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.

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.

Am I really ready?

I’m finding it hard to believe, but I think I’m finally ready. I have re-done the fine details of this over and over to make sure that it all makes sense and there is not a better way. I have been disappointed in how long it took me to get here because I have been unhappy with how the information was synthesized together and how I would have to describe it on the legend page. So I have been combining and simplifying over and over to make it as generalized and accurate as possible. I think it’s finally done. The process anyway (at least until I have to consider cortex and epigenetics more carefully).

Here is a shot of the spreadsheet for now. I try to upload a copy of it tonight after putting in the rest of the relevant links in. I like the idea of having a file handy for critics.

On the Left side is some general information on the details that I am representing. On the Right side is a box arrangement with some creative cell filling to indicate wires and processing centers. The positioning is relative to how it will be in the model. The pink regions are to indicate different anatomical directions. The blue bar is showing the most general structure. The Yellow boxes are either somatosensory ganglia or neurons. The Orange box represents the receptive field (where the sensation comes from and what it is) for the temperature and pain sense, and the blue boxes represents the touch sense (which is spread between the Vo and Vi sub-ganglia that they call “Pars Interpolaris” and “Pars Caudalis”). The yellow boxes on the right are the destinations of the secondary neurons that reside in the ganglia. The grey box represents the Ganglial Contact Zone (they just call it the Vi/Vo transition zone) that I needed to add as an element. I do not know if there is a GCZ between the Vo and Vi portions of the STN but I will be leaving place holders in the spreadsheet until farther notice.

On the left side of a ganglia/GCZ box I put any inputs to that body and in nearby cells I have receptor/cell type information that I will choose a bead for if necessary (cell type for sure due to message speed being an important factor).

I am also changing the box border colors when appropriate (inhibitory/excitatory signals, etc…). It’s going to get some tweaks because I think I can represent some of that better but at least I have a final piece spreadsheet!


The system that the Spinal Trigeminal Nucleus functions within is the somatosensory system (above). I chose to make somatosensory structures (pipe cleaner and plastic) yellow because that is an indicator of an “alert” color that might not be bad choice.

I chose to make pain sense a red bead (wire) or red glitter (processing center). I chose to make Temperature sense an orange bead or orange glitter. I chose to make touch a blue bead or blue glitter.

I want to get the legend up so I will put this in , finish the legend, and then add pictures of the finished STN (2/3 of it anyway, I’m doing Vo next). I just hope that I don’t get really picky about how it looks. I’m going to try to do a good job of course, but the last three weeks have been a bit ridiculous. There are few things that I have been as picky about…

It’s weird. I don’t know if I am doing anything unusual here but I have definitely seen some interesting things happen as I have worked on this. It feels like I’m doing something I could call “analogical thinking” where I’m just blurring things a bit in my head and looking for shared elements when I think about all of this, and how to convey the information. This also happens when I am researching and reading the material. Or maybe prying open an “analogical aperture” might be the right word? I’m still trying to figure this out and a lot of the impressions that I get about what is being written about my head are not things that I can really talk about with enough authority yet. I don’t like to carelessly discuss science.

I have seen my physical tics undergo some changes that have actually forced me to slow down as well. Since I started all this typing I have developed hand and knuckle related tics. Also when I am particularly engrossed in what I am doing sometimes I catch myself doing a particularly elaborate thing that goes from my neck all the way down to one arm. The finger ones are concerning me because I am getting sore knuckles. I am investigating Tai-Chi as a means to gain some more physical awareness so that I can perhaps get better at moving these tics around to less sensitive areas.

At least I hope that is possible. The literature I have read about Tourette syndrome suggests that the tics might be the result of emotional signatures in the cerebral cortex that were left unerased from some sort of generalized rule-making procedure. Coincidental encounters between current cortex activity and the old stuff may result in tics that are essentially partial memories of previous actions, or inappropriately placed memory signatures. The rule based aspects of our language system are historically based off of an evolutionary “copying” of the rule-based parts of the motor system. It’s looking to me like there is a point where the person with Tourettes chooses how to focus the “TO DO” urge. Some choose sports and music with their respective rules to throw the urge at. Maybe others can access a different system that has to do with the rules that determine our symbolic thought processes. Hopefully one of the professionals that I am emailing will be willing to take a look at all this at some point.


So I have essentially been rewriting the “design principles” page in it’s final form, and making all the final choices for the first piece so that I can have it finished and included as an example.

First pieces actually, since the delay included a new design element I am actually making three pieces, two processing regions and the contact zone between them (I changed that “Inter-ganglial regulatory interface” thing, it’s just “ganglial contact zone”). I’m doing the spinal trigminal nucleus caudalis, interpolaris, and the regulatory zone in between. I know it’s not much compared to what I wanted at this point, but here is a quick shot of what I have outlined.

The full design principles page will be the “Map Legend” page. I’m “almost” done and it’s at~8700 words. I had no idea that all that was lurking in my head. I’m glad that I took the time to outline this in full form because ADHD and disorganization. I am a learning process apparently…

Proof! :)

I want to apologize to those of you reading that did not realize that this was a lab manual.

One thing I should have said more obviously is that this is a process as well as a model. So what I am finishing for you is a story and a map legend. I’m calling it a “Legend” page because it’s all the background that any random person would need to figure out what they were looking at. It has,

  1. Why the model is important to me (It shows how information moved through the brain which lets me understand how I think).
  2. Why I had to make it look like I did (The design elements:Wires, processing regions, and interfaces).
  3. What the elements mean.
  4. How to look it up for themselves.

I’m trying to make it like lab meeting of the kind that I would have done in graduate school for fun. I am trying to get it done as fast as I can, but I realized that it would be really important to have and made delaying construction worth while.

Just for fun here is one of the analogies that I am using to offer something.

Yep! I really do think that parts of the brain can be understood in terms of similarities to specific generalities of the computers we use!


My routine.

Last update line to this post (7/13/12). The summary is that I got started on making the first piece of my model and found something new that I needed to include as a design principle.

As of 6/4/2012 this is an unfinished post! Since it is a creative work in progress on exactly how I turn brain information into a piece of art, I thought there might be preliminary interest before I was finished. It’s also nice having a record of the process for my own benefit 🙂

Most recent update

6/20 I Have Dye!

I’m almost done with the Legend. My next steps are to Finish the Legend, revisit the material briefly, and sketch the piece. I should be deliberate about this too. Even though the parts are easy, I want to do them right.

Note: My intentions are to update a couple of times and then make a final post.

6/5 update: Added the final decision on a trio of ganglia and the logic from source A1

6/7 update: Complication due to ambiguous structure, and doing figures right the first time. Below…

6/8 Finalized the method of diagramming the in-put/out-put logic! I think it’ MUCH cleaner and more understandable.

6/10 The weekend is a time for mentally resetting. This is valuable. I want to explain this someday 🙂 Essentially I need to add a new major element to the design so things got a bit slow while I was thinking. Now I have a solution!6/19

6/12 My apologies on the lack of updates. I have to order a black dye that I can use in the plastic so it might be a few days…

I’ll get some figures into this post. (…and yes I realize that I put beads into my figures twice…)

6/18: The dye will be here today hopefully. That would let me start tomorrow. This stuff has been designed in my head for over two weeks now and I’ve been going a bit nutty wanting to start. But the wait was worthwhile though because a legend page is a great idea. This one is turning out kind of neat because it’s like a lab meeting for you guys like the kind I used to always do during graduate school. A lot more fun than the real ones of course! (Unless the science is fun even when drier like it is for me 😉 )

6/19 I have no dye. Otherwise this will be the best map legend ever, or it will be horrible:)   I’m at 3049 words and really enjoying myself.


Now hopefully I can get a routine down to get this thing going in earnest! This will be the day to start good patterns and habits.(This will please you if OCD, maybe…)

Create a routine and just do one for now and as long as necessary. In fact that is what I am doing here. Blogging the experience of my first research attempt on my first model piece so that you can get an idea about the level of detail, and the thinking processes that I was engaging in while I was figuring out what I needed for every piece so that I can say the info is “GOOD”. It’s a model for the following work that I can refer to for anyone who is curious.

For every one of these brain processing centers I need the following information:

  1. The logical decision that it makes/role that it takes.
  2. Every known structure that it connects to.
  3. The logical nature of each of those connections (activation, inhibition, etc…).
  4. The number of connections (if possible, it might be important).
  5. The ultimate beginning and nature of the information that it carries/conveys. (For this and #6 it is to keep us in the “big picture both functionally, and experience-wise”)
  6. The ultimate end and nature of the information that it carries. (See #5 for context)
  7. Known Epigenetic regulation (for future use)
  8. What it looks like (might as well have some more context…).

For most readers 1-6 are of decreasing importance. 7 has to do with cutting edge things that are so new I can’t really do more than book mark it so I can build something into the model later when my brain spits out visual solution that is sensible in the information hierarchy. 8 will be useful to people in medicine or brain science. They will be more likely to have a mental link to the shape and it will be more interesting.

Of course I will add more as necessary, but that should be a good place to start. I have a system, I have a plan, what is the first piece!

#1 Spinal Trigeminal Nucleus

From Yahoo. Thank’s yahoo! (Trigeminal = “thrice twinned”. The freaking root is the “nerve”. Nerve is one of the most abused words in science. Its a linguistic whore…

Interesting context though. I almost feel like I’m in the room with Grey

Looks I have a more challenging piece for my first attempt. I like to Wikipedia first as a broad overview and it says,

The spinal trigeminal nucleus is a nucleus in the medulla that receives information about deep/crude touch, pain, and temperature from the ipsilateral face. The facial (cranial nerve 7), glossopharyngeal (CN9), and vagus nerves (CN10) also convey pain information from their areas to the spinal trigeminal nucleus.[1]. Thus the spinal trigeminal nucleus receives input from cranial nerves 5,7,9,10.

This nucleus projects to the ventral posterior medial nucleus in the dorsal thalamus.

That’s pretty bare for Wikipedia so either its pretty simple, or there is not much work with it yet. On top of that the source is gone. Would you trust that? The talk page just leads to a general medical portal, and the revisions just get simpler. This is when I start going to Pubmed, but later because this is a good example of what I keep running into when studying brain info:

Lack of specificity: Due to the long and complicated nature of brain research, this article uses historical Grey’s Anatomy images. This image is only useful when combined with other information because when Grey first did this work he numbered the cranial nerves I-XII, and their root ganglia I-XII. Since then they have discovered that these nuclei are more complicated than they thought because these nerves carry motor, sensory, place-in-space and other information from different places and for different purposes! So the Wikipedia page lists 12 cranial nerves, but 24 cranial nerve nuclei that translate and pass on the information. Annoying! The history has value, but that value is relative to the public’s utility. As long as the ultimate purpose of telling the history is honored in education (or fun), the information needs to be reorganized by everyone in biological sciences.

The Trigeminal Nerve, A TL;DR history.

It’s interesting that my first nuclei is actually mostly not about the body despite being at the bottom of the brain (or at least very low and central to the brain stem structure). That might say things about how human segments are arranged. In fact I think it suggests that the brain stem, should actually be thought of as the “Brain’s Spine”, combined with the information transfer of the “Body’s Spine” So the general information flow in the head looks like this…

…so far. In fact I think that a diagram of the information flow will be a necessary part of this project and I will draw one as I go. Fortunately Wikipedia even helps me here!

The brain stem is actually an interestingly complicated structure that literally routes information that impacts your entire body. It’s the most important information routing intersection in terms of overall structure at a “horror movie” or “that’s disturbingly interesting” level. So it’s actually a nice contrast that this structure has a complicated history when it comes to learning about it, and it being the first piece I make.

It was named as it looks, and the most obvious feature a centuries old anatomist would notice is that there are three huge nerves splaying from the cut zone. So yeah the old folks do the best with names that they can. The Trigeminal Nerve is interesting to me because the details of the information it handles shows us just how the “Human Worm Segments” of our head are arranged in gross detail.

Using Wikipedia on 6/4/2102, The nerves that feed this structure information mostly have to do with the face on the opposite side of the axis from the ganglion. But that information can be divided into two groups:

  1. Information about “…deep/crude touch, pain, and temperature from the ipsilateral face.”
  2. Physical routing of pain information from “The facial (cranial nerve 7), glossopharyngeal (CN9), and vagus nerves (CN10) also convey pain information from their areas to the spinal trigeminal nucleus.[1]. Thus the spinal trigeminal nucleus receives input from cranial nerves 5,7,9,10.” (We will see this link a lot. I will have to make a Link archive. I have to add proper citations to my routine anyway…)

The output is to the:

There’s that language again. Remember this old thing? I will need to make a new version with some more terms…

Ipsilateral means “same side”, Contralateral means “opposite side”. I think the entire reason that the brain does the side switching thing with information is to create a “Logical Contrast” so that it can tell a difference.

So we have the more “primal” type of pain, touch, and temperature from the face.

In addition we have unspecified pain information traffic for the face (facial nerve, “face/mouth nerve”), the mouth/throat(Glossopharyngeal nerve, “tongue-throat” nerve), and one of the most important nerves in your body, the Vagus nerve. Just pain information.

All that chaos above tells us that the ordered structure that we see in almost every human (there will always be exceptions) has rules, but we don’t understand them. So to properly understand the human body absolutely (if you are into that kind of thing) involves knowing the rules of the growth of the structures. That’s right, embryology.

Oh boy! A new toy! …and some old ones…

I know almost nothing about embryology, but the reason I am willing to play in an unfamiliar field is because I have enough experience with the fundamentals, and would have no problem internalizing a few new basic principles like the diffusion of chemicals in an embryo. (Sorry folks, it’s not a miracle. It’s only complex, which is why all the pain and suffering pops up too often.)

If you can see the results…

…you can get conceptual hold of any topic.



Developmental Biology

Now I’m only going to include the bits relevant for us, but when development becomes important for functional understanding, I will bring it up. I guess in general I will need a couple of recent reviews on the structure/ganglia/nuclei mass just to make sure I have everything. I always try more than one kind of search so I don’t bias myself so I am trying (I already warned you there are cultural effects in the science and the medicine of the Brain/Mind).

A. [Spinal and trigeminal and nucleus], B. [Trigminal and Nerve]. 272, and 1680. That difference is due to the fact that one plugs into another, time, and because doctors don’t see a STN, they something that their intellectual ancestor called something like a “..special nucleus of gray substance…”, which is to say they don’t see a computer, they see meat.

For A, Sorted by date

  1. “The role of trigeminal interpolaris-caudalis transition zone in persistent orofacial pain.” is the most recent review that is really “meaty” and detailed. A
  2. “Neurochemical properties of the synapses in the pathways of orofacial nociceptive reflexes.” is a more “molecular/cellular/tissue angle. Not a review, but they will have background. It’s the kind of thing that I could actually explain if anyone was curious. I used to do something called “In-situ Hybridization” and it was fun! I made yeast cells glow red and blue and genetically modified the creature myself. Life can be legos sometimes. Although I have to assemble it myself with Word and screen grabs…
  3. “Anatomy of the Rostral Nucleus of the Solitary Tract.” A book chapter. I love these people. Not the same nucleus but also in the brainstem so will give context. More screen grabs…

For B

  1. This one is Meaty and fun if you have the stomach. A review investigating new scanning technology on a live patient! This is the benefit of broadening your search criteria on anything. Let your tastes guide you.
  2. “Non-Invasive Mapping of Human Trigeminal Brainstem Pathways” is the brainstem relevant, uh yeah… more Word and screen grabs though…
  3. If I need one after the fun stuff above…

I think that is a good start so Now I read and diagram out a mini logical structure of the region of the general Trigeminal nerve nuclei, out one heirarchy level from the the Spinal Trigeminal Nucleus. I have defined my artistic link to the brain…


After reading “The Role of Trigeminal Interpolaris-Caudalis Transition Zone in Persistent Orofacial Pain” (A1 above) I have come to the conclusion that I must have a nod to actual structure in the model. But how to do this and not have it overwhelm the computation? I may just do it in metal wire that I can paint with a UV reactive substance so you can see the structure “light-up” over the computer bits…

The rear/bottom part of the STN is the Vc (Nerve V, caudal nuclei) This does the pain and crude touch part of this nucleus. It will be Yellow plastic with Black and Red glitter. The logic of the connections that I could strip out of “The role of trigeminal interpolaris-caudalis transition zone in persistent orofacial pain.” is in this image. Looks like I’m building in interesting trio and then attaching the group!

6/7 Update

So where is that model piece you promised!

The reason this was done in a pseudo-“live blog” was that I knew complications would arise and that I would need adjust things. I am prone to internalizing bad habits. It take effort for me to get a bad routine out of my head and I love routines! So with something as long term and detailed as this I need to get it right early. So what is at issue?

  1. That really shitty diagram above
  2. ambiguous structures.

One is easy but it took me some time yesterday to think it through. I decided to take the Grey’s anatomy images and convert them to figures in Microsoft PowerPoint (you can do SO MUCH with MS office and Photoshop. Did you know you can copy/ paste from one to the other in many cases?).

That still needs some work but is MUCH better than the previous. Still too busy for most readers, but better for now.

Two is a little harder. When I read that first source and discovered this Vi/Vc transition zone, I discovered that it was a very important network hub for a lot of important processes, and it’s still being intensely studied. So while this model is really adaptable to having elements replaced, I need a way to present things like this transition zone. I am working on the second source above (“Neurochemical properties of the synapses in the pathways of orofacial nociceptive reflexes.”) and it includes even MORE extra info about this same transition zone! I hope to have that integrated by the end of the day, after I figure out how to present this hub of a transition zone. It’s more fun than frustrating, but when I say I am going to do something I need to be more specific to your guys…


Final method of showing the in-put/out-put logic! Three separate diagrams for each of inputs, outputs, and “unknown logic”

Next, and hopefully last before modeling something, how do I show these extremely important inter-ganglial transition regions? They are extremely important apparently! Look at all those outputs! I need a way to make them seem obvious when differentiated from the ganglia proper, but still related to the functional class…

6/10 Post one.

I think having a period where you just have fun and relax will one day be a constitutional right if we can define it. Chances are when I am done here we will discover that creativity as a process requires spacing and thinking. The more employers dump on employees, the more mental reset points will probably be necessary. This would probably be to ensure that the physical basis of practice and more importantly, internalization is achieved under the least stress. You can take that as a scientific hypothesis…

To make up for the weekend gap I am now adding a “Legend Page” where the design elements will be explained in specific terms, and the way the elements interact will also be explained so that you can understand how the picture becomes the data that create our experience. In general terms at least. Since science will always be adding to what we know about ourselves, this model is by design extremely easy to alter by nature. It’s an expression of the scientific method.

Here is a preview since it is still in progress. I hope I “code in” permanent elements today at the very least.