA's recent expedition aimed at learning more about the planet Mercury. Despite being relatively close to us in the solar system (a few scant planets away), we know relatively little about this rocky planet. MESSENGER is an attempt to answer some long-standing questions about the planet, including (if you remember from my previous post) what half of the planet even looks like! I figured it was about time to give you an update on what MESSENGER's been up recently.

Some of the latest news to come from the MESSENGER mission concerns the origin of Mercury's magnetic field. The question of what exactly is a magnetic field opens the door to a big area of physics called electricity and magnetism. I'm not going to go into a lot of detail about magnetism - at least, not right now. I will tell you that a magnetic field is a a field that permeates space and exerts a magnetic force on moving electrical charges and magnets (otherwise known as magnetic dipoles). Earth (as I'm sure you know) has a magnetic field; this fact gives us north and south. There does not appear to be a simple answer for why Earth has a magnetic field. It seems that it has something to do with our rotation. We believe this because the planet Venus, though it has a similar iron core to Earth's, has a different rotation pattern and has no magnetic field itself. Earth's rotation may generate something called a dynamo effect, causing the fluid iron in the core of our planet to circulate. At the same time, convection occurs, drawing the hottest part of the molten iron away from the center of the planet towards the surface. This combination of rotation and convection generates electric currents, which in turn generates and sustains our magnetic field.

Now, while it's long been known that Mercury has a magnetic field (though it is about 100 times weaker than our own), why it does so has been a mystery. Scientists had believed that Mercury's iron core was thought to have cooled long ago; a lack of fluidity in the core would make it incapable of generating a dynamo effect. But it turns out that Mercury's core is not as quiet as they once believed. The latest news from MESSENGER seems to indicate that a combination of volcanic activity and fluidity in Mercury's core is responsible for the generation of this magnetic field.

Of course, as is always the case in science, as soon as one question is answered, another is posed. The question now is not "why does Mercury have a magnetic field," but "why is Mercury's core still molten?" For the answer to that one, however, it looks like we'll have to wait for more data from MESSENGER, and another announcement from NASA.

In the meantime, here are a few other facts about Mercury that NASA has announced from the latest data from the spacecraft:
1. Mercury appears to have active volcanic vents around something called the Caloris basin, This is one of the solar system's largest and youngest impact basin - a basin formed by an impact with an asteroid or comet during the first billion years in the history of the solar system.
2. The planet has shrunk in on itself more than anyone had ever expected - in fact, the planet seems to have shrunk one-third more than anyone predicted
3. The magnetosphere around Mercury is more complex than scientists had predicted. The magnetosphere (a kind of bubble around the planet that contains atomic and molecular particles) contains more complex particles than had been expected, given how close it is to the sun. In fact, many of the particles themselves originate from the planet, and are not carried there by solar wind.

MESSENGER is supposed to make another flyby of the planet in October, so I'm sure that more news about Mercury will be coming shortly. Until then, if you want to see a really interesting picture from the latest set of data, check out picture of the Caloris basin on the MESSENGER website at:
http://messenger.jhuapl.edu/gallery/sciencePhotos/image.php?gallery_id=2&image_id=193

Octopus - up close and personal

2008-08-05T10:02:00.000-07:00

I wanted to write a quick post about a topic I've written on before - octopus. In May, I wrote an entry about the intelligence of octopus (and I don't know about you, but some of what I learned certainly surprised me!). Well, my husband and I recently came home from a vacation in Hawaii. We both love to snorkel and scuba dive, and though we weren't able to do any scuba diving this trip, we did get in some great snorkeling. And this time we saw something we've never seen before while in the ocean - an octopus.

Now, we strongly suspect that there are octopus all over the areas where we often snorkel. The rocks and coral have so many cracks and fissures that there are ample hiding places for them. There are also significant numbers of moray eels in the area, and octopus are a tasty snack for a moray (if it can catch one, that is). And finally, we've heard other people say they've seen octopus around there before. So we knew that they were there. But we've never seen one before.

I think there are 2 main reasons for this. First, octopus are nocturnal, and we always snorkel during the day. And second, octopus are really, really, really good at hiding - especially when it comes to camouflage! An octopus sitting motionless in a crevice looks just like a rock - brown and bumpy. Put that "rock" 10 feet below the surface of the water, and a snorkeler swimming over the top of it will never see it.

However, this year we were extremely fortunate. We managed to see an octopus as it was moving to a new hidey-hole. It was fairly easy to see it when it was in motion; moreover, once it was settled into its new spot, we knew where to look for it, and were able to watch it quite easily. It was pretty big, maybe 2 feet long from the head to the tips of the arms, much longer than I ever expected to see in the wild. And perhaps the coolest thing about it was the way that it would rapidly change colors when one of us swam close to it. It would instantly switch from rock-brown to dark red, then fade back to brown when we backed off. I think that means we were spooking it a little bit!

We saw quite a few other interesting sea creatures while snorkeling this year, as well, including both the largest and the smallest moray eels we've ever seen (the largest being probably close to 4 feet long, and the smallest being only several inches), and a huge devil scorpionfish. This has to be one of the uglier fish I've ever seen. They sit on the bottom of the ocean, disguising themselves as rocks. They kind of look like a fishy equivalent of a gargoyle, actually - lumpy, brown, and extremely grumpy looking. And while you don't want to touch these guys (yes, they are poisonous), being able to find one is actually quite a treat. (Can you see the face of this one on the right-hand side of the picture, with a fin in the bottom left corner?)

I'm sure there were all kinds of interesting creatures in the ocean where we were snorkeling that we never even saw. But I think we were very fortunate to find the things that we did! Of course, the next time we go, I'll be on the lookout for even bigger and better things.

All about popcorn

2008-07-16T11:14:00.000-07:00

Did you know that popcorn is made from a special kind of corn? I had never really thought about it before, but if asked, I would have guessed that you could use any old corn to make popcorn. All you have to do is dry some kernels, then heat them up and they'll pop, correct?

Actually, no, it turns out that popcorn is a little more sophisticated than that. In researching how it's more sophisticated, I've learned some things about corn that I never knew before.

All corn is a type of maize, of which there are 6 kinds - pod, sweet, flour, dent, flint and pop. The kernels of all kinds of corn are made of 3 things - the germ, the endosperm and the pericarp. The germ is the only living part of the kernel. It's right in the middle of the kernel, and contains the information necessary for that kernel to produce a whole new corn plant (genetic material, enzymes, vitamins and minerals). It's also the part of the kernel that produces corn oil - about 25% of the germ consists of corn oil. The endosperm is the largest part of the kernel. It accounts for over 80% of the kernel's dry weight, and consists largely of starch. The endosperm lies between the germ and the pericarp, or outer hull. The pericarp is very tough, and is designed to prevent moisture loss from the inside of the kernel, as well as protecting the delicate germ from being eaten by bugs or microbes.

Different kinds of corn differ in how much of these 3 components the kernels have, as well as their starch and oil composition. Dent corn, for example (the leading type of corn grown on US farms), has an endosperm consisting of horny starch on the sides and soft starch on the top. As the kernels age, the soft starch shrinks, making a characteristic "dent" in the top of the kernel. Flint corn has no soft starch at the top of the endosperm, so it does not make a dent as it matures. The endosperm of flour corn consists mainly of soft starch, which makes it very easy to grind into flour. Sweet corn, grown for human consumption, has much less starch than any other kind. That's because the sugar in the kernels is not converted into starch in the endosperm - hence the sweet nature of the food. Pod corn is a very pretty kind of corn, with kernels that often turn a variety of colors. It is not eaten very often, but instead is grown to use for decorative purposes. And then, of course, there is popcorn.

Popcorn is specifically - and scientifically - known as Zea mays everta. It is a derivative of flint corn, and is distinctive in that it has a very thick pericarp. The thickness of its pericarp allows for the popping process to occur. When the water inside the germ is heated, it turns into steam. The thick pericarp holds the steam in, where it begins to gelatinize the internal starch and protein in the endosperm. Once the pressure of the steam gets too great, the pericarp bursts, releasing the starch protein and steam in a big pop. As the starch expands, it cools and solidifies into its distinctive popcorn shape.

There are several variables that go into how well popcorn will pop. One important factor is how quickly the popcorn is heated. The internal temperature has to reach about 180 degrees celsius (356 degrees fahernheit) before it will burst. If the kernel is heated too quickly, the external portion of the endosperm will release steam too quickly, bursting the pericarp before the internal part cooks properly. If it is heated too slowly, the building steam may leak out of the tip of the kernel, and it won't pop at all. Popping quality also depends on how much moisture the kernel contains. If there is a lot of moisture in the kernel, it will pop into chewy, soggy pieces of popcorn. Also, very moist kernels of popcorn tend to go moldy easily. If the kernel is too dry, however, it will not produce enough steam to pop well. So popcorn growers usually carefully control the moisture level of their popcorn kernels, and try to dry them out to around 15% of the total kernel weight being moisture.

There are lots of other interesting facts about popcorn that I came across when writing this entry. Here are a few of my favorites:

1. Popcorn usually pops in one of 2 shapes - mushroom (on the left) or snowflake (on the right). Different kinds of popcorn can produce exclusively one shape or the other, or a mix of the 2. Snowflake popcorn is usually used for eating straight as popcorn, which mushroom popcorn is usually used for popcorn confections (like caramel corn).

2. Popcorn kernels can move a distance of up to 3 feet when they burst.

3. "Popability" refers to how many kernels of a given batch of popcorn will pop. Some kernels simply do not pop, and are known in the popcorn industry as "old maids." They are assumed to either by too dry to produce enough steam, or have too leaky a pericarp.

4. Popcorn is the official state snack food of Illinois - which, by the way, produces a lot of the US supply of popcorn.

5. Scientists have found popcorn kernels over 1000 years old in tombs in both Peru and southwestern Utah.

Personally, I really enjoy eating popcorn. And I'm not alone. Apparently, Americans consume an average of somewhere around 17 billion quarts of the stuff per year. That's a lot of popcorn!

Sitting in the catbird seat

2008-07-11T09:33:00.000-07:00

I was in the car this morning, and one of my favorite programs on NPR came on the radio. It's a short little thing, usually just 2 or 3 minutes long, but it's always so interesting! The program is called "Bird Note," and every episode describes something about birds. Wild or tame, big or small, common or rare, showy or drab - it runs the gamut. The narrator sometimes talks about the behaviour of the birds, or their environment, or their plumage. One particularly interesting one a few weeks ago compared how much effort it would be for a human to build a nest comparable to that made by a robin. (It would actually be really, really difficult!) Today's show was about a bird called a catbird. Actually, it was about an idiom in which the catbird features prominently - as you might have guessed from the title, the idiom is "sitting in the catbird seat."

I'd never heard this phrase before, but the narrator explained that this phrase means having an enviable position, the upper hand, or the greater advantage in a situation. And the reason it means this is perfectly explained by the behavior of the catbird.

Catbirds are American birds of the mimid family. "Mimid" is Latin for "mimic," and mimids are known for the vocalization abilities. Other mimids include thrashers, mockingbirds and tremblers. The catbird's standard call sounds roughly like a yowling cat, actually, though it can also imitate other birds. (It's alarm or warning call sounds startlingly similar to a male mallard.) There are two kinds of North American catbirds. The grey catbird is the most common, and is found across the US in all kinds of environments (rural, suburban and urban). They are medium-sized and dark in color, with the only notable coloration being a rust-colored patch under their tails. The other kind of catbird is the black catbird, which is found more in Central America and Mexico.

So what does the catbird do to deserve having an entire idiom phrased after it? The catbird (like many animals) relies on height to assert superiority or dominance. If a catbird feels threatened, it will go to the highest position it can find to call out its warning call. The higher that position, the more likely the intruder will back off. In addition, if two male catbirds are jockeying to be the top male in the area (and thus attract the best female), they will take gradually higher and higher perches, trying to outsing the other, until one is at the highest point. The bird who gets the highest is the winner. And, of course, the high perch from which he claims his victory is called "the catbird seat."

So there you go. Sitting in the catbird seat means getting the most advantageous position.

I love finding examples of how something science-related has worked its way into everyday life and language. Okay, so maybe this phrase isn't the most common, everyday phrase you'll ever hear. But now, if you ever do hear it again, not only will you know what it means, you'll also know where it comes from!

Anyone have any other suggestions for phrases or idioms that have their origins in science?

The science of fireworks

2008-07-03T14:42:00.001-07:00

In recognition of the fact that tomorrow is the 4th of July, I'd like to spend today's post talking about fireworks. I love watching fireworks - the colors, the shapes, the sizes, and the different ways they twirl and burst and shimmer and sparkle are all entrancing to me. In thinking about fireworks, I wanted to investigate and see if what I think I know about fireworks is really true. In particular, I wanted to look into the science behind what makes fireworks different colors. I believe that I already know a little bit of the answer (as may you), but since it never hurts to have our knowledge expanded upon, here we go...

First, let's talk about the kind of firework that we are most familiar with in fireworks displays during the 4th of July - skyrockets. Skyrockets are projected into the air before they explode (unlike ground fireworks such as catherine wheels, which are like small, glowing ferris wheels that spin as they burn). These are built around a basic design - paper or pasteboard tubing filled with a combustible material, called pyrotechnic stars. Different tubes filled with different pyrotechnic stars can be combined in various ways to make the many shapes, sizes and colors that are seen when the firework explodes.

Pyrotechnic stars contain 5 basic components. First, there must be a combustible fuel to burn. Second, there is an oxidizer. This provides the oxygen required to start the burning process in the first place. (For a reminder about oxidizers, you can read my entry on flaming gummy bears.) Third, there is also something to hold the entire firework together, called the binder. And finally, there are chemicals which burn to provide the color, as well as another chemical to help strengthen the color of the flame produced.

So I was right - the color is provided by the burning of certain chemicals. Here's something I didn't know - a few of the chemicals that are used in producing fireworks displays:
Red: strontium or lithium salts
Orange: calcium chloride or calcium sulfate
Yellow: sodium salts such as sodium nitrate or cryolite
White: magnesium, aluminum or barium oxide
Green: Barium chloride
Blue: Copper chloride
Silver: Titanium or magnesium

Apparently, the most difficult color to achieve is blue. That's because copper is a tricky metal to burn. If it does not reach a high enough temperature, it will not emit enough light to be seen. However, if it gets too hot, it will fall apart before it produces any light at all. So consider yourself lucky if you wee a blue firework! Actually, all of the color-producing chemicals have to be handled carefully to achieve the right color. If there is a small amount of chemical impurity, thee metal will not burn properly. In particular, trace amounts of sodium burn so well that they easily overpower the intended color, producing yellow-orange instead.

I think my favorite kind of firework is called the willow firework. What's a willow firework? Well, your basic firework is called a peony. It makes a spherical burst of colored stars. Building off that, your next most common firework is the chrysanthemum, which is like a peony but with longer burning stars which leave a visible trail behind them. The willow firework is a variation on a chrysanthemum, but it has extremely long burning silver or gold stars. These burn so long that a long trail of sparks can be seen falling gracefully to the ground, just like a weeping willow tree.

Unfortunately, this year we probably will not watch a display of fireworks ourselves, but we may get to watch one on TV. Of course, it's not quite the same as in person, but it's better than nothing!

Catnip - a really good kitty drug

2008-07-01T08:53:00.000-07:00

I've said it before, and I'll say it again - science is everywhere, all around us, in so many different things that we see all the time. I am reminded of that quite frequently when I spend a few minutes looking at our cats. There are many things that our two kitties do that spark questions in my mind, and today is no exception. What I want to explore today is the following question - how does catnip work?

For those of you with cats, you are probably familiar with what catnip does to a cat. But for those of you who don't, let me describe a scene for you. We have a toy for our cats that is a catnip-stuffed mouse. Fairly standard, as far as housecat toys go, but this one is a cut above most catnip-stuffed mice in that it has a pouch inside of it that you can refill with new catnip. So as the cats play with the mouse, though the catnip (a) slowly loses potency and (b) slowly leaks out of the pouch, it doesn't matter, because we can put new, fresh catnip in. Now, right after we fill the mouse with new catnip, it's quite amusing to watch our cats play with it. They rub their faces all over it, they lick it over and over again (until it's drenched in cat spit), they bat it around and around and around, and then they run like maniacs chasing it. And, just so you know, this is the only toy that causes them to act like this. (This is not really normal behavior for them). It's the fresh catnip - they love it. Love, love, love, love, love it! And from what I understand, our cats are not alone in their catnip obsession. Many cats love catnip. About 70-80% of domestic cats have some sort of reaction to it. They love to smell it, roll in it, lick it, rub their faces in it, and it tends to make them go a little bit nutso. Honestly, it's like a kitty drug!

So I was watching this unfold the other day, and I wondered - why does catnip affect cats so strongly?

Catnip is an herb related to mint. It's native to Europe, Asia and Africa, but has long since been established in the Americas, too. It's not entirely clear why it has such a potent affect on most cats, but here's what I've been able to find out. Catnip leaves contain a volatile oil (volatile means that it vaporizes easily) called nepetalactone. The nasal passages of cats is sensitive to this oil; when cats smell the oil, it stimulates sensory neurons that transmit messges to several parts of the cat's brain. In particular, it stimulates the amygdala (which controls emotional response to stimuli) and the hypothalamus (which regulates lots of different activities including emotions). The stimulation of these two areas of the brain cause the intense emotional reaction to the herb.

There are a few things that should be noted about catnip. First, cats will become desensitized to it after a few minutes. This seems to be analogous to how our noses become desensitized to a particular odor if we'rearound it long enough. A cat will only respond to catnip for a short while, then it ceases to have an effect. However, if they walk away from it for a while, then come back, their noses will be sensitive to it again. Second, it is not addictive. Cats do not become dependent on it, no matter how much of it they have. Third, it apparently has no effect in humans. This is presumably because our noses do not have the receptor for the nepetalactone oil. And finally, even large cats like tigers and lions appear to be susceptible to it.

I think it would be fairly amusing to watch a big, ferocious tiger rolling around, rubbing his face in a catnip bush! It would strike me as fairly undignified, for what is otherwise a thoroughly dignified animal.

New creatures

2008-06-23T16:15:00.000-07:00

As I was scanning through the news this morning, I came across a story on msnbc entitled “Top 10 new species: only the coolest, weirdest – and deadliest – made the list.” Intrigued, I scrolled through the pictures on new life forms that have been discovered in various places on the planet over the last year. Here are a few highlights from the article:
Magaceras briansaltini: this is a new kind of rhinoceros beetle. Rhinoceros beetles are certainly nothing new, but this one has a completely different kind of horn than anyone has ever seen. Well, that’s not completely true – the horn has been seen before, but only in an animated cartoon. Remember Dim, the beetle from the Pixar movie “A Bug’s Life”? This new beetle looks exactly like him – only it’s black, not cartoon blue.
Xerocomus silwoodensis: This new mushroom species was discovered, surprisingly enough, in the relatively high-traffic area of Silwood Campus, a campus of Imperial College in London. Odd, how no one noticed it before this year, isn’t it?
Oxyuranus temporalis: This is the second most poisonous snake ever discovered. The other snakes that compete with this guy in terms of lethality are its 2 closest relatives – the inland taipan snake and the coastal taipan snake (which are ranked numbers 1 and 3 on the scale of snakes you don’t want to bite you). It was found in an isolated region of Australia.
Desmoxytes purpurosea: This one tops the list of these new creatures on my “yuck” scale, because it is a big bug with lots of legs. (You might remember from several of my previous posts that I’m not a big fan of bugs.) It’s a millipede, and what makes this species worthy of note is its shockingly bright pink color. It’s so pink, it almost looks fake – but apparently, its notable color is enough to scare away most would-be predators. That’s good for the predators, of course, since this creature also happens to be very inedible – spiny and poisonous.

The list also had a new jellyfish (highly toxic), a tubular plant (described as “having the appearance of the Michelin man”), and a frog specimen preserved in a museum that is now believed to be extinct in the wild. I knew that this list was merely the 10 new species this particular author found most interesting, and I wondered what other new species have been reported in the last few years that didn’t make the cut. Here are a few of the other new creatures that I’ve come across that I thought were worth note:
Rhynochocyon udzungwensis: This is a new type of giant elephant shrew, or sengi. The size of a house cat, this creature looks a but like a cross between a small anteater and a miniature antelope – 4 spindly legs, a stout, amber-colored body, a grey face, and a long, flexible snout. Despite its name, it’s not really a shrew at all, but a relative of African mammals like elephants and aardvarks. There are some 15 species of sengi previously known, but this one had never been sighted before, until first caught on film in the Ndundulu Forest in Tanzania’s Udzungwa Mountains in 2005.
Melipotes fumigatus: This is the only bird I’ve included in my list. It was discovered in New Guinea, on the same expedition that found numerous other species (including 20 new frogs that I won’t talk about here.) This bird is also known as a smoky honeyeater, and it is the first new bird species to be discovered on New Guinea for nearly 70 years.
And finally, Dendrolagus pulcherrimus: This species is more commonly referred to as the golden-mantled tree kangaroo. Also discovered on New Guinea, it’s the rarest arboreal, jungle-dwelling kangaroo in the world. Actually, I’ve cheated a little by including this species, since it was already known to exist in the Foja Mountains of Indonesia, but this is only the second place in the world that the animal has been sighted. But I included it, because I think it’s the cutest of the entire bunch I’ve looked at!

All in all, hundred of new species have been described over the last year. These creatures run the gamut in type, habitat, size, shape and purpose - parasites, plants, fungi, insects, fish, birds, mammals, and amphibians. Of course, since they’re so new, not much is known about many of them yet! I think it’s amazing that, despite the global nature of today’s world, there are still so many things about our planet that we don’t know. And these mysteries are not always even found in the deep jungles of New Guinea – sometimes they’re found right under our noses, or in the courtyards of the Imperial College in London.

The power of oses

2008-06-10T09:47:00.000-07:00

Today I’d like to write about oses. What, you might wonder, are oses? Well, that’s actually a nickname I’ve come up with for the wide variety of sugars that are found in the foods that we eat. Since the proper name for all sugars ends in –ose (I’ll give you a few examples in a minute), I like to call them all “oses.” (It saves me some effort.)

When I say sugar, you might think of granulated sugar, that gritty white stuff we use to sweeten things when we cook. But that is only one specific kind of sugar – specifically, it is sucrose. (See, it ends in –ose.) There are actually dozens of varieties of sugars in the world. What, chemically speaking, is a sugar?

Sugar is a carbohydrate. Carbohydrates come in 2 basic varieties, actually, sugars and starches. Starches are the biggest source of carbohydrates that we eat, but sugars are themselves very important sources of carbohydrates, as well. There are 4 major kinds of sugar that we come into contact with regularly – 3 come from plants and 1 from animals. The 3 plant sugars are called sucrose (what we know of as baking sugar), fructose and glucose.

Fructose is the sweetest of all natural sugars. Its chemical structure is very simple – 6 carbons, 6 oxygens, and 12 hydrogens. It is found in a variety of plant sources, including tree fruits, berries, melons and root vegetables. Chemically speaking, it is actually very similar to glucose; they both have the same numbers and types of atoms, those atoms are simply connected differently in the 2 different sugars. Glucose is the least sweet of the three major plant sugars, but it is the primary source of energy for living cells of all kinds (plants and animals). Sucrose is also commonly known as saccharose, and it is known as a disaccharide. That means it is made up of 2 pieces of glucose and fructose that are bonded together in a specific way. It is the plant sugar that is intermediate in its sweetness between its 2 cousins.

Various food items that we think of as sweet usually actually contain a mixture of the three plant sugars. For example, honey is a mixture of glucose, fructose and sucrose (80% sugars, 20% water). Maple sugar (which makes up maple syrup) is mostly sucrose. Molasses is a byproduct of sugarcane or beet sugar, which is also primarily sucrose. High fructose corn syrup is actually only about 45-55% fructose, the rest of the sugar being a mixture of sucrose and glucose.

The 1 major animal sugar is called lactose. Lactose is found in the milk of all mammals, though it is not as sweet as the plant sugars That means that, though milk has a relatively high sugar content, it doesn’t taste as sweet as something sweetened with sucrose, fructose or glucose. Of course, the rest of a mammal’s body (blood and muscles) also contains sugar in the form of glucose. After all, it is the major energy supply for metabolism. However, mammals do not synthesize glucose out of the constituent atoms – they produce it by converting any other kind of sugar they eat into it.

I know that sugar gets a bad reputation, some of it deserved. After all, our diets are higher in sugar (eg higher in sucrose) than is probably good for us. And a little sugar goes a long way, so we don’t really need to eat as much as we do. But sugar does have a very important place in our metabolism, as well as in making food palatable (actually, making it quite yummy sometimes). So don’t throw the baby out with the bath water, equating sugar with all things bad and horrible. Like everything, just take in moderation.

Antacids - chemistry in action

2008-06-02T10:21:00.000-07:00

Since becoming pregnant, I’ve become acquainted with an uncomfortable stomach reality – heartburn. Or, more properly termed, pyrosis. If you’ve never had heartburn before, let me introduce you to the phenomenon. Your stomach is a very acidic environment – it has to be, to digest everything that you eat. The acid produced by your stomach is supposed to be kept in your stomach and out of your esophagus (the tube connecting your mouth to your digestive tract) through the action of the esophageal sphincter. It’s supposed to be a one-way valve that lets food and liquid from the esophagus into the stomach, but not the other way around. However, sometimes that sphincter doesn’t work very well, and stomach juices push up out of your stomach and into your esophagus. And as these juices are strongly acidic, they can burn whatever they touch; in this case, that would be the lining of your esophagus. This doesn’t really have anything to do with your heart, making heartburn rather poorly named. But since the burning sensation occurs right behind your breastbone, and in severe cases, radiate through the rest of your chest, I guess it makes sense for it to have gotten that name somewhere in the past.

Okay, so that’s heartburn – a burning sensation occurring in your esophagus. Fortunately for mild cases, there is a very simple remedy. Antacids. How do antacids work? It’s actually very simple chemistry in action. To stop heartburn, you want to stop the ability of the rising stomach acid to burn your esophagus. In other words, you want to neutralize the stomach acid. The opposite of an acid is a base. If you combine an acid and a base, they cancel each other out , resulting in something either neutral or closer to neutral than you started with (depending, of course, on the strength of each one). So, very simply, antacids contain some sort of base to help neutralize the stomach acid they encounter.

There are multiple kinds of antacids, each using a different chemical formulation to help neutralize stomach acid. Some, like Tums, use calcium carbonate. Others, like Alka-Seltzer, use sodium bicarbonate instead. There are also magnesium salt-based antacids, like Maalox and Mylanta. Each formula works very effectively, but there are limitations to them. People with hypertension have to be careful not to ingest too much sodium, so sodium bicarbonate antacids may not be recommended. And excess calcium or magnesium can cause kidney stones, so you don’t want to take too much of the other ones, either. All in all, antacids are like any over-the-counter medicine, I guess – you still have to be smart with what you take.

Incidentally, pregnant women frequently experience heartburn because there is less and less room in the abdomen as the baby grows. This puts pressure on the bottom of the stomach, often pushing the stomach juices up into the esophagus. But it’s not really that big a deal, at least for me. A few Tums usually clears things right up!

Yay for chemistry in action!

The rubella vaccine

2008-05-27T10:32:00.000-07:00

Today I want to write about something that has bothered me for a while, but which has intensified since I became pregnant. And I know that I run the risk of jumping into a rat’s nest of controversy, as there are many people who passionately believe in one side or another of this controversy. But hey, science is sometimes controversial, so I’ll just take a deep breath and plunge right in.

I want to talk about childhood vaccinations.

You might have heard a lot of stories on the news or in the papers in the last few years about the controversy over vaccinations. Do kids really need them, should they get them, or (and this is really the favorite topic in the media) is the increase in the rate of vaccinations connected with the increased rate of autism in today’s children?

I consider myself very well educated on these topics, and let me just put my position out there. I do not believe there to be any credible scientific backing behind the purported link between vaccinations and autism. I think any “scientific” evidence supporting it is spurious at best. I understand that autism is on the rise among today’s children, my heart breaks for those families with autistic children, and I easily understand how they might want an answer for what has caused the condition. But the science just does not support their claim that it is due to vaccinations.

That’s all I want to say about the recent controversy over vaccines. The main focus of what I want to say about the decision of whether to have your children vaccinated or not is not simply, as I have heard it said, a personal decision. Yes,, it is personal. But it is also a social decision as well. Here’s what I mean.

Rubella, or German measles, is not a very common disease these days (at least in the US). That’s because vaccinations against rubella have been going on for years – it’s a part of the MMR vaccine, and it’s very effective. Some may argue that it’s silly to vaccinate against rubella. Actually, compared to regular measles, rubella is usually pretty mild. You might have a rash, low grade fever, swollen glands, headaches and body aches. Or you might not ever really notice that you have it at all. But here’s the sticky thing. While rubella might not be all that dangerous for children or adults, it is devastating to pregnant women and their unborn children. A pregnant woman who contracts rubella within the first 20 weeks of her pregnancy has a significantly increased risk of spontaneous miscarriage. And even if disease doesn’t kill her child, it is at high risk for congenital rubella syndrome. This syndrome includes a host of birth defects, including heart malformations, deafness, mental retardation, eye defects, low birth weight, or problems with the spleen, liver or bone marrow. These problem can plague a child for the rest of his life.

The easiest way for mothers to protect their unborn children against congenital rubella syndrome is to be vaccinated themselves. That way, even if they encounter someone with rubella, they and their baby will be protected. But here’s what I worry about: I’m sure there are plenty of women who don’t know of the dangers that rubella poses. And so their vaccinations are not up-to-date. What if they come into contact with someone else carrying rubella because they believe that “whether or not I get vaccinated is strictly a personal decision that doesn’t affect anyone else”? I hope that you clearly see that suddenly this is not simply a personal decision. The unvaccinated individual has significantly increased the risk of someone else being born with a serious birth defect – or perhaps even caused the baby to not be born at all. That’s not personal. That’s social.

I realize that I’m not going to sway anyone’s opinion on whether or not they or their children should be vaccinated. (Especially if their belief is based on religious reasons.) However, I just want to make people aware. This really is not just a personal question, and it makes my blood boil, both as a scientist and an expectant mother, when people suggest that it is.

Incidentally, for everyone who’s reading this – have you been vaccinated against MMR?

The intelligent octopus

2008-05-23T15:55:00.000-07:00

I wrote about giant squid recently, which prompted thoughts on a related topic in my head. I’ve read before that octopus are really intelligent creatures. But I’ve never actually investigated that claim very closely; I’ve just taken it at face value. So I wondered – is it true? How smart are octopus, anyways? And how do we know how smart they are? Is there a little octopus IQ test given to all eight-legged water-dwellers currently residing in aquariums around the world?

Remember, an octopus is a kind of cephalopod. Cephalopods are classified by bilateral body symmetry, prominent heads, and a variation on a mollusk foot called a muscular hydrostat – aka arms or tentacles. (FYI, a muscular hydrostat is a piece of anatomy found in any animal that has muscle but no skeletal support and that is used to move stuff – such as food – around. Your tongue is a perfect example of one.) There are two major types of cephalopods – those with a mollusk shell (like the nautilus) and those without (like squid and octopus). The octopus takes being shell-less even one step further than many of its relatives, however, because it has no skeletal support at all. It doesn’t even have any vestiges of an internal shell or bones, unlike cuttlefish or squid. Its body is entirely soft.

You’d probably agree that an octopus does, indeed, have a noticeably large head. And housed within that head is a very large and complex brain. In terms of brain size relative to body mass, octopus brains rank higher than those of reptiles and fish. And while their brains are organized very differently from that of vertebrates, there is no denying that it is highly differentiated and organized into different sensory processing centers. So that brings us to the question of how intelligent these creatures are. If they have such large brains relative to their body size, it would make sense that they would be intelligent, right?

The answer is – maybe. It depends on whom you ask. Some scientists believe that the size of the octopus brain is not a sign of intelligence at all, but merely an indication that their entire brains are not built very efficiently. And there may be some backing for that. In fact, octopus have been discovered with spines lodged in their brains, from where a meal that they were eating went the wrong way through their system and got wedged in their heads. That’s a pretty good indication that there is something a little screwy about the way their digestive and nervous systems intersect.

However, others believe that octopus have large brains because they are intelligent. When they say “intelligent,” what they really mean is capable of highly complex behaviors above and beyond simple survival skills. Here are some examples of the evidence that scientists falling in to this camp cite as backing for their belief.

1. Captive octopi are extremely good escape artists. Lids of tanks must be heavily weight shut, or the creatures will use their arms to push their way out. Even then, the areas around octopi tanks are frequently carpeted instead of tiled. That’s because octopi can manage to squeeze through incredibly small spaces (remember, they have no bones). So even with a heavily weighted lid, they still sneak out. But they can’t crawl across a carpeted floor, so they have nowhere to go but back where they came from. When they do manage to escape, where do they go, you might wonder? Usually, they are found in neighboring tanks, snacking on whatever tasty treats they find there.

2. Octopi are highly adept at changing their appearance. They can change the color and texture of their skin at will to match their surroundings. Their appearance can change from solid colors to lightly speckled to dramatically striped very rapidly during hunting, courtship, male-to-male aggression and in response to a threat. They accomplish this through the stretching of chromatophores, which are multicelled organs consisting of pigment sacs and various colors. When their muscles fibers contract and expand, the chromatophores change within seconds, making the octopus much faster at changing appearance than any land-based camouflage artist.

3. Researchers have trained octopi to recognize shapes, colors and textures in much the same way that they would teach vertebrates like rats. In the 1950s and 1960s, scientists at the University of Cambridge taught young octopi how to recognize small and large squares, horizontal and vertical stripes, and black and white circles. And the octopi were quick learners, too, though it seems like their maximum level of knowledge is ultimately below that achieved by rats.

4. Octopi are highly skilled navigators underwater, and have been trained to run through mazes just like mice and rats. When presented with a new underwater terrain filled with holes, an octopus can quickly learn to navigate through the correct holes to get to its den (and a treat). And once it’s figured the route out, it is much faster at navigating it the second time through.

5. Octopi have been shown to be able to solve the “food in a container” challenge. If given a closed jar with a crab inside (crabs being a very tasty octopus snack), most octopi will figure out how to open the jar and get their treat, even if they’ve never seen such a jar before. Incidentally, this is a classic test of problem-solving ability in vertebrates such as non-human primates.)

6. There was even one study in 1992 claiming to show that octopi could learn by observing other octopi. According to the study, an octopus was allowed to observe another octopus being trained to prefer one color ball (red) to another (white). Later, the observer octopus showed a preference for red balls, even though he had not received the training himself. This study has been met with much skepticism, however, and it is generally agreed that it must be rigorously repeated before it can be taken at face value. To date, no one else has been able to reproduce the results under more rigorously controlled conditions, so the jury is still out on that question.

This debate rages on even now, as scientists try to come up with the perfect experimental set-up to test whether the octopus is really intelligent, or simply very good at navigating in its surroundings. Regardless, I love watching octopi at aquariums. Whether or not they are as smart as some claim, they are fascinating creatures nonetheless. I’ve never seen one in the wild, though I’ve often looked (while scuba diving). Who knows – maybe some day I’ll get lucky enough to see one in the ocean!

Why don’t they go bad?

2008-05-21T10:22:00.000-07:00

This post is for anyone who’s ever ordered coffee at a restaurant and wondered about the little cups of creamer that they bring with it. These creamers hold maybe a tablespoon full of cream that tastes actually tastes pretty decent in your average cup of coffee, but they also have an inherent mystery about them that has always puzzled me a bit. You see, unlike regular milk or cream, these little things do not need to be refrigerated. Says so right on the lid – no refrigeration necessary. And yet, if you look at the ingredients, there is actual milk in there. So why doesn’t it go bad?

To answer this question, let’s first look at how regular milk is processed for sale in the US. Milk (as well milk-related products like cream and non-dairy products like juice) undergoes a process called pasteurization before it is put on the market. Pasteurization is a process by which any liquid is heated to destroy any microorganisms in it, such as bacteria and mold. It’s named after Louis Pasteur, a famous French scientist who accomplished many things over the course of his life, including advancing the idea that diseases are caused by germs and for developing a vaccine for rabies. He also figured out that heating liquids to a temperature below their boiling point would significantly extend their shelf life (the amount of time before the liquid spoils). There are 2 major methods for pasteurization in use today – High Temperature/Short Time (HTST) and Extended Shelf Life (ESL) treatments. These different methods just use different machinery to achieve the same end. Pasteurization is different from sterilization, in that it is not designed to kill all of the microorganisms within the liquid. Instead, it results in a logarithmic reduction in their levels, reducing them to a point where they are unlikely to cause disease as long as the product is refrigerated. However, as anyone who has ever left a carton of milk in the fridge for too long knows, even a pasteurized product will go bad eventually. That’s because there are still some microorganisms left in the liquid that will cause it to curdle, sour, or otherwise go bad after enough time. If you were to leave the milk out at room temperature, the residual bacteria would spoil the milk even faster – even as fast as overnight.

So if they contain real dairy, why don’t those little creamer packages go bad when left out overnight, too? Well, it turns out that those things undergo a slightly different process called ultrapasteurization. This is also known as ultrahigh-temperature pasteurization, or UHT. Ultrapasteurization is really a process of sterilization instead of pasteurization. When a product is ultrapasteurized, it is heated hotter than in regular pasteurization. This results in the killing of all microorganisms within it – they simply can’t survive the heat. And without any microorganisms, the liquid simply won’t go bad – at least not for a very long time. You can keep ultrapasteurized dairy at room temperature for months if it has not been opened, and it will still be as good when you open it as when it was first produced. Of course, once it is opened, then you need to refrigerate it. That’s because there are numerous bacteria and mold spores floating around in the air, covering your skin, and on every surface in the world. So when that package is opened, those little beasties can get inside and work their destructive magic.

So there you have it. You don’t need to refrigerate little packets of creamer because they have been sterilized. Just another example of science making a difference in little aspects of life you may never have realized!

How to see the inner man (or woman)

2008-05-12T16:00:00.000-07:00

There is a major event happening in the life of my family right now, and I haven’t written about it yet but have been waiting for the opportunity. My husband and I are expecting our first child! There are so many things that I’ve thought about writing with respect to the science of pregnancy – what causes morning sickness, how amazing the pattern of development of the human body really is, how statistically unlikely it was that we would have twins (though lots and lots of people teased us about the possibility), and how much I hope our child grows up loving science as much as we do. But I held off, waiting for the perfect topic. And today, I think I’ve found it – I want to write about ultrasounds.

Actually, I’d like to write about some of the various ways that medicine has come up with to look at what’s going on inside the human body – short of surgery, that is. Three big techniques come to my mind, and I’d like to take a few minutes to discuss what each one does, how they are different from each other, and what their advantages are. These three are ultrasounds, x-rays, and MRIs.

I’ll start with the ultrasound (particularly near and dear to us at the moment). The word “ultrasound” actually means sound waves that are above the range of human hearing (20,000 hertz), so when we talk about ultrasounds in a medical sense, we are actually talking about ultrasonography. Ultrasonography has been around for about 50 years, and is extremely widely used in diagnostic procedures to visualize soft tissues, muscles, tendons, and some internal organs (including the heart, liver, gallbladder, kidneys and bladder). It is also commonly used to look at a developing fetus within a mother’s uterus. During the process, ultrasound waves are produced by a small wand, or transducer, which radiate out into the body to focus at the specified depth. This sound wave is partially reflected from the layers between different tissues – specifically, where there is a change in tissue density. The sound waves that get bounced back towards the transducer are detected by a sensitive microphone, which are then translated into an image on a computer screen. There are several big advantages to using sonography as a diagnostic tool. For one thing, it does not use ionizing radiation (as do x-rays), making it safe to use for developing babies. For another, it is relatively cheap compared to its high-power brothers like the MRI. However, it is limited in its ability to see certain structures within the body – it is not good at visualizing bones or the brain, for example.

So let’s go now to the next imaging technique on my list – the x-ray. The medical use of x-rays manipulates the physical properties of – you got it – x-rays. (Clever, huh?) An x-ray is a high energy type of light wave. The energy of a light wave can be measured by its wavelength – the shorter the wavelength, the higher the energy the wave has. In the visible spectrum, red light has lower energy (and longer wavelengths) and blue light has higher energy (and shorter wavelengths). Past the visible spectrum comes ultraviolet light, followed by x-rays. While visible light does not have enough energy to pass through your skin, x-rays have considerably more energy, and thus can pass right through your skin and muscle. However, they are not strong enough to pass through bone. So when you undergo a medical x-ray (for example, to see whether you’ve broken a bone or when you are at the dentist), the doctor will put you in front of an x-ray emitter, which sends x-rays through your body and picked up by a detector (usually a piece of film) on the other side of you. Places of your body where the x-rays pass through (eg muscles and soft tissue) show up as black, while pieces of your body where the x-rays were absorbed (eg bone and teeth) show up white. The film is developed, and the doctor can tell whether your bones are all as they should be – whole and unbroken (hopefully). X-rays are more powerful than sonograms, especially for diagnosing problems specific to the skeleton. However, their major drawback is that they use ionizing radiation in the process. Too much ionizing radiation can cause all kinds of problems for your cells and tissues; however, the exposure any of us will be likely to receive from medical x-rays over the course of our lives is minimal and of low risk.

What about the fancier techniques, like MRI? MRI stands for magnetic resonance imaging, and it uses an entirely different basic principle to visualize the interior of the human body. Instead of sonography (which uses sound) or x-rays (which uses high-energy light), MRIs use magnetic fields. When a person is subjected to an MRI, their body is immersed in a strong magnetic field, which has an effect on the hydrogen atoms throughout their body. The human body can be upwards of 75% water; in each molecule of water, there are 2 hydrogen atoms. Thus, the amount of hydrogen in your body from water alone is really high. And these hydrogen ions will all align with the magnetic field when you are in the MRI machine. So you sit there, with all your hydrogens aligned, and then your body is pulsed with a radio wave. This pushes some of the hydrogen atoms out of alignment with the magnetic field. The radio wave stops, and the hydrogens all slowly snap back into alignment. However, depending on what tissue they happen to be sitting in, they will snap back into place at different speeds. And the speed at which the hydrogens align themselves with is detected by the machine, then calculated to determine what tissue is what. An MRI is a very powerful technique, and can be used to diagnose a number of different medical conditions, including multiple sclerosis, brain tumors, torn ligaments, spinal hernias, tendonitis, and even strokes in the early stages. Another advantage is that they, like sonograms, do not use any form of ionizing radiation. And yet another advantage is that MRIs can be used to look at any plane of the human body – sideways, top-to-bottom, or any other way you can think of. There are some disadvantages, though. Certain people cannot receive MRIs, because the strong magnetic field would be dangerous for them (for example, people with pacemakers). MRIs take a very long time to do, as well, and they are extremely expensive – much more so than either x-rays or a sonogram.

All three of these techniques are powerful in their own right. They can be used to look at different parts of the body – soft tissue, organs, bones or ligaments – with different resolutions. Each one uses a different major method of visualization – magnetic fields, sound waves or electromagnetic radiation. Each one has different costs, risks and benefits. And all in all, I’m glad to live in a day and age where all three are used as a part of everyday medicine. Each one is so much safer than having to cut the body open to see what’s going on inside!

Oh, and by the way, we have had our ultrasound to check on our developing baby. All looks good – 2 arms, 2 legs, and all pieces where they should be! Now we just have to wait to see the little one in person!

The giant of the deep

2008-05-05T10:17:00.000-07:00

As you might have guessed from my various postings through the months, I like to write about animals. There are so many things about them that I find interesting – the purring of cats, lizards whose appearance hasn’t changed in a million years, goats that randomly fall over when they are startled, how kangaroos can’t walk backwards, and how, ounce for ounce, bats are one of the longest living mammals on earth. Well, today I’d like to talk about an animal that no one knows very much about, but one that I have found fascinating ever since I first heard about it. This creature is one of the great animal mysteries of the world – we know that it exists, but short of that, we know relatively little about it at all. The animal in question – Architeuthis. The giant squid.

What is a giant squid? Since it is not very creatively named, you’ve probably guessed that it’s simply a really, really big squid. But how big is it? How does it get so big? Where does it live? And why do we know so little about it?

First, let’s discuss squid and octopus in general. Your basic squid has a few standard anatomical features – 8 arms and 2 tentacles, each with hooks and/or suckers, a head (with a very large brain), a mantle (or torso), and 2 fins at the rear of the mantle. Your basic octopus is the same, except that it doesn’t usually have fins, and it’s arms and tentacles only have suckers, not hooks. (There are a few species of octopus with fins, however; they live off the coast of New Zealand and are considered primitive relative to other octopus. That’s why they are referred to as “Dumbo octopus.”) The tentacles of squid are generally much longer than the arms. In fact, there are 2 ways to measure the length of a squid. You can either measure the standard length, which is the length from fins to the end of the arms, or total length, which is the length of the fins to the tentacles. Most squid are quite small, reaching an average total length of almost 2 feet. Of course, that’s the size of most squid – except for the giant squid.

How big a giant squid can get is a matter of debate, since they are so hard to find. The largest reported giant squid ever found washed up in New Zealand in 1887, supposedly at a total length of 55 feet. However, since it was dead, it is likely that its tentacles became stretched like rubber bands once it died and washed up. Based on the length of its mantle, it is now believed to have been only around 30 feet long. Scientists now generally base their estimates of how big a giant squid can get on the remnants of them found in the stomachs of their only known predators, sperm whales. Based on these leftovers, it is now believed that they can reach up to 45 feet in total length. The only invertebrate believed to be larger than the giant squid, actually, is its cousin, the colossal squid (which may be twice as long).

Giant squid live in the depths of every ocean in the world. They are usually found near continental and island slopes of the North Atlantic, the South Atlantic, and New Zealand and Australia, and are rarely seen in tropical waters or near the poles. Unfortunately for scientists, they are often studied after they’ve died, whether they’ve washed up on a beach or are taken out in pieces from a sperm whale’s stomach. In 2004, however, major news was made when scientists off the coast of Japan filmed a live giant squid for the first time ever in its natural habitat. Finding live giant squid in the ocean is notoriously difficult. Scientists usually try to follow sperm whales in the hopes of finding one, but that has proved relatively fruitless. Unless we come up with a better way of finding these elusive giants, they might remain a mystery for some time to come.

Of course, just because we don’t know a lot about them scientifically hasn’t stopped us from using our imaginations to envision them. Giant squid have been a source of legend for thousands of years. Tales of them have been around among mariners since ancient times. In fact, it is believed that the giant squid probably gave rise to the legend of the kraken - a giant sea monster off the coast of Norway and Iceland that was capable of engulfing entire ships (and one that you might remember from the recent Hollywood blockbuster “Pirates of the Caribbean 2: Dead Man’s Chest").

I don’t know why I find these creatures so intriguing, to be honest. Perhaps it’s simply because of their mystery. Imagine – an enormous creature, swimming in the depths of the ocean, so well adapted to its environment that we can’t even find it. Something so large that it only has one predator it needs to fear. And something that, unlike sharks, has not successfully been made into the villain of a Hollywood movie plot such that we feel the need to hunt it down and kill it. Maybe someday we’ll know more about this giant animal. Until then, I must say that I kind of like the uncertainty.

Reversing revisited

2008-04-28T10:35:00.000-07:00

In my last post, I talked about the ability to walk backwards, with the following conclusions: kangaroos – no ability to walk backwards; emus – ability to walk backwards unverified. Apparently, in the book that I mentioned (“Emus can’t walk backwards: Another round of dubious pub facts”) I have been told that the author describes experiments done in Australia to demonstrate that emus can, in fact, walk backwards. I’d be interested to read it, learn the evidence for myself, and also to know whether it describes the origin of this fable. (Really, emus are not all that popular an animal to discuss in everyday conversation! So who started the idea that they can only walk forwards?)

Anyways, I’ll see if I can check it out from the library. This is good - this could save me a long time sitting in front of the emu exhibit at the zoo, waiting for one of them to back up.

Ready, set, reverse!

2008-04-24T09:58:00.000-07:00

Our cats really love to sit on the counters in our bathrooms. Every morning, as I’m getting ready for work, our older cat will come and sit on the counter for a few minutes – until I pull out the hair dryer, that is. The noise of this machine always scares her, and she inevitably jumps down off the counter and scampers away. A few days ago, however, she tried a new technique for getting off the counter. Instead of turning around and jumping down, she simply backed herself right off the edge. Not surprisingly, this didn’t work very well – she misjudged where the counter ended, and wound up with her rear legs in the trash can and her front legs on top of the toilet seat! (I guess I should be glad she didn’t wind up with her back legs in the toilet bowl.)

Now, I must admit, I laughed quite a bit at her predicament. (After making sure she as unhurt, of course.) But it sparked a question in my mind. She can back up quite well, but apparently she has to be level ground. And I wondered if that was a trait that all animals share. Can any creature that walks forwards also walk backwards? Or are there animals in the world that are physically unable to back up?

For the most part, animals that can walk forwards can also walk backwards. However, it is not universally true.

The one mammal that I came across that is unable to back up is the kangaroo. Kangaroos are marsupials that belong to the family Macropodidae, which means big feet. Other macropods include wallabies, quokkas, pademelons, honey possums, and wallaroos – in fact, there are over 50 different species of macropods. The most obvious difference between kangaroos and other species like wallabies and wallaroos is size. The 6 largest marsupial species are all referred to as kangaroos. In addition to really big feet, kangaroos have very powerful leg muscles, a strong tail for balancing, and a skeletal structure that makes them very efficient hoppers. But it also means that they can’t really walk. If a kangaroo has to move slowly, it forms a tripod between its tail and two forelimbs. You might see a kangaroo in this position if it’s eating something from the ground. But for general locomotion, hopping is much more efficient. And apparently if a kangaroo wants to retrace its steps (its hops?) it must turn around to do so. They cannot hop backwards, nor can they mince backwards in their tripod walk.

It has also been reported that certain birds are unable to walk backwards – in particular, ostriches and emus. These are the two largest birds on the planet; they are both members of the most primitive of modern bird families (including kiwis, cassowaries, and rheas). Both flightless, these guys rely on good old-fashioned leg power to get themselves around. Emus, in particular, can be quite speedy – they can sprint upwards of 30 miles an hour! They have a unique structure to their pelvic bones and muscles that allow them to move so quickly. They also have extremely powerful legs - in fact, emus are also the only birds that have calf muscles. Not only can emus run really quickly, their strong legs make them incredible jumpers. If startled, they can jump straight up almost 7 feet – which, considering that the bird itself is over 6 feet tall, is quite impressive. So they can move really well going forwards – but can they reverse? Unfortunately, though that statement is often thrown around as fact (and is even the title of a book – “Emus can’t walk backwards: Another round of dubious pub facts”), I wasn’t able to find any reliable source to tell me whether or not it was true. The evidence is mostly anecdotal. I guess the next option to me to verify this fact would be to camp out at the emu section of the local zoo and watch them for a few days to see if I can see any of them go backwards!

There may be other animals that cannot reverse their locomotion. One other suggestion my husband came up with was the centipede. With that many legs, I can imagine that it might very well be difficult for organize them all to go in reverse!

Anyone have any other ideas?

Yikes! Brain Freeze!

2008-04-21T10:28:00.000-07:00

Here in the Seattle area, we are going through a rather disappointing spring. With the exception of 1 very notable day, our weather has been much colder and wetter than usual. Now, I love warm weather. Give me sun, sun, sun! So I’ve been having a hard time being patient for the nice weather to return. When I think about warm weather, I think about lots of things associated with summer time – barbeques, running through the grass in my bare feet, seeing our cats sunning themselves in the windows, listening to the birds outside, and, of course, all the yummy summer food. Especially ice cream. I really like ice cream. The only downside to eating ice cream on a warm summer day, unfortunately, is the chance of developing brain freeze.

Have you ever had brain freeze - that feeling when you’re eating something really cold (could be ice cream, or a slurpee, or some ice cubes in a drink) and all of a sudden you get a horribly painful ache in the front of your skull? Fortunately, it only lasts a few seconds, which is a very good thing since it hurts so badly. Have you ever wondered what causes it?

Brain freeze occurs when your palate gets a little confused over the temperature. Your palate is, basically, the roof of your mouth. If you run your tongue over the roof of your mouth, everything from the ridge behind your teeth to the farthest back you can reach is the palate. It is made of both bone and muscle, and is covered by a layer of skin. It serves several important purposes, including separating your nose and nasal cavity from your mouth. There are many nerves and blood vessels situated in this region, which are all sensitive to the things you eat. When you eat something very cold very quickly, the nerves in your palate get a strong message that there’s something freezing here! These nerves then get a little confused – they think that your brain is in danger of freezing from the cold. And since a frozen brain would be very bad for your health, these nerves send an immediate message to increase the blood flow to your head. Increased blood flow would mean extra warmth for your brain, keeping it safe from freezing. However, the blood vessels holding this extra blood in your head expand so quickly that they cause pain. The pain is very short-lived – the increased blood flow stops as soon as your palate warms up a little, your blood vessels contract again, and the headache stops.

One thing that surprised me is that not everyone suffers from brain freeze. Apparently, it only happens in 30-40% of the population. (The American population, that is.) I guess that makes me one of the unlucky ones, since I definitely get them! I did learn one new way of getting the brain freeze to go away faster, though. When you feel it start to develop, press your tongue against the roof of your mouth. This will warm your palate up faster than it would otherwise, and stop the headache faster.

Or you could just eat your ice cream a little bit slower.

The Oregon earthquake swarm

2008-04-17T11:02:00.000-07:00

I live in western Washington, an area not as well-known as California for being earthquake-prone but which is nevertheless earthquake territory. That's because we're right on the edge of the North American tectonic plate, which runs almost directly up the western coast of North America. When you think about the fault lines created by this boundary, you might think first of arguably the most famous fault line in the US – the San Andreas fault. The San Andreas fault stretches approximately 800 miles up the coast of California; here, the passage of the North American plate (which moves southeast) and the Pacific plate (which moves northwest) generates the most memorable earthquakes of the region. This includes the devastating 1906 San Francisco quake, which was an estimated 7.8 on the Richter scale and responsible for some 3000 deaths.

Now, the San Andreas does not extend up into Washington state. However, being at the edge of the North American tectonic plate means that we also have fault lines capable of generating substantial earthquakes in the area. For us, however, the danger comes primarily from where the North American plate meets the Juan de Fuca plate. The Juan de Fuca plate is very small, extending from the southern border of Oregon to British Columbia, Canada; it was once part of a much large plate (the Farallon plate) that has largely subducted (meaning sunk) underneath the North American plate. There are three remnants of the Farallon plate still in existence - the Juan de Fuca plate off of the Washington coast, the Cocos plate off of Central America, and the Nazca plate along the western edge of South America. Subduction of the Juan de Fuca plate is responsible for the formation of the Cascade mountains which includes two volcanoes that you might be familiar with - Mount St. Helens and Mount Rainier.

The last major earthquake to occur off a fault from the Juan de Fuca plate was around 1700, with a magnitude of somewhere around 9.0 on the Richter scale. However, in the last 2 weeks, scientists have detected a rash of earthquakes off the Oregon coast – over 600 of them, up to a magnitude of 5.4. But here’s the odd thing – these earthquakes do not appear to be coming from any of the fault lines from the Juan de Fuca plate. Instead, they are centered in the middle of the plate – about 40 miles from its edge.

There are actually several odd things about these earthquakes. First, of course, is that they do not correspond to a fault line. But second, they do not follow the typical earthquake swarm pattern of a major shock followed by steadily decreasing aftershocks. It has been a steady stream of earthquakes of mostly equal size. That means this is unlikely to be caused by a fault internal to the plate itself. In fact, scientists really have no firm idea what’s causing these tremors to occur.

One of the major researchers studying this swarm is Dr. Robert Dziak, marine geologist from Oregon State University. Though he says that nothing like this has been detected in this region ever since monitoring has begun, he has a couple of suggestions as to what’s causing the swarm. It’s possible that a new fault is opening in the middle of the Juann de Fuca plate. Or it could be that the entire plate is under stress, being squeezed by the plates around it, which could cause it to crumple a little in the middle. Or there could be new volcano activity in the area immediately beneath this spot, injecting new magma into the middle of the plate and pushing the plate much faster than it has previously moved.

I should mention that these earthquakes do not appear to be any danger to the inhabitants of the Oregon coast. The quakes are too far away, too deep and too small to even be felt on the mainland. They are detectable by a system of hydrophones set up on the ocean floor – which were actually originally set up to detect submarine activity off the Pacific coast during the cold war. But they’ve been put to a more peaceful use as of late.

Not a lizard, and not a snake - but some of both

2008-04-14T11:45:00.000-07:00

Did you know that there is still a species alive on earth that roamed the planet alongside the dinosaurs?

It’s called the Tuatara. The tuatara is the last surviving species of the Sphenodontians, a group of animals that developed and thrived during the upper Triassic – nearly 220 million years ago. If you were to look at it, you might think the tuatara is a lizard – a triangular head, four squat legs with long spiny toes, leathery skin, and a long tail. However, while the tuatara is a reptile, it is equally closely related to both lizards and snakes. It is the only surviving species on earth that fits this description. Other relatives of the tuatara were the beak-headed reptiles (also known as Rhinocephalia), but the rest of them died out 100 million years ago.

The tuatara is sometimes referred to as a living fossil. Despite its ancient origins, the appearance of these animals has not changed very much in the last 200 million years. This means that they can be used to study what their ancient relatives looked liked. Because of this, they are of great interest to scientists who study the evolution of lizards, snakes, and diaspids (the group that includes both birds and crocodiles).

Interestingly, though the overall appearance of the tuatara has remained unchanged for millions of years, it now seems that they undergo relatively rapid molecular changes. By comparing DNA extracted from tuatara bones approximately 8000 years old to modern tuatara DNA, scientists now believe that this animal has the fastest rate of DNA changes ever measured. At an average rate of change of slightly over 1.5 subsitutions per nucleotide per million years, it beats out the previous record-holding fast molecular evolver, the Adelie penguin. The fact that the DNA of the tuatara changes so rapidly, while its overall body hasn’t changed in millions of years, is remarkable.

Tuataras live only in New Zealand. And though I refer to the tuatara as one species, there are actually 2 closely related subspecies of tuataras – S. punctatus and S. guntheri. S. guntheri is also know as the Brothers Island tuatara, and it is extremely rare, much more so than its S. punctatus relative. In reading up on these creatures, I came across a few interesting facts:
-They have the slowest growth rate of any reptile we know of. In fact, they keep growing until the reach about 35 years old, but only attain a final size of 20 inches.
-They can live to be over 100 years old, though their average life span is around 60 years.
-They can hold their breath for nearly an hour.
-They are nocturnal – for the most part. Adult tuatara hunt at night, but young tuatara will hunt during the day. This is because a really hungry adult will eat a young tuatara if it can catch it. In addition, because they are cold-blooded, they will bask in the sun during the day to regulate their body temperature.
-They have an extra eye besides the two in the front of the face. Called the parietal eye, it is found on the top of the head, and is visible only in the very young. After about 6 months of age, it becomes covered with opaque scales and pigment. Its function is unknown, though scientists have suggested it to play a role in circadian rhythms or the absorption of UV light to aid in the production of vitamin D.
-The hearing organs of the tuatara are very primitive, and look very similar to that of turtles. There is no eardrum, or even an earhole. The cells that respond to sound are relatively poorly specialized, and respond only to low frequency sounds.

If you have a few minutes, and want to see some pictures of these cool little creatures, you can check out the website of the Kiwi Conservation Club at:
http://www.kcc.org.nz/animals/tuatara.asp

The image of the tuatara was taken from:
http://www.wpclipart.com/imgpage.html?http:
//www.wpclipart.com/animals/T/Tuatara.png

A well-built skull

2008-04-10T09:53:00.000-07:00

Why don’t woodpeckers hurt their heads when they bang them into trees?

That question popped to mind the other day as I was working outside in my garden. We have a woodpecker that has taken to visiting one of our neighbor’s trees. Stay outside long enough on a decent afternoon, and soon you will hear the distinctive “rat-a-tat-a-tat-a-tat” of the woodpecker’s beak, as it rams over and over again into the trunk. These birds are tenacious when it comes to drilling holes in things! Not only are they tenacious, they are powerful. In fact, North America’s largest woodpecker (the Pileated woodpecker) can hit a tree 20 times a second, up to 12,000 times a day, with forces as high as 1,200 times the force of gravity with each hit. That’s roughly the same as hitting a wall with your face at 16 miles an hour – over and over and over again. Ouch. That makes my head hurt just thinking about it!

So how come they don’t hurt themselves?

Woodpeckers are highly adapted to this punishing lifestyle based on the design of their skulls and brains. First, the skull: a woodpecker’s skull is very thick and bony, but the bone itself is fairly spongy. There is also a think layer of cartilage at the bottom of the lower jaw bone that serves as a cushion. This cartilage and bone structure enables to force of the blow to be distributed to the base and back of the skull, rather than the brain.

Next, the brain: a woodpecker’s brain actually has several features that protect it from impact. First, it is small and packaged very tightly inside the skull cavity. Because of its tight packing, the brain does not move much more than the skull does. When a human hits his head, the brain can jostle around within the skull cavity, actually bumping against the bones. That bump causes much of the brain injury associated with a head trauma, such as a concussion. But woodpecker’s brains don’t move that way, so they can’t knock themselves out, get concussions, or incur brain bleeding. Second, there is not a lot of cerebrospinal fluid, either, because there is simply no room for it. This fluid helps transmit shock waves from the skull to the brain, which can also cause injury to the brain. Little fluid – few shock waves. Third, a woodpecker’s brain has a smooth surface, with a high surface area to weight ratio. This is unlike a human brain, which has ridges, folds and bumps all over the surface. We actually have a lot of surface area on our brains! That’s good for thinking, but bad for a head trauma. It means that any impact to the brain is felt over a small surface area. For a woodpecker, a blow to the brain is spread out over a larger surface area, which means that the impact on any given spot is smaller.

Finally, there is another very important fact that helps explain why woodpeckers don’t hurt their heads when they peck – it has to do with their pecking technique. Woodpeckers will always peck at a surface in a straight line, with no side-to-side twisting or torque. This prevents a specific kind of stress on the nerve fibers of the brain called “diffuse axonal injury” or DAI. DAI is one of the most common and dangerous forms of traumatic brain injury. DAI occurs when a sudden deceleration is coupled with some form of rotation, which can twist nerves apart like a lid coming off a jar. A brain impact that occurs straight-on will not cause DAI, because there is no rotational stress being applied to the brain. So it is vital that a woodpecker hit its target dead center and straight on with every hit. And, from all indications, they do!

Incidentally, an Ig Nobel prize was awarded in 2006 in opthamology to Dr. Ivan Schwab and Dr. Phillip R.A. May, for their work on woodpecker head trauma. In particular, they studied why woodpeckers are immune to retinal detachments, brain damage and spinal cord injuries with their repeated head banging. And in addition to the stuff I’ve talked about above, they did learn one additional thing. Woodpeckers always close their eyes with every bang of their beak.

Dr. Schwab did admit, however, that whether they do it to keep their eyeballs in or the wood chips out was an open question.

Roadrunners

2008-04-07T11:34:00.000-07:00

My husband and I were fortunate to be able to spend a few days last week visiting family in Palm Desert, California. Palm Desert is a beautiful oasis in Riverside County, a few hours east of Los Angeles. The weather there this time of year is gorgeous – 80 degrees, sunny, light breezes pretty much every day. Perfect weather for sitting out by a pool in the afternoon, which is mostly what we did! One afternoon, while engaged in this extremely pleasant activity, I looked over to the edge of the pool patio, and saw a funny little bird running underneath the shrubs. Lo and behold, it turned out to be a roadrunner.

I’ve never really thought about roadrunners that much (except, of course, for road runner in the Loony Tunes cartoon who always managed to get the best of Wile E. Coyote). But this was a neat looking bird. He had a long neck, a tuft on top of his head, and a very long tail. When he (or maybe a she, I don’t know exactly know what gender it was) walked or ran, his whole body went horizontal – head down, tail stretched out behind him. But when he stopped, his head came up, his tuft poofed out, and his tail rose up behind him. All in all, it was a very cute sight. I decided to investigate roadrunners a little bit more to see what I could find out about them.

A roadrunner is actually a kind of ground cuckoo. It is found in all of the southwestern states, but predominantly in the Mojave, Sonoran, Chihuahuan and south Great Basin deserts. Its prominent features include its tail and head (which I mentioned above), as well as its feet – it has 4 toes, 2 of which point forwards and 2 of which point backwards. The roadrunner can fly, and will do so if threatened or (apparently) if traveling downhill. But because it has a large body and weak wings, it can’t fly very well, so it usually prefers to walk or run. In fact, this little guy can run as fast as 17 to 19 miles per hour. (The fastest human in the world, incidentally, clocks in at around 22 miles per hour. But that’s for a distance of only 100 meters.)

The speed of this bird makes him well adapted to catching and eating other animals. Its diet consists almost exclusively of insects, scorpions, lizards, rodents, and other birds. They have been seen snatching dragonflies or hummingbirds out of air in mid-flight! They will eat fruit that they find on the ground, though, especially in the winter when prey becomes scarce. Roadrunners will even eat rattlesnakes – they are one of the few animals that can do this, actually. To catch this very dangerous snake without getting bit, the roadrunner will dart around, snatch the snake up by the tail, and whip it repeatedly against the ground until it’s dead. And here’s a funny tidbit that I happened across. A roadrunner will eat its prey whole; however, they have been know to catch snakes too big to eat in one sitting. So they will swallow as much as they can, then run around for a while with the rest of the snake dangling out of their mouths until the eaten bit has digested enough to make room for the rest of it! (Yuck.)

Interestingly enough, as long as the food that the roadrunner eats is high enough in moisture, the bird does not even need to drink any additional water. They also have special glands around their eyes that secrete extra salt from their bodies. This makes them very well adapted to living in the desert.

And no, they do not really say “beep beep” whenever they stop. Their vocalizations consist of a much more normal, bird-like cooing or whirring. The "beep beep" is, unfortunately, only in the cartoons.

The marvels of flight

2008-03-25T12:34:00.000-07:00

Now that spring is starting to appear, our neighborhood is awash with the song of birds singing in the trees. Every day while waiting for the bus, I see at least a few geese flying overhead on their way south. And the number of robins digging worms in our yard is actually kind of comical. As I watch all of these birds, I am frequently struck by the fact that birds are remarkable fliers. The ease with which they take off, maneuver in the wind, swoop and swoon like acrobats, somehow manage to avoid running into each other, and then land safely on any number of surfaces (trees, roofs, the ground, cars, electrical wires, or the surface of Lake Washington) is remarkable. How do they do it?

Flying is all about having enough upward thrust to overcome to force of gravity pulling an object to the ground. Birds achieve this thrust using their wings in 2 ways – by manipulating air that is already moving (as in gliding) or by moving air themselves (as in flapping).

Gliding is actually relatively simple. When a bird is already airborne, it can glide in much the same way that a hang glider does. For one, they use thermals, trade winds or updrafts. These are piles of air that are rising upwards. The air moving upwards creates a force on the underside of their wings, pushing them up. For another, the shape of the wings gives them upward thrust. As their wings move against the air, they push the air underneath the wings down. This is a force that must be counteracted (according the Newton’s law of every action having an equal and opposite reaction) by an equal and opposite force up. A force pushing up – and voila! Flight.

Okay, so that’s the easy case. What about flapping? How does that work? Well, when a wing flaps, it pushes air in a strong force downwards. This moves the bird up in the air. A curious question, therefore, is why doesn’t the upward stroke of a wing flapping create a force that pushes the bird down? Actually, bird wings are hinged – when the flap down, they are fully extended. But when they move back up, they are folded up, presenting less surface area to push against the wind. You can think about this like the oar on a canoe. If you paddle with the full surface area of the blade pushing against the water, you get a big push. But if you paddle with the blade parallel to the direction of motion, you don’t get much thrust at all. So just imagine a bird wing being like a canoe paddle that pushes air around, instead of water.

Well, it doesn’t sound too complicated, right? If that’s all it takes for flight, why haven’t humans invented self-flying units with retractable wings that we can use to take off, and why don’t we glide into work every day in our personal hang gliders? Well, a bird can fly not only because of the forces its wings can exert on the air, but because its body is uniquely adapted for flight in ways that a human body is not. For example, birds are extremely light. They have extremely strong, hollow bones – strong enough to get the job done, but light enough not to create too much weight to overcome. Birds have feathers, which are capable of trapping and dispersing more air than hair or skin. Birds have highly efficient respiratory systems, which are extremely good at extracting oxygen from the air. In addition, they have extra air sacs next to the lungs, so the animals never run out of breath. This is really important, as it takes a lot of energy (and thus a lot of oxygen) to maintain flight. And birds eat food that is highly energy dense for their body size, which (again) gives them the extra energy they need to carry out this tremendously difficult task.

The human body is all wrong for us to be able to fly on our own. We’re much too heavy, largely because we’re so dense. We don’t have any sort of extra light, fluffy, airy material like feathers to help us move air the way we want to; our arms and hands are neither strong nor big enough to create enough of a downward thrust to move us skyward. Our lungs are perfectly fine for our usual activity on land, but are nowhere near efficient enough for such an aerobically intensive feat as flying. In fact, we just don’t have enough energy, period.

Of course, we have found ways around our limitations as far as flying goes. We’ve built jumbo jets, ultralights, hang gliders, and powered parachutes. So it is possible to get us off of the ground. But if you were to compare the simplicity of a bird flying with all of the ways that we as humans do it?

Frankly, I don’t think it’s much of a contest which one is more elegant. So you can consider this another entry in my list of “ways in which nature is a much better engineer than man.”

(With apologies to all of the engineers I know out there.)

It’s a bird… it’s a plane… it's a squirrel?

2008-03-18T15:19:00.000-07:00

Today’s topic is one of those that makes me smile. Say these two little words to me, and I guarantee you that a silly grin will pop to my face. I don’t know why, exactly – it’s just irresistible to me. Want to know what the 2 words are?

Flying squirrels.

I find something irresistibly funny about the idea of squirrels flying loftily through the air. Squirrels! Those little, bushy-tailed sneaks who will do just about anything to get into a bird feeder, who sit and chirp just outside the patio door (tantalizingly out of reach of our cats), who like to play chicken and run across the road right in front of my car, and who have been brazen enough to steal entire grilled cheese sandwiches from picnic tables when my attention has turned. (That’s a true story, by the way.) I guess I find it funny that an animal like that can fly gracefully and elegantly through the sky.

Actually, we must get something straight. Flying squirrels can’t actually fly – they glide. They have a large, loose flap of skin that stretches between their front and back legs. When they jump from a tall tree, this skin stretches out, forming a shape much like a kite. Using the lift provided from these “wings” and their tails as rudders, the squirrels can glide up to 150 feet through the air to land on another tree trunk. The only true flying mammals in the world belong to the order Chiroptera, to which bats belong. Flying squirrels belong to the order Rodentia (yes, they are rodents), the family Sciuridae (meaning squirrel), and the subfamily Pteromyinae (meaning flying squirrels). There are two major subfamilies of flying squirrels – Northern and Southern. These differ in their geographic distribution, forest preference, and subtly in their appearance – for example, Northern flying squirrels tend to be larger than Southern ones.

While the flying squirrel is possibly the most well known mammalian glider, there are other ones, as well. There are several species of gliding possums, including 11 belonging to the family Petauridae. These guys have great names, including the Great-Tailed Triok, Tate’s Triok, Leadbeater’s Possum, the Biak Glider, and the Sugar Glider. There is another species of flying squirrel called the scaly-tailed flying squirrel (an African rodent that’s not actually related to squirrels at all, it just looks like them). There are also 2 species of flying colugos, or lemurs. It’s not a bad list, considering that mammals really do not have the right body shape or structure for flight at all!

What prompted my decision to write about flying squirrels? I came across an article recently in National Geographic about efforts to design a jumpsuit that will allow humans to skydive without a parachute – instead, they’ll glide to safety in the same way a flying squirrel does. It’s called a wingsuit. Actually, wingsuits do currently exist; they have large fabric panels between the arms and legs of the suit that allow the skydiver to maneuver in freefall. However, the current generation of wingsuits are not advanced enough to allow the entire flight to be parachute-free – you still need that for the actual landing. That’s because while the gliding action of the wingsuit slows your vertical speed down dramatically, it translates it into horizontal speed – upwards of 90 miles an hour. That’s plenty of speed to do some damage to your body! Designers are trying to create a wingsuit that will allow the skydiver to manipulate their “wings” at the last minute before landing, slowing their horizontal speed.

Now, the jury’s still out as to whether or not this will actually work. I think we can be certain of one thing, though. Nature still has mankind beat when it comes to creative ways to handle complex problems. What we will only be able to do with extreme effort, these squirrelly little rodents have been doing effortlessly for years. Kind of humbling, don’t you think?

Happy Pi day!

2008-03-14T10:36:00.000-07:00

This is more about math than science, but I thought I’d write a brief note about it anyways. Today is March 14th, which translates to 3/14. For those of you who remember your geometry, that sounds an awful lot like the beginning of that most mysterious of all numbers – Pi.

Pi is a mathematical constant, which can be calculated by taking the ratio of a circle’s circumference (the distance around its edge) to its diameter (its width at the widest point). No matter what size circle you use, the calculation comes out to be the same. Pi is an irrational number, which means it has an infinite, non-repeating decimal. The numbers to the right of the decimal point never repeat, and thus pi can never be written as a fraction (not accurately, anyways). Modern computers have calculated pi out to more than a trillion digits – and there is still no end to the number in sight.

To celebrate Pi day, at 1:59 pm at the San Francisco Exploratorium, a group of Pi enthusiasts will gather to really celebrate their favorite number. Why 1:59 pm? Well, 3/14, 1:59… that’s otherwise known as 3.14159.

I don’t think anyone can celebrate more digits of pi with better precision than that.

One hardy little worm

2008-03-13T15:45:00.000-07:00

As I’ve mentioned before, I am a cellular and molecular biologist. My specific area of research is in the cellular biology of aging – why do cells (and whole organisms) get old and die? To do this research, my colleagues and I use a model organism called Caenorhabditis elegans (or C. elegans, for short). C. elegans is a small roundworm that lives in the soil of temperate environments throughout the world. It was first developed for use in biological research in the 1970s, and has become a premier organism for studying development, neurobiology and aging. C. elegans is a cool animal with lots of really neat features (at least, neat to a biologist), but I’m not going to go into a great amount of detail about the organism itself right now. Instead, I want to write about how amazingly sturdy these worms are.

A group of C. elegans was on board the space shuttle Columbia when it exploded upon re-entry into the earth’s atmosphere on February 1, 2003. A week later, their containers were found amidst the vast amounts of debris left over from the explosion. Three months later, the containers were opened. And to everyone’s amazement, the worms were still alive.

The Columbia performed approximately 60 different experiments while it was in space. Many of those experiments involved various animals – including worms, insects, spiders, fish, bees and silk worms. Worms had been sent into space several times before this, to study the effects of space radiation and microgravity. This time, the experiment was very simple – would the worms survive well in space if fed a synthetic diet instead of its usual bacteria? Had the Columbia survived its re-entry, it’s doubtful whether the results of the experiment would have even made the mainstream media. However, as we know, the Columbia did not survive. And everything of board died – except for the worms.

The worms were growing on Petri dishes, which were enclosed within aluminum containers, which were themselves enclosed in a locker around the mid-deck of the shuttle. The locker itself was discovered, and still contained some moss used in another experiment onboard the space shuttle. (However, the moss had been killed with a preservative before re-entry.) The 5 canisters each contained 6 to 8 petri dishes. Only 1 of the dishes had melted, and those worms died. But the others were still alive. Some of them had gone into a super-stress resistant hibernation mode, which has long been known to allow them to live under conditions of high heat, low food, and extreme stress. But others hadn’t even gone into the hibernation mode – they were still crawling and active.

Even in the midst of the Columbia disaster, many scientists greeted the news of the worm’s survival as groundbreaking. It has been used as an argument for the notion that life on earth may have come here on a meteor from elsewhere in the galaxy. After all, if a worm could survive a gigantic explosion upon coming into the atmosphere, why couldn’t sturdy bacteria do it if it was embedded within a meteor? Now, I don’t want to weigh in on that particular topic. But I do think it incredible that something – anything – could have survived a disastrous re-entry and explosion the way that these worms did.

Of course, it would have been great if we had never had to learn this lesson – because then we wouldn’t have lost the Columbia.

That’s some powerful blood!

2008-03-07T11:26:00.000-08:00

Today, I’m going to write about something that I’m certain has directly impacted every single person who reads this entry – and yet I’d bet that no one has ever heard about it. This is a story about how a simple, uninspiring-looking animal with prehistoric roots has become essential to the world’s modern medical field. This ungainly creature is directly involved in proving the safety of injectable medicines; in fact, no medicine can be injected into a single patient in the US without first being tested against the blood of this animal. And it might surprise you to learn exactly what animal I’m talking about. It’s not the rabbit. It’s not the rat. It’s not even the mouse.

It’s the North American horseshoe crab.

I’ve never seen a horseshoe crab in person. In fact, I learned about this topic myself recently from a Nova special on PBS, and what first got me watching the show was the sight of these really odd, lumpy-looking critters on a beach on Delaware. My first thought was – “what on earth is that thing on the beach? It looks like an old army helmet.” The show was fascinating, however, and I learned how amazing – and important – these creatures really are.

So what is a horseshoe crab?

Horseshoe crabs are arthropods, more closely related to spiders, ticks and scorpions than to other crabs. They are aquatic, and the North American species is mostly found in the Gulf of Mexico and along the eastern shore of the North America. (There are other related species off the coasts of Japan and India.) Their bodies are shaped like teardrops, with a long tail coming off the tapered end. They have a large intestinal system, a nervous system with a bulbous brain, and a long heart that extends almost the entire length of its body. They have numerous appendages, including legs for walking, pincers (or chelicerae) for putting food in its mouth, and book gills, which are used both for breathing and for propulsion under water. Their bodies are covered with a hard, curved shell (or carapace). This shell protects the crab from predators, who have a hard time turning them over to get at their soft, edible underbellies. (It’s also this shell that makes them look like army helmets when they’re on the beach.) Their tails serve several purposes, including working as a rudder to help steer the crab when swimming and to help flip the crab over if it gets turned upside-down while out of the water.

Horseshoe crabs have an amazing optical system. They have 2 compound lateral eyes, which are mostly used to find mates. They have 5 additional eyes on the top of their shells, some sensitive to visible light and other sensitive to UV. They have 2 more eyes on their undersides, located near the mouth, which may help keep the animals oriented while swimming. And if that weren’t enough, they also have photoreceptors along their tails to help coordinate their circadian rhythms. Phew! That’s a lot of eyes for one animal.

Where this critter really gets interesting is when you start talking about its blood. Back in the 1960s, Dr. Frederik Bang of Johns Hopkins University was studying horseshoe crabs in Massachusetts. He found that when common marine bacteria were injected into the bloodstream of the horseshoe crab, their blood immediately began to massively clot. While horseshoe crabs lack a sophisticated immune system, they do have a simple way of preventing infections from bacteria, fungus and viruses. Their blood contains numerous compounds that bind to and inactivate the toxic components of such invaders. In the case of bacteria, that toxic component is called endotoxin; the amebocytes bind to any endotoxin and coagulate around it, forming a thick, dense clot. This serves 2 purposes – first, the endotoxin can no longer harm the crab, and second, the entry point by which the bacteria got into the crab is sealed. It’s a simple, but extremely effective, mechanism of preventing bacterial infection.

And this is where the horseshoe crab and modern medicine meet. It turns out that you can purify the compounds in the crab’s blood that cause it to clot in the presence of endotoxin. So let’s say you have an injectable medicine, and you need to test whether or not it is pure – free from bacterial contamination. You mix the medicine with some horseshoe crab blood and watch to see whether a clot forms. If nothing happens, the medicine is clean. However, if a clot does form, that means there is endotoxin – and thus bacteria – in the medicine. And that means it cannot be injected into human patients. All injectable medicines in the US – including vaccines – must be tested against horseshoe crab blood before they are used. This makes horseshoe crab blood extremely valuable. It’s estimated that a quart of the stuff is worth $15,000!

The good news is that we don’t have to kill the crabs to get their blood. They are collected from the water and taken to a designated facility, where some of their blood is removed. In fact, up to 30% of the blood volume from a crab can be removed at any one time without injuring it. Once the collection is done, the crabs are returned to the ocean. Once home, they recover their lost blood volume within a week. Crabs are only bled once a year, and studies have shown that crabs can be harvested year after year without any ill effect to their lifespan or breeding habits.

I think it’s amazing that I’ve never even heard of this before I saw this Nova special. Horseshoe crabs are really important animals! And now that I know a little more about them, I guess they don’t look that strange. In fact, I’ll consider myself lucky if I ever see one in person.

The image of the horseshoe crab was taken from:
http://scienceblogs.com/grrlscientist/2007/06/delaware_horseshoe_crab_harves.php

“Smells like science!”

2008-03-04T09:40:00.000-08:00

Today’s blog is a little different. I’m not going to talk about some new discovery, or a cool animal, or something from NASA, or even a scientific question I’ve always wondered about. Instead, I’m going to talk about my favorite TV show. Bear with me, this actually does have something to do with science!

The one TV show that we always watch regularly is called “Mythbusters,” and it’s been on the Discovery channel for 5 or 6 years. The premise of the show is that there are innumerable urban myths floating around our culture that people assume to be true. But are they really true? The cast of Mythbusters takes these myths and scientifically tests them to find out whether they are impossible, possible or true. (Actually, what they say on the show is whether the myth is busted, plausible or confirmed.) They test chemicals, explosives, cars, bridges, elevators, food, toys, sporting equipment, historical stories, things from the movies, boats, animal legends, famous criminal escapes… and on and on. The list of myths they have to test is seemingly endless.

There are 5 mythbusters on the show. While none of them have formal scientific training, most of them are engineers by trade, specializing in building robots, electronic gadgets and other high-tech toys. And though none of them are scientists, I am usually impressed by their ability to design and execute their experiments to test the myth of the day. Their experimental designs are highly scientific – hypothesis-driven, well controlled, and with a limited number of variables. They do their best to eliminate alternate hypotheses that could explain their results, and they seldom over-interpret what they see. All in all, I think they are actually very good scientists. (Actually, the title of this entry – “Smells like science!” – is one of the lines from my favorite cast member, Adam.)

There are many things I love about this show. First, it’s really fun. The cast works very well together, and they obviously have a lot of fun with what they do. Second, they demonstrate some really neat technology and concepts, both in science and engineering, with the robots and gadgets they make. Third, it’s fun to see the different ways that a scientific question can be tested. And finally, it’s really fun to guess whether you think a myth will be busted or confirmed – and even more fun when something that sounds completely impossible turns out to be true!

Here are some examples of the myths that have been tested on the show over the years (as well as their results):

1. If you drop a piece of toast, it will preferentially land butter-side down. (Busted – unless you drop the toast from a 5-story building.)

2. You can survive in a falling elevator if you jump right before the elevator hits the ground. (Busted – you can’t jump fast enough to counteract the speed of the falling elevator.)

3. You can carry on a conversation with someone while you are in free-fall (during parachuting). (Busted – there is too much noise from the wind.)

4. Sharks are afraid of dolphins. (Plausible – a shark is less likely to attack someone if they are swimming with a dolphin. They don’t know for sure whether this is because the shark is afraid of the dolphin, but the result was pretty clear, and supports multiple stories of shark attack victims being saved by a dolphin pod.)

5. You can stop a car from running if you jam a banana or a potato in its tailpipe. (Busted – the pressure of the exhaust pushes the banana or potato out.)

6. You can safely float to the ground from the top of a tall building if you use an umbrella as a parachute. (Busted – a huge golf umbrella will slow you down some, but it’s still a rough landing. A regular umbrella is too small to do anything.)

7. A needle in a haystack is really hard to find. (Confirmed – though that’s not surprising.)

8. In the old west, someone could be sprung from jail if you blew the bars of their cell out with a stick of dynamite. (Busted – the amount of dynamite you’d need to break the bars open would kill anyone inside the cell.)

9. You can raise a sunken boat from the bottom of the sea using ping-pong balls as ballast. (Confirmed – the only trick is getting enough ping-pong balls down there!)

As I said, this show has been on for several years now, so they have tested hundreds of myths. So if you haven’t ever watched the show, but would like to see some really fun and cool scientific principles in action, I would highly recommend that you check this show out. It’s funny, it’s goofy – but hey, it’s science!

Lasers and… modern alchemy?

2008-02-29T11:18:00.001-08:00

Now this is a cool discovery. Turns out the old idea of making gold from other metals is not as far fetched as you might think! Well, okay, so we can’t really turn metal into gold – but we can make it look like gold! At least, one scientist at the University of Rochester has figured out a way to do just that with lasers.

Dr. Chunlei Guo, professor of optics, published the paper in the journal Applied Physics Letters in January entitled “Colorizing metals with femtosecond laser pulses.” In it, the authors describe their technique of using extremely short laser burst to alter the surface of a metal. These bursts – lasting only quadrillionths of a second - melt and vaporize the atoms on the surface, which subsequently rearrange themselves in nanostructures. These nanostructures include holes, globes and rods. These structures respond to incoming light in new ways from the original atomic structure; their reflection of light is highly dependent on their size and shape. So simply by changing the laser, Dr. Guo can change the resulting nanostructures, and thus change the reflected light to be a different color. This process is different from a coating or a finish, since it actually physically changes the properties of the metal. So it won’t wear away, peel or fade. And it cannot be felt by your finger. The altered structures are simply too small for our nerves to detect, so the metal still feels like normal. As far as we are able to detect, a golden aluminum that results from this method is indistinguishable from real gold.

So far, Dr. Guo has been able to make aluminum, platinum, titanium and silver look like pure gold. For that matter, he’s also made them look black, blue and gray. And he believes he can create any color he wishes, including multi-colored iridescence like the wings of a butterfly. It’s only a matter or trial and error to find the right setting for the lasers and the metal.

So what’s the practical use of this technique? Dr. Guo has suggested uses from the fanciful – etching a family photo on the metal door of a refrigerator – to the practical – producing cars and bicycles of different colors without having to use paint. Or, perhaps, custom-designing jewelry to match the eyes of your beloved? Apparently he’s already been contacted by jewelers about that possibility.

The Devil Frog

2008-02-26T11:17:00.000-08:00

Fossils are such interesting things. They allow us to see glimpses of a world gone by, of creatures we could have only imagined. Remember the giant sea scorpion? (November 29th, 2007 – “A super sized insect.”) Or perhaps you recall the reptilian mammals of the Permian extinction. (January 4th, 2008 – “The Permian Extinction.”) There have been some really unusual creatures on our planet over the years! Well, scientists are at it again. This is another example of a fossil of something that’s still around today – it just used to be a lot bigger!

Paleontologist David Krause of Stony Brook University in New York and Susan Evans of the University College London have recently announced the discovery of the largest frog to have ever lived. Published just a few weeks ago in the Proceedings of the National Academy of Sciences, it is called Beelzebufo – meaning Devil Frog. This thing was approximately the size of a bowling ball – 16 inches tall and weighing in at 10 pounds. The largest frog currently in existence is the Goliath frog of West Africa, which can reach up to 7 pounds. However, Beelzebufo – which was found in Madagascar - does not seem to be related to African frogs at all. Instead, it is related to a group of big-mouthed horned frogs in South America called ceratophyrines – also known as Pacman frogs for the size of their mouths.

Apparently, ceratophyrines are quite aggressive, especially for frogs. They are ambush predators, and with their large mouths, will try to eat just about anything that walks by. Dr. Krause thinks that the Beelzebufo was probably much the same way. It also sported some heavy armor and teeth, prompting the speculation that this guy could have been strong enough to take down hatchling dinosaurs. This guy was not an aquatic frog hopping among lily pads. He likely lived in a semi-arid environment, and hunted by camouflaging himself and jumping out at his prey.

The fact that the devil frog seems to closely related to frogs in current-day South America has given new life to the long-lived speculation as to where Madagascar actually came from. Traditionally, scientists have believed that Madagascar broke free from Africa approximately 160 million years ago, and then India almost 90 million years ago, to its current isolated position. However, some scientists have recently suggested the presence of a land bridge connecting Madagascar, Antarctica, and South America. This theory is supported by recent discoveries showing close relations between dinosaurs found on Madagascar and South America. While it would be possible for animals to migrate over the ocean, either by swimming or by being carried on some sort of float, Dr. Krause believes it unlikely that the devil frog could have done either. Frogs are not adept at dispersal across marine barriers – they cannot live in saltwater, so would not have survived a swim of that nature. And the distance between South America and Madagascar makes the float idea “sort of impossible to believe,” he says.

While this is definitely in the lead for the largest frog to have ever lived, it is certainly not the largest amphibian ever. For example, the crocodile-like Prionosuchus reached an estimated 30 feet long when it was around during the Permian period. Once again, I am glad I live in an age where the frogs, crocodiles, and bugs are all a much more reasonable size!

I wonder if they were snoring?

2008-02-22T10:09:00.000-08:00

I came across a funny – and intriguing – article in the journal Nature yesterday - “Sperm whales found fast asleep at sea.” A team of researchers off the coast of Chile was studying calls and behaviors in sperm whales when they came across an unusual sight. A pod of whales was hanging completely motionless at the surface of the water. Their noses were poking out, but the rest of their bodies were hanging vertically. And they were completely unresponsive. From all indications, they were fully asleep. They didn’t stay that way for very long – only 10 to 15 minutes. But it was enough to make Dr. Luke Rendell and his colleagues believe that they had actually observed the first example of a whale in full sleep mode.

Scientists have previously believed that whales, like dolphins and other air-breathing ocean mammals, only slept with half of their brains at a time. This would leave the other half awake to carry out essential functions like breathing and watching for predators. (You can refresh your memory on this in my entry entitled “Zzzz…” from September 20, 2007.) However, using remote monitors, scientists had also observed that sperm whales tend to spend approximately 7% of their time drifting inactive in shallow water. Before now, no one knew what they were doing. Now scientists think they do – the whales were grabbing power naps.

No one knows whether this is the only sleep that the sperm whales engage in. They may be capable of sleeping both in this full mode as well as in the half-sleep mode previously know about. Their circumstances would dictate whether they would be able to engage in full sleep or half sleep. However, it is also possible that this is the only kind of sleep a sperm whale needs. If that were the case, then that would make the sperm whale one of the least sleep-dependent mammals known.

The current record-holder on that, by the way, is the giraffe. Giraffes only sleep about half an hour a day, which is usually broken up into about six 5-minute naps. Wow! That makes me tired just thinking about it.

You can see the video of the sleeping whales at:
http://blogs.discovery.com/news_animal/2008/01/view-harrowing.html

A shark and a discovery

2008-02-20T16:18:00.000-08:00

I recently learned something new about a shark - the hammerhead shark, to be specific. Now, I’m not the world’s biggest shark fan. I appreciate how they are incredibly adept hunters, how they are perfectly adapted for their environments, and how they are in essential part of the balance of the earth’s oceans. But there is something a little creepy about them – their big bulging eyes, their row after row of jagged teeth, and the way they can be whipped up into a feeding frenzy with the right conditions. But of all the sharks that I know of, one of my hands-down favorites is the hammerhead. Quite frankly, I think hammerhead sharks are some of the coolest looking sharks around!

There are 9 different kinds of hammerhead sharks currently known – scalloped, great, smooth, whitefin, scalloped bonnethead, squarehead, scoophead, shovelhead and smalleye. The great hammerhead is the biggest, capable of reaching up to 20 feet long. Most of them are much smaller than this giant, though, around 10 to 11 feet long. By far their most noticeable characteristic is their heads – they all have a wide, flat head that extends out past their body to look somewhat like a flattened hammer. Their eyes and nostrils are at the tips of the extensions, allowing them to thoroughly scan the oceans for food. The different kinds of hammerheads vary in several ways, including size, distribution, and the shape of their hammers. The scalloped hammerhead has a wavy edge along the front of its head, while the smooth hammerhead has – you guessed it – a smooth edge. The great hammerhead is the largest, but has only 2 distinct bumps along the edge of its hammer. The bonnethead shark is relatively small, around 3 feet long, with a very smooth and rounded head. The smalleye hammerhead is very poorly understood. It has very small eyes relative to other hammerheads, hence the name. However, it also goes by the name golden hammerhead, because it is a really unusual golden color.

Whatever their differences, though, hammerheads all have one thing in common – their big, flat heads. It's very strange, don’t you think? What possible advantage could having a ridiculous looking head afford the shark? Well, actually, there are several advantages to it. One advantage is that it allows a very large area for the sensory organs that help it detect its prey. Called ampullae of Lorenzini, these are electrolocation sensory pores that help detect the electromagnetic fields put out by living organisms that the shark might eat. Popular prey for the hammerhead includes fish, crustaceans, and stingrays (apparently a favorite of the great hammerhead). Not only does the increased surface area for their electrolocation sensory pores help them hunt better, their nasal passages are much larger, too, giving them better smelling ability. So I already knew that. But here’s what I recently learned that I think is really neat. The hammerhead also helps the shark maneuver. The wide, flat surface of the head allows them to turn very tightly without losing stability. In addition, the head provides the shark with a lot of lift as it swims, much as a wing provides lift for a plane.

So, a wide head gives better hunting and better swimming. All in all, I'd say that's pretty smart.

Now, this may not be the most groundbreaking discovery ever – that the hammers of hammerhead sharks help them swim more efficiently. But I think there is a very important principle at work in my discovery that there was more to the hammerhead that I had previously known. There are so many things in the world that I think I know the answer to. But when I dig a little deeper, I find that there is always something new that I can learn. And that is the greatest thing about science!

The hammerhead shark picture was taken from:
http://www.sharkdiving.us/images/hammerhead/01.jpg

Go dog, go!

2008-02-15T09:46:00.000-08:00

I’ll freely admit – I love pets. I’ve written about our cats before several times, and though we don’t have a dog right now, we’d love to get one in the future. In fact, one of my and my husband’s favorite activities every February is to follow the goings-on at the Westminster Kennel Club dog show. For those of you who don’t know, the Westminster Kennel Club dog show is the second longest continuously held sporting event in America (just one year behind the Kentucky derby). It is organized by the Westminster Kennel Club, America’s oldest organization dedicated to the sport of purebred dogs. Every February, dogs from over 150 breeds from around the world descend on New York to compete against each other, trying to be the dog that best matches the ideal standards of their particular breed. And we love to learn about all the different breeds of dogs! From giant St. Bernards to tiny Chihuahuas, from skinny Whippets to stocky English Bulldogs, from active Border Collies to pampered Pomeranians, domesticated dogs are a highly variable group, coming in all shapes, sizes, colors, features and temperments. In fact, domesticated dogs are the most highly variable mammal on the planet!

The domesticated dog, also known as Canis lupus familiaris, is a domesticated subspecies of the wolf. According the DNA evidence, the wolves that gave way to modern domesticated dogs began diverging from other wolves over 100,000 years ago; these wolves gave way to dogs some time later. (The exact time is disputed, and ranges anywhere from 15,000 to 100,000 years ago). Over time, dogs have diverged from each other in appearance because humans have selectively bred them to enhance for the traits they want. Let me give you a few examples of features that you might think are totally useless, but are actually integral to the dog’s purpose:

Corgis have extremely short legs relative to their body size. These dogs are particularly well-designed for herding cattle. Their short legs mean that when the cows kick, the dogs don’t get hit – they duck right under.

Daschunds also have short legs, but unlike corgis, their bodies are small and wiry. This is so they can crawl into dens and hunt out badgers, foxes and rabbits. This goes hand in hand with their tenacious and persistent (aka prone to barking) personalities.

Bloodhounds are extremely wrinkly dogs. Their faces seem to have about twice as much skin as they actually need! The reason for this is simple – the extra folds help funnel scents in from the air to the nasal passages of the hound. This allows them to be among the most sensitive scent hounds around – under optimal conditions, they can smell as few as 1 or 2 human skin cells.

Chesapeake Bay Retrievers are uniquely adapted to a watery life. Their coats are in 2 layers – a harsh outer coat and a dense woolly undercoat, both of which are oily and water-repellant. In addition, their hindquarters are especially strong and their back toes webbed, to allow for better paddling ability. All of this is very useful to the Chesapeake Bay Retriever, who was bred to retrieve fallen ducks from the frigid waters around the Chesapeake Bay when their masters were hunting. These dogs have been known to retrieve up to 200 ducks a day for their owners!

Bullmastiffs are big, broad, stocky dogs. They have barrel-like chests and very thick skulls. This makes them well-suited for their original purpose – finding and immobilizing poachers by knocking them over and pinning them to the ground.

But here’s something interesting - despite the many unusual traits that these and all dogs have, dogs are not particularly genetically diverse. They retain the same basic characteristics of their ancestors – sharp teeth, strong jaws, powerful muscles, fused wristbones, and a cardiovascular system that supports both sprinting and endurance running. There are a few genetic distinctions that we know about among dogs breeds. For example, scientists have discovered that large dogs and small dogs have differences in a gene called insulin growth factor 1 (IGF-1). The IGF-1 gene of small dogs (like Chihuahuas and Pomeranians) tends to be of one variety, which is different from the IGF-1 gene of large dogs (like St. Bernards and Irish Wolfhounds). And while there are other genetic differences known to exist between breeds, scientists do not really know how those differences correlate with the different appearances of the dogs. So most of the differences may be primarily superficial – skin-deep, as opposed to DNA-deep.

And on a final note, this year’s Westminster Kennel Club dog show was particularly enjoyable. The winner of best in show was a 15-inch beagle named Uno. The beagle just happens to be one of my favorite breeds of all time, so I was really happy. How could you not love a face like this?

The following images were used in this entry:
Pembroke Welsh Corgi: http://www.dogbreedinfo.com/images10/PembrokeLucy2.jpg
Daschund: http://www.justusdogs.com.au/images/daschund.jpg
Bloodhound: http://www.greatdogsite.com/admin/uploaded_files/thumbnails/
bloodhound333x_1190777749500.jpg
Chesapeake Bay Retriever: http://www.dkimages.com/discover/previews/793/
75023959.JPG
Bullmastiff: http://www.dogbreedinfo.com/images16/BullmastiffShirley1
halfStand.JPG
Beagle: http://blog.mlive.com/kzgazette/2008/02/large_Uno.jpg

More cool images from outer space

2008-02-07T13:30:00.000-08:00

I recently wrote about how 2 of Saturn’s lesser-known moons were recently shown to look astonishingly like flying saucers. (“Saturn’s flying saucers” from January 11, 2008.) Well, it looks like NASA is at it again. They’ve just released pictures of the planet Mercury, showing scientists a side of the planet never before seen by human eye.

Mercury is the smallest planet in our solar system (now that Pluto is no longer considered a planet, of course). It’s about one-third the size of Earth, with a diameter of around 3000 miles. (That’s roughly the distance from Los Angeles to Maine.) Being closest to the sun, Mercury has a very rapid orbit – it circles the sun once every 88 earth days. It doesn’t have a normal orbit, though, it has an elliptical one. The distance from the sun to the surface of Mercury varies from 28 million to 43 million miles. While there was much speculation some years ago as to why Mercury has such an eccentric orbit (including the theory that there was another planet even closer to the sun that was tugging on it), it now appears that this elliptical orbit is explained in Einstein’s General Theory of Relativity. Despite the fact that it orbits the sun very rapidly, it rotates on its axis relatively slowly. Mercury only rotates 3 times for every 2 orbits that it makes. (This would make for some very odd sunrises and sunsets on the surface!)

A lot of interesting comparisons can be made between Mercury and Earth. Both planets have similar densities. Also, both planets have similar cores made of iron. However, Mercury’s iron core is much larger than ours - it seems to make up around 42% of the volume of the planet, and is at least partly liquid. Like Earth, the core of Mercury is surrounded by a rocky mantle and crust; however, Mercury’s mantle and crust is much smaller than our own, coming in at approximately 370 miles thick. This crust is highly cratered, and actually looks a lot like the surface of our moon. Both Mercury and Earth also have magnetic fields (of the 4 rocky planets, they are the only 2 to have one.) Mercury might have even had an atmosphere, except for the fact that it is so close to the sun - its atmosphere is constantly getting blasted away by solar wind. Being so close to the sun has other consequences, too. Temperatures at the equator have an 1100 degree Fahrenheit difference between day and night – and despite the possibility of extreme heat, there is evidence of the existence of ice at the poles.

Mercury is visible from the surface of Earth, but just barely. It’s hard to see because it stays so close to the sun; this makes it hard to see except at twilight and dawn. In fact, about the only information we had until this year about the surface of Mercury came from NASA’s Mariner 10 spacecraft, which mapped about 40% of the planet’s surface in 3 fly-bys in the 1970s. But here’s the odd thing about the Mariner 10 mission. The combination of Mercury’s elliptical orbit and its slow rotation means that the same side of Mercury is always illuminated by sunlight when it is closest to the sun. So that’s the only side that the Mariner 10 was able to see in its pictures! That means that there was an entire half of the planet we’d never seen.

So, on August 3, 2004, NASA launched the MESSENGER spacecraft to do a detailed mapping of Mercury’s surface. (MESSENGER stands for Mercury Surface, Space Environment, Geochemistry and Ranging.) MESSENGER will make 3 flybys of the planet over the next 3 years before it settles in to a stable orbit around it. During those passes, the spacecraft will pass within 124 miles of the surface, allowing for some highly detailed images. And the first set of pictures, released in January, did not disappoint.

I think my favorite image is the giant spider crater. It’s a massive crater with faint lines radiating out from the center of it, kind of like a squished spider. Scientists think that this may be the remnants of a volcano. There are also other neat images, though. For example, there is one taken near Mercury’s terminator – the line between the side of the planet lit by sunlight and the side in darkness. This image shows a vast plain of craters, which are enhanced because of the long shadows that exist at the terminator. And another shows a double ringed crater – it actually looks kind of like a doughnut on the surface. Scientists hope that these images will allow them to better understand the physical properties of Mercury, as well as its geological history. (For example, whether there has been volcanic activity on the planet.)

I highly encourage everyone to check out the website of the MESSENGER mission. You can see all of the images I’ve described (this is where I got the spider crater picture), as well as others that will be released as the spacecraft does more flybys. (The next one is scheduled for October of this year.)
http://messenger.jhuapl.edu/index.php

Mmmm…. Tastes good!

2008-02-05T11:57:00.000-08:00

When you put something in your mouth tonight for dinner, a complex array of flavors may await you. You might not like all of the flavors, of course! But you can taste them, nonetheless. Have you ever wondered how?

Taste is a chemical sense. In that regard, it is similar to the sense of smell. Both taste and smell give us information about the chemical nature of our surroundings – taste giving us information about the chemical nature of what we’re about to eat, and smell giving us information about the chemical composition of the air we’re breathing. The senses of taste and smell are, in fact, closely related. Actually, the concept of flavor is really a combination of the taste, smell and texture of a substance. You’ve probably experienced how food tastes much more bland when you have a cold and can’t smell it. That’s because half of your ability to sense the flavor is lost when your nose is stuffy.

You might know that we have long believed to have only 4 basic taste sensations in our mouths -bitter, sweet, salty and sour. However, recent evidence seems to indicate that there may be 1 more thing we can taste – it’s called umami, or savoriness. Umami is the taste of non-salty flavorings like MSG. The combination of all 5 taste sensations provides the taste of any given substance. And these taste sensations are controlled by your tongue.

The tongue is a very rough, ridged surface, containing ridges and valleys called papillae. There are 4 types of papillae, 3 of which contain taste buds. Taste buds are onion-shaped groupings of 50 to 100 taste cells that protrude up into the surface of the papillae. When food is dissolved by the saliva in your mouth, it breaks up into different chemicals, which interact with different proteins on the surface of the taste cells. These proteins are called taste receptors.

The bitter taste receptors are a family of 30 or so related proteins called T2Rs (identified in 2000). Sweet taste receptors are combinations of T1R2 and T1R3 proteins, while umami is tasted by combinations of T1R1 and T1R3 proteins (all found in 2003). All of these proteins function in a similar manner. When triggered by their chemical, they change other proteins inside the cell, ultimately resulting in the transmission of a message of bitterness, sweetness or savoriness to the brain. Nothing passes in or out of the taste cells with these taste proteins.

There is currently only 1 candidate sour receptor protein, called PKD2L1 (discovered in 2006). This protein acts in a different way. Sour tastes are usually acidic, thus they contain hydrogen ions. These hydrogen ions block the channels for other ions (such as potassium). As a result, the ion concentrations in the taste cells change, which results in a sour signal being sent to the brain. While the salty receptor protein is currently unknown, it is believed that it probably allows sodium ions into the cell. This increase in sodium ions would result in the transmission of a salty signal to the brain. For all of these taste receptors, their underlying mechanism is the same – changing ion concentrations results in different taste signals being sent from the taste cells to the brain.

So now that these signals have been sent to the brain, the next challenge is for the brain to decode them. And here’s where we get to the real mystery of it. We don’t really understand how our brain interprets the signals that we get from our taste buds. In fact, the sensations of taste and smell are both really poorly understood at the levels of our brain. So unfortunately, I can’t tell you how that part works. Maybe someday we’ll have a better understanding of it!

Until then, all I can do is wish that you get to taste something you really enjoy today. (For me, that would definitely be chocolate…)

Flaming gummy bears!

2008-01-31T09:30:00.000-08:00

I just stumbled across an amazing – albeit a little obscure – fact: if you ever drop a gummy bear into potassium chlorate, be prepared for a big bang!

The experiment is simple. Put a small amount of potassium chlorate into a glass test tube, and gently heat it. Now drop in a single gummy bear – and stand behind a protective shield. The gummy bear will burst into a flame-shooting reaction for about a minute.

Don’t believe me? You can see an example of this at:
http://blog.wired.com/wiredscience/2008/01/video-gummy-bea.html
(I really recommend watching this video. It’s amazing how many flames a single gummy bear will produce!)

So I have 2 questions about this flaming gummy phenomenon. (1) Why does it happen? And (2) Why should I care?

First, why does it happen? Potassium chlorate is a powerful oxidizer – a substance that burns when you give it a combustible fuel, since it easily gives up oxygen to fuel the reaction. In this case, the combustible fuel is the sugar in the gummy bear. Sugar is a molecule that stores a lot of energy. When that molecule is oxidized rapidly, all of the energy gets released in one quick step. So the amount of energy released by the potassium chlorate is the same as what you would get by metabolizing the gummy bear in your body – the energy is just released more quickly.

So mix the 2 together, and the potassium chlorate releases oxygen molecules, which oxidize the sugar, producing energy in the form of lots of big flames. It’s that simple!

So why should I care? I think it’s a great example of how to illustrate simple chemical concepts in a really fun manner. The concepts here – the amount of energy stored in sugar, and the process of oxidation. If you were to just describe how sugar is a great holder of energy, and oxidizing agents can burn spontaneously, it sounds kind of boring. But show someone a picture of a gummy bear bursting into flames, and all of a sudden science becomes much more fun!

Serious – and not so serious – research

2008-01-24T14:14:00.000-08:00

The Nobel Prize in Medicine. A serious award about serious science. Nobel laureates have made a significant, lasting, and important contribution to our understanding of the scientific world, work that has dramatically changed what we know about how our world works and how we conduct research. For example:

In 2006, Andrew Fire and Craig Mello were awarded the Nobel for the discovery of RNA interference - gene silencing by double-stranded RNA. This is an experimental technique used by thousands of scientists today.

In 2002, Sydney Brenner, H. Robert Horvitz and John E. Sulston won the prize for the genetic regulation of organ development and programmed cell death. We now understand that cells have dedicated mechanisms not only to keep themselves alive, but also to kill themselves when necessary.

In 1999, Gunter Blobel received his Nobel prize for learning that proteins have intrinsic properties that dictate their movement and final place within a cell. This property forms the basis of a huge field of current biological research – protein trafficking.

And in 1993, Richard Roberts and Phillip Sharp were given the Nobel for discovering split genes. It had previously been thought that genes were always one long, continuous unit. Drs. Roberts and Sharp clarified that genes are often broken into multiple sections, which get cut and pasted back together in a process called splicing. This presented a dramatic shift in the understanding of how genes are regulated.

Yes, the Nobel prizes are inspiring and dramatic. They are the serious side of research. But there is also a less-than-serious award about less-than-serious science, which I personally find highly entertaining. An award ceremony held every year celebrates the not-so-inspiring research, the research that doesn’t really change our world, but (quite often) the research that makes us laugh – and hopefully remember why we love science. They’re called the Ig Nobels.

The Ig Nobels are awarded by an organization called Improbable Research. Their stated goal: “The Ig Nobel Prizes honor achievements that first make people laugh, and then make them think. The prizes are intended to celebrate the unusual, honor the imaginative -- and spur people's interest in science, medicine, and technology.” To give you an idea of the kinds of research that are awarded Ig Nobels, here are a few examples of the winners for 2007. (Remember, this research is all actual research, published in real, peer-reviewed scientific journals.)

In Medicine: Brian Witcombe and Dan Meyer – Sword swallowing and its side effects. Based on: “Sword Swallowing and its Side Effects” published in the British Medical Journal

In Physics: L. Mahadevan and Enrique Cerda Villablanca - How sheets become wrinkled. Based on: “Wrinkling of an Elastic Sheet Under Tension” published in Nature

In Chemistry: Mayu Yamamoto – Extracting vanilla from cow dung. Based on: “Novel Production Method for Plant Polyphenol from Livestock Excrement Using Subcritical Water Reaction”, internally published in the International Medical Center of Japan

In Linguistics: Juan Manuel Toro and Nuria Sebastian-Galles – Rats sometimes cannot tell the difference between a person speaking Japanese backwards and a person speaking Dutch backwards. Based on: "Effects of Backward Speech and Speaker Variability in Language Discrimination by Rats," published in the Journal of Experimental Psychology

In fact, if you look back at all the Ig Nobels awarded over the last 10 years, you’ll find a variety of topics that will probably make you sit up and say – “someone studied that?!?” This includes the attraction of mosquitoes to limburger cheese, how herrings communicate with flatulence, calculating the surface area of an elephant, the levitation of frogs with magnets, helping make clams happier by giving them Prozac, and whether humans can swim faster in water or syrup. Wow. Now that’s some funny science!

My personal favorite, though, has to be the 2004 award for psychology. It was awarded to Daniel Simons and Christopher Chabris for demonstrating that when people pay close attention to something, it's all too easy to overlook anything else.

Dr. Simons and Dr. Chabris made a video of a group of 6 people tossing a basketball amongst themselves. In the middle of the video, a person in a gorilla suit walks into the middle of the circle of people. The video was shown to test subjects, who were told to count the number of times the basketball changed hands. After they watched the video, they were asked about what else they saw besides the basketball. And here’s what’s really funny. An astonishingly large percent of the test subjects did not notice the person in the gorilla suit. They were so focused on the task at hand – counting the passes of the ball – that they completely failed to see a six-foot tall person walking around in a gorilla suit. Now that’s what I call focus!

Now, the Ig Nobels may seem silly and inane. But I think that they serve a very important function. Science is serious. It’s significant. It can be intense. But science is also supposed to be fun. It’s supposed to intrigue and excite people. It’s supposed to make you think about things you never knew before. It’s supposed to stimulate your imagination. And what better way to make science fun than to show people a video with someone walking around in a gorilla suit!

By the way, if you want to watch the basketball and gorilla video yourself, go to: http://viscog.beckman.uiuc.edu/media/ig.html
Click on the link “View the “basketball” video." I hope it makes you laugh!

Laundry science

2008-01-22T10:13:00.000-08:00

Have you ever wondered how dryer sheets work?

I have. I tend to collect static electricity - my hair, my clothes, even my cats. So I absolutely have to have a dryer sheet in the dryer whenever I’m doing a load of laundry. If I don’t, I’m doomed to be a crackling, zapping, static-y mess. So in goes a dryer sheet, and out comes nice, static-free laundry. It’s like magic!

Well, actually, it isn't magic, it's science. Here’s how they work.

First, let’s talk about static electricity. Static electricity occurs when an electrical charge builds up on a surface. Electrical charge is made of electrons. (“Electrons” and “electricity” sound so similar because they are from the same root.) What are electrons? They are one of three major particles that make up atoms, along with protons and neutrons. The names of these things refer to the electrical charge that they carry: neutrons are neutral – not charged; protons have a positive charge; electrons have a negative charge. So when the negatively charged electrons flow in a stream – that’s considered an electric current. Or when electrons build up on an unmoving surface – that’s considered static electricity. (It’s called “static” because it doesn’t move.)

One other important thing to know about protons and electrons is that they are attracted to each other. When an atom has equal numbers of electrons and protons, all of the positive charges and negative charges cancel each other out, leaving the overall charge neutral. If an atom has more electrons than protons, it is negatively charged, and, of course, if there are more protons than electrons, it is positively charged. Neither of those situations is very stable – atoms like to be neutral. So a negatively charged atom will try to find a positively charged atom and stick to it.

So if atoms like to have their protons and electrons balanced out, how do you get a buildup of electrons on a surface to make static electricity? When clothes are tumbling in a dryer, they are rubbing together like crazy in a warm, dry environment. This heat and friction makes the charges on the surface of the clothes separate. Take a look at this diagram, which shows the separation of charge on a sock. Some socks will get extra electrons, and other socks will lose their electrons. This is an unstable situation for the socks. The atoms want to regain their neutral charge. So as the socks are tumbling in the dryer, a sock with a negative charge will find another sock with a positive charge and stick to it. Now when you pull the socks out of the dryer, they will remain stuck. It doesn’t have to be socks, of course. It could be sleeves of the same shirt, folds of a skirt, shirts to each other, underwear to pants. They will stick together. Voila. Static Cling.So let’s go back to dryer sheets. Dryer sheets reduce this buildup of static electricity by releasing extra protons into the dryer during the dry cycle. These extra protons stick to the negatively charged clothes that are building up. And because these negatively charged clothes are now balanced with extra protons, they no longer stick to other pieces of clothing. So you get a nice, non-sticky load of warm, dry clothes at the end of the cycle.

This is a perfect illustration of how science can be found everywhere you look – even in something as mundane as doing the laundry. And I think we should all give a big hand to the science of static electricity – and those who figured out a way eliminate it.

The chemistry of fire

2008-01-17T15:42:00.000-08:00

One of my favorite activities on a chilly winter night is to snuggle on the couch in front of a roaring fire in the fireplace. There’s something so cozy about it! Now that I think about it, fire is kind of a strange thing. It gives warmth and light – but it can also be highly destructive. It can sustain life – or it can destroy it. But what is it? When I have wood burning in my fireplace, what exactly is going on? What is fire?

Fire isn’t a thing. It’s a chemical reaction. Specifically, fire is a chemical reaction that releases heat and light energy as matter changes from one state to another.

Okay, sounds good. But what does it mean?

Let’s deal first with the first part of that definition – it’s a chemical reaction. Chemical reactions are wide and varied, and include everything from nails rusting to the bubbling of alka-seltzer tablets in a glass of water to the metabolism of sugars in your cells to produce energy. A chemical reaction simply means that 2 or more things (molecules, ions or atoms) interact and change to something else. So let’s look at a nail turning rusty. This is an example of an oxidation reaction. When iron is exposed to water and oxygen, the water and carbon dioxide in the air form a weak acid (called carbonic acid). Carbonic acid dissolves the iron, and also breaks more water down into hydrogen and oxygen. Free oxygen (from the water) and dissolved iron (from the nail) combine to form iron oxide – which is rust. The net result is that iron has changed into iron oxide - a completely different molecule than it was when you started.

So what is the chemical reaction that occurs in fire? For fire to occur, you must have 3 things - something to burn, oxygen and an ignition. So let’s look at the burning of wood. The ignition spark – which can come from any number of places (such as a match, a lightning bolt, or friction) - must bring the wood to about 300 degrees Fahrenheit. At this temperature, the cellulose in the wood begins to break apart. This breaking of the cellulose releases three things - volatile gases (namely oxygen, hydrogen and carbon), char (which is pure carbon) and ash (all the rest of the unburnable minerals from the wood). We see the volatile gases as smoke. For the wood to catch in flames, the temperature must now get to 500 degrees Fahrenheit. Now the molecules in the cellulose start to break apart into atoms. The atoms recombine with oxygen, forming water, carbon dioxide, and other stuff. The recombining of those atoms into new molecules produces a lot of energy, which takes the form of heat and light.

So you start with wood, heat and oxygen – and you wind up with water vapor, ash, and smoke. And all of the heat and light energy that is released in the transformation? That’s fire.

So the next time we have a fire in our fireplace, I hope that I can remember that this process of fire is really a great example of some fundamental chemistry. Maybe then I won’t take it for granted quite so much!

Diseases you never want to get

2008-01-14T09:35:00.000-08:00

I recently received a tetanus booster shot. Actually, it was called DTaP, and it was a combination vaccine against tetanus, diphtheria and pertussis. As I recovered from the booster shot (I had quite a sore arm for several days), I started wondering about these diseases. I wanted to know: what, biologically speaking, are they, anyways?

Let’s start with tetanus. Tetanus is caused by a soil-dwelling bacterium named Clostridium tetani. It can enter your body through a deep tissue wound that gets dirt in it (the classic example is stepping on a rusty nail). Other injuries involving dead skin, however, such as frostbite or burns, can also allow the bacterium a way into your system. There is also a form of neonatal tetanus, which can occur when a baby is delivered under unsanitary conditions. Once the bacterium is in the body, it produces a neurotoxin called tetanus toxin, which acts as a poison on your neurons. It stops the ability of the nerves controlling your skeletal muscles to turn themselves off; the risk is that these nerves will be firing signals at the smallest stimulus. This means that a small touch on your skin that would normally be ignored by your nervous system will result in a large, spastic muscle movement. The classic symptom of the disease is lockjaw, though other symptoms include difficulty swallowing, severe muscle spasms, and seizures. The spasms may continue up to 4 weeks, unless death occurs (in approximately 10-20% of the cases).

Sounds dreadful, doesn’t it? So here’s some good news: vaccination against tetanus is very effective. Even if you are behind on your tetanus boosters, there is even a post-exposure tetanus prophylaxis that you will receive if needed. Because of this, tetanus is very rare in the US. There have been fewer than 40 cases per year in the US since 1999. Phew!

How about diphtheria? Diphtheria is caused by Corynebacterium diphtheriae, There are 2 types of diphtheria – one in the upper respiratory tract, and one on the skin. The cutaneous (meaning skin) form of diphtheria is usually a secondary infection of a pre-existing skin wound. It is considered a mild form of the disease. Respiratory diptheria, however, can be very severe. It is spread very easily through respiratory droplets (such as those made by a cough or a sneeze) of an infected individual. The disease manifests as a sore throat, low-grade fever, swollen glands, and weakness. The most prominent symptom, however, is the accumulation of a thick, gray membrane over the throat and tonsils. This membrane can make swallowing and breathing difficult. Once established in the respiratory system, it can also spread to other organs, such as the heart and kidney. One in ten infected individuals will ultimately die from such an infection.

Corynebacterium diphtheriae is scientifically very interesting. It colonizes local tissues of the throat, then produces a toxin called diphtheria toxin, which interferes with a cell’s ability to make protein. This interference is lethal; any such cell affected by the toxin will die. There are actually 3 different substrains of this bacteria, each of which is capable of producing different amounts of toxin. The gravis strain can produce the most toxin, thus it causes the most severe form of the disease. However, toxin production is controlled not only by the genetics of the bacterium, but also the environment of the throat. In particular, inorganic iron prevents the synthesis of the toxin. So if you don’t have much iron in your bloodstream, the bacterium can produce much more toxin.

I know, this sounds horrible, too. But here’s the good news: diphtheria is also very rare in the US, again due to good vaccination protocols. There are fewer than 10 cases reported across the country every year. If someone does become infected, treatment options are pretty good. Immediate hospitalization and treatment allows most patients to recover from the disease.

And for the final disease of the day – pertussis. You may know pertussis better as whooping cough. This is a highly contagious disease of the upper respiratory tract. It is caused by the bacterium Bordetella pertussis, which lives in the mouth, nose and throat of mammals; there is no other known environment in which is bacterium is found. It is pathogenic only in humans. B. pertussis causes this disease because it, too, produces a toxin. Petussis toxin alters a cell’s ability to regulate internal levels of a molecule called cAMP. Elevated cAMP levels in a cell results in it losing fluid and ions. Pertussis toxin also has a very specific effect on cells of your immune system called phagocytes. Phagocytes normally engulf and destroy foreign matter in your body, such as bacteria. However, phagocytes affected by pertussis toxin can no work in this way, and a primary line of defense against the B. pertussis bacterium is lost.

The outcome of infection progresses in several stages. The first stage resembles a simple cold – runny nose, sneezing, low-grade fever and mild cough. The second stage is when the disease is at its worst. The cough becomes very severe. Infected individuals will have uncontrollable fits of coughing, following by a characteristic high-pitched crowing, or “whoop,” as the person breathes in. (This is why it is commonly called whooping cough.) The coughing fits can be so violent that they can cause the person to turn blue from lack of oxygen, or they may vomit once it is over. Between coughing episodes, the person will appear normal; however, they can count on around 20 such fits a day. The third phase of pertussis is the recovery phase, during which symptoms gradually disappear. There are many possible complications from pertussis, including pneumonia, ear infections, dehydration, seizures, encephalopathy (abnormal brain function due to oxygen deprivation) and death. The disease is most severe in young children; older children and adults usually have an easier time of it.

I was very surprised to learn about the frequency of pertussis in the US. Cases reached an all-time low in 1976 (1,010 cases reported); but that number has been slowly rising. According to the CDC, 5000 to 7000 cases of the disease are reported every year. One of the reasons for this is that immunity from infection or vaccination is not life-long; boosters are required to maintain immunity. But because it is so rapidly transmitted, anyone behind on their boosters can get a mild form of the disease, which is then transmitted. It is believed that more of these mild cases are now being recognized, whereas they would have previously been treated as a regular respiratory infection. There is some good news, though – treatment for established cases of pertussis is very good, and the number of reported deaths is very small.

After learning about all of this, I’m really glad that I was recently vaccinated against all of these things! None of them are anything I’d ever want to contract.

Saturn’s flying saucers

2008-01-11T09:15:00.000-08:00

Did you know that there are flying saucers around Saturn?

Okay, I confess, they’re not really flying saucers. They’re moons. But they sure look like flying saucers. At least, they look like the flying saucers from the space alien movies from the 1960s. You know, the ones that look like this:

The 2 moons in question are called Pan and Atlas. They’re really small; Atlas is only about 25 miles by 15 miles in size. That’s tiny compared to the size of Saturn’s biggest moon, Titan, which has an equatorial radius of 1600 miles. (Incidentally, that makes Titan larger than the planet Mercury, and much bigger than the ex-planet Pluto.)

These small planets have confused scientists ever since they were discovered by the Voyager 1 and 2 spacecraft in the early 1980s. Recently, the Cassini spacecraft has provided highly detailed images of the moons, showing us how oddly-shaped they really are. A research team from the Space Science Institute in Boulder, Colorado, believes it may have the answer for why these moons have such an odd shape.

Saturn’s rings lie in a flat disc that corresponds to the planet’s equator; the moons are actually embedded within those rings. Atlas lies within the A-ring, the outer of Saturn’s 2 brightest rings. Pan is within the Encke Gap of the A-ring. (The diagram here shows the naming convention of the A- and B-rings, as well as the Encke Gap.) Scientists had previously argued that the moons were made up solely of fragments left over from collisions of larger moons. However, scientists from a team led by Carolyn Porco have concluded that the moons are made up primarily of material just like the rings themselves – light, porous and icy. In fact, as much as two-thirds of the moons might consist of this matter, which is quite unlike the dense, massive material that would be the leftovers of other planetary bodies.

Porco’s research group believes that the cores of Pan and Atlas likely came from these planetary leftovers. But over the millennia, the moons may have drawn dust and ice slowly to themselves, building themselves up. Two important features of the moons are consistent with this model: the ridges around the equators of the moons are in the same plane as the rings of Saturn, and they are as thick as the vertical distance that the moons cover in the rings. So it makes sense that they could likely have picked up material as they orbited Saturn to make themselves larger. This accumulation would likely have occurred in several stages, the last of which would have resulted in the strange ridges that give them their flying saucer shape. That’s because the moons act as “accretion discs;” as matter falls towards a gravitational pull, it gradually builds up into discs. In fact, this is quite possibly comparable to how Saturn’s rings themselves were made.

However, it is also believed that Pan and Atlas have reached their final shape, and will not grow any larger. That’s because their orbits are thought to prevent any additional material from being able to stick stably to their surfaces.

But don’t worry. Despite appearances, Martians are not making their way towards Saturn in their flying saucers. I guess these are just another one of the bizarre things in our universe!

The following image was used in this entry:
Flying saucer: http://www.altfg.com/blog/biography-obit/bernard-gordon/

Something really weird about whales

2008-01-07T10:24:00.000-08:00

Did you know that whales have earwax?

I discovered this fact while investigating human earwax (for my entry “Funny things about humans”). And as I thought about it a bit, I came up with a few questions about whales. What are some of the main features of a whale’s body? What kinds of features distinguish different whale species? What’s the smallest whale in the world? And do all whales have earwax?

There are 2 kinds of whales – baleen whales and toothed whales. Baleen whales are also known as whalebone whales, great whales, or Mysticeti. They are one of 2 suborders that make up Cetacea (that is, all whales, dolphins and porpoises). The main feature of these whales is their lack of teeth. Instead of teeth, they have baleen plates that filter food from water like a sieve. Baleen plates are composed mostly of a protein called keratin, and they are arranged in 2 parallel rows that grow out of the upper jaw. It looks like combs of thick hair. A baleen plate can be anywhere from 2 to 12 feet long, and weigh up to 90 pounds, and will grow continually throughout the lifespan of the whale, with the end continually wearing away. In contrast to baleen whales, toothed whales (also known as Odontoceti) have teeth (though you probably had guessed that already). These teeth are mostly used for eating, though they can also be used for aggression. There is a wide variety in teeth among toothed whales. Some dolphins have over 100 teeth in the jaws, while the narwhal whale has a single tooth (which looks like a tusk protruding from the left side of the mouth).

Baleen whales and toothed whales also have different kinds of blowholes. A whale’s blowhole is analogous to our nostrils, the hole in the head through which the animal breathes. In contrast to mammals, though, a whale’s blowhole does not actually connect to the esophagus (the tube that food goes through from the mouth to the stomach). It only connects to the trachea (the windpipe). Because of this, a whale cannot breathe through its mouth. It must breathe through its blowhole on the top of its head. Baleen whales actually have 2 blowholes positioned in a V-shape, while toothed whales have a single blowhole.

Baleen whales tend to be larger than toothed whales; in fact, the largest mammal in the world is a baleen – the blue whale. Other baleen whales include fin whales, minke whales, humpback whales, and gray whales. There are small baleen whales, too – the smallest is the pygmy right whale, which is around 20 feet long. The largest toothed whale is the sperm whale. At an average of 60 feet long, sperm whales are actually the largest toothed animals in the world. The sperm whale is unusual, though, as toothed whales tend to be small. Examples of toothed whales include dolphins, porpoises, narwhal whales, beaked whales, killer whales, pilot whales and beluga whales. The smallest whale in the world is the toothed dwarf sperm whale, otherwise known as the Owen’s pygmy sperm whale. These guys average around 8 feet long, weighing in at around 300 pounds. That makes them even smaller than dolphins.

As far as earwax goes, it has only been found in baleen whales. I have found references to earwax in both fin whales and humpback whales. Whale earwax serves a different purpose than our earwax. Its primary job is to prevent water from entering the ear canal, and it is not shed. In fact, baleen whales accumulate layers of wax as they get older; the more layers of earwax, the older the whale. Fin whales add 2 layers of wax a year, while humpback whales add 4. Scientists can use these layers to approximate the age of the whale. Actually, that’s the only way of aging a baleen whale. Toothed whales can be aged by looking at their teeth, because teeth grow in layers. You can count the layers of a whale’s tooth and see how it was. But baleen doesn’t grow that way. So the only way of knowing how old a baleen whale was is by counting the layers of its waxy ear plug.

I wonder if toothed whales also have earwax? They all have ears, which are just holes in the side of their heads immediately behind their eyes. And presumably they all need a way to keep water from flooding their ear canals. Maybe they have some other way of keeping water out of their ears. Or maybe we just haven’t looked hard enough yet?

The images I used were taken from the following sites:
Narwhal whale: http://concise.britannica.com/ebc/art-6694/Narwhal
Blue whale: http://en.wikibooks.org/wiki/Adventist_Youth_Honors_Answer_Book/
Nature/Marine_Mammals

The Permian Extinction

2008-01-04T10:04:00.000-08:00

In a recent entry (“A super-sized bug”), I mentioned that ancient sea scorpions disappeared from the fossil record around 250 million years ago, during a time known as the Permian extinction. What was the Permian extinction? In short, it was one of the most cataclysmic mass extinction events ever to happen to life on earth. There have actually been 5 massive extinctions over the earth’s history. They are the Ordovician extinction (440 million years ago), the Devonian extinction (370 million years ago), the Permian extinction (250 million years ago), the Triassic extinction (210 million years ago) and the Cretaceous extinction (65 million years ago). The Permian was by far the biggest. In total, 70% of all land-based species became extinct; 95% of all marine life was killed. It has been referred to as “the mother of all mass extinctions.”

The Permian period lasted from approximately 286 to 248 million years ago, and was the last period of the Paleozoic era (which lasted from 540 to 248 million years ago). During the Permian period, all of the earth’s continents were in 1 giant land mass. It was called Pangea; shaped like the letter “C,” it spanned the equator. The mouth of the C was a sea called Tethys, while the rest of the world was covered by a giant ocean called Panthalassa.

This configuration of land and ocean led to an expansion and diversification of both terrestrial and marine species. Therapsids were the dominant land-based tetrapod (which means 4-legged creature), and have also been called “mammal-like reptiles.” There were multiple kinds of therapsids, including dinocephalians (a dog-like crocodile), gorgonopsians (a large reptilian saber-toothed tiger), therocephalia (smaller than the gorgonopsians), and dicynodonts (the only herbivores in the group). There were also several primitive turtle-like and reptilian-like creatures, including pareisaurs (armoured herbivores reaching a whopping 9 feet long), procolophonids (chunky lizards with big skulls), and diapsids (which still exist in the form of reptiles and birds). Dominant insects were mostly cockroaches (upwards of 90% of insects were some kind of roach), though dragonflies were also abundant. Terrestrial flora changed dramatically during this time. Pangea had large areas of relatively dry land, as opposed to the damp, jungle-like climate that had existed previously. Swamp-loving trees were replaced with conifers (pine trees), and gingkos, cycads and ferns also become prominent. The marine environment was full of exotic life. Great reefs harbored giant sea scorpions, armoured fish, mollusks, sponges, trilobites, brachiopods (bivalves that look like clams), nautiloids (to which the modern nautilus belongs), and ammonoids (related to octopus and squid).

The organisms of Pangea during the Permian period were vast and varied. But after the Permian extinction, very few of these creatures had survived. What happened to destroy so much of this varied and exotic life? At the moment, there are several theories to explain the massive die-off.

One theory is that massive volcanic eruptions coated the landscape of the present-day Siberian Traps with basalt lava, causing environmental stress, an elevation of the earth’s temperature, and mass extinction. An expansion of this theory says that the increased temperature resulting from the basalt lava would not be enough to destroy so much life. But it could result in the release of methane gas from below the ocean floor, which would further increase global temperatures. Yet another related theory is that the basalt lava decreased the ability of the oceans to dissolve oxygen. Because of this, deep-ocean bacteria thrived (they don’t use oxygen), and they produced massive amounts of hydrogen sulfide. The hydrogen sulfide escaped into the atmosphere, causing acid rain and destroying the ozone layer. In fact, recent evidence from David Bottjer, professor of earth and biological sciences from the University of Southern California, supports this model of an uprising of hydrogen sulfide from the deep ocean. In a paper published in the November issue of the journal Geology, Dr. Bottjer reported evidence that deep-sea organisms were the first to die off, followed only later by creatures dwelling in shallow water. Many people also believe that this model could explain the later Cretaceous extinction event that wiped out the dinosaurs. (That was the second largest extinction event in the world.)

Whatever the cause, the effects on life on earth were nothing short of disastrous. While 70% of land species and 95% of marine species died out during this extinction event, on an individual level, perhaps as many as 99% of all individual organisms died as a result of whatever happened. This clearing of the landscape provided room for the emergence of other well-known species, including the dinosaurs and modern mammals. So in retrospect, it wasn’t a total loss. But it certainly was a tough time for everything involved.

To sleep, perchance to dream

2007-12-21T10:13:00.000-08:00

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

2007-12-17T10:31:00.000-08:00

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…..

2007-12-13T09:57:00.000-08:00

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!

2007-12-10T10:11:00.000-08:00

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

2007-12-04T16:15:00.000-08:00

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?

2007-12-04T12:28:00.000-08:00

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

2007-11-27T14:23:00.000-08:00

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

2007-11-26T13:11:00.000-08:00

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!

2007-11-20T11:07:00.000-08:00

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

2007-11-16T16:14:00.000-08:00

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

2007-11-13T16:48:00.000-08:00

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!

2007-11-08T14:29:00.001-08:00

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!

2007-11-05T12:45:00.000-08:00

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

2007-11-02T09:34:00.000-07:00

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

2007-10-30T09:43:00.000-07:00

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

2007-10-25T11:19:00.000-07:00

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

2007-10-24T09:26:00.000-07:00

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)

2007-10-17T11:25:00.000-07:00

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

2007-10-15T09:56:00.000-07:00

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?

2007-10-09T09:17:00.000-07:00

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!

2007-10-04T09:29:00.000-07:00

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.

When sleep goes awry

2007-10-01T15:48:00.000-07:00

In a previous entry (“Zzzz….”), I talked about sleep – why we need it, what happens when we don’t get it, and how the sleeping habits of animals across the world compare to our own. Having delved into what constitutes normal patterns of sleep, I wanted to know about what happens when sleep goes awry. If sleep is such an important part of our biology, why do some people have so much difficulty with it?

The term “sleep disorder” encompasses a wide variety of sleeping problems. Sleep disorders can be grouped into 4 main categories: dyssomnias, parasomnias, proposed disorders, and medical/psychiatric disorders. Of these, dyssomnias and parasomnias are the most prevalent. Dyssomnias are disturbances in the timing, amount or quality of sleep. Common dyssomnias include: insomnia, narcolepsy, restless leg syndrome, sleep apnea, jet lag and shift-work sleep disorder. Parasomnias interfere with the transitions between sleep stages, and include: sleepwalking, sleep talking, sleep terrors, bedwetting and teeth grinding. While much work is being done on many of these different sleep disorders, one in particular has been extensively studied in terms of its biological cause. This condition is called narcolepsy.

Narcolepsy is a sleep disorder that affects almost 150,000 people in the US (about 1 in 2,000 people). It is a neurological condition characterized by excessive daytime sleepiness and abnormal REM sleep. (Remember, REM sleep is that stage in our sleep cycles when our brains are active but our bodies are inactive.) A narcoleptic often becomes so drowsy that they will fall asleep wherever they are, irresistibly and without warning. There are additional manifestations of narcolepsy, including sleep paralysis (inability to talk or move upon waking), hypnagogic hallucinations (auditory or visual hallucinations while falling asleep or waking up) and cataplexy (a sudden episode of muscle weakness that is triggered by strong emotions). While symptoms of excessive daytime sleepiness, sleep paralysis and hypnagogic hallucinations are sometimes seen in people who are not narcoleptic (usually people who are extremely sleep deprived), cataplexy appears to be exclusive to narcolepsy.

Narcoleptics who are having an attack of cataplexy is a truly unusual thing to watch. There are several fairly well known videos of narcoleptic dogs, including Rusty the narcoleptic daschund and several from the Stanford Center for Narcolepsy. Typically, the dogs in the videos are playing and seemingly having a great time, then suddenly their knees buckle and give way and their necks and jaws go slack. The dogs fall down and become paralyzed for a period of time, during which all of their reflexes are lost. After some time, they recover with no ill effects, and resume their previous activities.

So why does this happen? I’ve said it before, and I’ll say it again – it’s not fully understood. Sleep researchers have shown that over 90% of narcolepsy with cataplexy is caused by defective signaling from 2 related chemicals in the brain. These chemicals – hypocretin-1 and hypocretin-2 – regulate activity in the hypothalamus, the part of the brain that regulates sleep and appetite. Scientists have shown that the inherited form of narcolepsy in dogs is caused by genetic mutations that make their brains unable to respond to hypocretin-1 and hypocretin-2. In humans, it appears that the chemicals are physically absent, because the cells that make the hypocretins are mysteriously missing. The current thinking is that those cells have been killed off by the body’s own immune system. But why that happens is still unknown, as is what causes narcolepsy without cataplexy.

I guess I shouldn’t be surprised that there are so many ways that sleep can go awry, as well as the fact that we don’t really understand why yet. After all, sleep is an enormously complicated part of the brain, and it integrates a huge number of different factors of genetics and environment. It’s amazing that our brains and our bodies handle it as well as they do.

Lunch break

2007-09-25T12:33:00.000-07:00

I’m about to break away from my lab bench and go eat lunch. And in doing so, I will be putting to use a part of my body I don’t think about very often – my stomach. Being curious in nature, I wondered - chemically and biologically speaking, how does the stomach work?

The stomach is the second stop in your body’s gastrointestinal tract (the first being your mouth), and it is designed to break down large food molecules into smaller ones that can be absorbed by your small intestine. It achieves this primarily because it is a balloon filled with acid. Acidity is measured on a pH scale, ranging from 0 to 14 - the lower the number, the more acidic a liquid is. A liquid is considered neutral – neither acidic nor basic – at a pH of 7. Everything above 7 is basic, while everything below 7 is acidic. Here are some examples of the pH of commonly encountered liquids:
-chlorox bleach = 11.4 (base)
-pure water = 7 (neutral)
-lemon juice = 2 (acid)
-sulfuric acid = 0.3 (strong acid).
The pH of your stomach varies between 1 and 4, depending on several factors including the time of day and what foods have been eaten. And the culprit responsible for this acidity? Gastric acid.

Gastric acid is one of the main secretions of the stomach. It is made up mostly of hydrochloric acid, along with small amounts of salts, and is secreted by a specific type of cell in the stomach, called parietal cells. The gastric acid serves to break apart large molecules like proteins. This strong acid in your stomach poses a potential difficulty for your body – if any of that acid was to escape the stomach, it would wreak havoc with whatever it touched. Anyone who experiences heartburn knows what this feels like! Heartburn occurs when acid from the stomach makes its way into the esophagus. The burning sensation is, actually, the stomach acid burning the lining of your esophagus. Your stomach, therefore, must have a strong acid-proof barrier to keep all of the gastric acid contained. That barrier is the stomach lining – actually, those cells called secretory epithelial cells.

Of the 4 major types of secretory epithelial cells lining your stomach, the mucous cells are the primary defense. They protect everything else from the gastric acid by secreting mucus - a basic, thick, sticky fluid. Actually, there are mucousal cells lining all of the body cavities that are exposed to the external environment – not only the stomach, but also places such as the nostrils and mouth. The mucus in your stomach neutralizes the acid before it eats away the cells underneath.

The mucous cells lining your stomach are actually organized several layers thick. The cells at the top (closest to the acid) are simple columnar epithelial cells. That means that they are shaped like cubes, taller than they are wide, stacked one layer thick, tightly packed together without any gaps. The cells are strictly oriented with a top and a bottom based on their connections with each other and with the cells underneath. Though they are protected from the stomach acid by the layer of mucus on their tops, they still live a harsh – and short – life. Your stomach lining, in fact, has of the most rapidly dividing population of cells in your entire body – the mucosal cells are replaced approximately every 20 hours.

What happens if the mucous cells can’t produce enough mucus to protect themselves from the stomach acid? The result is called a gastric ulcer. Gastric ulcers (which are ulcers specifically in the stomach, as opposed to peptic ulcers, which take place in the small intestine) are most commonly the result of an infection by the bacteria Helicobacter pylori. When H. pylori establishes an infection in your stomach, it produces compounds preventing the production of mucus. No mucus, no protection, and damage to the lining of your stomach can result. The good news, though, is that your stomach has amazing regenerative powers. Removal of the bacteria results in the regeneration of mucus and the mucousal cells.

I haven’t even touched on the rest of digestion, such as how nutrients get absorbed into the bloodstream and how the intestines work, and already I’m impressed. The stomach is an amazing organ that has to face a lot of challenges just to accomplish its job. Makes me appreciate it all the more!

Okay, enough about the stomach. I'm hungry.

Zzzzz....

2007-09-21T09:43:00.000-07:00

I wonder how many of you will have yawned by the time you get to the end of this entry. Not because it’s boring (I hope!), but because of the power of suggestion. The topic?

Sleep.

Sleep is a part of life - at least, it is if you are a mammal, reptile or bird. Like it or not, your brain needs to sleep. A sleeping person is a funny thing to watch. Someone who is asleep is usually lying down, eyes closed, and they are unresponsive to most soft noises. Their breathing is slow and steady, and their muscles are completely relaxed, though they will move around from time to time (usually once or twice an hour). In short, they are completely detached from most of the things happening in their surroundings – though they can be aroused with a strong enough stimulus.

Let’s delve into what happens to our brains and our bodies when we sleep. Human sleep architecture follows an oscillating cycle of REM (rapid eye movement) and NREM sleep (non rapid eye movement). REM sleep usually accounts for 25% of our slumber, with NREM making up the rest. In REM sleep, the brain is active while the body is inactive; NREM sleep is the opposite, with the brain being inactive and the body being active. The cycle usually lasts around 90 minutes, and it goes as follows:
NREM stage 1 (light sleep): you are somewhere between waking and sleeping
NREM stage 2 (sleep onset): you become disengaged from your surroundings, and your body temperature drops
NREM stage 3 and 4 (deep, restorative sleep): breathing slows down, blood pressure drops, muscles relax, hormones are released, and most tissue growth and repair occurs
REM sleep (dream sleep): eyes dart rapidly back and forth, muscles become immobile and stiff, brainwaves speed up to awake levels, and dreams occur
So when you fall asleep, your brain will pass through NREM stages 1 through 4, and then enter REM about 90 minutes after. REM sleep usually lasts from 5 to 30 minutes, and then you repeat the cycle every hour and a half. During NREM sleep, your body will unconsciously move around, turning over and rearranging itself. This is your body’s way of making sure that no part of your skin or body has its circulation decreased for too long a period of time.

That’s what sleep is – but why do we need it, anyway? In short, we don’t really know. Scientists have shown that sleep is essential for survival, but no one has the definitive answer of why. Evidence indicates that enough sleep is essential for a healthy immune and endocrine system, tissue repair, and may play a role in diseases such as hypertension, obesity and diabetes. It also seems to be important in higher cognitive functions. People who are sleep deprived have decreased memory and attention, complex thoughts, motor responses and emotional control. In fact, people who are sleep deprived sometimes function more poorly on tests measuring motor control and coordination than someone who is legally drunk.

As I mentioned before, sleeping is a part of life for all mammals, not just humans. If you have pets, it might seem like your furry friends do nothing but sleep! Dogs sleep somewhere between 13 and 18 hours each day, while cats clock in an average of 16-20 hours a day. (That equates to about two-thirds of their lives, by the way.) Koala bears manage at least 19 hours of shut-eye each day. However, even koalas are not the sleepiest mammal around – that record belongs to armadillos, opossums and sloths. They sleep an average of 80% of their lives (almost 20 hours every day). That’s a lot of time slumbering! Water-bound mammals, such as whales and dolphins, have slightly different requirements for sleep. They are conscious breathers (they actively decide when to breathe, unlike humans, who breathe without thinking about it), so they have to remain at least partially conscious to stay alive. Because of this, only half of their brains sleep at a given time. If you ever see a dolphin “logging,” or swimming slowly near the surface, they are probably taking a nap.

What about non-mammals? Reptiles and birds exhibit true sleep, but in a different manner than mammals. Reptiles become unconscious, but they do not have a dream component of their sleep cycle. (Yes, snakes can still sleep even though they don’t have eyelids – they sleep with their eyes open.) Birds are very light sleepers, and they rarely fall into a deep sleep stage at all. This means that they, like reptiles, rarely dream (if ever). Fish and amphibians reduce their awareness of their surroundings, and spend time in an energy-saving state called “rest.” But scientists have found no evidence of the changes in the brain waves of fish and amphibians that would indicate that they are really asleep.

Incidentally, I’ve known a lot of people in my day who claim that they really don’t need very much sleep to function. (Many of these were during my college years.) Sorry folks, but the science has you beat. You may function okay with a greatly reduced sleep schedule. But you’d function a whole lot better if you slept more.

When is a kilogram not a kilogram?

2007-09-17T11:53:00.000-07:00

Here’s a funny headline that caught my eye today: Kilogram Mysteriously Loses Weight. Interesting. I always thought a kilogram was defined as an unchangeable measurement of mass. How can a kilogram be less than a kilogram? Isn’t that like saying that the mile has inexplicably just gotten shorter?

Well, not exactly. What the article was really talking about was International Prototype Kilogram (the IPK), the reference cylinder at the International Bureau of Weights and Measures in Sevres, southwest of Paris. The cylinder itself, used to define what a kilogram really is, seems to be shrinking.

Hold on a second - if this cylinder itself is the definition of a kilogram, it’s shrinking in relation to what? The IPK was made in 1879, made from a platinum and iridium alloy, and is 1.54 inches in diameter and height. For years, it has been used to define the measurement of “kilogram.” Duplicates of this reference point were made and shipped around the world. And since then, the original object lives in an ultra-secure vault in a chateau in Sevres, rarely coming out to see the light of day. In fact, the only time it comes out is to be compared back to the duplicates, just to make sure that everyone is following the same metric standard. Recently, the IPK weighed in at 50 micrograms less than all of the other kilograms. (In case you’re wondering, 50 micrograms is roughly equivalent to the weight of a fingerprint. In terms of everyday life, this changing reference won’t matter very much. However, if you are a physicist calculating something complex like electricity generation, it will matter a little bit more.)

This is quite a puzzle for scientists. Apparently, these reference objects are made from the same material, at the same time, and they are kept under the same conditions. And yet their masses are drifting slowly apart. To be honest, physicists at the International Bureau of Weights and Measures don’t know whether it’s because the IPK is shrinking, or the duplicates are getting heavier. However, scientifically speaking, only the original IPK in Sevres defines the kilogram. The duplicates are defined as incorrect.

Because of this problem, scientists would like to have a better definition of a kilogram. So it’s likely that the kilogram will have to undergo a facelift in the near future. There is plenty of precedence for this. Many other standards of measurement have changed over the years. For example, take the meter. Over the years, the definition has gone through the following permutations:

1/10,000,000th of the distance from the pole to the equator (1793)

the distance between 2 marks on a platinum reference bar (1799)

1000000 / 0.64384696 wavelengths in air of the red line of the cadmium spectrum (1906)

the length traveled by light in vacuum during 1 / 299 792 458 of a second (1983).

Keep in mind that these changes have not altered the distance of a meter, merely the precision by which it is measured. Maybe soon we’ll have a newer, more precise definition of what makes a kilogram.

Until then, I think we just have to concede – a kilogram just isn’t what it used to be.

Much Ado About Nothing

2007-09-14T09:21:00.000-07:00

Today, I’d like to talk about some science a little farther away than the life sciences I’ve written about so far. Actually, it’s literally farther away – out in space. Outer space encompasses everything else in the universe outside of earth’s atmosphere, from the moon (a mere 250,000 miles away) to the Abell 2218 galaxy (a much farther distance of close to 13 billion light years), and everything in between. As I’m sure you are aware, that’s a pretty big area. No one really knows how large the universe is, or if it even has edges at all! (It’s possible that the universe is infinitely large.) The most distant galaxies seen by the Hubble space telescope are at about 13 billion light years away, and the visible horizon of the universe (that is, as far as we can detect) is about 15 billion light years away. Within that area, there are differences in the distribution of celestial objects. However, even with an uneven distribution, scientists have always observed that most of outer space has something in it. Even if it’s not filled with stars, space contains things like galaxies, black holes, gas and dark matter (that strange and mysterious material). At least, no one has ever found a significant region of space that is void of any of these objects – until August.

At the end of August, researchers from the University of Minnesota announced that they discovered a vast chunk of space with nothing in it. This area is 1 billion light years across – that’s 6 billion trillion miles of emptiness. If we assume that the Milky Way is 100,000 light years across, the void is 10,000 times larger. And it appears to be truly empty – no stars, no galaxies, no black holes, no gas and no dark matter. Nothing.

While scientists have observed other areas of space with nothing in it, the sheer size of this cosmic void has taken everyone by surprise. For example, there is a small cosmic void fairly close to Earth – only 2 million light years away. It’s called the South Pole Void, so named because it occupies the sky directly above the southern pole of the Milky Way galaxy. But the region discovered by the Minnesota team is roughly 1,000 times the volume of any other known void, including the South Pole void. That’s close to comparing the volume of the Great Lakes with the volume of the Atlantic Ocean. Sure, the Great Lakes are really large. But the Atlantic is much, much larger.

How on earth did these astronomers find something with nothing in it? To accomplish it, they relied on pictures from the National Radio Astronomy Observatory. The NRAO, headquartered in West Virginia, designs, builds, and operates some of the world’s most advanced radio telescopes. Unlike standard telescopes, which visualize light waves, radio telescopes “see” radio waves generated by interstellar objects. These radio waves provide a much clearer view of stars, galaxies, and planets because they can pass through much of the gas and dust in space without distortion, unlike visible light. And many celestial objects produce much stronger radio waves than they do visible light waves, so radio telescopes can see them in much greater detail. Lawrence Rudnick’s team studied radio pictures taken from the NRAO’s Very Large Array (VLA) telescope. Their careful study of the NVSS data showed a remarkable drop in the number of galaxies in a region of sky in the constellation Eridanus. Further study showed that, not only is the region devoid of galaxies, it is devoid of nearly all matter.

Scientists say that it is possible that this giant empty space is simply a fluke of nature. After all, with a virtually infinite area of space and a finite amount of matter to disperse in it, it’s possible to get a large area devoid of objects. However, the chance of that happening is pretty small, according to James Conlan, an astronomer at the National Radio Astronomy Observatory. Conlan, though not a part of the Minnesotan research team, is investigating this empty region of space further. He believes that even though further investigation may discover a few objects in this space, it will still be the largest least dense region of space ever discovered.

What causes such a large region of empty space? Brent Tully is an astronomer at the University of Hawaii who studies the near-Earth void. According to him, empty regions of space are likely caused by a gravity battle. Areas of space that are more densely packed with matter have bigger gravitational pull than areas that are packed less densely. Over time, dense space will pull matter away from less dense space. Of course, the effect will increase over time; as more and more matter gets added to the dense space, its gravity will increase, which will pull in more matter, which will increase its gravity, and so on. After billions of years, this could eventually lead to a hole in the universe – areas where there is simply nothing left.

It’s fascinating to learn that not only are there objects in space that are worth studying, it is also worth studying, well, nothing! According to retired NASA astronomer Steve Maran, "This is incredibly important for something where there is nothing to it."

A tribute to Alex

2007-09-11T11:27:00.000-07:00

When reading the news today, I came across a story about the death of an exceptional bird - Alex the African Grey Parrot, to be precise. Alex was a part of psychologist Irene Pepperberg’s research at Brandeis University in Waltham, Massachusetts. For the last 30 years, he has been remarkable for his advanced language and recognition abilities. While parrots are widely known to be remarkable mimics, mimicry is not necessarily a sign of intelligence. Alex, however, went beyond merely aping back the sounds that he heard. He seemed to grasp abstract concepts, a benchmark of higher cognition. According to Dr. Pepperberg, Alex did not simply imitate human speech – he vocalized thoughts that were a result of reasoning and choice.

Alex (derived from Avian Learning Experiment) became a part of Dr. Pepperberg’s research in 1977, when she bought him from a pet store in Chicago. Alex, who was only a year old at the time, had no particular pedigree, and no particular indication of intelligence, but Dr. Pepperberg wanted to study him anyways. It turned out to be a very smart move. Over the years, he learned to count to 6 (including 0), identify colors and objects, express frustration with both his human and avian companions, and understand the concepts of “same,” “different,” “bigger,” “smaller,” “over” and “under.”

Here are some examples of his abilities. When asked about the color of a common object (such as corn), he would tell you the correct color of the object (in this case, yellow) even if it was not in sight. You could hold up a tray full of complex objects of different shapes, colors and materials, and he would pick an object based on shape, explore it with his beak, and tell you both what material it was made of and its color. He occasionally told other parrots in his room to “talk better” if they were mumbling. If you showed him 2 objects of different shape, color and material, and ask him what was the same, he would reply “none.” And he would say things like “I want” something, or “I want to go” somewhere. Dr. Pepperberg argues that these abilities require abstract thought – an understanding of color and objects, similarities and differences, location labels, and the concept of nothing-ness. He had the emotional equivalence of a 2-year old, and the intellectual equivalence of a 5-year old. Not bad for a creature with a brain the size of a walnut!

Of course, sometimes he was stubborn, too. (If you’ve ever encountered an African Grey Parrot, you know what I’m talking about. Sometimes they have the mindset of a mule!) I came across a story where Dr. Pepperberg was attempting to show a journalist Alex’s ability to distinguish colors, and he didn’t want to play along. He just wanted a treat.

While scientists agree that Alex’s abilities were remarkable, they do not all necessarily agree on what it really means. Do birds such as Alex really understand the words they are using? There have been past examples of scientists claiming that they have shown intelligence in an animal. Perhaps the most famous is a horse named Clever Hans. At the turn of the 20th century, Clever Hans could supposedly count, tell time, and make change by tapping his hoof on the ground. However, further studies showed that Hans was responding to his trainer, who tipped him off to the right answer by movements with his head. And studies from the 1970s on chimpanzees claiming to demonstrate that they could generate grammatically correct sentences have also been shown to be the result of the chimps mirroring their teachers. However, the experiments on Alex have withstood the test of time and close scrutiny. Effects on Alex’s abilities being influenced by his keepers have been rigorously controlled for. Studies on Alex have been published consistently in well-regarded journals such as the Journal of Comparative Psychology. He has been featured not only in scientific literature, but also in the popular press. He made appearances on PBS, the BBC, and Discovery. He was well known for interacting with host Alan Alda in an episode of Scientific American Frontiers, as well as in the PBS nature series “Look Who’s Talking.” He has been featured in the USA Today, New York Times, and the Wall Street Journal. He even has a book entitled “The Alex Studies.” Even his skeptics all agree. There was something unique about Alex.

So let me just say that science is better off for having known a small African Grey Parrot named Alex. I’m sure he will be missed.

A beautiful insect

2007-09-07T12:52:00.001-07:00

And now for a brief digression into a lovely topic – butterflies.

I was thinking about my garden the other day, and my thoughts strayed to our butterfly bush. I don’t really know why it’s called a butterfly bush, since it doesn’t really seem to attract them! (It’s awfully pretty, though.) As I thought more about butterflies, though, I realized how little I really know about them. For example, what makes a butterfly’s wings so colorful? How far can they fly? What’s the difference between a butterfly and a moth? And why on earth are they called “butterflies,” anyway?

Butterflies are insects belonging to the order Lepidoptera. There are actually 3 subfamilies of butterflies in this order – the true butterflies (superfamily Papilionoidea), the skippers (superfamily Hesperioidea) and the American moth-butterflies (superfamily Hedyloidea). There are 5 families of true butterflies in the world – the swallowtails and birdwings, the cool whites and yellows, the gossamer-wings, the metalmarks, and the brush-footed butterflies. All of these families encompass butterflies of all sizes and colors.

The reason for their beautiful and varied colors is found in the composition of their wings. Butterfly wings are covered in scales, which is the reason they are Lepidoptera (which literally means “scaly wings”). The brown and black scales are caused by pigments called melanins. However, for brighter colors such as blue, green, red and iridescence, the butterflies rely not on pigments but on the physical structure of the scales. This structure causes light to scatter when it reflects off the surface, creating a rainbow of colors. Their beautiful appearance is not primarily about ascetics, of course. Butterflies would provide a tasty snack for many hungry creatures, so many of them are also toxic if ingested. The toxic species tend to be brightly colored; of course, non-toxic butterflies don’t want to get eaten either, so they are brightly colored to pretend like they are toxic!

Of course, their appearance varies depending on which type of butterfly you are talking about. There are approximately 28,000 species of butterflies all over the world. While over 80% of them live in the tropics, a significant number are found in North America (over 700 in the US and Canada and roughly 2,000 in Mexico). The largest butterfly currently known is called the Queen Alexandra’s Birdwing butterfly, measuring in with a wingspan of almost 12 inches. Next to the world’s smallest know butterfly, the Pygmy Blue (with a ½ inch wingspan), it really looks like a giant!

Butterflies can fly immense distances over their lifetimes. The Monarch butterfly is perhaps the most famous migratory butterfly, traveling north from Mexico upwards of 3000 miles. There are other well-known butterfly travelers, however, including the Painted Lady, which migrates between Mexico and North America, as well as Europe and northern Africa. Other migratory species include Cloudless Sulphurs, Gulf Fritillaries, Red Admirals, Common Buckeyes, Clouded Skippers, Long-tailed Skippers, Mourning Cloaks, Question Marks, and several of the Danaine butterflies. (Boy, butterflies sure have some great names, don’t they? I want to know who named the Question Mark butterfly.)

So what’s the difference between these guys and moths? I was surprised to learn that the answer is not completely clear. There are some physical differences distinguishing them, including the shape and structure of their antennae, the organization of their wings, the type of pupa that they form between the caterpillar and insect stage, wing color and body structure. There are also a few behavioral differences, too, namely in the time of day most of the species are active. However, there are many examples of some moths that exhibit traits of butterflies, and vice versa. For example, butterflies usually have antennae shaped like a club at the end, while moth antennae are unclubbed at the end - unless you’re talking about the Castniidae moths, which have butterfly-like antennae, or the Pseudopontia paradoxa butterflies, which have moth-like antennae. Butterflies pupate by forming what is called a chrysalis, while moths form a cocoon - unless you’re talking about Hawk moths and gypsy moths, which form a butterfly-like chrysalis. And most butterflies are active during the day, while moths are nocturnal - unless you’re talking about Gypsy or Sunset moths, which are active during the day. So while science has divided moths from butterflies in their taxonomy, apparently, the question of the difference between butterflies and moths is still not settled!

And as for where butterflies got their name? One possibility is that it is a permutation of “flutter by,” which is, of course, what butterflies do! Alternatively, the English word might derive from the old Anglo-Saxon tradition of naming them based on their appearance. Since the most common butterfly back then was a yellow brimstone butterfly, they called them “butterfloege,” Another possibility comes from folk lore of North American colonies, where people claimed that witches and fairies would turn into these creatures at night, fly by, and steal people’s butter. Yum.

And in case you wanted to know, here’s what butterflies are called in a few other languages. The Russian word for butterfly, “babochka,” means “little soul.” In ancient Greece, butterflies were known as “psyche,” which also means “soul.” (Modern Greek, however, refers to them as “petalouda.”) The French refer to butterflies as “papillons,” also the name of a very cute kind of little dog with enormously fluffy ears. And the Sioux Indians call butterflies “kimimi,” meaning “fluttering wings.”

I don't know about you, but just thinking about all these butterflies makes me smile. Truly they are beautiful insects. And I'm not even that big of a big fan of insects!

The Power of Modern Microscopes

2007-09-04T09:41:00.000-07:00

Today’s entry is a little different than ones I have entered before – it’s not so much about a discovery as it is about a technology. This technology, which has advanced rapidly over the years I have been in science, is the microscope. I use microscopes in my research, as do most life scientists. Most of the ones I use are relatively low on the technology scale. But there is a vast range of microscopes available, for everything from low resolution light microscopy to extremely sensitive atomic resolution electron microscopy, and they are making it possible for us to look more closely at the inner workings of tissues, cells, and molecules than we could ever have dreamed possible.

Conventional compound light microscopes use a system of glass lenses to bend light and magnify an image. The magnification ability of a light microscope is limited, therefore, by both the size and shape of glass lenses and the physical properties of visible light. Standard compound microscopes usually have a magnification range of 40 to 1000-fold. However, where compound microscopes typically run into problems is with resolution. Resolution is the ability to distinguish 2 very small and closely spaced entities as being distinct. If you blow up a standard digital picture from 4x6 to something much larger, like poster size, you will get a very magnified, fuzzy picture. That’s because you have poor resolution – and no matter how much more you blow it up, you can’t make it any clearer. With microscopes, the story is the same - even if you have enormous magnifications, poor resolution just means you have a bigger picture of something fuzzy.

What if you want to look at something more closely than a light microscope will allow? One way is to use a Scanning Electron Microscope. Scanning Electron Microscopes (SEMs, for short), have a magnification ability up to 200,000-fold. The resolution limit of SEMs is very good; some of them can resolve objects down to 5 nanometers. (That’s 5 x 10-7 centimeters, roughly a quarter of the size of the thinnest known spider web!) It achieves this resolution because it does not use visible light to magnify the image; instead, it uses electrons. The sample to be examined must be able to conduct electricity; to do that, it is coated with a conductive material like gold. The sample is placed in front of a beam of electrons, which is sent through a series of magnetic lenses designed to focus them very tightly in one spot. The spot of electrons is focused back and forth across the specimen, row by row. As it scans, it knocks electrons off the surface of the sample, which are detected by the microscope. An amplifier condenses all of this information into a final image, built up from the number of electrons emitted from each spot on the sample. SEMs are commonly used to look at very small surfaces; for example, the compound lens of a fly eye looks quite beautiful when visualized by SEM.

SEMs are extremely powerful, but they are not the ultimate in microscopy. The most powerful microscope available in the world is the atomic force microscope, or AFM. AFM has, simply put, the most magnification and resolution power of any microscopy system on the planet. The principles of AFM are fairly straightforward. An atomically sharp tip is created on the end of a flexible cantilever that bends in response to force between the tip and the sample (kind of like a diving board). A laser sends a beam of light towards the tip, which is reflected at a certain angle. The tip is then moved across the sample of interest. As the tip moves in response to the sample, the angle at which the laser beam is reflected changes. This change is detected by the microscope, which is then turned into a 3-dimensional picture of the item being scanned. The resolution limit of AFMs is extremely high; they can reach a lateral (side-to-side) resolution of 1 nanometer (1 x 10-7 centimeters) and a height resolution of 1 angstrom (1 x 10-8 centimeters). That’s powerful enough to look at the structure of individual proteins!

Most scientists do not need to look at an object in that great of a detail. However, for those that do, these advances have made possible looking at things that would have been unimaginable 20 years ago. It kind of makes me wonder – 20 years from now, what kind of microscopes will we have? And what currently unimaginable things will we be able to see? Individual atoms? Subatomic particles? Now that’s what I call small!

Class is in session!

2007-08-27T09:35:00.000-07:00

With the advent of September, children all across the country are gearing up for another year of backpacks, books, and peanut butter and jelly sandwiches. That’s right, it’s time for school. In school, children develop new skills, learn new information, and establish patterns of thinking and behavior that will serve them their entire lives. And their teachers - people whose jobs it is to teach others what they do not already know – are one of the driving forces behind the process.

Teaching sounds so simple that you might be surprised to learn that it has always been believed to be exclusively human. You might think that there are many examples in nature of animals teaching each other. After all, don’t mother cats bring live mice to their kittens to show them how to kill and eat live prey, and don’t baby birds learn how to fly from their mothers? True – but that’s not the kind of teaching behavioral scientists like to study. There are, in fact, two kinds of teaching – social teaching and active teaching.

In social teaching, a youngster learns by watching and copying adults performing a task. In active teaching, an individual is a teacher if it changes its behavior in the presence of an uninformed observer at some initial cost to itself. This change in behavior sets an example so that the uninformed individual learns more quickly than it would on its own. In social teaching, knowledge is passed on passively, without deliberate initiation by the knowledgeable individual. In active teaching, the teacher initiates the instruction solely to pass knowledge along. Thus a young duck learning to migrate by flocking south with other ducks was not “taught” the process, since the experienced ducks would have flown south regardless.

Here is classic example of social learning. Dr. Michael Noonan is a professor of animal behavior at Canisius College. He has reported how orcas in a Canadian marine preserve set “water traps” to catch and eat seagulls. In one case, one orca (Alpha) set the trap with apparent success; some weeks later, the killer whale’s brother (Beta) began setting the same trap. After study, Dr. Noonan concluded that this was the result of Beta watching Alpha and then mimicking the technique, not due to an active teaching role of Alpha. Alpha was not a teacher. He was merely an example.

While there are many examples of social teaching in nature, scientists have only recently proved that active teaching takes place in non-humans. The results come from two surprising animal species – a tiny British ant (Temnothorax albipennis) and the plains-dwelling meerkat (Suricata suricatta).

In one study, Drs. Nigel Franks and Tom Richardson from Bristol University showed that ants use a technique called “tandem running” to teach each other about a source of food. This technique involves an ignorant ant (the student) closely following an experienced ant (the teacher). The student uses its antennae to periodically stop the teacher to determine its location relative to local landmarks. This process results in a slow initial journey to the food of interest (in fact, at least 4 times slower than the teacher would take on its own); however, the student learns the location of the food so well that it subsequently takes any number of paths to and from the food without the need for random foraging. The scientists concluded that all the requirements for active teaching are in place, thus proving this ant species as the first non-human species to teach each other.

Shortly thereafter, Drs. Alex Thornton and Katherine McAuliffe from the University of Cambridge demonstrated teaching in wild meerkats. Meerkats live in social groups of a dominant male and female (who produce the pups), a variable number of adult helpers (who rear the pups), and the pups themselves. The meerkat diet consists of insect and animal prey, some of which can be quite dangerous to an untrained pup. A scorpion sting, for example, can be crippling or even lethal for an animal the size of a meerkat. Thornton and McAuliffe showed how the helper meerkats teach pups to disable and then eat scorpions without being stung. This teaching takes more time and effort for the helpers than would merely providing the pups with a diet of dead scorpions. However, it results in a decreased scorpion sting rate and faster development of the hunting skills for the pups. Again, the data was clear. Meerkats, like humans and British ants, actively teach their young.

So this marks the first non-human species to be proved as engaging in active teaching. (Of course, I suspect they probably do not wait until September to start their lessons as humans do.) Admittedly, ants, being insects, do not have nearly the same appeal that meerkats do. So while ants are able to teach each other, I suspect it’ll be a while before we see any television shows featuring “The Ant Food Finding School.” But for all of you who enjoy watching “Meerkat Manor” on Animal Planet, I’d like to propose a possible sequel on the Learning Channel. It’s called “Meerkat Elementary School.”

What is it about tickling?

2007-08-24T09:16:00.000-07:00

In a recent entry (“Let’s talk about feet”), I discussed some of the amazing features of human feet, including the fact that feet are ticklish. That sparked a question in my mind – what makes us ticklish? Why are some parts of our bodies more ticklish than others? Why are some people extremely ticklish, while others can stand seemingly hours of feathers-on-the-toes temptation without even cracking a smile? And is it really true that you can’t tickle yourself?

Ticklishness is neurologically hardwired into our brains. The sensation of tickling is controlled by a highly developed part of the brain called the cerebral cortex. The cerebral cortex is one of the largest parts of the brain; it contains all of the centers that receive and interpret sensory information, initiate movement, analyze information, reason and experience emotions. Neurologically, a ticklish response is similar to a developed defense response against dangerous creepy-crawly critters like poisonous spiders and bugs. This explains why we tend to be ticklish on exposed or vulnerable parts of our bodies – like our feet, armpits and stomachs. Make sense, right? The sensation of tiny little legs crawling across my toes would easily make me jump, brush the area vigorously, and remove whatever’s causing the feeling. Sounds a lot like what happens when someone tries to tickle my feet!

Ticklishness might be more than simply a neurological phenomenon, though – scientists also believe that it is a learned response. Two essential factors must be in place for tickling to occur. First, there must some form of a mock attack. Someone else must be coming at you in such a way that your brain interprets as potentially hostile. But second, and equally importantly, there must be a perceived lack of real threat. In other words, I must believe both that you can make me laugh uncontrollably and that you won’t actually hurt me in the process. If a good friend suddenly tickles you from behind, both of those criteria are met – it’s startling, surprising, and maybe initially scary, but there’s also no real threat. As the Encyclopedia Britannica says to describe when a child will find tickling enjoyable, “The child will laugh only – and this is the crux of the matter – when it perceives tickling as a mock attack, a caress in mildly aggressive disguise.”

Tickling also has a relational aspect. Robert Provine, professor of neuroscience at the University of Maryland, Baltimore County and author of "Quest for Laughter", believes that tickling is an important form of non-verbal communication. For children, tickling is most often done during a time of playing, either with their parents, siblings, or playmates. Above the age of puberty, tickling usually is a form of flirtation, and is often done in the context of a sexual relationship. All in all, Dr. Provine points out that tickling is always done between people who have a good relationship – parents and children, siblings, good friends or spouses. Strangers or coworkers don’t usually try to launch a tickle attack!

So what about the idea that you can’t tickle yourself? Once again, our brains provide the answer. The human brain knows what feelings to expect whenever the body performs a certain motion. The region of the brain that controls this is called the cerebellum. The cerebellum is a relatively primitive region at the base of the brain that monitors movement and sensation. We don’t pay attention to most of these things – for example, our brain ignores the feeling of clothes on our skin. If we had to pay attention to every sensation our bodies experienced, we’d be overwhelmed! Instead, our brains are wired to pay attention to startling, surprising or unexpected sensations. This is the neurological reason why we can’t tickle ourselves. When you move your hands towards your feet, your brain expects the associated sensations, realizing “Oh, it’s just me. No problem.” Without the surprise, unease, or feeling of mock attack, it simply doesn’t tickle. That’s not to say that you can’t stimulate the nerves in your feet to feel funny when you try – but you’re probably not going to break out laughing in the same way as if someone else was doing it to you.

And just in case you were wondering, humans are not the only ones who are ticklish. Chimpanzees have been observed tickling each other when playing. (Does that qualify as monkeying around?) And even other animals can get in on the fun. In 1999, two neurobiologists at Bowling Green State University published results from a tickling study on rats. When the rats were tickled at the napes of their necks, they chirped and kicked their feet. I guess that’s what it sounds like when a rat giggles!

The "small animal, short life" phenomenon

2007-08-20T10:35:00.000-07:00

The question of why we get old is a very hot topic in life science research right now. (Of course, it’s been a hot topic of human interest for hundreds of years! Consider the story of Ponce de Leon and the quest for the fountain of youth.) But only relatively recently has science delved deeply into what makes us age. There have been lots of theories put forth over the years to try and explain aging. Many years ago, scientists studying aging discovered something interesting, which is this: the predicted life span of a mammal generally correlates with its body size. To explain this, let’s take a look at some examples, and I’ll show you how it works.

Your standard pet gerbil, weighing in at around 0.3 pounds, will live somewhere between 2 and 4 years. Holland Lop rabbits, a bit heftier at 5 pounds, can be expected to last 7 to 12 years. Golden retrievers, around an average of 70 pounds, usually survive 12 to 17 years. Let’s move away from domesticated pets and head on up mammal size chart. How about camels? Weighing in at 1,500 pounds, they hang around an average of 40 years. Going even larger still, elephants, which weigh anywhere from 6,000 to 16,000 pounds, typically live somewhere around 70 years. And what about the largest mammal of all, the blue whale, being a hefty 100 tons? Since whales don’t have teeth, which are typically used to determine age, it’s a little difficult to say exactly. But some scientists believe that blue whales can survive upwards of a hundred years. In fact, if you were to pick a mammal at random from the entirety of the natural world, you’d be pretty safe betting how long it could be expected to live based on its average body mass.

This brings up an interesting question - why do big mammals live longer than little ones? Perhaps it’s because bigger mammals are harder to eat than smaller ones, and are less likely to turn into someone else’s dinner! I’m just kidding. The average life spans I’ve listed above are the length of time until a “natural” death, not death from predation or disease. Actually, scientists really don’t know why small animals live short lives. It might have something to do with metabolism and metabolic rate, or it might be related to the fact that small mammals produce babies extremely rapidly. The question is still up for debate.

But now that I’ve said all that, here’s what I find really the most interesting. There are some very notable exceptions to this “small mammal, short life; large mammal, long life” phenomenon. And just as scientists don’t know why small body size usually means short life span, they also don’t know why some animals are completely off the charts.

One animal I find particularly intriguing is the bat. Even though many people don’t like them, bats have a ton of interesting features that I might discuss in a future entry. For today’s purposes, suffice it to say that bats live much, much longer than you would expect for their size. On average, though they have a high infant mortality, once they reach adulthood, they live between 10 and 30 years. The oldest bat ever recorded was a wild caught banded little brown bat, 34 years old. Amazing, considering the average banded little brown bat weighs in at 8 grams – or 0.01 pounds. Comparing different animals, in fact, bats live longer per ounce of body weight than any other mammal on earth. The only mammal capable of true flight, with the ability to echolocate and an amazing anatomy, is also the longest-lived per ounce. Who would have thought that?

Let's talk about feet

2007-08-16T10:12:00.000-07:00

Today’s topic – the wonders of feet. That’s right, feet. I don’t know exactly why, but I find feet to be one of the more fascinating parts of human anatomy. They are an incredibly intricate and complex piece of the body, stand the heavy stress of bearing our full body weight every single day, take a lot of abuse by getting crammed into uncomfortable shoes, and are generally ignored. (Unless, of course, you’re talking about tickling – but more on that later.)

Here are a few of the more amazing facts about feet that I’ve come across:
-Human feet contain over a quarter of the bones found in the entire body – 26 bones per foot (or 28, depending on how you count).
-There are approximately 250,000 sweat glands in the average pair of feet – that’s enough to produce a pint of sweat every day.
-When you walk, you produce 2-3 times your body weight in pressure on your feet. When you exercise, the pressure gets even worse – they can cushion as much as a million pounds of pressure in 1 hour of strenuous activity!
-The average individual will walk over 115,000 miles over his lifetime – that’s enough to go around the world 4 times.
-The skin on the soles of your feet is 20 times thicker than the skin on the rest of your body.

Incredible, isn’t it? These amazing pieces of anatomy at the ends of our legs just keep on working, day in and day out, bearing enormous pressures, step after step. But do you want to know the thing that I find the most intriguing of all? For all the strength and resiliency of our feet, they are also one of the most sensitive areas on our bodies for being tickled. I know some people who can’t stand anyone else touching their feet, because it tickles too much. They can stand on them for hours, walk thousands of steps, balance on one or the other, and clothe them in socks, shoes and slippers of various materials, and yet a delicate touch by human fingers is unacceptable.

Personally, I find it fascinating how this part of our anatomy is put through such rigorous and grueling use – and yet is still sensitive enough to reduce us to helpless giggles.

Science involves all the fun activities!

2007-08-15T11:24:00.000-07:00

"Science involves all of the fun activities--sitting still, being quiet, paying attention, writing down numbers--yes, science has it all!"
--Principal Skinner, “The Simpsons”

I’m a scientist. Actually, I’m a post-doctoral fellow in the field of cellular and molecular biology, but that’s rather a mouthful, so I usually just say I’m a scientist. I work in a research lab, conducting experiments, collecting data, writing results. And if you were to follow me around on any given day, what you’d see is a lot of the following: looking through a microscope, typing numbers into my computer, reading papers about other people’s experiments, and sitting at my desk, thinking about what experiments I’m going to do to repeat the whole process the next day. Sounds like Principal Skinner was right – I do a lot of sitting still, being quiet, paying attention, and writing down numbers!

But I’m here to tell you, all this notwithstanding, that science is fun.

That’s right, science is fun. It’s exciting. It’s cool. It’s got a lot of gee-whiz-ness to it. There’s always something new, something unexpected, something that’s, quite frankly, downright unbelievable. Granted, the things I find fascinating do not all come directly from my lab bench – or my department, or even my institution. But it comes from scientists out there just like me. Let me give you a few examples of some of the latest science tidbits I’ve learned recently that make me sit up say “wow.” Did you know…
…that if the nerves in your skin were stretched out end-to-end, they would reach an average of 45 miles - almost the same distance as from the northern to southern edge of Rhode Island.
…that the average human cell contains enough DNA to wrap around the outside of the cell 15,000 times – yet it is packaged tightly enough to fit with no trouble.
…that bats have a ridiculously long life span for being such a small mammal. They can live up to 20 or 30 years– even though other mammals of comparable size, such as mice and rats, typically only live a few years.
…that there are places in the Atacama desert in Chile, sandwiched between the Andes mountains and the Pacific ocean, that do not see any rain for hundreds of years at a time. Some spots have been rainless for 400 years! Still, some plants, animals, and even humans live there – sustained by tiny pockets of fog that come in from the ocean.
…that the magnetic field of the earth wanders – and sometimes the poles even completely reverse themselves! This happens fairly infrequently, though – reversals happen sometime between every 5000 to 1 million years.

With this blog, I plan on discussing these and other wonders of the scientific world. I plan on writing about a variety of topics, including life sciences, medicine, astronomy and geology. Some of my topics will be brand new discoveries, and others will be long-known items that I find particularly intriguing. My hope is that you will come away from everything that I write knowing something that you didn’t know before. And I hope that it tickles your interest. Let the wonders begin!