The Spinal Trigeminal Nucleus Caudalis

It’s still a process, not a map. So of course my first meeting with the materials did not go as planned (more below). The good news is I have my first piece! Meet your Spinal trigeminal nucleus caudalis! (This link gives the larger context. You don’t need it.)

Here is the context for that piece so that you know where it is in your head. This is not something that you can just google to find an easy picture of unfortunately because these are delicate brain structures that don’t tend to get individual attention in surgery very often (from what I can discern). You can’t actually find a picture of this ganglia dissected out. I guess these tissues tend to not be represented in that manner very often.

This piece spans the region around your first to second vertebrae, and is probably not much bigger than a pencil. Remember that this is one sub piece of a larger group of ganglia that collectively make up the Spinal Trigeminal Nucleus (bottom to top, caudalis, interpolaris, and oralis sections). Above all that you still have three more trigeminal ganglia, the “Main” Trigeminal Nucleus (crude touch, discriminative touch), the Mesencephalic Trigeminal Nucleus (proprioception:”place-in-space” for the face) and the Trigeminal Motor Nucleus (controlling your face).

I realize that the brightly colored glittery monstrosity is not really what you would expect to see associated with brain science, but I like to get things really conceptually simple if possible. I think it works and if my particular choices on appearance don’t work in the long run I can always change it. Besides, I don’t know if I really think much of someone who might get scared away by brain science just because I chose to involve glitter. Here is a breakdown of the information in the piece.

*The yellow color is what I chose for the general Somatosensory system (Pain, temperature, touch, and “place in space”) that acts as a part of your “sensory suit”. Structures having to do with this system will be yellow.

*Running from bottom to top are seven green paper clips (bottom) and three silver ones (top) with the ends sticking out from the plastic resulting in twenty places for a pipe cleaner to attached.

*There is red and orange glitter glued to the surface of the ganglion to represent the information that the structure processes (picture, not diagram).

*The Green paperclips indicate excitatory connections from the primary axons arriving from the trigeminal ganglion that carry the pain and temperature information from the face. Seven is not a random number! You have seven Dermatomes in your head and neck that are arranged like an onion from your nose back and I thought it would be a good idea to have that information represented.

*The Silver paper clips represent connections that exist, but with unknown logic. There are direct connections between the STN Caudalis and the Contact Zone with the Interpolaris (the Vi/Vc GCZ that I has to incorperate as a design element), there are connections with the Vi and Vo sub-ganglia. There may also be connections with the motor nucleus so I may be adding features.

*The pipe cleaners are yellow (somatosensory) and represent the primary sensory afferents (the first data wire sending a signal) for Pain (red beads) or temperature (orange beads) sense.

So what this piece does, is to take the the incoming pain and temperature information from the face, eyes, mouth, teeth, larynx, and sinuses (from one side for each ganglion), and and passes it on to your thalamus and your cerebral cortex where your conscious sensation of these will take place. This piece does this in a way that creates a literal physical map of your face/etc in how the information is passed along. This is called somatotopy (preserving the physical location information as the information goes from one part of the brain to another). In your Primary Motor Cortex and Primary Somatosensory Cortex your entire body is represented, in physically distinguishable form.

Parts to be added!

I knew that I needed to get used to modifying pieces while they are on the model so I have not yet added the secondary somatosensory afferents (the second data wire) that move the signal from the Spinal Trigeminal Nucleus to the Thalamus (specifically the VPM, the ventral posterior medial nucleus of the thalamus). I will be experimenting with attaching paperclips to the dorsal (rear in humans) part of the piece so I can have those connections.

Technical issues.

So any plan of attack that exists gets altered when it meets reality. My attempt to understand and convey the brain was no different. First, here are some 25g test pieces that I made to see how well the dyes worked on the InstaMorph. I put 25g of plastic beads into a short mason jar with three drops of dye and one tablespoon of water. This was put in a pan of water set to 3.5 (~160-170F) on the stove. This was done with the red, blue, yellow and black dyes. After a half an hour I folded the plastic about 15x (after washing my hands) to mix everything up and put it back in the water if needed. The results were what could be expected with randomly buying plastic and dyes.


This worked the best. So at least I was lucky enough to be able to build my first piece. This only needed the three drops, and only needed to be folded the one 15x session.

Blue and Red

These had similar issues. The dye does not stick to the InstaMorph as well. I ended up folding in two 15x sessions, and cutting grooves into the surface of the pieces so they would have more surface area contact with the plastic. You can tell when the dye will not stick as well when there is dye left in the small pool of water in the mason jar. Over time I had some dye stick to the plastic, and some stick to the glass in the jar. However it looks like I will be able to use them, I just need to remember to incubate longer or add more dye to the jar.


Yeah. So since black is the absence of all color, a lazy ( but normally fine) way to make black dye is to mix the primary colors because that way the object absorbs all color resulting in a black appearance (you don’t really see color, you see the unabsorbed visible light reflecting off of objects). That can result in problems…

I don’t want to spend more money at the moment so I might try finely ground activated charcoal…

The weird stuff.

This should have been built a week ago but the strangest thing happened. I got ritualistic about building the first piece. I don’t really have any other way to explain it. Since I have spent the last two months with this brain modeling among my primary interests, the act of bringing it into reality made me get emotionally sensitive about it in weird ways. I did not want to do it unless that was the only thing I was going to do that day (no other distractions). I got anti-social (I have mostly stayed away from internet social areas and real-life social areas). It also distracted me in other areas of my life that has caused some disruption (My hobby needs to be de-emphasized a bit). I guess this has meant more to me than I thought…


I can’t really do time tables anymore because while I am finally building a routine, I need to make that routine compatible with my life. If I am truly pushing against something that nature was uh, nice enough to give me access to, I have to start admitting some realities. It is having some kind of psychological impact. It’s minor at this point but I am getting more forgetful lately. I have a hypothesis that if TS is giving me some kind of altered access to rule-governed forms of language processing, over-reliance on that form can make me lazy with associational memory. I was always bad with names, phone numbers and such. But now when I get into more heated internet “discussions” I have started dropping bits of sentence structure and confusing others. I have not read enough about grammar structure to analyze copies of these discussions, but what I have allowed myself to think about makes me thing there is a weird blurring of categorical information, and lack of transitions. I have a problem giving people context. That makes me feel like a jerk…

1. As I have mentioned off and on, I am building a legend page to go with this effort that is actually supposed to work like a guide so that anyone could in principle do what I am doing. The reason that I decided to set it up this way is because back when I first started this, I realized that just drawing, sketching, and building pieces of the brain made a huge difference in my ability to internalize the information. Not only does it get me to remember what each piece is or does, but my brain seems better able to snap everything I read into an appropriate context. Lots of little things have become easier to conceptualize. For example I can see how the shapes and paths I am seeing were laid down by development. Also the way that incoming information is changed from a locational organization, to a computational organization after the primary sensory ganglia (Trigeminal Ganglion in this case) puts how everything is organized into a different picture and renders all the meaty bits more sensible because I am managing to uproot my assumptions about the brain from the limitations that my mind has put on it.

The mind is not nearly as mysterious as I was led to believe…

2. While I should look some more, I have yet to find any information on the internet about Tourette Syndrome or ADHD from the point of view of someone who not only has it, but can read the scientific literature as deeply as I can (I know they exist, I just need to find them). That makes me feel like I have a duty to present it in all it’s meaty glory with detailed citation lists way too long for the internet. Normally anyway. Since I’m still pretending that Tourettes is letting me translate information differently, I aim to make all that complicated crap sensible to everybody. Right now one short bit on google-fu is too little for me. I have mostly been waiting because the longer I took to build the first piece, the harder it was to think about TS or ADHD pages. I have a lot to say about both and I’m eager to see if it looks as impressive on a page as it does in my head. I’ve been wrong before.

3. The “Philosophy Grinder”. A couple of weeks ago I was going to do a post about me and philosophy. That has been boiling in my head for a while and that weird idea is now something I want to call the Philosophy Grinder. This is a very preliminary idea, but the gist is this. The information that your brain turns into your mind has very specific logical routes,l characteristics, and consequences to how our minds work. What would happen if one were to make a way to line up a philosophy next to the reality of how we process our reality? There are very real differences between associational and rule-based aspects to our social minds. There are very real biases that we place on the information that comes in and how we apply assumptions to it. There are many many more things that could be discovered if such a comparison could be made. I have not yet put the information into a single picture, but these five images contain most of the general idea in outline.

4. Next piece? I’m not sure. If I went to the thalamus from the STNVc I would learn more. But I will give in to a sense of completeness and finish the Other four parts of the STN.

I guess I will Post a few more images from the process for now and hopefully I will have a legend up as soon as I can.

In the beginning, the summer project…


So, how do I do a first post on my new and first blog? I guess by pointing out some information that I have put together that explains what this is all about.

I am a former research scientist who now works in public education. I left because I was not naturally cut out for the research environment, and if you want that story it’s here, as well as the entire reason I want to do this experiment.

I was diagnosed with ADHD as a child and thought I got over it. It turns out that was not the case (I saw a neurologist), rather I got used to it but it still made me too inefficient to survive in today’s academic research environment. I could have earned my PhD and tried to stay in academia, but I would have ended up a miserable person. While I was getting my bad news about the ADHD the neurologist also dropped another tag on me that I had no idea I had, Tourette Syndrome.


The popular stereotype of Tourette Syndrome is the person who can not stop cussing. Those folks do exist, but they are a minority within a minority, so of course they are even more misunderstood than me.

The best way to describe what it is like to have TS is to say that you always want “to do”, just “TO DO”! It’s like when you get electrocuted and your muscles keep contracting except that it never stops no matter how tired you are. You can’t stop it unless you focus on it, but of course life won’t let you spend your attention that way, so when you are not paying attention, you twitch, or move joints, or hum, or engage in a collection of other interesting behaviors ( Once while sharing driving duties with my wife for 16 hours I got physically stir crazy enough that I burst a capillary in my eye 😉

I always knew that I was a twitchy kid, but that was not something that I expected, and I had no idea what that meant beyond the stereotype. Fast forward a couple years while attempting to become a teacher in a bad economy and eventually all those internalized science routines needed an outlet, bad.


More info here. You see, I had joined this community of individuals who became obsessed with a children’s cartoon and believe it or not I think it is related. About nine months ago I got caught up in one of the most creative fandoms that have ever existed (It’s my blog, argue away) and I am now am a full-blown Brony, which is the name taken by adult male fans of the modern reboot of “My Little Pony” (Friendship is Magic). There I was, this mostly antisocial person who was now surrounded by people writing, drawing, animating, and I was having all these excited emotions running through me that were, not new but in a different context and I did not know how to handle it. I was reading about ADHD and TS at the same time and I had all this science in my brain, my background and it was like I went a little crazy for a bit. I was analyzing everything, and especially things having to do with brains and it felt like some weird OCD. I actually had to work to stop being analytical! (pity my wife)


I did a lot of writing during that time in order to have an outlet from what I think might be a weird combination of the TS and the socially triggered creative impulses. There was something trying to come alive in my head and it did not have the proper tools (connections?) to properly express itself. What ended up reducing the intensity of the analytical OCD was my research about ADHD, TS, and brains. Or it was just time and I’m reading too much into it. I don’t know for sure.

So the point of all of this is that I am trying to research the brain well enough so that I can figure out what the changes in my brain mean in real cognitive experience. If I can figure out what I am, I can figure out how to live. To that end this blog will be a journal documenting the construction of a logical model of the brain that is as accurate as I can possibly make it, and visually understandable.

If I do this right I won’t be the only one benefiting so I hope that you the reader will let me know if I am doing my job!