Monday, 27 August 2012

Eyes are weird

And the award for the weirdest, craziest, most mind-bogglingly boggled piece of the body goes to...THE EYE.

The eye is often held up as the pinnacle of biological design. It's not. It's a backwards mess. An awesome backwards mess, yes. A useful and wonderful backwards mess, yes. But it's still a mess. There's all sorts of ways in which the eye seems like something that evolution bashed together during a hundred million bad days. It's amazing that it works at all.

Anatomy of the eye. The retina covers the whole back layer of the eye. The optic nerve goes to the brain. From

WEIRD THING #1: Your eye is upside-down
The lens flips images, so they are upside-down when they hit the retina

When you see something, what you're seeing is light reflected off objects and into the eye. This light passes through a part of your eye called the lens. The lens focuses light, making images nice and sharp, and letting you see things that are close or far away. It focuses the light on the retina, which is a layer of neurons at the back of your eye. But because of the way the lens works, the image gets flipped, so what the retina sees is upside-down. The retina sends the picture to the brain. It's the brain's job to flip it so it's right-side-up again.

WEIRD THING #2: Your eye is backwards

Close up on the retina. From
The retina is made up of lots of cells. Some of these cells are specialized neurons called rods and cones. The job of the rods and cones is to sense light, and send this information on to your brain. But the rods and cones are at the back of your eye, as far away from the light as it's possible to get and still be part of the eye. All the cells that the rods and cones connect with on the way to the brain are actually closer to the image than the rods and cones are. Light has to penetrate through all those cell layers to hit the rods and cones. Those cell layers filter the light, so it's dimmer than it was at the start. It's kind of like the eye's version of flying from San Francisco to San Diego with a stopover in New York. You still get to San Diego, but only after going thousands of miles out of your way. And because you went so far out of the way, you're tired and cranky and not feeling very bright.

WEIRD THING #3: When your eye turns off, your brain turns on

When rods and cones sense light, they turn off. Yeah, that's right. Off. In the dark, your eye is "on". In the light, it's "off". Which, in my mind, wins the award for the silliest of all the silly eye things.

The rods and cones send information (in the form of action potentials) to another layer of neurons in the retina called the retinal ganglion cells (RGCs). (This is one of those layers of cells that light has to pass through in order to hit the rods and cones in the first place - in the picture its the layer closest to the light).
When the rods and cones are on, they release a neurotransmitter which inhibits the RGCs. "Inhibits", in this case, just means "turns off". So here's how this works:

The light is on
If I flip on the lights in my room, my rods and cones turn off. They stop inhibiting the RGCs, and the RGCs turn on. They then send action potentials to the brain, which interprets the message as light.

The light is off
If I flip the lights off, the process reverses. The rods and cones turn on and start to inhibit the RGCs. The RGCs stop talking to the brain, the brain interprets this as darkness.

In pop culture there's a phrase: "Go into the light." If someone is dying in a movie, (usually in a hospital bed with no hope of recovery), they say, "I see a light!" and other people say, "go into the light!" The light is supposed to be the afterlife. It's not. I don't know if there's an afterlife, but I do know that "the light" isn't evidence of one. But "the light" is real. People who have near death experiences often report seeing a bright light. But what they're seeing is their rods and cones turning off as their eyes start to die. The rods and cones turn off, and the brain interprets this as bright light.

I think that's a pretty neat factoid. As weird as the off/on thing is, it's also super cool. Like I said, the eye is a cobbled-together mess. But it's a fascinating cobbled-together mess. I love it. It's this sort of slap-dash path to awesomeness that is one of the things that makes me so excited to learn and teach about the brain.

Monday, 20 August 2012

ACTIVITY: 2-point discrimination (a.k.a. meet your homunculus)

Ever wonder how the brain processes all the information from your senses? Your brain has to constantly be aware of what you're seeing, hearing, smelling, tasting, and feeling. It has to know what parts of your body are moving and what parts are still. That's a lot of information to keep track of. Today we're going to do an activity which will show you how the brain "sees" your body. This activity is about your sense of touch, but the punchline applies to all your senses and also to muscle movement. I usually do this activity with middle school students, but I the first time I did it when I was in high school.


1 friend or parent. This is a two-person activity.
2 things you can poke with. The tips should be as small as you can get them without them actually being sharp and painful. Sharpened pencils work well, or un-folded paperclips, or compasses from math class. For the rest of the experiment, I'm going to call these "the pokers".
1 pencil, or some other thing you can write with.
1 ruler
This chart (print or copy it down, whichever works for you):


1.      Have your partner close their eyes. If they peek, the experiment won't work. 

2.      Take your pokers, one in each hand, and press them into your partner's upper arm at the same time. Have them spaced about four inches apart. You should press just hard enough that your partner feels them, not so hard that it hurts. If your partner is wearing sleeves, have him/her roll them up first. The experiment works best on skin. Ask your partner how many pokes they feel. They should say "two".

3.      Move the pokers closer, and ask how many pokes you partner feels. Keep moving them closer until your partner says "one."
4.      Now move the pokers farther apart, in tiny steps, just until your partner says "two." Then move them closer, until your partner again says "one". Your goal is to find the point where your partner stops feeling two pokes and only feels one

5.      Use the ruler to measure the distance between the two pokers.

6.      Write the distance on the chart, in the section for "Partner #1" and "Arm".

7.      Repeat steps 1-6, this time on the fingertips, the palm, the back, the leg, and the bottom of the big toe. Write down your answer on the chart. Do you notice anything?

8.      Now reverse the roles. Let your partner poke, and you close your eyes and try and see whether you feel one thing or two things.


In some places on your body, like the fingertips, the distance at which the person first feels only one poke is very small. At other places, like the back, the distance is very big. What does this mean for your brain?

Every part of your body is covered in sensory neurons. (If you don't know what I mean by "neuron", read this post.) These neurons carry touch information to your brain. Your brain has a certain amount of area set aside for processing the touch information it gets from each part of your body. In the activity, the distance number for the fingertip was very small. This is because your fingertips are covered with lots and lots of neurons, which makes them more sensitive. More sensitivity means that your fingertips are able to feel small or light things. These neurons go to your brain, which has a huge amount of space set aside for all those neurons. Close your eyes, grab an object, and run your fingers along it. Can you tell what it is? Most of the time, you can. That’s because there’s so many neurons carrying touch information from your fingers to your brain.

How about your back? The distance you wrote down for your back was probably very big, maybe the biggest number you got. What do you think this means? The touch neurons in your back aren't nearly as dense as they are in your fingertips. Because there’s fewer neurons, it’s more difficult for you to tell the difference between one poke and two pokes. There's also much less brain space for your back. If you think about it, this makes sense. Do you need to have sensitive fingers? Yes. Does your back need to be sensitive? Does it type? Or write? Do you stick your back into your pack, rummage around, and find your lunch? No! You use your fingers! Your back doesn't need to be super-touch-sensitive.

Now think about the other parts of the body that you tested. Was the number big or small? Why? Think about what you use the part for. Does it need to feel things with high sensitivity in order to work? How sensitive do you think the parts of your body that you didn't test are? (Like your cheek or your stomach.) Test them. Were you right?



Remember how I said that each body part has a certain amount of space in the brain? A neuroscientist named Wilder Penfield figured out just how much, and realized that your brain actually contains a map - a mini-you, with all the parts there. The size of the parts is relative to how touch-sensitive they are. Penfield came up with this drawing, which he called the "homunculus". ("Homunculus" means "little man".)

Your sensory homunculus. Imagine putting a knife at the top of the brain, so that is was on a line from one ear to the other, and slicing down. You'd get a slice that looks like the yellow part of the picture. (See the pic of the brain in the corner if you don't understand what I mean. The right side of that pic is the front of the brain). The yellow part is actual brain. The pink body parts are an adaptation of Penfield's original homunculus drawing.


Your brain sees the world in maps. The maps are distorted, depending on how you use each sense, but they’re still maps. Almost every sense has a map. Most senses have multiple maps. You have a "tonotopic" map, which is a map of sound frequency, from high-pitched to low-pitched, which is how your brain processes sound. You have a "retinotopic" map, which is a reproduction of what you're seeing, and it's how the brain processes sight. Your brain loves maps.

You even have maps of your muscles. This is a picture of your motor homunculus, which is how your brain “sees” and controls your muscles. It's on the right. Compare it to your sensory homunculus, on the left.

Touch is on the left, muscles are on the right. What's different?

If you took your motor homunculus, and made a model that looked like an actual "little man", this is what you'd get:

Motor homunculus. Check out the mouth and fingers! Huge! Think about it. Of all the muscles in your body, the ones in your fingers and mouth have to do the most precise, intricate movements. Otherwise, you wouldn't be very good at talking. (from

Let's relate this back to the activity. Look at the picture of the sensory homunculus (the first pic). Huge fingers, small back. Big lips but not much of an arm. The more touch sensitive an area is, the more brain space it has. For muscle movements, the finer, more detailed the movements are, the more brain space those muscles have. Cool, huh? Just wait until you see what happens to the maps if you lose a finger. That's a real mind-blower. (Future post alert!)

Tuesday, 14 August 2012

Phineas Gage

WARNING! This post contains graphic images of an injury to a skull and brain. Older kids and adults only, please.

Phineas Gage and the tamping iron.
A while ago, I said that Henry Molaison (a.k.a. HM) was the most famous patient in the history of neuroscience. I think, on reflection, that I was wrong. Since I study learning and memory, HM is more relevant to my work than the man I’m going to talk about today. But if I’m being honest, HM is only the second most famous patient in the history of neuroscience. Phineas Gage is the first.

He’s also the first patient. You could argue that the moment that spike went through Phineas Gage’s brain was the moment that neuroscience was born. The first neuroscientist (the man we consider to be the father of neuroscience), Santiago Ramon y Cajal, wasn’t even born until four years after Gage’s accident.

In 1848, Gage was a railroad foreman. He was setting up an explosion, using a tamping iron to pound blasting powder into a hole deep in a rock. A tamping iron is a long, metal rod. The iron struck the rock, there was a spark, and the powder exploded. The tamping iron shot through Gage’s cheek, out through the top of his head, and landed on the ground 80 feet (25 meters) away.

The first amazing thing about this story is that Gage didn’t die. This was a time before antibiotics were widely used. He not only survived a spike shooting through his brain, but he also survived any infection. Major props to Dr. John Harlow for keeping Gage alive.

But it wasn’t until after Gage recovered that things got really amazing.

Before the accident, Gage was reliable and intelligent, an energetic worker, and just an all-around good guy. After the accident, he was rude and unreliable. He couldn’t hold down work. He urinated in public. He had a terrible temper. He was a different person than the one he’d been before.

Holy cow! Phineas Gage suffered an injury to the brain, and his personality changed completely! How?

The rod went through an area of Phineas Gage’s frontal lobe called the prefrontal cortex. The prefrontal cortex is what makes humans human. Specifically, Gage lost the sections that are important for decision making, planning for the future, and impulse control and following social rules (i.e. the bits that tell you it isn’t okay to urinate in public or swear at fancy ladies). All the bits of the brain responsible for muscle movement, language, and basic survival were still present. So Phineas Gage survived, and he could still walk and talk, but personality-wise, he was unrecognizable.

A digital reconstruction of Phineas Gage's injury. This is just a computerized image, not a real brain! I'm showing you this because I want you to see exactly where in the brain the injury happened. This is from a study done by Hanna and Antonio Damasio.

The prefrontal cortex is in yellow. From Wikipedia.

This is all super-interesting from a basic neuroscience standpoint, but it’s also super-interesting from another perspective. Something as small as railroad spike changed Phineas Gage from a person of virtue to a person of disgrace. If a brain injury can change our personalities, what does that say about who we are? Are we, in the end, just a product of neurons firing, or is there something more? I know what I think, but it’s up to you to decide what you think.

And here are some more questions for all the budding neuroscientists out there. Serious brain injuries happen to people every day, and not all of them can be fixed. Phineas Gage died over 150 years ago, but knowing what we know now, we still wouldn’t be able to return him to the person he was before the accident. But maybe that's just because we don’t yet know enough. So here are the questions: Is it reversible? And if it is, how? What do we still need to learn? If you decide to be a neuroscientist, you might be the one who figures out how to fix the modern-day Phineas Gages.

Thursday, 9 August 2012

Olympics special: Think your way to success at sports

The Vancouver Olympic torch. That was such a fun two weeks.
          Okay, I admit it. That title’s a bit of a lie. You can’t become good at sports just by thinking about it. But you can give yourself a leg up, pun totally intended. Training your muscles is critical, but there’s no question that thinking in the right way can increase your chances of doing well in sports.
          I’m not talking about dreaming, or wanting, or never giving up, or all that other stuff that Olympic sportscasters talk about. Drive and desire are important. They’re as critical to sports as to, say, getting your Ph.D. in Neuroscience. But drive isn’t what this post is about. This post is about a very specific way of training your brain, so that your brain is better at training your muscles.
          But before I get to that, I first have to give you two crash courses:

Crash course 1: Learning in the brain

          In this blog, I’ve talked a lot about neurons, which are the cells that make up your brain. Neurons connect to each other at points called synapses. When neurons are active (we call this “firing”), they release chemicals at the synapse. This is how neurons talk to each other.
          When you learn, you’re causing certain neurons to fire over and over again. This repeated firing causes your synapses to change. They become more sensitive to neurotransmitters. They become stronger. These changes last from days to years. This process underlies learning and memory. From a cellular neuroscience perspective, learning and memory are the same thing.
The synapse is where neurons talk to each other, and it's where learning happens. (All the other labels are various parts of neurons - see this post)

Crash course 2: How the brain controls muscles

The parietal lobe, cerebellum, and spinal cord.
          Let’s pretend that I want to get to my kitchen, because I’m hungry. First, an area in my brain called the parietal lobe brain comes up with a lot of possible plans. I could get to my kitchen by skipping, sprinting, uncoordinated somersaulting, or walking. The parietal lobe sends these plans to another brain area called the basal ganglia. The basal ganglia picks “walking” as the best plan (though uncoordinated somersaulting was a close second). It tells the parietal lobe the plan. The parietal lobe confirms it, and sends the "walk-to-kitchen" plan down the spinal cord and to the muscles. The muscles move. As they move, my cerebellum kicks into high gear, making sure I turn right just before I crash into my kitchen counter, and that I jump over my dog (he loves to get in my way and beg for cuddles). Part of the cerebellum’s job is to make quick changes to muscle movements while they’re happening.
The basal ganglia are blue. The caudate, putamen, and globus pallidus are all part of the basal ganglia. The amygdala is not - its job is emotions, not muscle movement. In real life, the basal ganglia are located deep inside the brain. You can't see them from the surface.

          This involves a lot of neurons, and a whole lot of synapses. Millions of synapses would be a low estimate. Since synapses are where learning happens, that’s millions of chances to learn.

How do you think your way to success at sports?

          You visualize. Over and over and over again. Picture those movements. See yourself catching that ball. Dancing that toe-touch. Swimming that breaststroke. Watch it in the movie of your mind whenever you can. Scrutinize it. Is your wrist turning properly? Is your kick high enough? If not, change the picture. See yourself doing the movement perfectly.
          As far as your parietal lobe and basal ganglia are concerned, this is exactly the same as doing the movement. By visualizing the movement, you activate all those planning pathways. Those neurons fire, over and over again. Which is what needs to happen for your synapses to strengthen. In other words, by picturing the movements, you’re actually learning them. This makes it easier for the parietal lobe to send the right message to the muscles. So when you actually try to perform a movement, you’ll get better, faster. You’ll need less physical practice to be good at sports.
          This doesn’t work for general fitness. You still need to train your muscles and heart and lungs to become strong. But it’s very good for skilled movements. Basketball lay-ups. Gymnastics routines. Six months ago I earned a black belt in taekwondo. I’m certain that one of the reasons I passed the technical portion of the test is that I visualized my forms, kicks, and self-defenses over and over and over again, whenever I could. (The physical test was another matter – the only way I was going to get my body to do 150 push-ups in 5 minutes was to do a gazillion training push-ups, and I HATE push-ups.) But for techniques, visualization worked like charm. I trained my brain, and that made it easier to train my muscles. This doesn’t only work for sports. Music, for example, also requires skilled muscle movements.
          So if you find yourself sitting around with nothing to do, or bored in the shower, or lying in bed trying to fall asleep, turn on your mind-movie, and picture yourself doing your sport. Keep it up, and I’ll bet you improve.

Two more years until the next Olympics action! This picture was taken at Vancouver 2010, so the countdown's a wee bit off now.

Saturday, 4 August 2012

Olympics special: Exercise makes you smarter

It's the Olympics! Woohoo! I love the Olympics, so I'm going to celebrate with a series of sports-and-brain related posts.

Taken by me at the Vancouver 2010 Opening Ceremony. Awesome, eh?
          You are born with hundreds of billions of neurons in your brain. They wire together in vast networks that control all your thoughts and feelings, and everything that you do. And then they start to die.
          I've got some bad news for you. Throughout most of your life, your brain cells are dying. The good news is, that isn't always a bad thing. You're born with more neurons than you need. When you're very young, those extra neurons die, but that's okay. If they all wired into the network, it would be like being stuck in an overcrowded room with 50 different people trying and have deep conversations with you while the lights flash and the floors rumble and the music blasts forever. In other words, it would be too much for your brain to handle. You'd have a seizure. Really. That's not an analogy. If those extra neurons didn't die, you would seize. So it's a good thing that some neurons die during infancy and early childhood.
          But not all neuron death is good, especially when you're older. There's a group of diseases called the neurodegenerative diseases, where too many neurons die, leading to difficulties in memory, muscle movement, learning, and, in many cases, death. Even in healthy people, neurons are always dying. About 5-6% of them die every year. This is a large part of the reason why even healthy elderly people are less able to remember things. Even people in their late 20s, like myself, don't learn or remember as well as they did when they were kids.
          The good news is, you can slow this down. The better news is, even though your neurons are always dying, they're also always being born. You have a potentially endless supply of new neurons just waiting to be born. This is huge news. It's the great big thing in neuroscience right now. When I was in school, I was told that new neurons were never born. A person was born with all the neurons they would ever have, and once those neurons started to die, too bad! There was nothing to be done. But thanks to the work of neuroscientists over the last decade, we now know that this is a myth! New neurons can be born. Thank you, neural stem cells!

This picture shows new neurons being born in an area of the brain called the hippocampus, which is important for learning and memory. The red neurons are the newborn ones. I got this picture from Wikipedia, but it's originally from Faiz, et al., BMC Neurosci, 2005

           And not only are new neurons being born all the time, but you can increase the rate at which they're born. You can make new neurons! You can slow neuron death! You can't reverse the process completely, but you can start to apply the brakes.
          One way is to keep your brain active. Do puzzles, learn new things, debate issues, read books, and for the love of all that is good and brainy, get away from that TV.
          The other way is to keep your body active. That's right! Exercise your way to a smarter brain!
          One of the hot topics in neuroscience right now is that exercise increases neurogenesis. "Neurogenesis" means "neuron birth". When you exercise, new neurons are born. This translates to better memory and faster learning. You don't have to do much. No one's asking you to be an Olympian. But take the stairs instead of the elevator. Bike a mile instead of driving. Grab a ball and some friends and get your sport on. The type of exercise doesn't matter, just that you do it.
           Keeping both your brain and body active is a great way to slow neuron death, increase neuron birth, and increase the number of connections that neurons make with each other. That means faster learning and longer-lasting memories. To me, that sounds like an excellent reason to work up a sweat.

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I now have a Twitter account! Holy social networking, Batman! You can follow me at @TheBrainGeek, and get fun brain thoughts and facts that don't make it on to the the blog.

Wednesday, 1 August 2012


            Before I start the post, a little something for your viewing pleasure:

           Why am I showing you a video of a man walking around obstacles? If you read the title of the video, you already know (darn Blogger and YouTube giving away the punchline!). But I'll tell you anyway.
           This man is blind.
           That's right, blind. As in, unable to see. But look at him avoid the obstacles! If he's blind, how's he doing it?
           This blind man is able to avoid the obstacles thanks to a phenomenon known as blindsight. Blindsight exists because not all blind people are actually blind. Some of them can see. They just don't know they can see.
            To understand blindsight, you need to know how visual information is processed in the brain. Here's a picture of the brain's visual pathways:

This picture shows how visual information moves from the eyes into the brain.

            Visual information leaves the eye via the optic nerve. The optic nerve splits, and sends information to the lateral geniculate nucleus (LGN) and superior colliculus (SC). Both areas get the same information from the eyes. In other words, both areas "see" the same thing.
            The pathway from the LGN to the visual cortex is the conscious pathway. When you see things, and know that you see them, that's visual information moving through the LGN to the visual cortex.
            When visual information moves through the SC however, you aren't conscious of it. It doesn't go to the visual cortex, and you don't know that you see it. But it's still very important. Most animals have an SC. Not all animals have a visual cortex. Amphibians have an SC. They don't have a visual cortex. Humans have both.
            Imagine you're a frog. A black dot buzzes across your vision. Do you sit there and ponder it? What is the meaning of the black dot? Is it food? If it's food, is it tasty food? Are you hungry enough to eat the black dot raw? Or do you feel more like a dragonfly stir-fry instead? Or are you hallucinating, and the black dot is only a figment of the imagination. And if the black dot is only a figment of your imagination, what does that mean about you? What's the meaning of life, anyway?
            Or, instead of pondering for an age and a half, do you just eat the black dot?
            You, Mr. or Miss. Frog, will stick out your tongue and snatch that black dot, because it's a fly and flies fly and you want to eat it before it flies away.
            But you don't think about it.
            My point, with the whole black dot story, is to give you an example of a time when an animal needs to react to visual information very quickly, without time for thought. Eating something speedy, for instance. For humans, who don't often catch tasty flies on their tongues, avoiding danger is a time when we would want to react fast without thought. Or, walking around an obstacle that might make us trip and slam painfully to the ground. If you add thought into the mix, your reactions will slow down. Humans can think fast, but not that fast, especially when a baseball is heading for our foreheads at 100 mph.
            It's important to have an area of the brain that can respond to danger with lightning speed, faster even than thought. That's the SC. When you dive out of the way of a speeding baseball, it's the SC. If you've ever thought, "Wow! I can't believe I jumped out of the way so fast!", you can thank your SC. It doesn't need you to think and tell it what to do. It sees danger, and it acts.
            Back to blindsight...Imagine a scenario where an injury or a stroke wipes out your visual cortex, which is part of the LGN pathway. What does this mean?
            Well, your eyes are still intact. You can still see. But your conscious visual pathway is broken. You don't know that you can see.
            But - and here's the key - your SC still works. Which means that unconscious danger-avoidance pathway still works. So if a doctor starts to lead you down a obstacle-packed hall, just like in the video at the top of the post, you'll be okay. Your SC will keep you from running into things. If someone then asks why you made that sudden right turn, your answer would be something along the lines of, "I don't know. It just felt right." Because you don't know. You're acting without conscious thought. It's only later that you realized you moved.
            That's blindsight.
            It doesn't work for all blind people, only those with damage to the conscious visual pathways in the brain. You need working eyes to have blindsight.
             If there's a take-home message to this post, it's this: Not all blind people are completely blind. And blindness doesn't always happen in the eyes. The eyes can work perfectly, and the damage is in the brain.
             Another take-home message would be: The brain is awesome. But you already knew that.