Monday, 30 April 2012

Jet lag

                Last Friday afternoon I was sitting in my favorite coffee shop in Vancouver, Canada. It was bright and sunny (shocking, I know, for all those familiar with rainy Vancouver), and I was WIDE AWAKE.
            Then I got on a plane.
            For nine hours.
            After a 6 hour delay.
            The plane was delayed again for an hour in a holding pattern over London Heathrow Airport.
            I finally arrived in London, England on Sunday night, tired, hungry and dying for a shower.
            By 2 am, I was WIDE AWAKE.
            4 hours and a giant snack later, and I was still WIDE AWAKE.
            By Monday afternoon I was ready for a mega-nap.
            Darn jet lag...
            I’ve now been in England for a week, and my sleep schedule is finally sorted out.
            Have you ever been jet lagged? Ever wonder why? The simple explanation is that it’s because you’ve just jumped forward or back a number of hours, and this screws up your sleep cycle. But there’s a lot of interesting information hidden in that little blurb.
            First of all, why do we jump forward or back? Do you know why London is eight hours ahead of Vancouver? (Hint: The answer is in astronomy, not in neuroscience.)
            Why we feel jet-lagged is a quirk of neuroscience. We all have a clock in our brains called the circadian clock. The clock is on a 24-hour cycle, just like a real clock. Every day the clock resets itself based on light.
            When it’s dark, the pineal gland in your brain releases a hormone called melotonin. Melotonin acts like a neurotransmitter. At night, melotonin levels are high, and you are sleepy. During the day, when it’s bright out, melotonin levels are low.
Melotonin levels change over the course of the day. Chart modified from
            What happens if you suddenly jump forward eight hours, as I did last week? Your pineal gland can’t keep up with the sudden change. I landed in London at 7 pm (11 am Vancouver time). I’d managed a few hours sleep in the plane, and when I woke it was bright above the clouds. My brain thought it was morning. My melotonin levels were low. My pineal gland can’t read a clock, and didn’t know it was really 7:00 pm.
            Fast forward to 2 am that night (6 pm Vancouver time). My melotonin levels were still low, because my brain thought I was in Vancouver, where it was late afternoon. But it was actually the middle of the night. My melotonin levels should have been high. They weren’t. So instead of sleeping, I sat WIDE AWAKE in the kitchen of my cousin’s house reading a book and munching on toast and marmite. And cheesy crackers. An apple. I think there was a sandwich in there as well. Oh, also some brownies. I was hungry.
            The problem was that my body was in London, but my brain was still in Vancouver.
            It took a few days of normal, 24-hour cycling sunlight/darkness, for my brain to figure out that I wasn’t in Vancouver anymore.
            Now I’m well rested and happy. My melotonin levels are normal and I'm and loving my vacation! asleep

Friday, 20 April 2012


            For several posts now, I’ve talked about neurons and how they talk to each other. I described what a neuron is and the various parts, the action potentials that are triggered when you need to use your brain, and the neurotransmitters that are the words neurons use to talk to each other. Now it’s time to end that story with the synapse itself.
            The synapse is the space between the axons of one neuron and the dendrites of a second neuron. There are thousands of synapses on every neuron. Synapses are tiny. 1000 of them lined up in a row would be about as long as the head of a pin!
            Synapses are like neuron phones, or neuron mouths. They’re how neurons talk to each other. Have you ever heard the saying, “no man is an island”? It means that each person needs other people in their lives. No person can succeed all by themselves. Neurons are the same way. No neuron acts alone. Nothing in the brain happens because just one neuron fires. For anything to get done, lots of neurons have to talk to each other.
            Here’s a picture I drew, close up on a synapse:
             Remember, 1000 of these things can fit on the head of a pin. You’re looking at a tiny section of the axon and the dendrite, and the space between them, which is the synaptic junction. See the red and blue things? Those are ion channels. The red ones open when they sense a change in electrical voltage. I’ll talk about the blue ones later. The green circles are neurotransmitter vesicles. These are packages full of neurotransmitter. In the picture, the neurotransmitters are yellow stars.
            A lot of what I’m going to talk about is similar to the electrical stuff from the action potential post. Specifically, ion channels, and how positive ions like to move into the negatively charged neuron. At the synapse, the positive ion is calcium (Ca2+). You can imagine the synapse and the synaptic junction as swimming in a soup of calcium ions.
            When I left off, our action potential was charging towards the end of the axon at the speed of a racecar. What happens when it hits the end of an axon?
            This happens:
The five steps are:
  1. The electrical current of the action potential causes voltage-gated ion channels to open, and calcium flows into the axon.
  2. The vesicles “sense” the increase in calcium, and they know an action potential has just happened. They fuse to the membrane of the axon. (The membrane is like the axon’s skin.) The vesicles open up.
  3. Neurotransmitter flows out of the vesicles and into the synaptic junction.
  4. Neurotransmitter binds to the receptors. These are the blue things in the picture. Receptors are ion channels. Neurotransmitter makes them open, letting calcium, sodium, and other positively charged ions into the dendrite.
  5. The inside of the neuron becomes positively charged. If you remember your action potentials, you know that when the neuron becomes positively charged, it sets off a huge racing electrical current. So what do you think happens when the neurotransmitter opens the receptor channels? Yep. Of course you got it.
     Action potential!

      Now the message travels down the second neuron, and eventually to a third and fourth and maybe a hundredth or a thousandth neuron, until your muscles twitch or the lightbulb goes off in your head and you suddenly understand what your teacher was talking about.
      It takes a lot of receptors opening to start up an action potential in the second neuron. Sometimes it doesn’t happen at all, which is why you don’t notice a lot of what goes on around you, especially when you aren’t paying attention. The neuron can change the number of receptors on a synapse. In this way, some synapses become stronger, and more likely to trigger an action potential. That’s called learning, and if I’m doing my job, it’s happening in your brain right now.
            How? Well, that’s a subject for another post!    

Friday, 13 April 2012


            In an earlier post, I talked about what happens when neurons “fire”. When something important happens, electrical impulses travel down the axons of neurons in what is called an action potential.
            But what happens when the message gets to the end of the axon? Does it just flutter off into the vacuum of brain space? Of course not! The message transmits to the next neuron in line. If you see something you want to grab, your neurons need to talk to each other: a neuron in your eyes needs to talk to a neuron in the brain’s visual cortex which talks to a neuron in the brain’s motor cortex which talks to a neuron in your muscles. Except that a lot more than four neurons are chatting to each other. Thousands are. How do they all connect?
            Enter the synapse. This is the connection point between the axon of one neuron and the dendrites of another.
Zooming in on neurons and synapses. Picture from, arrows are my own.
            The synapse is a HUGE topic. Why? Because this is where everything happens. Personality, memory, mood, it’s all encoded here, in these tiny little synapses, thousands of which stud a single dendritic tree. (Not sure what I mean by “dendritic tree”? Check here).
            (Personal confession time! I’m biased. I like synapses so much because I study them in my lab. I’m interested in how brains grow, and how synapses are formed in young brains. By “young” I mean before birth through the first few years of childhood. I think synapses are a SUPER AWESOME FANTASTIC topic, so I’m going to spend several posts talking about them.)
            For two neurons to talk to each other, they have to have some way to communicate. Humans use words to communicate. Dogs bark. Bees dance. Birds sing. Neurons communicate with neurotransmitters.
            Neurotransmitters are chemicals, but you can think of them as the words that neurons use to talk to each other. Just like words, there are lots of neurotransmitters, and each one has a special meaning. Some cause you to feel specific emotions, like happiness or sadness. Some help you learn. Others move your muscles or make you feel sleepy.
            When an action potential reaches the end of an axon, the axon releases a neurotransmitter, which is received by the dendrite. I’ll talk about how this happens in a later post. Until then, think of the axon as waving down the dendrite, then shouting a bunch of words over and over until the dendrite gets the message.
            Here are some examples of the words, or neurotransmitters, that axons use:

    A neurotransmitter "word." This is serotonin.
  • DOPAMINE: This causes feelings of pleasure and reward. Addiction results from imbalances in dopamine levels. 
  • SEROTONIN: Another “happy” chemical. If you don’t have enough serotonin, you feel sad and depressed.
  • GLUTAMATE: This one is responsible for learning and memory.
  • ADRENALINE: You’ve heard of this one, right? It’s the “fear” chemical, but you can also get fun doses of it from roller-coasters or the last ten nail-biting seconds of a close sports game. Often, the brain releases glutamate at the same time as adrenaline. Can you guess why? (answer at the end of the post)
  • ACETYLCHOLINE: (Say: a-see-til-koh-leen) This chemical makes your muscles move. Snake venom works by preventing your muscles from recognizing acetylcholine. This causes paralysis and, if you don’t get to a hospital quickly, death.
  • ADENOSINE: Too much of this and you get nice and sleepy. When you wake up, adenosine levels in the brain are low, but they increase during the day until you just can’t keep your eyes open anymore and crash into your bed at night. The caffeine in coffee or soda works in part by making your neurons unable to respond to adenosine.

(Answer to the question: It’s to help you stay alive. If adrenaline and glutamate are released at the same time, you’ll have strong memories of scary things. You’ll avoid those things in the future, and stay alive longer.)

Wednesday, 11 April 2012

The folds of the brain

Thanks to Kiban for this post idea!

So wrinkly!
            If you’ve ever seen a picture of the brain, you know the brain is wrinkly. But what’s the purpose of the wrinkles? Because they do have a purpose, and it’s very important.
            The general rule of thumb is: more neurons = smarter brain. But the size of your brain is limited by your skull. This is where the wrinkles come in.
            The surface of your brain is called the cortex, and the cortex is the part of your brain that contains your neurons. The more surface your brain has, the more cortex it has. The more cortex it has, the more neurons it has. The more neurons it has, the smarter it is. All the better to see you with, my dear, as a certain wolf once said. (Or hear you with, talk to you with, play basketball with, and on and on and on.)
            This gets into a concept called surface area, which is usually something geometry nerds talk about, but it’s important for brain nerds too. Surface area simply means the amount of surface something has. If you were to peel off the top layer of something, no matter how wrinkly that something is, and lay that top layer out flat, what you’re looking at is the surface area.
            More folds = more surface area. That means that a wrinkly brain can hold more neurons than a smooth brain. The wrinkles are so important that scientists even have science-y names for them. The ridges are gyri (singular: gyrus) and the folds are sulci (singular: sulcus). Even individual wrinkles have names. Neuroscientists talk about the “fusiform gyrus” or the “inferior temporal sulcus”.
            We have lots of evidence that gyri and sulci are positively linked to intelligence. (Remember, more wrinkles = more neurons.) Human brains are wrinklier than the brains of any other animal. For the most part, we’re all as wrinkly as the next person, but not always. Some people are born with a condition called lissencephaly. This means “smooth brain.” It causes severe mental retardation, and children with lissencephaly often die within several months of birth. We also know that declines in brain function in the elderly are sometimes due to widening of the sulci. A gradual widening of the sulci late in life (which also means a gradual thinning of the gyri), means fewer neurons compared to when a person was young. Some neuroscientists are trying to figure out why this happens, and how to stop it.

Monday, 2 April 2012

Build your very own zombie

(Note: this post is about zombies, which do not exist but can be scary. Older kids only, please)

            The world seems to be sending me a message.
            First, I watched the entire second season of AMC’s The Walking Dead in the space of four days.
            Next, I was hanging out in my favorite coffee shop in Vancouver, ran into a friend there, and ended up getting into a spirited discussion about zombies. Specifically, what bits of a brain need to be functional for a zombie to exist?
            Then, when I linked my “Parts of the Brain” post to my Facebook page, it started up another conversation about…what else? Zombies.
            Fine! I’ll write a post about zombies!
I love this movie
            Zombies and I go way back. As hipsters would say, “I liked zombies before they were cool.” I remember the days when my lab mates and I would sit around at lunch and argue over which was scarier: a vampire apocalypse or a zombie apocalypse. The basic argument came down to the ability of vampires to form intelligent plans versus the power of stupid people in large groups. But which is truly the more frightening option: the sparkly, love-sick vampires from Twilight, or the brain-munching, intestine-gobbling, world-destroying hordes from George A. Romero’s Living Dead movies? I rest my case. And I still think a bunch of zombies running rampant in a shopping mall is one of the coolest set-ups for a movie, ever.
            Alright, so if we’re going to make a zombie, what do we need?
            According to Dr. Wade Davis, we need tetrodotoxin, which is a toxin that comes from pufferfish. We also need drug that causes hallucinations, like the plant datura. Dr. Davis wrote a book called The Serpent and the Rainbow, in which he told the story of Hatian voodoo bokors, or shamans. The bokors would give someone these drugs, and the person would appear to die, then reawaken as a zombie. They would have muscle control and be able to follow orders, but have no ability to plan or make decisions or interact socially. It was believed that these people had come back from the dead. The Serpent and the Rainbow probably contributed to the zombie myth as we know it. Pop culture later added the brain eating and it being contagious through bites.
            Most scientists think Dr. Davis was wrong. It’s unlikely that someone could actually make a zombie using these drugs, or keep them in the drug-induced zombie trance for years, as Dr. Davis claimed was possible. But the zombie myth lives on, even though the story that helped spawned it is now dead. It’s quite fitting, really.
            Still, let’s pretend you can make a zombie. What bits of the brain do you need? (See this post for a review of the parts of the brain.)
            Clearly, you need a functional spinal cord, because zombies can walk. Your spinal cord contains a central pattern generator, which controls the basic walking pattern. This means you don’t have to think about walking. Until you trip. Then you’ll start paying attention. The point, though, is that you don’t need a brain to be able to walk.
            Your zombie’s also going to need a hypothalamus, because it’s HUNGRY. If it has a hypothalamus, it will also be capable of feeling cold and heat and thirst. Try burning or freezing your zombie foes, or separating them from delicious water.
Your zombie won't be needing most of this.
            Apparently zombies can see, so let’s give our zombie an occipital lobe. They can also smell and hear, so let’s add in the olfactory bulb and the hearing centers of the temporal lobe, but not the language or memory centers. Zombies can’t talk and they don’t remember their loved ones. Our zombie doesn’t get a limbic system either, as it apparently cannot feel fear and, as I just pointed out, it has no memory.
            Our zombie will not need a frontal lobe, and probably not a parietal lobe either. We’ll give it a cerebellum, so it can move its arms and claw at you. Since it doesn’t have a functioning heart, blood won’t be flowing to the brain. This means that a head wound, that classic destroyer of all things zombie, might not work. A head injury might not destroy the necessary brain centers, and the zombie can’t bleed to death. Even fully healthy humans survive head injuries on a pretty regular basis, so why should a head injury take out an already-dead zombie? (Note that the key word here is survive. Head injuries = not fun.)
            Which raises the question of how you actually go about killing a zombie…I guess you’d need very, very good aim, so you can shoot the right sections, like the hypothalamus. (I should point out that my experience with guns is zero. Pretty much limited to what movies told me, which isn't exactly reliable.) Or you could go the smashy-smash route and completely destroy everything from the neck up.
            It’s 1:05 am and my imagination is going haywire. This whole post is more for fun then actual correctness. What are your thoughts? Do you agree or disagree? What parts of the brain do you think the modern, discerning zombie needs? What’s your preferred method of zombie destruction?
            Also, before you say it, I’m aware that I’ve thought about this way too much.

Sunday, 1 April 2012

Parts of the brain

           Your brain is not one big disordered jumbled mess of neurons partying together in an electrical and chemical slurry. It’s tightly organized. Each part does something special. Today I’m going to talk about the seven major parts of the brain (or, at least, the seven parts that I think are most major).
            How we learned all this is an interesting story in itself. You can’t crack open a person’s head and go mucking about in there to find out what everything does. Shocking, I know. But sometimes head injuries happen. While head injuries are obviously a bad thing and no one wants one, they’re also a source of information about the brain.
            When someone has a head injury – like the case of Phineas Gage who got a railroad spike through his frontal lobe – they don’t always die. But often, things change. Personality or memory gets messed up. Maybe they go blind, even though their eyes are working perfectly. By looking at what the person can no longer do, and comparing it to which area of the brain is injured, we can figure out what each area of the brain does. It’s from studying these unfortunate individuals that we figured out what most of the parts of the brain do.
             Head injuries were a big source of information in the early part of the 20th century, when the study of neuroscience was still young. We now have machines like MRIs which allow us to look inside a person's brain without injuring them. Obviously, this is better for all involved, especially for the person who's brain is being studied.
            So now I bring you...BITS OF THE BRAIN 101:

  1. The frontal lobe: Personality, attention, and social interaction. Humans have the most developed frontal lobe of any animal in the world.
  2. The parietal lobe: Sensation, particularly the sense of touch. Also, muscle control.
  3. The temporal lobe: Hearing, certain types of memory, and language.
  4. The occipital lobe: Vision. That’s all. Vision. Sight is the only sense with its own dedicated lobe. There's more brain space devoted to processing sight than any other sense. This is why it's the most important sense in most people. In blind people, the hearing, touch, and smell centers of the brain invade the occipital lobe, which means more brain space for these senses. This is why the blind people have such sharp senses of hearing and touch compared to people who can see. 
  5. The limbic system and hypothalamus: This is a collection of structures located deep inside your brain which control the actions you take in order to keep yourself alive. The hypothalamus is responsible for hunger, thirst, and temperature regulation. The limbic system is in charge of emotions like fear and desire. It’s also involved in memory and sense of smell. 
  6. The cerebellum: Muscle control and muscle memory. When you go through a complex series of movements without thinking about it, like playing a musical instrument or doing a basketball jump shot, that’s your cerebellum taking over. 
  7. The brain stem: This is absolutely, completely, 100% essential for your survival. That’s because the brain stem controls your heart and your lungs. It’s also involved in pain, regulating sleep-wake cycles, and transmitting information from the brain to the spinal cord and down to rest of the body. In the picture on the left, this is the bit which includes the pons and medulla oblongata.

CHALLENGE: I mentioned Phineas Gage, who survived a railroad spike going through his frontal lobe. He survived, but he wasn't the same. Based on what I just told you, what do you think happened to him? Answer in a future post.

And yes, I know I still owe you the end of the action potential story - the synapse. That's coming up too.