The brain model design principles.

A blueprint for us…

How do you understand something as big as the hardware and software that is what you are? By trying to line up as many facts about it as you can. To that end I want to build a computationally accurate model of the human brain and I want it to be visually understandable! Now what the heck does that mean? What that means is that I am going to identify every little part of the brain that I can that science has been able to discover. I will then build a really simple, yet very visually informative model that shows the interaction of of the various computational components. That’s right, it’s time for plastic and pipe cleaners 🙂

Here is the prototype so far. Sorry about the fuzziness, I’ll fix the lighting issue soon.

Left: Prototype ganglia constructed from InstaMorph plastic. This plastic can be embedded with dyes, glitter all sorts of things to differentiate otherwise similar bodies. Paper clips can anchor many things including pipe cleaners of many colors. These prototype ganglis took about ten minutes to construct! Below: Prototype framework of the brain. At the bottom is an outline of the spinal cord at c2 (I will add detail wire for the white/grey seperation). Ganglia will be attached to the dowling rod with smaller rods tapped into drilled holes.

This model is going to be really cool! So far I am incorporating the following design principles.

  • Easy, simple construction that can be modified on the fly for any reason. Dowling rods with drilled holes and bracelet wire for framework. Ganglia will be represented by plastic structures that can be easily put on projecting smaller rods. Nerves will be pipe cleaners twisted around paper clips embedded into the plastic (really cool InstaMorph, below).
  • Easy visual assessment of the nature of the information flow by: choosing different colored  pipe cleaners for different kinds of data, Differently dyed ganglia to represent different classes of processing organized by main process (motor, sensory, autonomic, etc…), and sub-process (each kind of sense that can be tied to a single axon. Golgi tendon organ, muscle spindle, vibration touch, sharp pain, dull pain, many more…). Colored thumb tacks to represent the kind of neurotransmitter used. Colored paperclips that will indicate the nature of the cell/cell connection (activates, inhibits), tiny strips of colored electrical tape to indicate anything I did not thing of like if a nerve is on all the time or not. This is still ongoing but to give you an idea about how complex this might get, here is a source I am using for the brainstem.
  • Anything else I can possibly do to make this easy, obvious, and accurately reflect reality!



Now there is a limit to how much I can show in a useful manner, especially since there are aspects to brain science that we are still figuring out. But we are a lot farther than the vast majority of the population realizes, and it could be so useful people who need it except for one HUGE problem. Most of the discoverers of knowledge try to own all the language, and on top of that most of them don’t bother learning how to communicate what they know with everyone else.

The Language Barrier

That confusing and vague statement refers to the problem of jargon and life. For the non-scientists present let me say that I understand. Life is really really complicated and you don’t have the time to learn lots of new words, and even worse learn them in a way that lets you understand them on a useful level (internalizing the definition and not just the letters). I’m not trying to be insulting in any way here! I was the lone science person in a family of soldiers and preachers, and that gives you access to lots of different kinds of people. Also I work in public education so I meet lots of children from lots of backgrounds. In a bad economy the last thing a parent, or job-seeker, or anything else dealing with what life hurls wants to do is learn vocabulary. I’m on your side, at least in part. If I were dictator for a day I would add a constitutional amendment that required that any licensed, accredited, degreed, or otherwise specialized person to have to be able to explain what they do in words that the maximum number of people would understand. What’s the point of experts if they aren’t able to sell their expertise to the rest of us? The other side of that contract would be that society would make it a priority to be willing to actually look things up when they want to have opinions on things, and that we all actually try to condemn ignorance as a species. Yeah I’m an idealist, I like to complain about the sun rising too 😉

The second point I was making above has to with the fact that there are something like five related, but still distinct symbolic systems trying to describe the brain, and all of them are impenetrable to the average person. The study of the brain spans centuries, structures are in Latin words that describe the way things look, cells are described by things like speed, and activity level, chemicals have names with no bearing on their role in sensation, computer science is increasingly used to discuss the relationship between structures, etc. Biochemistry, Neurobiology, Cell Biology, and once the main function of a part is discovered, the culture that found it usually avoids the one thing that would help everyone, name it after the function in a way that suggests it’s connection to everyday experience!

So one very important thing I am going to do at some point is rename everything so that it has two names, the “real” one, and my name that will try to be informative.

Everyday experience.

Now how am I going to make sure that the function of each structure does what scientists really think it does? I have to look at a small collection of facts that will make the identification of function as accurate as possible.

  1. Scientific Consensus: I will use more than one source of information that emphasizes peer review. What this means is that I will use Wikipedia whenever available, and at least two review articles that discuss the structure in question so that I know the scientific consensus (broad agreement) on the function.
  2. Evolutionary Comparisons: I will try to identify existing organisms that do, and do not have the structure that are as closely related as possible so that we can have an idea of what the presence and absence of the structure contributes to behavior. This is tricky as these structures have been modified by evolution over time, but there are lots of brains out there!
  3. Paleontology: I will try to identify when the structure evolved, and what that world was like as closely as I can in order to identify the selective advantage of the function of the structure. Evolution operates within natural selection. With no selective advantage, evolution will not likely keep any mutations around so if we can figure anything out about the environment our ancestors lived in, we can figure out what that brain part might do.
  4. I will try to find examples of what occurs when this part breaks in real people. It’s in unfortunate fact of science that the victims of injury are a valuable resource in brain science.

Using these four things as filters I have a very excellent chance of really figuring out what the function of a structure in the brain actually contributes to the whole. In addition I might be able to connect it to every day experience! I will add more information filters as their necessity is discovered.

Moving the information your reality is made from.

I am modeling the “nerves” out of pipe cleaners. The reason I am doing this is because you can get them in a huge variety of colors so I can choose colors to represent the nature of the information that is carried by the bundle of nerve cells, or individual cell when necessary. One of the really neat things about the nervous system is that one can compare the structure of it to the inside of a complicated piece of machinery where the data cables are bundled by function. (Yep! I’m going with the Command/Control cable analogy, especially in the spine. No this does not imply a designer, I’ll do an embryology post sometime).

Processing the data.

I am going to model all the little “bits” (Ganglia*) out of a material called InstaMorph. This stuff is really neat because it is a plastic that can be made transparent and mold-able by putting it in boiling water. When it gets back to room temperature it is hard again! Here is a neat example I found. It can also be dyed so I can color the pieces by some functional color scheme. When I start making the pieces I will probably provide a video of some of it.

*Ganglia are where the processing of data occurs in the brain. In a very real way your brain is made from lots of little brains, as well as other ways creating functional separation of the data that is coming in from the outside world. How that data relates to stored information is another matter entirely 🙂

Decisions to be made.

*Part of how the “data” of long term memory is stored involves layers present in other parts of the brain such as the cerebral cortex, and other areas that function similarly. I am thinking of using colored felt to indicate functional regions at this time like the somatosensory homunculus, or the motor homunculus.

*How much to distort my model versus reality because I have to make functional identification of relationships a priority.

*How to incorporate cutting edge issues like epigenetics which has the potential to be even more controversial than evolutionary psychology.

*There is always etc…

To be continued…

One thought on “The brain model design principles.

  1. Pingback: In the beginning, the summer project… | Brains and Bronies

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