1.1 --- a/thesis/cortex.org	Mon Mar 31 00:18:26 2014 -0400
     1.2 +++ b/thesis/cortex.org	Mon Mar 31 00:35:31 2014 -0400
     1.3 @@ -377,7 +377,7 @@
     1.4     #+caption: Here is the worm from figure \ref{worm-intro} modeled 
     1.5     #+caption: in Blender, a free 3D-modeling program. Senses and 
     1.6     #+caption: joints are described using special nodes in Blender.
     1.7 -   #+name: worm-recognition-intro
     1.8 +   #+name: worm-recognition-intro-2
     1.9     #+ATTR_LaTeX: :width 12cm
    1.10     [[./images/blender-worm.png]]
    1.11  
    1.12 @@ -763,7 +763,7 @@
    1.13     #+caption: Program for iterating through the nodes in a blender file
    1.14     #+caption: and generating physical jMonkeyEngine3 objects with mass
    1.15     #+caption: and a matching physics shape.
    1.16 -   #+name: name
    1.17 +   #+name: physical
    1.18     #+begin_listing clojure
    1.19     #+begin_src clojure
    1.20  (defn physical!
    1.21 @@ -970,7 +970,7 @@
    1.22      control functions.
    1.23  
    1.24      #+caption: Program to give joints to a creature.
    1.25 -    #+name: name
    1.26 +    #+name: joints
    1.27      #+begin_listing clojure
    1.28      #+begin_src clojure
    1.29  (defn joints!
    1.30 @@ -1004,7 +1004,7 @@
    1.31      #+caption: With the ability to create physical creatures from blender,
    1.32      #+caption: =CORTEX= gets one step closer to becoming a full creature
    1.33      #+caption: simulation environment.
    1.34 -    #+name: name
    1.35 +    #+name: physical-hand
    1.36      #+ATTR_LaTeX: :width 15cm
    1.37      [[./images/physical-hand.png]]
    1.38  
    1.39 @@ -1027,7 +1027,7 @@
    1.40     #+caption: jMonkeyEngine supports multiple views to enable 
    1.41     #+caption: split-screen games, like GoldenEye, which was one of 
    1.42     #+caption: the first games to use split-screen views.
    1.43 -   #+name: name
    1.44 +   #+name: goldeneye
    1.45     #+ATTR_LaTeX: :width 10cm
    1.46     [[./images/goldeneye-4-player.png]]
    1.47  
    1.48 @@ -2107,7 +2107,7 @@
    1.49      #+caption: floor and the ball. Notice that when the ball causes 
    1.50      #+caption: the cube to tip, that the bottom face can still feel 
    1.51      #+caption: part of the ground.
    1.52 -    #+name: touch-cube-uv-map
    1.53 +    #+name: touch-cube-uv-map-2
    1.54      #+ATTR_LaTeX: :width 15cm
    1.55      [[./images/touch-cube.png]]
    1.56  
    1.57 @@ -2124,10 +2124,10 @@
    1.58     damage to the spinal cord or brain, and when they do, they loose
    1.59     the ability to control their own bodies without looking directly at
    1.60     the parts they want to move. In [[http://en.wikipedia.org/wiki/The_Man_Who_Mistook_His_Wife_for_a_Hat][The Man Who Mistook His Wife for a
    1.61 -   Hat]], a woman named Christina looses this sense and has to learn how
    1.62 -   to move by carefully watching her arms and legs. She describes
    1.63 -   proprioception as the "eyes of the body, the way the body sees
    1.64 -   itself".
    1.65 +   Hat]] (\cite{man-wife-hat}), a woman named Christina looses this
    1.66 +   sense and has to learn how to move by carefully watching her arms
    1.67 +   and legs. She describes proprioception as the "eyes of the body,
    1.68 +   the way the body sees itself".
    1.69     
    1.70     Proprioception in humans is mediated by [[http://en.wikipedia.org/wiki/Articular_capsule][joint capsules]], [[http://en.wikipedia.org/wiki/Muscle_spindle][muscle
    1.71     spindles]], and the [[http://en.wikipedia.org/wiki/Golgi_tendon_organ][Golgi tendon organs]]. These measure the relative