1.1 --- a/thesis/Makefile	Sat Mar 29 22:46:05 2014 -0400
     1.2 +++ b/thesis/Makefile	Sat Mar 29 23:01:49 2014 -0400
     1.3 @@ -12,5 +12,6 @@
     1.4  	rm cortex.tex abstract.tex
     1.5  
     1.6  
     1.7 +scp:
     1.8 +	scp "r@aurellem.org:/home/r/thesis/$(THESIS_NAME).pdf" .
     1.9  
    1.10 -

     2.1 --- a/thesis/cortex.org	Sat Mar 29 22:46:05 2014 -0400
     2.2 +++ b/thesis/cortex.org	Sat Mar 29 23:01:49 2014 -0400
     2.3 @@ -364,7 +364,7 @@
     2.4     - I built =EMPATH=, which uses =CORTEX= to identify the actions of
     2.5       a worm-like creature using a computational model of empathy.
     2.6     
     2.7 -* Building =CORTEX=
     2.8 +* COMMENT Building =CORTEX=
     2.9  
    2.10    I intend for =CORTEX= to be used as a general-purpose library for
    2.11    building creatures and outfitting them with senses, so that it will
    2.12 @@ -374,7 +374,7 @@
    2.13    possible, so that =CORTEX= may be used for things I have not
    2.14    forseen.
    2.15  
    2.16 -** COMMENT Simulation or Reality?
    2.17 +** Simulation or Reality?
    2.18     
    2.19     The most important archetictural decision of all is the choice to
    2.20     use a computer-simulated environemnt in the first place! The world
    2.21 @@ -437,7 +437,7 @@
    2.22      doing everything in software is far cheaper than building custom
    2.23      real-time hardware. All you need is a laptop and some patience.
    2.24  
    2.25 -** COMMENT Because of Time, simulation is perferable to reality
    2.26 +** Because of Time, simulation is perferable to reality
    2.27  
    2.28     I envision =CORTEX= being used to support rapid prototyping and
    2.29     iteration of ideas. Even if I could put together a well constructed
    2.30 @@ -460,7 +460,7 @@
    2.31     simulations of very simple creatures in =CORTEX= generally run at
    2.32     40x on my machine!
    2.33  
    2.34 -** COMMENT What is a sense?
    2.35 +** What is a sense?
    2.36     
    2.37     If =CORTEX= is to support a wide variety of senses, it would help
    2.38     to have a better understanding of what a ``sense'' actually is!
    2.39 @@ -538,7 +538,7 @@
    2.40     #+ATTR_LaTeX: :width 10cm
    2.41     [[./images/finger-1.png]]
    2.42  
    2.43 -** COMMENT Video game engines provide ready-made physics and shading
    2.44 +** Video game engines provide ready-made physics and shading
    2.45     
    2.46     I did not need to write my own physics simulation code or shader to
    2.47     build =CORTEX=. Doing so would lead to a system that is impossible
    2.48 @@ -562,7 +562,7 @@
    2.49     from the base system, other researchers can turn to this community
    2.50     for help when doing their research.
    2.51     
    2.52 -** COMMENT =CORTEX= is based on jMonkeyEngine3
    2.53 +** =CORTEX= is based on jMonkeyEngine3
    2.54  
    2.55     While preparing to build =CORTEX= I studied several video game
    2.56     engines to see which would best serve as a base. The top contenders
    2.57 @@ -604,7 +604,7 @@
    2.58     write my code in clojure, an implementation of =LISP= that runs on
    2.59     the JVM.
    2.60  
    2.61 -** COMMENT =CORTEX= uses Blender to create creature models
    2.62 +** =CORTEX= uses Blender to create creature models
    2.63  
    2.64     For the simple worm-like creatures I will use later on in this
    2.65     thesis, I could define a simple API in =CORTEX= that would allow
    2.66 @@ -641,7 +641,7 @@
    2.67     #+ATTR_LaTeX: :width 10cm
    2.68     [[./images/empty-sense-nodes.png]]
    2.69  
    2.70 -** COMMENT Bodies are composed of segments connected by joints
    2.71 +** Bodies are composed of segments connected by joints
    2.72  
    2.73     Blender is a general purpose animation tool, which has been used in
    2.74     the past to create high quality movies such as Sintel
    2.75 @@ -957,7 +957,7 @@
    2.76      #+ATTR_LaTeX: :width 15cm
    2.77      [[./images/physical-hand.png]]
    2.78  
    2.79 -** COMMENT Eyes reuse standard video game components
    2.80 +** Eyes reuse standard video game components
    2.81  
    2.82     Vision is one of the most important senses for humans, so I need to
    2.83     build a simulated sense of vision for my AI. I will do this with
    2.84 @@ -1254,7 +1254,7 @@
    2.85      community and is now (in modified form) part of a system for
    2.86      capturing in-game video to a file.
    2.87  
    2.88 -** COMMENT Hearing is hard; =CORTEX= does it right
    2.89 +** Hearing is hard; =CORTEX= does it right
    2.90     
    2.91     At the end of this section I will have simulated ears that work the
    2.92     same way as the simulated eyes in the last section. I will be able to
    2.93 @@ -1555,7 +1555,7 @@
    2.94      jMonkeyEngine3 community and is used to record audio for demo
    2.95      videos.
    2.96  
    2.97 -** COMMENT Touch uses hundreds of hair-like elements
    2.98 +** Touch uses hundreds of hair-like elements
    2.99  
   2.100     Touch is critical to navigation and spatial reasoning and as such I
   2.101     need a simulated version of it to give to my AI creatures.
   2.102 @@ -2034,7 +2034,7 @@
   2.103      #+caption: The touch profile for the touch-cube. Each pure white 
   2.104      #+caption: pixel defines a touch sensitive feeler.
   2.105      #+name: touch-cube-uv-map
   2.106 -    #+ATTR_LaTeX: :width 10cm
   2.107 +    #+ATTR_LaTeX: :width 7cm
   2.108      [[./images/touch-profile.png]]
   2.109  
   2.110      #+caption: The touch cube reacts to canonballs. The black, red, 
   2.111 @@ -2049,7 +2049,7 @@
   2.112      #+ATTR_LaTeX: :width 15cm
   2.113      [[./images/touch-cube.png]]
   2.114  
   2.115 -** COMMENT Proprioception is the sense that makes everything ``real''
   2.116 +** Proprioception is the sense that makes everything ``real''
   2.117  
   2.118     Close your eyes, and touch your nose with your right index finger.
   2.119     How did you do it? You could not see your hand, and neither your
   2.120 @@ -2183,7 +2183,7 @@
   2.121      #+ATTR_LaTeX: :width 11cm
   2.122      [[./images/proprio.png]]
   2.123  
   2.124 -** COMMENT Muscles are both effectors and sensors
   2.125 +** Muscles are both effectors and sensors
   2.126  
   2.127     Surprisingly enough, terrestrial creatures only move by using
   2.128     torque applied about their joints. There's not a single straight
   2.129 @@ -2326,7 +2326,7 @@
   2.130      in humans and completes the sense of proprioception begun in the
   2.131      last section.
   2.132      
   2.133 -** COMMENT =CORTEX= brings complex creatures to life!
   2.134 +** =CORTEX= brings complex creatures to life!
   2.135     
   2.136     The ultimate test of =CORTEX= is to create a creature with the full
   2.137     gamut of senses and put it though its paces. 
   2.138 @@ -2349,7 +2349,7 @@
   2.139     that will test everything. 
   2.140  
   2.141     #+caption: A full test of the hand with all senses. Note expecially 
   2.142 -   #+caption: the interactions the hand has with itself. It feels 
   2.143 +   #+caption: the interactions the hand has with itself: it feels 
   2.144     #+caption: its own palm and fingers, and when it curls its fingers, 
   2.145     #+caption: it sees them with its eye (which is located in the center
   2.146     #+caption: of the palm. The red block appears with a pure tone sound.
   2.147 @@ -2358,7 +2358,7 @@
   2.148     #+ATTR_LaTeX: :width 16cm
   2.149     [[./images/integration.png]]
   2.150  
   2.151 -** COMMENT =CORTEX= enables many possiblities for further research
   2.152 +** =CORTEX= enables many possiblities for further research
   2.153  
   2.154     Often times, the hardest part of building a system involving
   2.155     creatures is dealing with physics and graphics. =CORTEX= removes