Why is brain science so difficult to understand anyway?

In which I take a step back…

First let me say that there are good reasons for the names and terms that need to be changed. When they were first bestowed they did not know what the parts did in the brain. Also keeping a name the same (no matter how silly) can make it easier to do science between folks from different countries. But that usefulness loses it’s relative value once the function of a part of the brain becomes better defined. At some point tradition has to give way to reality and

the name should be changed to something that represents it’s function so that non-scientists can use that information as soon as possible. Especially with something as potentially useful as brain science.

But here is where I can almost understand why there might be a genetic component to conspiracy theories. It might look like I’m seeing hierarchies everywhere, but it’s not crazy if it’s true and I can demonstrate it. A bunch of old sciences are joining together into something new and that new thing has to be useful to people. Brain science needs to do renaming and in a real way the organization of the colors in the model are a process for doing that.

Science and Naming

Science is a constantly evolving discipline because it is a process, and the things that come out of that process can change the outside appearance of the whole enterprise. Part of that is due to the fact that science sometimes gets things wrong and better information is found later.  But what is “wrong” is usually the best that they could do at the time. I don’t stick my nose up at alchemy because it was a hypothesis, and chemistry was it’s competitor. Chemistry won, for the most part (I suppose nuclear chemistry is close enough to alchemy in some respects ;)…) As an example the rhetorically abused “paradigm change” that occasionally does occur, such as the eventual acceptance of plate tectonics.

Here is a good story about Alfred Wegener and how he changed Geology.

From Wikipedia’s Continental Drift article.

But another part of that is also because multiple fields of study discover that they are really parts of the same thing and it can take a while to get everything worked into a whole with language that everyone uses. This happened with DNA. At first they knew nucleic acid existed, and that there was something in the cell that stored the genetic information. Eventually the right experiment was done and the two fields, DNA and genetics, were merged.

Here is Wikipedia’s description of the Hershey-Chase experiment which is the one they show us in Molecular Biology to tell the history of how they knew that DNA was where our genes were.

Martha Chase and Alfred Hershey. From The Cold Spring Harbor Laboratory DNA Learning Center.

Brain science is a lot like the second one except that these fields knew that they were related from the start. It’s just that the brain had so many dimensions to how it functioned that it’s study started in many different places at different times.

  • Molecular biology: The study of the nature and structure of the chemical networks inside of cells, focusing on the molecules that do the chemistry. Biochemistry (think chemistry specific to biology) is a big part of this field.
  • Cell biology: The study of the behavior of cells and the interactions between cells.
  • Neurobiology: The study of the cells of the nervous system and their interactions. This roughly blends into,
  • Anatomy of the brain, psychology, sociology, more!

The reason all the names and interactions suck to learn is that when these things were first being investigated, the scientists often times did not know what they were dealing with so they had to have something, anything to create differences that they could use to sort and study parts.

It started with anatomy.

Here is a free online version of Grey’s Anatomy (the book, not the comedy). Back then they had very little idea what this stuff was all about. There were some items known in general terms from specific brain injuries, but the structures were mostly all named according to what they looked like, in Latin, or French, or…

Cerebellum (little brain), medulla oblongata (middle body), median fissure (middle division). It can be a little intimidating.

Then there was Cell Biology and Neurobiology.

Cells had the same problem with naming. You have lots of names having to do with names, shapes, and now electrical properties as well. This was not just for the nerve cells either, your brain has more non-nerve cells in it than nerve cells believe it or not. The general name for those cells is Neuroglia, nerve glue! I’m sure at the time it was fine, but for everyone else? Here is a small selection;

Neurons: Pyramidial cell, Purkinje cells, uni- bi and multipolar cells…

Glia: Microglia, Schwann cells, astrocytes, satellite cells

On top of that now the cells are also being divided by electrical activity. This overview of the somatosensory system (touch/pain sensing system) shows cells being named by the speed of the impulse, the voltage peak (literally detected by micro voltmeter)

Now admittedly this last bit is far more useful because these features do give me information that can be used in organization and study. But I maintain that it is useless to regular folks who have a relative with a problem, or their own problem and a life to deal with.

Then there was modern brain science, and more crazy naming.

Here is where my issues with naming and science start to become unfair, which is why it’s a process and not a rule. If the role of a part of the brain is unambiguously known, or known well enough that it’s primary function is known, that is when the name should be changed. But when you are sitting on the cutting edge things are still too fuzzy for that. Here are some examples of things that can’t really be renamed that I will have to take into account somehow;

  • Structures/cells/molecules with still unknown functions and/or relationships.
  • Whole fields that are not yet known well enough to integrate into brain science.


They name these things whatever they have to to understand them. I will have to have a way of making “function unknown” visually obvious in a way that does not detract from visually appreciating what is known. I will probably have a color, or obvious texture, or similar reserved for that purpose. I’m hoping to make some basic decisions this week.

How carefully do I need to do this? Here is an image from one of my sources that I found freely available on the web. This is a section of your brain stem (there are 25 pages of these).

From “Organization of Human Brain Stem Nuclei” by Yuri Koutcherov, Xu-Feng Huang, Glenda Halliday, and George Paxinos of The Prince of Wales Medical Research Institute The University of New South Wales. Brain nuclei are literally small brains that have jobs in processing information for your body. The are information nodes in a net work, and they are sensible and understandable!

This is the most fascinating part of the brain to me because what I am most interested in are the very oldest things in our ancestors. If I had managed to get my PhD I wanted to study Origin of Life issues. This is close too!

The brain stem is the most ancient structure evolutionarily speaking. There is a rough progression from oldest to youngest as you move from the bottom of the brain stem through to the forehead. What that means is that if you find that you share something with a creature that is REALLY distantly related to you and it’s in the brain stem, you probably have something really mentally universal and fundamentally important. This is where the model starts.

The brain stem is the origin of ME, and YOU in that big grand ultimate sense that we mean when we want eternal life, the propagation of the self and our memories and experiences into continued existance. This is where Brains began because this is where an ancestor that was a worm-like thing first made* something “different” at the front in terms of how information flowed in it’s body. This is like a worms brain. This is;

  • Vomiting, Sneezing, Coughing (Generalized “Get the toxin out!”)
  • Breathing
  • Heart Beating
  • Sleeping (It’s that old…)

Go back much farther and you lose things that are bilateral. Yes, not long after a tube shaped body appeared evolution took advantage of cells that communicate in a way that made the “self” possible.

To start organizing it I printed out all these pages and started coloring things with colored pencils by category of function as best as I could. No particular color but I toyed with making certain some colors certain categories.

Just look at that organization! Sometimes I sympathize with Creationists. If you don’t know how to understand Embryology it can look deliberate. But in the end it’s still just the Arrogance of Ignorance…

I just want to start making hypotheses about why it’s organized the way that it is and what that says about our ancestors!

The book chapter lists these categories. In the parentheses afterward I will try to convey what they mean to you in a personal sense. The colors are matched to the colored pencil colors as closely as I could manage and the regions with black shading are the white matter (wires) and areas unshaded with black are the nuclei/ganglia (information processing centers). This is all human specific information and I will not include animal information until I get to the model.

  • Autonomic Regulatory Centers
  • Reticular Formation
    • The Brainstem’s brainstem. Very old parts. (Maintaining tone, balance, and posture–especially during body movements. Sends eye and ear signals to the cerebellum so that the cerebellum can integrate visual, auditory, and vestibular (balance) stimuli in motor coordination. Gaze centers, which enable the eyes to track and fixate objects, and central pattern generators, (programmed muscle movements) which produce rhythmic signals to the muscles of breathing and swallowing. Cardiovascular control.  Pain modulation.  Sleep and alertness (all or nothing conspicuousness?). Habituation – This is a process in which the brain learns to ignore repetitive, meaningless stimuli while remaining sensitive to others.
  • Tegmental Nuclei
    • Cognition, motivation, drug addiction, intense emotions relating to love. May be involved in modulating sustained attention or in mediating alerting responses, and also in the generation of REM sleep. Head direction.  Arousal, attention, learning, reward, and voluntary limb movements and locomotion.
  • Locus coeruleus involved with physiological responses to stress and panic.

I think you get the point. See how the language sucks. But there is so much information there that could be more helpful if it was better presented for the public.

They know TONS about how these bits connect together, what the bits do, and lots of the logic (computational rules like “On”, “Off”, more…) between them. If you are a philosopher and you are not reading neurobiology at whatever level you can, you are being professionally negligent. But it’s only partially your fault, hence this effort.

These networks and how they differ on an individual basis is what I hear used as the term neurodiversity in public. Ignore it at your peril. We are a spectrum, not black and white. Mental illness is the definition of the extreme. I know that some of the science readers here might get a bit uncomfortable with the term because there are a lot of bad ideas associated with some folks who use the term. But it is accurate and that is what I care about.

Stuff that is new in a BIG way

There are two that I can think of: RNA interference and epigenetics (I’m preparing a cool post about that, eventually). RNA interference is basically when RNA plays a role in shutting off gene expression instead of being a messenger molecule. Epigeneitcs is something that I will have to do a post on all by itself at some point. This is when a trait gets inherited for a limited number of generations, or gets inherited with no actual change in the DNA. What gets inherited are little “marks” on the DNA that change the expression. While I have not yet explored RNA interference and the brain yet, epigenetics is VERY involved in brain function. In fact I’m of the opinion that this will be next decade’s controversial research subject due to it’s implications.

So there is a bit more on the level of detail that I want to take this model. Right now I am entering nuclei into a spread sheet and adding relevant details about connections, role (human and animal studies), neurotransmitters, everything.

Next post. Something different. My weird relationship with philosophy.