Attract a mate in three easy steps

Are you looking for someone to nest with? Someone with whom to share a bowl of millet seeds? Are you a male zebra finch?

Wikipedia

If you answered 'yes' to all of these questions, the solution to your solitude is the solution to a set of coupled ordinary differential equations.

The worst kept secret in zebra finch dating is the power of song. Females go crazy for it. Unfortunately, Green Sleeves won't cut it. Women want a spectrally complex, consistent, and loud song, a tall order for regular zebra finch guys who have to squeeze singing lessons into days already packed with dehusking seeds and preening. So maximize your singing strategy by studying the dynamics of song production.

The syrinx, from http://thediagram.com/4_5/syrinx.jpg

1. Tension

What's the difference between normal breathing and song? In part the answer is tension between the vocal folds. In humans, the vocal folds are in the larynx at the top of the trachea,  but in songbirds, the vocal membranes are at the bottom, in a structure called the syrinx. Perhaps the most distinctive difference between the larynx of mammals and the syrinx is that the syrinx has two sets of independent membranes, enabling songbirds to sing two tones at once. By bringing the membranes together, airflow is restricted through the syrinx and the vocal membranes begin to oscillate, producing song. The greater the tension between the vocal membranes, the greater the pitch of the resulting tone. Trying singing a high note, do you feel the tension?

2. Pressure

You can't produce song without pressure. In mammals, pressure is generated by the diaphragm and lungs, but songbirds have specialized air sacs which pump air through the lungs in a single direction. Pressure coming up from the air sacs cause the vocal membranes in the syrinx to oscillate, producing song.

3. Bifurcations

This fancy sounding word has a simple meaning for singers. At any given time, a bird can either be A) not singing or B) singing, and any time you'd like to start singing, you need to transition from A to B. This called a bifurcation. To undergo a bifurcation, both pressure and tension are needed. Tensing the syrinx without any pressure will not create song, neither will exhalation without any syringeal tension. Pressure and tension can be thought of as two dimensions, like latitude and longitude. Some locations in this space result in beautiful tones, other locations are noisy, others produce no sound at all.

There are two types of bifurcations seen in the syrinx. The first is called a Hopf bifurcation, in which oscilations start very small and grow, like feedback from a microphone, into full-fledged song. The other type of bifurcation is a called a saddle-node bifurcation, in which pressure breaks through the membrane like a flood bursting through a dam, in a sudden, large bending of the membranes.

Putting it all together

Below are simulations of a model syrinx and sound created as the pressure and tension are modulated. The top graph shows the pressure/tension state, while the bottom graph displays resulting movement of the syrinx.

 

That was probably too fast to be useful, here is the same song, slowed down 20 times.

Now get out there and practice! Use this digital syrinx to work on your song. Try moving from the steady state to oscillations via Hopf- and saddle node bifurcations.

Go the the syrinx simulation.


Good luck finding your mate!

Wikipedia

Skulls in motion

While chowing down on a delicious slice of pizza (and no, definitely not Chicago-style even though I live in Chicago), I realized yet again how bizarre we humans are. Not because we're bi-pedal or hair-less or take an incredibly long time to reach adulthood (for the record I am quite content with this last one -  the longer I can lavish my nieces and nephews with birthday gifts the better!).

No, it's because we only move one bone in our skull when we eat: our lower jaw. While I'm relishing the greasy goodness of my pepperoni pizza my lower jaw is tearing off pieces and then breaking them down into a manageable mush that can be swallowed. But all the other bones in my skull are (hopefully) staying right where they are.

So why is this bizarre? If you were to watch other vertebrates (things with backbones) while they eat you'd see the bones in their skull going crazy! It's like a humming engine with gears spinning, levers turning and pistons pumping. Take for instance this video (courtesy of my PhD advisor Mark Westneat) of one incredible vertebrate: the slingjaw wrasse (Epibulus insidiator). The slingjaw wrasse captures unassuming prey by throwing its jaw out ahead of its body. There are whole sets of inter-jointed bones in the skull (engineers call these linkages) that enable muscles at the back of the head to propel the jaws forward.

Sure, the slingjaw wrasse is an extreme example, but most fish have skulls with many moving bones (aka kinetic skulls). One other huge group of vertebrates with kinetic skulls are birds. Check out this awesome video made by Megan Dawson and colleagues at Brown University using XROMM. The video shows how the bones in a duck skull move while its eating.

Kinetic skulls can be found among fish, birds, plus many lizards and snakes. This makes kinetic skulls a great system for studying how bones, muscles and joints interact to create movement. Inspired by my advisor's work on the kinetic skulls of fishes, I have been studying how the bones in bird skulls move and how skull shape relates to beak shape and function. Check out this 3-minute video to learn more about my research:

Though we may be bizarre among vertebrates with our non-kinetic skulls, every time we reach, jump, walk, grasp, lift, bend, breathe we use complex musculoskeletal systems with many moving parts. In this way, we really are not too different from other vertebrates. For that reason, by studying other members of our vertebrate family we really do learn more about ourselves. On that note and having finished my pizza I think it's time I moved a few more bones in my body than my jaw and fingers to type this entry. To quote a wise professor here at the U of C, I think tis' time for a constitutional walk!

An Arm That Isn't There

Imagine a normal day. You wake up, get dressed, walk out the door and say “Hello” to your neighbor. But something is different. When you say “Hello,” you hear nothing. Suddenly, you can no longer hear yourself speak.

How sure would you be that you just said “Hello”? Your “Hello” could have been anything. You might have said it correctly, normally. But maybe it was different. Maybe this time, you said “Hello” in a British accent. Maybe you thought you said "Hello," but you accidentally said “mayo.” You’re still able to talk, but now every word comes with a bit of fear. What did I just say?

Just like shooting a jump shot or bending into a perfect plié, speech is a motor behavior we practice over and over again to get right. And just like seeing the ball ricochet off the rim, or feeling the unexpected shift in balance from a dropped posture, we need to be able to hear our speech in order to tell when we’ve made a mistake. With any motor skill, feedback is a critical part of learning.

Some researchers believe that stuttering speech in some individuals may be a problem with the feedback mechanisms of the auditory system, rather than a motor control problem. Here is one example of a dramatically effective speech therapy that modifies auditory feedback. Change the feedback, change the behavior:

A Brand New Arm

Ten years ago, Jan Scheuermann lost the use of her peripheral nervous system. She could no longer control her arms or legs. But now, researchers at the University of Pittsburgh are trying to give Jan a new arm. They have plugged hundreds of little antennas into the top of her brain (the motor control centers of her cerebral cortex) and are listening for electrical signals. Some cells are saying “move right” and others are saying “move left” and some are saying “grab that chocolate.” And when a whole bunch of neurosurgeons and engineers and computer scientists and one adventurous woman all work together…

All that, and no feedback. The researchers are listening for incoming signals, but not sending any signals back out. Jan's thoughts are being sent to her arm, but her arm isn't sending any information back about where it is or what it's touching. Her new arm might as well be talking without hearing. 

Imagine how well she’ll do when she feels her arm for the first time.

Neural control for simple rhythmic behaviors

Consider the gruesome euthanized chicken, who runs headless around the farmyard.

If movement is controlled by brains, and brains occupy heads, how does the chicken manage its running?

Trick query. Although brains are critical for many aspects of elaborate flexible movement, simple rhythmic behaviors can be managed using pools of neurons outside the brain--for example, in the spinal cord.

These small circuits are called central pattern generators = CPGs, because they produce rhythmic outputs without needing rhythmic inputs. When we walk, run, or breathe, it is (largely) because of neural events that are localized within our spinal cords and brainstems, rather than our midbrains and forebrains.

Central pattern generators have been studied extensively in that favorite edible arthropod, the lobster. Do you remember that lobsters are invertebrates, definitionally lacking spinal cord? (They have exoskeletons though!) Their CPGs reside elsewhere, in the stomatogastric ganglion.

Above: Cells of the stomatogastric ganglion, with three associated nerves.

(ref. scholarpedia)

How do CPGs produce rhythmic outputs? As a case study, here's a simplified look at the lobster's Pyloric CPG.

The simplified pyloric central pattern generator is a three-neuron circuit. Each of these neurons exhibits steady activity in isolation--meaning they cause their own firing, without needing excitation from other neurons. Connections between the three neurons serve to interrupt this otherwise steady activity. When one neuron fires, it briefly communicates with two others, forcing them towards silence (away from their firing threshold).

Across the three cells, the strength of these inhibitory connections control the timing of firings. The result (at equilibrium) is a repetitive sequence of firings in the network:

uno uno uno uno uno, dos dos dos dos dos, tres tres tres tres tres;

uno uno uno uno uno, dos dos dos dos dos, tres tres tres tres tres;

uno uno uno uno uno, dos dos dos dos dos, tres tres tres tres tres... .

But changes in connectivity can disrupt this stereotypy.

These three neurons also communicate with three muscles, contracting their corresponding muscle at every firing. Triggered by their afferent neuron, each muscle contracts in turn.

1. During the first neuron's bursting, the pyloric sphincter at stomach's entrance gets pulled open. Food moves in.

2. During second neuron's bursting the sphincter is closed again, retaining its new contents.

3. The third neuron triggers ripples on the stomach wall that advance the food forward.

1. The pyloric sphinter reopens...

Fly to the interactive visualization

Explore a simple model of this rhythm! Click on the large-circles (cell bodies) to artificially silence them. Strengthen the influence of inhibition between neurons by clicking at their junctions (synapses).

Which neuron opens the pyloric sphincter?

How much can you dilate the pyloric sphincter?

Can you reorder the characteristic 1, 2, 3 sequence?

Larval Zebrafish

The prey - a paramecium 


Large black eyes stare down on the micro-scaled paramecium as it propels through the fluid. Hundreds of cilium protrude from the circumference of the paramecium’s single-celled body move synchronously but slightly out of phase give the illusion of a wave sweeping through the tiny hair-like cilia. 





Paramecium slowly moving through fluid. Other faster moving paramecia can be seen briefly as well.

The predator - larval zebrafish


Unaware, past the ebony of the predator’s eyes, the cilia strike the fluid in a whiplash fashion pushing the paramecium forward. Motionless, the predator larval zebrafish stares at the minuscule paramecium yet inside its brain, millions of neurons fire in response to its predatorily instincts. What exactly is happening inside of the zebrafish’s head? See for yourself! 


Florescent dyes injected inside the transparent larval zebrafish react to calcium ions indicative of neural activity. The video shows the zebrafish’s mental activity in response to the swimming paramecium. [Reference]

Smaller than a centimeter, wielding less than a couple hundred neurons, and being fully transparent, larval are a popular specimen for exploring how neural systems function. Larval zebrafish are popularly used in labs to study their swimming and prey-capture behaviors to explore the underlying neuronal architecture and function and helping us to comprehend nature and answer questions like how a zebrafish moves. 





Larval zebrafish as seen under a microscope. Cellular activity such as blood circulation can be seen through the transparent zebrafish.


How a zebrafish moves - from a neural perspective






A larval zebrafish hunts down its prey, the paramecium. Observe that when the zebrafish swims, undulations or traveling waves can be seen along the tail of the zebrafish.

At the larval stage, swimming behavior is achieved by rhythmic propagation of neural waves down the tail is observed. These traveling waves activate and hence contract (shorten) muscles in an alternating left, right pattern. When for example a muscle on the right side of the body is shortened actively by the electrical neural signal, the muscle on the left side of the body will be passively lengthened. The alternating muscle contraction pattern produces undulatory movement. [Reference] 


How a zebrafish moves - from a physical perspective



In order to swim forward, zebrafish must overcome frictional drag and pressure drag (the force needed to the water in front of its body). Frictional drag is largely overcome by the slippery body coating of the fish. To overcome pressure drag, fish use force produced from their muscles. 


A large percentage of the zebrafish is comprised of layers of muscles called myomeres. The neural traveling wave neuronal signal described above propagates from the brain down to the tail resulting in the contraction and relaxation of alternate myomere layers producing undulations.

The undulations are mechanical force waves which interact with the surrounding water producing thrust of sufficient magnitude to overcome drag and propel the zebrafish forward. [Reference]

As the fish swims forward, flow circulation and pressure differences created from the beating tail produces a jet of fluid in the direction opposite of swimming. A vortex ring (ring of rotating water particles) encircles the jet. [Reference] If these vortices are large enough, the zebrafish can use the stationary rotating vortices to push against to gain more momentum. However, larval zebrafish are low Reynolds number swimmers, meaning the vortices they produce dissipate in the fluid very rapidly, to fast to take advantage of the extra “kick.”

Simulation of a zebrafish displaying vorticity magnitude 



This is a simulation of a zebrafish swimming based on kinematics acquired from experimental data and feed into the numerics. The advantage of doing such simulations is to study the hydrodynamic forces and vorticity to help understand why a zebrafish swims the way it does.

Directional Tuning of Neurons in Motor Cortex

Mukta Vaidya

What do Anakin Skywalker’s arm (Star Wars, Luke Skywalker’s hand (Star Wars), Del Spooner’s (Will Smith in I, Robot) arm, and Geordi Le Forge’s visor (Star Trek) all have in common? They are all prosthetics, artificial devices that are meant to replace or aid missing or dysfunctional body parts. Prosthetics are by no means limited to science fiction! Modern prosthetics include hearing aids, artificial heart valves, artificial knees, and artificial retinas just to name a few. Part of my own research involves using what we know about how the brain coordinates and controls movement to develop ways to control a robotic arm using just signals from your brain! The reason I get to work on these types of projects is because of all of amazing scientists and engineers that have come before me that are working on one seminal question: how does your brain control how you move?

The part of your brain that is primarily responsible for motor learning and control is called motor cortex (see figure above). People have been studying motor cortex since the late 19^th century, and trying to map out its organization and function since the late 20^th century. Although we have been able to discover an incredible amount of information on how motor cortex works through both experimentation and modeling, to me, it is equally amazing how much more we still have to left to learn. Nevertheless, significant contributions have been made by many, many amazing researchers.

In this post, I’d like to pay tribute to one in particular. In 1982, Apostolos Georgopoulos published a very important paper entitled, “On The Relations Between The Directions Of Two-Dimensional Arm Movements And Cell Discharge In Primate Motor Cortex.” A pdf version of this paper can be found here: http://www.jneurosci.org/content/2/11/1527.short .  In this study, monkeys were trained to make arm movements in one of eight directions in two dimensional space. While the monkeys were performing this task, he recorded electrical activity from neurons using microelectrodes that were lowered into the arm area of the brain. He also used electromyographic signals (http://en.wikipedia.org/wiki/Electromyography) to monitor muscle activity, as well as electrooculograms (http://en.wikipedia.org/wiki/Electrooculography) to measure eye movements. He found that the frequency of discharge from neurons that were active during this task (i.e. how often they were firing), varied systematically with the direction of movement. Neurons would fire with the highest frequency (fastest) when the monkey’s arm movements were in its preferred direction. As the direction of movement moved further and further away from the neuron’s preferred direction, the neuron would fire at increasingly lower frequencies. Thus, this study found that each neuron had a roughly bell-shaped tuning curve. In addition, Georgopoulos and his colleagues also found that tuning curves for neurons overlapped to a large degree, and proposed that this was useful for a population code, where several neurons would contribute in encoding a movement direction.

Much has been learned about the motor cortex since 1982, including advancements by Georgopoulos and his colleagues. Neurons in motor cortex do much, much more than just encode one movement direction each. They represent things like position, velocity, force, movement trajectories to name just a few, and work together in lots of different ways to do so.  These representations aren’t static either—motor learning and plasticity (changing in brain organization) is also an area of great interest and research.  However, this paper by Georgopoulos and his colleagues was a very important step in understanding the role and function of motor cortex, and laid groundwork for not only cortical motor control research, but brain machine interface research. Understanding different ways that your brain represents information about movement (such as having neurons that are directionally tuned), allows you to come up with models that you can use to decode actual signals from the brain in order to control artificial devices (such as a joystick or robotic arm).  As a graduate student studying how motor cortex works, as well as working on a brain machine interface project, I am truly amazed and thankful to all of the incredible researchers who have come before me. This includes my current advisor, shoutout to Hatsopoulos lab (http://pondside.uchicago.edu/oba/faculty/Hatsopoulos/lab/ )!

How do we move?

Sarah Wohlman

The science of studying how we move is called biomechanics. We move in countless ways throughout our environment without thinking twice about how our joints and muscle work together. Do you think in the 9.58 seconds Usain Bolt is running 100 meters he is thinking about how to move his leg by rotating his knee, hip and ankle all at the same time? ...Probably not!

Let’s break it down to the basics. Biology is the science of living organisms. Mechanics is the science of motion and the forces that produce motion. Therefore, biomechanics is concerned with the integration of these two sciences to answer the question…How do living organisms move?

Many organisms, including humans move by shortening our muscles or more scientifically contracting our muscles. Let’s start briefly with how muscles work. Muscles only PULL, they do not push. That’s why we have muscle on both sides of our joints. Let’s focus on our elbow. The bicep flexes our arm, bringing our forearm closer to our upper arm. But if the bicep can only pull (pulling forearm to upper arm), how do we extend our arms? The answer is our triceps, which is located on the other side of the arm, pulls our forearm away from our upper arm. Therefore, when the bicep contracts it flexes our arm and when the triceps contracts it extends our arms. This means that these two muscles are antagonists. We have sets of antagonist muscles through our bodies, quadriceps and hamstrings in our thighs, trapezius and deltoids in our shoulders, etc.

Muscles pull on bones meaning they create a linear force. But don’t we move by our joints rotating (think about your knee rotating when you walk)? So, now the question arises: how do our muscles, which create a linear force by pulling on bones, cause joints to rotate? To start, first we already know that our muscles contract, meaning they create an equal force that is applied to both the origin and insertion of that muscle (i.e. the start and end of the muscle). We need to transform our muscle force to a joint rotation (also, called a joint torque or moment). This is a common mechanics principle where a torque is created when a force is applied at a distance from the axis of rotation.

To apply this to our biceps example: our torque is our elbow rotation, our force is our biceps or triceps force, and the axis of rotation is our elbow. A term used throughout the biomechanics community to refer to the distance the force is applied from the axis of rotation is the moment arm.

As we know though, our bodies have more than one muscle on either side of our joints. For instance, there are 6 major muscles that cross and power the elbow, 4 flexors (biceps brachii, brachialis, brachioradialis, and pronator teres) and 2 extensors (triceps brachii and anconeus). But we also know that we mainly only use our elbows in two ways, flexion and extension. So why do we need more than one extensor muscle and one flexor muscle? It is important to note here that all our muscles also have very different shapes, sizes, and orientations in the body. Therefore, you can start to understand that all our muscles have different roles based on their anatomy and location.

Let’s think about some ways that muscles vary. As we already learned, muscles cause joint rotation because they create a force that is a distance from our elbow. Therefore, if muscles are different distances from the axis of rotation then the amount of rotation they cause at the joint varies. So their location changes what they do. Or if a muscle can generate a big force, another variable to create a rotation, then it may be used mostly when we need to pick up a big load. So their size changes what they do.

It is pretty interesting to start thinking about all the ways that we can move our bodies. We need a lot of muscles to be able to create all the different actions that we do. Each muscle serves a purpose in our bodies. We have evolved to have an extremely efficient musculoskeletal system because in order to contract our muscles they need energy. How do our muscles get energy? Well, that is a question that will be addressed in future blogs so make sure you come back to check out more.