Two weeks of perspective…

So it’s been two weeks since I last worked on any of this. I had spent the last three months before that tearing through scientific literature like a madman trying to make a system to model how a brain thinks and I had to make sure that I’m not obsessed or anything. I would be lying if I said I was not concerned about it. The whole thing was kind of manic. Fortunately my priorities seem to be OK. While I can’t say I did not think about going back to the model, I managed to have lots of fun with other things.


But where to next? Well I need to get at least two pieces of writing out of the way before I make anything else. The Legend, and a general page on Tourette Syndrome. I should probably do the Legend page first, especially since I’ve mentioned it a bunch of times. But I have to do the TS page first. This one has bee eating at me for almost half the time I have been doing this. It’s the thing that defines my personality, whether I like it or not. It’s the thing that I think influences my burning desire to do this project in the first place, and if I am lucky it has even given me a different way of reading and writing. I don’t know, but I have to write it next because it’s the next bat that wants to fly out of my belfry and I can’t ignore it’s flapping anymore. So I guess we will see what happens next.

Colors and Sorting. Final decisions so I can start modeling ganglia.

I had a really cool post on philosophy and neuroscience planned, but I was too sick to brain that much so it became petty color day last week.

I’m starting this model out from the bottom where the spine becomes the brain stem. There really is no set place where “Brain” starts and “Spine” stops. I have a couple of places in mind, but the outline on the very bottom of the wire frame is based on spinal segment C2. So I might just start with everything neural from there.

Left: Course of wires (nerve bundles) in the Brain Stem. Center: Anatomy of the nerves, muscles, and circulation of the upper neck and brain. Cerebellum removed. Right: Location of all Cranial nuclei I-XII.

The following is the organization that I am using to convey information on the nerves using color and pattern. The “Wires” of the body, the nerves are kind of complicated in science and medicine.

Doctors are unbelievably awesome people in terms of what they do, but training them has become a very intense process that is hard to change. So they all still learn the body by all the little complicated Latin names that have some meaning the tells you what the part looks like, and where it is. Because of that, The Original “Grey’s Anatomy” is still useful, and publicly available.

Right: Brain Stem with parts of Cerebellum removed, Rear (Posterior) view. Center: Cross-section of spinal cord showing Control (Motor, Red)) and Command (Somatosensory, Blue. Top is Rear/Dorsal, Bottom is Front/Ventral, and Supplemental Computer Control (Spinocerebullar, Blue also *sigh*), Right: Brain Stem from the Rear/Side (Poster Lateral)

But scientists who do all the mad scientist stuff that needs to be done to understand brains, talk in microscopic structures, and chemistry, and tissue, and genetics. So color and pattern is really the only thing I can use to translate that divide.


  • The wires going into the brain stem are the nerve bundles in the spine. These bundles represent outgoing command signals for movement, and incoming signals for data that we interpret as some of the classical five senses. These bundles are highly organized and the nature of the data is known to pretty detailed levels.
  • Here is a some general information on the nature of the white matter spinal nerve bundles. These are called “ascending tracts” or “descending tracts” which makes sense. You will also see “afferents” which is ascending, and “efferents” which is descending (link above).
  • You would feel it as “Movement” and “Touch/Pain/Hot/Cold”. To science it is Somatosensory data and Motor control.
  • This is a complicated model…

After staring at the information for a while I came up with the following set of information that I needed for every sense.

To the right is a screen grab from an Excel spread sheet where I am using to partially organize all of this craziness. These are all significant features that give me information that helps me to understand the data that these wires carry.

Commonly understood sense: This is not what you think. This is not Touch, Taste, Smell, Sight, and Hearing. This is the Somatosensory system, Gustation, Olfaction, the Visual System, and perception of sound. I’m afraid it’s much more complicated when you are an object instead of a subject. All that symbology…

Organ/system: Location: “sensor” substructure: This describes the physical nature of the minimal “thing” that detects the sensation after the simple receptor which would only bind a chemical, or move, or something. Examples include Muscle spindles that detect muscle stretch and let you unconsciously know where you are in space, or the Eye and it’s organized receptive fields.

“Receptor” ultimately responsible for “signal”: This is what we perceive from a single kind of receptor that detects something that we can interpret in experience. I got a lot of the ideas for whole list by looking at the receptors that we use to detect touch from here. What this describes are what is known in general terms about the different ways that we “feel” and these ways are defined at least partially by the receptor and the type of wire that carries the sensation. Examples of senses underlined as there were presented: muscle length and velocity, muscle tension, joint movement, joint angle, joint torque, touch flitter or movement, vibration, skin stretch, touch movement, fine touch, sharp pain or cool/cold, Dull aching pain or touch or warm…(always dot dot dot…)

Sensation common language: What you would call the feeling. I had those above.

Processing variations: This is where the real complexity starts. I got this idea from seeing how pain is processed and discovering the fact that there are at least three levels to how your body processes pain. These are called the Neospinothalamic tract, the Paleospinothalamic tract, and the Archiospinothalamic tract. Basically New, old, and ancient pain processing pathways. Think about it, do you react the same to a pinprick and a pool-cue through the abdomen? The “thalamic” part refers to the Thalamus which is a HUGE part of emotional processing and acts like a informational switchboard. One of my hypotheses is that these three divisions are mirrored in more than just pain perception. I believe that these represent three computational modes that we engage in and they have a huge impact on everything we do.

Body Region specific info: I am not ruling out the fact that there may be unknown information that body region can give me.

General Reflexes: Most of what you sense is carried out below the conscious level. Did you know you have multiple pathways controlling your movements and only one is “consciously controlled”? Many reflexes such as the stereotyped knee-tap don’t even need the brain at all except to let you know that it happened. I wonder if there are social reflexes…

Axon:Group:Diameter/Velocity: This refers to the behavior of the data as it travels along the wires in terms of speed and intensity. This matters A LOT. The next time you get a short stabbing pain pay attention. There is a noticeable distance between the time you feel the stab, the when you feel the throb (especially if you get a finger tip crushed). That is the difference between Aα and C fibers

Lower Body/Upper Body Routes: Just like peeking into the innards of an airplane, your wires are bundled too! 1′ refers to the first single cell in a series of connected wires. Some can go from your toe to your brain, one cell. There is usually a processing center at the site of connection and things you are consciously aware of tend to have very few stops. 2′ is the second wire that the first ware attaches (synapses) to. 3’… Reflex arcs might need information presented differently here since the paradigm changes a bit.

Face Routes: The same general principles but here things get complicated by the fact that humans are segmented like insects. It’s just that their segments are easier to see than ours. In general each human segment is represented by the bit where one nerve and vein/artery pair travel off of each side. So if you look at human segments this way you want to understand what is traveling in the Cranial Nerves and their ganglia.These have a very confusing course and they will be one of the later parts of the model.

If you were to stretch out a human by the segments and look at the function, we would be pretty weird. I’m sure that even more detail will come out later but for now…

  1. Smell
  2. Sight
  3. MoveEye/EyeRespond
  4. MoveEye
  5. FeelFace/Chew
  6. MoveEye
  7. ShowEmotion/Taste/Salivate
  8. Hear/SenseGravity/SenseMovement
  9. Taste/Salivate/Swallow/Speak
  10. RestAndDigest/Swallow/Speak/MoveTongue
  11. RestAndDigest/Swallow/Speak/MoveHeadAndNeck
  12. MoveTongue/Swallow/Speak

  • Side Note : You would be correct to think that I really, REALLY want to explore the evolutionary consequences of that series. Part of it involves understanding something called Hox genes, part is evolutionary biology, and part is developmental biology. After all if you look at a fly, or a Worm or two (Lots of cousins to choose from), you see really weird things. It’s thought segmentation evolved more than once. In fact the starfish is technically a bilateria, but somehow regained radial symmetry! That is a weirdness that I intend to pursue

Representing Nerves: Spinal Wire Data. Pipe cleaners, glitter, and tape!

I have these pipe cleaners and glitter. Buying this with a Dremel tool got me really funny looks…

Options for showing differences in the same color of pipe cleaner include a strip of clear tape with glitter of one, or multiple colors depending on the information transmitted. I could also use a small piece of colored electrical tape or duct tape to add new layers of information that I might need. The nature of the connections that the wires make will be represented with colored paper clips (below). All of this can be changed easily if I discover a better way, but I have to start somewhere…

In the above Spinal cord cross section, I mentioned that there were Command (descending paths, or efferents, Red), and Control (ascending paths, or afferents, Blue) lines that represented the data that travels up and down your spine.

  • Side Note: some afferents and efferents are part of the same system, such as cerebellar  feed back loops that help with balance (The Cerebellum is pretty much the biggest regulatory computational region the brain has. That’s why it looks like a small brain. It’s big and old too…). They had to start somewhere so “This in/That out” was what they started with…


These command lines are in two categories.

The first are the voluntary, conscious pathways that you use to directly control your movements. I use White pipe cleaner because it tends to be culturally represented as “Good” in a neutral, universal way (I have ideas about this that do not involve race…). You are trying to move, it could be good or bad. The data that controls your conscious movement comes in three paths. The first two, the Anterior/Lateral Corticospinal tracts (Front/Side), control most of your movement. The Lateral path is the main path and controls arm and leg muscles for the opposite (ipsilateral) side of your body. The Anterior path also controls opposite arm and leg muscles, but for muscles located more centrally to the body. I am using Black/White tape to separate the two paths. The remaining voluntary path, the Rubrospinal tract, is an interesting path. It and the corticospinal tract can make up for the absence of the other so it seems to be some kind of extra level of movement control, but it is much smaller in humans than it is in other animals. I am marking that path with Red tape.

The second are the involuntary command lines that your body uses to make your movements correct, smooth, and precise. The Retuculospinal tract is responsible for other things as well, but this part is helping with balance and posture. Orange and Red Glitter are chosen because they are controlling you (from one perspective) and work together to do similar things. The Tectospinal tract is responsible for helping you to keep your head on a particular target. I thought the Light Blue glitter was good for vision. (Not to be confused with the Spinotectal tract, below). The Medial Longirudinal Fasciculus is another complicated tract. But a good part of it is devoted to similar roles as the TectoSpinal tract, controlling eye movements. It is Green glitter (also good for vision). Note that the poorer the knowledge of the function is, the worse the naming gets. Yeah, Tectospinal means Tectum-Spine in path. That’s it… Finally detection of gravity, motion and rotation and use of that to maintain posture is the job of the Vestibulospinal tract. I make that Purple because purple is what they use for royalty. A powerful force that can be good or bad…

Voluntary Motor

Involuntary Motor


I have to apologize but the organization changes a bit here in the text because I have to adapt to the brain info and not the other way around.

Yellow pipe cleaner is the Fasciculus Gracilis or Cuneatus sensory nerves that carry “Place in Space” (proprioception), Deep Touch, Vibrational Touch, and Viscreal (organ) Pain) for the Lower Body, Trunk, and Upper Body respectively.They will simply be physically separated because they are easy to see.

Silver glitter on a Yellow pipe cleaner is “Place in Space”

Black glitter on a Yellow pipe cleaner is “Deep Touch”

Brown glitter on a Yellow pipe cleaner is “Vibrational Touch”

Yellow glitter on a Yellow pipe cleaner is “Viscreal Pain”

Blue pipe cleaner is the “Place in Space” proprioceptive information of the Dorsal, Ventral, and Rostral Spinocerebellar tracts. The nature of this information is still being investigated, but it certainly has to do with detecting limb and joint position. The Dorsal/Ventral pair work together and in different ways for the legs and trunk only. The Rostral tract does the same for the head and arms. Since other categories are likely as I look through the literature they will be Black and White as I think about what other information needs added. It’s the cutting edge in this section. Some sources report (I’ll flesh this out later) some touch and pressure as well for the dorsal tract so I will have to be careful or add other colors as I discover info.

Red pipe cleaner is the Lateral Spinothalamic tract because it carries pretty intense information: Pain and Temperature. Pain will be Red, Orange or Yellow glitter depending on the particulars (Sharp, throbbing and ???). The Anterior Spinothalamic tract will be Green in comparison because it carries Itch, and Crude Touch. Itch will be Red glitter, and Crude Touch will be Black.

The ascending Spinotectal tract is easily confused with the descending Tectospinal tract (above). So much so that Wikipedia is not as useful here, especially since this is still a mysterious tract. In fact their Anterolateral system page includes the wrong one! There are very few papers that look at the Spinotectal tract, but those that I can look at tend to think it has to do with detecting vibrations. That seems like a good use for the Purple pipe cleaners as any.

The Spino-olivary tract is yet another tweak involving propriception. This at least has a bit more research than the spinotectal, but Wikipedia is still not very useful.

Processing Centers (Ganglia)

It’ really interesting reading about brain organization. It’s like the brain has two mismatched “halves”, connected by a smaller brain. The top half they call the Cerebrum, the bottom half they call the Midbrain, and the small brain is the Cerebellum. If I were to assign identities to these parts I would call the Cerebrum “Consciousness and You”, the Midbrain “Why I’m doing this/How I feel about this/This is how you are doing/This is what you need to do” and the Cerebellum is “The Puppeteer”.


There is a weird transition in structure from the Midbrain to the Cerebrum. The Cerebrum is mostly made out of Cortex, which I still need to decide how to represent. It’s basically layers of cells that you can even see. Somehow (they are still working this out and I need to read more) this region processes your conscious experience in columns that are also communicating with the regions next to them, and other regions of cortex by way of the Basal Ganglia.

The Cortex is a layered structure where most of the memory storage somehow involves connections between layers. “A” in this image is in the middle of the cortical layers. While this is not human cortex, the more animals that have a structure, the more basic it is to our common experience, the more general conclusions you can draw. The circled area above is the Hippocampus which is involved in long term memory formation and the meanings of other abbreviations can be looked up here.


The Midbrain is mostly nerve bundles and  Ganglia which act like little processing centers that make logical connections, and logical decisions. (There is supposed to be a little cortex in the Midbrain and eventually I will find that info. The kidney has adrenal cortex…).

Here is the Basal Ganglia which is particularly relevant to me because it is involved in both ADHD and Tourette Syndrome. You don’t need to look at them but I thought more examples of ganglia would be nice.  (A Couple of sources for this image)

Now that image is not quite done, but I just wanted to start it for now because I am trying to work on the ADHD and TS posts too. The take home message from the links is that the Basal Ganglia is/are part of how your brain prevents you from making mistakes, and it/they are constantly cycling though different connections in your cortex as you are consciously interacting with the world. It has a direct (activating) and indirect (inhibitory) path that is constantly making, and breaking connections between cortical regions. Guess which one I have problems with 🙂


The Cerebellum is a structure that helps you to learn to do things, mostly motor things, and makes sure that you do things right like an ever present teacher that is holding your hand while showing you how to color without going outside the lines. There is a lot of evidence that is operates outside of the motor system too.

The only other feature worth mentioning is that there is a third “structure” in the brain that is the oldest, and least organized. It is called the Reticular Formation. It seems to be a looser collection of networks and ganglia that handle unconscious and very ancient tasks like balance. posture, sleep/wake cycles, cardiovascular control, respiratory control, pain, and habituation (the ability to learn to ignore things). This will be modeled, but will be challenging.

I first started by looking at anatomy in recent review articles like this one about the Brain Stem, and the Wikipedia entry. That was really important to get a general feel for the field and how it is described and discussed. But when I found this Anatomy text available for free (above image), that had to be how I started making the ganglia models.

This has 29 individual ascending sections of a human brain stem. This not only gives me each little tiny processing center in the brain stem (up until 2004), it gives me the nerves, and cells that have to do with neurotransmitters, and more that I can use for info later. In the previous post I pointed out how when I shaded these ganglia by functional class, the organization started to really show up well!

So right now I am entering all the names of the brain stem ganglia into a spreadsheet and looking up functions and links to papers so I can connect them in the model. I don’t know if I am unrealistically ambitious but I’m going to try damn it.

The list has over 300 items that I still need to categorize, but between that, Grey’s Anatomy, and the Wikipedia entry on the cranial nerves I am going to start with:

  1. Spinal trigeminal nucleus (Vs)
  2. Spinal accessory nucleus (11, or XI))
  3. Nucleus ambiguus (11, or XI)
  4. Solitary nucleus (Connected to IX and X according to Grey)
  5. Dorsal motor vagal nucleus (X)
  6. Central Cervical Nucleus
  7. medial pericuneate nucleus
  8. Medial Reticular Nucleus of the Medulla (and internal arculate fibers?)
  9. Inferior salivary nucleus IX
  10. Hypoglossal nucleus XII

Why? They are central, and low so would be the best place to start pragmatically. I’ll try to say something about them as I make them and display progress here. The stuff in quotations are things I’m still thinking about.

Representing Ganglia: Dyed InstaMorph plastic embedded with paperclips, dye and glitter! Thumb tacks used too!

I need a material that is fast and easy to use, modify, and place. This seems to work just fine Colors will be chosen similarly to the wires above. To represent a logical decision that is made by the wire/ganglia connection I will attach the pipe cleaner to the ganglia with a colored paperclip that will indicate the kind of connection. Red for inhibitory, Green for excititory.(Off or ON)

An adjacent thumbtack (actually I may changes this to a colored bead on the pipe cleaner) will indicate the neurotransmitter that is used in the signal transfer.

I will find another solution (like the bead) to represent any details having to do with the signal pattern of the firing, or the logical consequences of such ( (Example: spiking interneurons).

After the primary sensory wires meet the first data transfer centers, who knows what I will need to do to properly represent the way the information is transformed? This could get really interesting…

I’m just starting to realize how crazy this could get, but it feels possible…

Pant, pant, pant…