“One of the difficulties in understanding the brain is that it is like nothing so much as a lump of porridge.” – Richard L. Gregory


The brain is annoyingly hard to understand. Maybe this guide helps a little.

If we look at the brain, we see that it’s a network of calculators that connect together. Those calculators are brain cells called neurons. Each of those cells takes an input, does some calculation, and gives an output.

Each neuron is a calculator which takes an input at the dendrites and gives an output through its axon


Each calculator consists of millions of different molecular machines that work in harmony, to ensure that each neuron is able to do its calculation function.

How do these machines know what to do?

They don’t! The machines work just by following the laws of physics and stochastic probability. For example if such a molecular robot is positively charged, he wants to go to an area that is negatively charged. Or if some area is too crowded, he wants to go where it’s less crowded.

Some of the best visualizations of the inner workings of a cell are created by XVIVO Scientific Animation, who produced several educational videos for Harvard University, like this one:


The calculation function of a neuron is not always the same. Neurons are able to adapt and change their calculation functions, based on past inputs. They do this by changing their internal structure, or the structure of their connections to other neurons, based on the patterns of how they get activated. Much like a tree which grows in the way the wind blows.

The rule of how those connections change is:

“What fires together wires together”

It means that, if two neurons activate at roughly the same time, their connection gets stronger. If they no longer fire synchronously, their connection gets weaker. These changes in the connections between neurons are the physical basis of our memories.

Neurons are never moving still. They are constantly stretching their dendrites, like they are searching for other neuron-buddies that they can hold hands with.


Billions of neurons connect together to form feedback loops. There are various feedback loops in your brain doing things like regulating your body temperature, heart rate or your breathing patterns. Basic functions like that are regulated by deep structures of the brain, like the brain stem, which connects the spinal cord to the rest of your brain. There are also feedback loops doing more complex stuff that involves cognition, like when you are driving a car.

On top of the brain stem there is the limbic system – often referred to as the reptilian brain. Its primary function is regulating your emotions and telling you what behavior to do more or less via the feedback signals “pleasure” and “pain”.

Pleasure - do more of what you are currently doing. Pain - do less of what you are currently doing´.


Above the limbic system, we have the neocortex which generalizes over all situations that we experience and detects patterns. Basically our brain is a multi-layered pattern recognition machine. That machines enables us to detect patterns within patterns within patterns and so on…

In other words: The brain is clustering information into higher and higher levels of abstraction. On the highest level our brain creates a mental simulation of the world (including ourselves).

Neurons in the cortex are organized in small circuits called cortical columns, made of around 100 – 400 neurons each. There are around 20-100 million columns in the brain, which all act as single units that talk to their neighboring columns to form larger computational units. Once this has a certain size it is called a brain area.


Brain areas talk with each other and form a processing stream. A common metaphor is that the brain works like an orchestra, where each brain area is like an instrument to make up the music of the mind.

In reality, there are just few brain areas that seem to be highly specialized. The brain is, at its heart, an interconnected organ. It is very difficult to define clear-cut purposes for individual regions. It’s like each player in the orchestra would switch instruments all the time and sometimes playing the flute, trombone and the piano all at once. It’s kind of a mess.

There are a few small nuclei that make up your arousal system. You could say they produce the weather that is going on in your brain. They can flood your system with dopamine, serotonin, acetylcholine and other neurotransmitters to make you calm, focused, stressed, motivated, sleepy or social. You can take drugs to affect the weather in your brain quite drastically.


Your mind is spread across two hemispheres. There is a persistent myth that the right brain is the creative one and the left brain is the logical, analytical one. This is bullshit. The real difference is that the right hemisphere has a wider focus on things and thinks more globally, while the left hemisphere thinks more narrowly and is concerned with details. But both hemispheres are involved in creativity, and both hemispheres are involved in reason. They just use different kinds of attention.

The hemispheres are connected by the corpus callossum – a communication highway between the left and right brain that ensures that both hemispheres make up a coherent self.

Cutting your corpus callossum would create basically two human beings in one body. Each hemisphere would develop their own personality, which goes as far as having a christian hemisphere and an atheist one, which was observed in a patient by Indian neuroscientist Ramachandran.

The strange thing is that you wouldn’t even realize that you are two persons. One reason for that is that one of them – the right brain – cannot speak because spoken language is produced in the left brain.

Another reason is that the hemispheres wouldn’t be entirely disconnected. They still merge at another area – the brain stem. But it’s a longer route, with a lot less axons, which makes the integration not as coherent as it was with the corpus callossum intact.

Left brain: Fragmented, decontextualized, narrow-focused attention, categorizing the world. Right brain: Holistic, context & implicit meaning, broadly vigilant attention, connecting to the world.


That’s it. The thing, that you think is you, is a squishy lump of cells. Billions of calculation machines that take inputs from exterior reality (or each other) to create a simulation of the world including yourself.

There are a thousand ways of how stuff can go wrong in there and I think everyone comes, at some point, to the conclusion that every human has developed and curated his or her own personal insanity.

Although it seems we already know a lot about how the brain works, there are even more open questions that we cannot answer yet, like:

  • How do single neurons compute?
  • How do circuits of neurons compute?
  • Why do we sleep and dream?
  • What is the neural basis of subjective experience, cognition and attention?

It’s one of the most fascinating fields that you can study these days.

This post is based and build on Joscha’s talk at the Chaos Communcation Congress 2016. Check him out, he’s awesome.

If you are currently studying neuroscience, check out my summary that may help you get an overview about the basic topics: