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.
Tuesday, September 25, 2007
Friday, September 21, 2007
Zzzzz....
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.
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.
Monday, September 17, 2007
When is a kilogram not a kilogram?
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.
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.
Friday, September 14, 2007
Much Ado About Nothing
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."
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."
Tuesday, September 11, 2007
A tribute to Alex
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.
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.
Friday, September 7, 2007
A beautiful insect
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!
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!
Tuesday, September 4, 2007
The Power of Modern Microscopes
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!
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!
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