1.1 --- a/thesis/cortex.org	Sat Mar 29 23:55:47 2014 -0400
     1.2 +++ b/thesis/cortex.org	Sat Mar 29 23:57:29 2014 -0400
     1.3 @@ -364,7 +364,7 @@
     1.4     - I built =EMPATH=, which uses =CORTEX= to identify the actions of
     1.5       a worm-like creature using a computational model of empathy.
     1.6     
     1.7 -* COMMENT Building =CORTEX=
     1.8 +* Building =CORTEX=
     1.9  
    1.10    I intend for =CORTEX= to be used as a general-purpose library for
    1.11    building creatures and outfitting them with senses, so that it will
    1.12 @@ -374,7 +374,7 @@
    1.13    possible, so that =CORTEX= may be used for things I have not
    1.14    forseen.
    1.15  
    1.16 -** Simulation or Reality?
    1.17 +** COMMENT Simulation or Reality?
    1.18     
    1.19     The most important archetictural decision of all is the choice to
    1.20     use a computer-simulated environemnt in the first place! The world
    1.21 @@ -437,7 +437,7 @@
    1.22      doing everything in software is far cheaper than building custom
    1.23      real-time hardware. All you need is a laptop and some patience.
    1.24  
    1.25 -** Because of Time, simulation is perferable to reality
    1.26 +** COMMENT Because of Time, simulation is perferable to reality
    1.27  
    1.28     I envision =CORTEX= being used to support rapid prototyping and
    1.29     iteration of ideas. Even if I could put together a well constructed
    1.30 @@ -460,7 +460,7 @@
    1.31     simulations of very simple creatures in =CORTEX= generally run at
    1.32     40x on my machine!
    1.33  
    1.34 -** What is a sense?
    1.35 +** COMMENT What is a sense?
    1.36     
    1.37     If =CORTEX= is to support a wide variety of senses, it would help
    1.38     to have a better understanding of what a ``sense'' actually is!
    1.39 @@ -538,7 +538,7 @@
    1.40     #+ATTR_LaTeX: :width 10cm
    1.41     [[./images/finger-1.png]]
    1.42  
    1.43 -** Video game engines provide ready-made physics and shading
    1.44 +** COMMENT Video game engines provide ready-made physics and shading
    1.45     
    1.46     I did not need to write my own physics simulation code or shader to
    1.47     build =CORTEX=. Doing so would lead to a system that is impossible
    1.48 @@ -562,7 +562,7 @@
    1.49     from the base system, other researchers can turn to this community
    1.50     for help when doing their research.
    1.51     
    1.52 -** =CORTEX= is based on jMonkeyEngine3
    1.53 +** COMMENT =CORTEX= is based on jMonkeyEngine3
    1.54  
    1.55     While preparing to build =CORTEX= I studied several video game
    1.56     engines to see which would best serve as a base. The top contenders
    1.57 @@ -604,7 +604,7 @@
    1.58     write my code in clojure, an implementation of =LISP= that runs on
    1.59     the JVM.
    1.60  
    1.61 -** =CORTEX= uses Blender to create creature models
    1.62 +** COMMENT =CORTEX= uses Blender to create creature models
    1.63  
    1.64     For the simple worm-like creatures I will use later on in this
    1.65     thesis, I could define a simple API in =CORTEX= that would allow
    1.66 @@ -641,7 +641,7 @@
    1.67     #+ATTR_LaTeX: :width 10cm
    1.68     [[./images/empty-sense-nodes.png]]
    1.69  
    1.70 -** Bodies are composed of segments connected by joints
    1.71 +** COMMENT Bodies are composed of segments connected by joints
    1.72  
    1.73     Blender is a general purpose animation tool, which has been used in
    1.74     the past to create high quality movies such as Sintel
    1.75 @@ -957,7 +957,7 @@
    1.76      #+ATTR_LaTeX: :width 15cm
    1.77      [[./images/physical-hand.png]]
    1.78  
    1.79 -** Eyes reuse standard video game components
    1.80 +** COMMENT Eyes reuse standard video game components
    1.81  
    1.82     Vision is one of the most important senses for humans, so I need to
    1.83     build a simulated sense of vision for my AI. I will do this with
    1.84 @@ -1254,7 +1254,7 @@
    1.85      community and is now (in modified form) part of a system for
    1.86      capturing in-game video to a file.
    1.87  
    1.88 -** Hearing is hard; =CORTEX= does it right
    1.89 +** COMMENT Hearing is hard; =CORTEX= does it right
    1.90     
    1.91     At the end of this section I will have simulated ears that work the
    1.92     same way as the simulated eyes in the last section. I will be able to
    1.93 @@ -1555,7 +1555,7 @@
    1.94      jMonkeyEngine3 community and is used to record audio for demo
    1.95      videos.
    1.96  
    1.97 -** Touch uses hundreds of hair-like elements
    1.98 +** COMMENT Touch uses hundreds of hair-like elements
    1.99  
   1.100     Touch is critical to navigation and spatial reasoning and as such I
   1.101     need a simulated version of it to give to my AI creatures.
   1.102 @@ -2049,7 +2049,7 @@
   1.103      #+ATTR_LaTeX: :width 15cm
   1.104      [[./images/touch-cube.png]]
   1.105  
   1.106 -** Proprioception is the sense that makes everything ``real''
   1.107 +** COMMENT Proprioception is the sense that makes everything ``real''
   1.108  
   1.109     Close your eyes, and touch your nose with your right index finger.
   1.110     How did you do it? You could not see your hand, and neither your
   1.111 @@ -2183,7 +2183,7 @@
   1.112      #+ATTR_LaTeX: :width 11cm
   1.113      [[./images/proprio.png]]
   1.114  
   1.115 -** Muscles are both effectors and sensors
   1.116 +** COMMENT Muscles are both effectors and sensors
   1.117  
   1.118     Surprisingly enough, terrestrial creatures only move by using
   1.119     torque applied about their joints. There's not a single straight
   1.120 @@ -2326,7 +2326,7 @@
   1.121      in humans and completes the sense of proprioception begun in the
   1.122      last section.
   1.123      
   1.124 -** =CORTEX= brings complex creatures to life!
   1.125 +** COMMENT =CORTEX= brings complex creatures to life!
   1.126     
   1.127     The ultimate test of =CORTEX= is to create a creature with the full
   1.128     gamut of senses and put it though its paces. 
   1.129 @@ -2358,7 +2358,7 @@
   1.130     #+ATTR_LaTeX: :width 16cm
   1.131     [[./images/integration.png]]
   1.132  
   1.133 -** =CORTEX= enables many possiblities for further research
   1.134 +** COMMENT =CORTEX= enables many possiblities for further research
   1.135  
   1.136     Often times, the hardest part of building a system involving
   1.137     creatures is dealing with physics and graphics. =CORTEX= removes