Why I am not building anything for two weeks or so. Orgainzing is everything in this project.

Building is the easy part! I need to tie together lots of brain info…

Preparation: Organization principles

This is where I think the Tourette Syndrome helps, I’m still working on the ADHD angle and yes I will get to those pages soon!

One theme that I keep seeing come up over and over and over is the theme of the hierarchy. Hierarchies are everywhere in biology and the brain is made up from interconnected hierarchies. Our language is hierarchical!

You should already be familiar with the hierarchy if you are a human being. That is the way that we organize ourselves when we need to get anything done. The military ranking system is the most obvious example. Also many government bodies will display a hierarchy of the organization somewhere such as this example.

Our countries are nested hierarchies that have states, and counties. Our cities have a hierarchy too with the capital acting as the center to organize the whole mess. These are divided in turn into districts, etc…

Because they are so important to us we play with hierarchies. Russian nesting dolls, child’s games that demand “who is the leader!”, so many social groups like,  political parties, school clubs, religious organizations, corporations, universities, Ad infinitum as we evolve.

It’s a never ending process where we try to organize ourselves in better ways using the same general outline that is literally millions, tens of missions, maybe hundreds of millions of years old. But there is a remarkable thing that gets overlooked, our brain contains hierarchies too.

In fact my hypothesis (the reason I am doing this) is probably why I keep writing in those little bites. My mutation affects some part of a hierarchy that deal with conceptual processing and my comfort with writing in smaller paragraphs is a result. (No really, it’s a habit…)

As outside, reflected within. Or is it?

When brain research started, the first attempts to understand the meat that contains our mind, they did not have a whole lot work with, it being hundreds of years, to fifty years or so from the way the lectures discuss the history today. On the hundreds of years scale they were discussing body snatching gangs in British universities for subjects, texts were written that are so legendary that TV shows of dubious quality are named after them, and it’s all in language that does nothing for memorization unless they teach Latin in public schools again (good luck with that). Brain parts are named after what they look like or some dead person’s name (most of the time). Sure you get “Medulla Oblongata” with Bugs Bunny (I least I think I remember that reference) but regular folks just can’t deal with that.

On the order of around half a century ago (hi Grandpa!), they were finally tinkering with the plumbing, and finding an organic computer in the most general of terms. Animal models of the easy senses (vision) were giving us lots of information. What we learned is that vision is processed in a hierarchical manner! The eye assembles images out of sets of contrasts!

*Drama Prevention Department*

Protip from “The Rustler”

Drama prevention department tip One: The ghost in the machine.

Quick aside for some sensitive readers: Brain computation is a valid search term when perusing scientific documents. Eyes processing visual information hierarchy-style is a visual fact in text-books. You can even see part of it. When it’s in your hands it hard to avoid talking about it.


Above: The Optic Chiasm(2) is the structure where the data from the eyes is organized as it travels to the back of the brain (visual cortex, 6). The information travels from the eyes (top) towards  the Chiasm (below the hypothalamus) where some of the data travels to the opposite side and some stays on the same side. From the Chiasm the data on both sides travels to at least four destinations along multiple paths along the Optic Tract, each of which deals with more processing of the information.

I know talking about the brain as a thing, a computer seems rude to some folks, but that is what I am doing, and more importantly that is what brain science is doing. So please be thoughtful if you are offended by any of the issues in this project. I am willing to be challenged but you need bring your best game if you can not control your emotions. In return I will do my best in the same way.

My belief (hypothesis) is that the way we deal with society is also hierarchical in the brain. A piece of evidence is that we are obsessed with hierarchies, and for good reason, it is how reality lets us organize information. Just google [Mythology and Hierarchy]…

My challenge is to translate and integrate the hierarchies into the model, and maybe discover some new ones that relate to social pain. I want this to make  sense to everyone.

The above warning goes for religious folks, non-religious folks, libertarians, feminists, anti-feminists, communists, and any other “-ist” that follows the programming manual from one individual, for a specific place, in a specific time. Behave yourselves or I will summon the “Rustler” (source). Some of those above groups I also share when it comes to philosophy, but none of it is out of bounds.

Drama prevention department tip Two: I’m sorry Fluttershy…

This is going to be a tough one, but lots of research is simply impossible without killing animals. I will keep out images of anything unpleasant, but the fact remains there are cats involved, and rabbits (Angel better start behaving…), rats, mice, primates of all kinds and lots of other animals that science is impossible without. Again challenges and feelings of any kind are fair, but be thoughtful. The Rustler has a soft side however…

The Rustler has many faces…many names…and a heart…


Contrasts and the hierarchy…

Note: I am willing to help anyone in the comments understand the material in this section more than others because understanding the Cell Biology based biological hierarchy of the nervous is critical to understanding the brain!

A contrast is intimate knowledge if you are a photographer, or in any kind of professional visual art category. For everyone else the simplest contrast is a black and white issue, literally.

Anything that computes needs to be able to tell a DIFFERENCE in a computational sense, the same one they taught you about in school. What matters is, what are the units of that difference? For most of you it was dogs, cars, bottles, rocket ships, anything. Now you use your wallet mostly because the issue is subtraction. But in your eye it’s light. Not just just one kind of light…

Red, Blue, Yellow during the day, and slightly blue/green at night. Yep! Rods and cones. Each one detects the presence of a small range of light frequencies, and collections of these cells turn a spot or edge into a on/off signal at a Center/Surround.

Below: Connections between the cells as seen in neurobiology textbooks (From a great program called “Webvision” from individuals working at the University of Utah! Awesome images!!!)

They call these Center/Surrounds “Receptive Fields” in neurobiology (which is another hierarchy made from Cell biology/Anatomy/Biochemistry/Molecular Biology), because they discovered them from the outside, they named them inside-out. If you are an artsy type that is why Photoshop faqs like this one exist.

You would perceive it as a Center/Surround if you had conscious access to that system, a circle inside of a circle, which is easy for nature to make. What matters is that when the light coming from a spot or edge strikes your eye, you detect it because there is a circle in there that turns a cell on or off, inside of a circle that turns a cell off or on in opposite manner to the other circle. The first step to visually sensing your world is this structure whose sole purpose is to detect a spot of light

The Visual system’s center/surround circuit that detects spots and turns them into single “on/off” (0/1, right/wrong, good/evil whatever) signals that go to the brain.

Note: Don’t get too involved with details on the images below (Unless you want to), they are just there to demonstrate that the cells in your eye are indeed arranged in a clear hierarchy.

Top: The structure of the human retina from “Grey’s Anatomy” Center: The cell relationship seen by Gray.

The Center/Surround and why you see the world the way you do.

The center/surround detects an spot, and these are assembled into the basic features of our world by passing single “spot Yes/No” signals to the brain. All the little cells in the receptive field eventually converge their signals onto a single cell sends it’s signal to the brain.

Motion is detected as particular collections of spots in and moving across your visual field over millions of center/surrounds. This processing is carried out at the very back of your skull in the visual cortex where the basic aspects of scenes are assembled.

This basic system is duplicated to let you see different contrasts, but here is where the science gets fun and a bit more difficult because this is where medical students and such are.

These contrasts are detected by three classes of cone cells and one class of rod cell:

  • Cone S (short wavelength): Responds to a range of light centered on 564 nanometers, basically Blue. Makes up a smaller amount of total cones (5-10%).
  • Cone M (medium wavelength): Responds to a range of light centered on 534 nanometers, basically Green. These are present in larger numbers and in about equal number to Cone L.
  • Cone L (Guess…): Responds to a range of light centered on 420 nanometers, basically Red.
  • Rod: Responds to a range of light centered on 498 nanometers. They are responsible for night vision and peripheral vision.

Note that the three types of cone cells contribute to color vision by responding to one of the three different frequency ranges, and the intensity of the light (about one hundred gradations of intensity).

Here is where it gets heavy and I will try to be gentle. But that can not be helped because we just hit the cutting edge! I will do a post that diagrams out the specifics eventually, but maybe not until I get to that part of the model. A free review that summarizes some of this information as it connects together is here,

“Neural models and physiological reality”

The mind interprets three basic contrasts. These contrasts oppose one another to give you the vision that you use in normal day “bright-light” conditions:

  • Blue/Yellow contrasts are detected in a system involving cells that respond to the difference between Blue and Red/Green (half is called “blue-ON/yellow-OFF opponent response” in sciency talk). Damage to this system results in Blue/Yellow color blindness. While individual cells detect yellow or blue, the actual color is detected through the opposition of the signals responding to the individual colors.
  • Red/Green contrasts are detected in a system involving the difference between Red and Green. This system again uses the opposition of the red and green signals to determine the actual color. Damage to this system results in Red/Green color blindness.
  • Black/White contrasts which I am still reading about.


Scientific American article


Take Home Message…

  • Your Brain puts your picture of the world together out of little basic features that it has to assemble into a form that can not only constantly assess what is going on, but also compare what you see to your memory.
  • The process of building up that picture is done through a hierarchical process that takes the little bits and assembles them.
  • The function of the eye is one of the best known of those processes and it is a good model for how those other processes can be understood.
  • My grammar may suck, feel free to be a Nazi…

Next time: Creating a hierarchy for the data that travels in the spine. Making the brains command/control cables visually sensible.

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