Dealing with the issues Body, soul, and science in

I am myself of microbiologist and physiologist, having studied these issues at Göteborg University and after that, taught Biology in Sweden for 29 years in K9 schools.
I have also experience of multiple strokes, the last one and biggest in Insula in September 2014.

Writing about body, soul and spirit, I understood that I needed to take a look at cognitive neuroscience to find biological explanations of the religious and philosophical terms of soul and spirit. I started with a section about neuroscience at but I decided to create a separate page for neuroscience due to the extent of this scientific issue.

Phineas Gage with his horrible accident in 1848 and his dramatic change in personality, had doctors discover that brain parts were responsible for specific human behaviors.

Phineas Gage’s case and the symptoms he got, started the cognitive neuroscience research.

I share in this page my notes and screenshots from two videos. One with Dr. Octavio Choi and one with a neuroanatomist Jill Bolte Tailor, who got a severe stroke on her right brain hemisphere.

Dr. Octavio Choi starts his lecture (see video below under Brain basics) with the Gage case.

I will on this page collect data on the various parts of the brain and their functions.



Neuroscience -definition

About neuroscience, Merriam Websters says that it is

a branch  (such as neurophysiology) of the life sciences that deals with the anatomy, physiology, biochemistry, or molecular biology of nerves and nervous tissue and especially with their relation to behavior and learning

I would add that there are different parts of neuroscience like

neuroscience has use of other disciplines like:

  • biochemistry of substances like neurotransmitters
  • cellular biology, cytology about  neurons 
  • psychology
  • a psychiatrist working with drug addiction and mental diseases

Recent neuroscientist like Susan Greenfield, now ask for cooperation with 

  • mathematicians
  • quantum physics



This issue was dedicated to in August 1018:

This part of neuroscience looks at brain activity with MRT  during spiritual exercises and meditation. Pope Francis was among other religious people examined. Read more at


Cognitive neuroscience

This part of neuroscience tries to understand the brain activity of various conscious states, like awakened, sleeping, dreaming, sedation and drug intake, and other euphoric activities.

Before going into cognitive neuroscience it is good to define what consciousness and conscience are, like Octavio Choi in his lecture below.

I dedicated a separate page about consciousness. read about these definitions in


Cognitive bias in animals

Science talks about:

  • cognitive bias
    “Cognitive bias refers to a systematic (that is, nonrandom and, thus, predictable) deviation from rationality in judgment or decision-making.
  • judgment bias
    “In its simplest explanation, judgment bias describes optimistic and pessimistic decisions made under ambiguity.”
  • Attention bias
    “is the tendency to drive or sustain attention to specific stimuli or types of information before others.”


Studying how early humans understood sacred scriptures like Genesis I stumbled upon the concept of “cognitive bias”. It is defined as 

“… a systematic error in thinking that occurs when people are processing and interpreting information in the world around them and affects the decisions and judgments that they make.

The human brain is powerful but subject to limitations. Cognitive biases are often a result of your brain’s attempt to simplify information processing. Biases often work as rules of thumb that help you make sense of the world and reach decisions with relative speed. Read more at )

Where did this bias come from and why?

It has been important for humans to simplify information to be able to make faster decisions and to survive. We have to go back to Africa when humans were still at the evolutionary level of homo Erectus or earlier animal-like levels.

I think therefore it is important to look at cognitive bias in animals.

As an article abstract at says “people in negative states attend to threats, retrieve negative memories, and make negative judgments about ambiguous stimuli more than happier people. …a new research area investigating the possibility that such affect-induced ‘cognitive biases’ also occur in animals.

Judgment Bias in Animals

I read the article “Judgment Bias” by Sanne Roelofs and Franz Josef van der Staay in 08 June 2017

In its simplest explanation, judgment bias describes optimistic and pessimistic decisions made under ambiguity. It is a bias in the judgment of ambiguous information, influenced by emotional state.”

The experiments to test Judgement bias in animals is explained in the article.
“The animal is first trained to associate:

  1. a positive reference stimulus (eg. low-frequency tone) with an appealing reward (e.g. meatballs)
  2. and a negative reference stimulus (eg.  a high tone frequency tone) with a less appealing reward (e.g. garlic) 

After discrimination training, ambiguous stimuli (e.g. middle frequency tones) are sent.

  1. When the animal performs the behavioral response it associates with a positive outcome (approaching the left goal box), this is scored as an optimal choice.
  2. When the animal performs the behavioral response it associates with a negative outcome (approaching the right goal box), this is scored as a pessimistic choice.

Read more  in



The peripheral nervous system

Images were taken from


The central nervous system,
involved in consciousness

Images and info in this part is taken from  Tony Nader’s video I shared in my page about consciousness.

The nervous system involved in consciousness is divided into these main parts:

  • The brain has
    • the brain
      • cortical areas
        • Primary sensory areas for vision, sound,  etc

          • occipital lobe visual information
        • associative regions for vision, sound, etc
          this region takes in subconscious information from the corresponding primary sensory area, and transfer it through different associative region levels and finally to the cortex where we become aware/conscious about the information.
      • subcortical areas
        • Thalamus
      • the brainstem has a 
        • the reticular formation
          that has the function to modulate awareness among others wakening us up from sleep.

When we see an image, the image comes to the information that goes through the primary vision sensory area, the occipital lobe in the back of the brain. You are not aware of it yet. But it is first when the image information goes though the associated area levels for vision, that you become conscious of the image. Each associative area are nearby and is divided into several levels. See the arrows from the different primary sensory areas. the same consciousness mechanism is valid also for touch and auditory signals.

You must be awake to become aware of signals. The reticular formation is a modulator for consciousness, like a thermostat that turns up and down awareness.

An alarm clock activates the reticular formation that activates your associative area for sound so you become aware that the clock alarm is ringing.



The brain basics

Dr Octoavio Choi, Chief Academic Psychiatrist, Oregon State Hospital Director, Forensic Evaluation Services, made a good and short presentation of some brain basics. Many images on this page are screenshots from his video.


The triune brain

Cortex means covering. the cortex is above and covers the limbic system and the reptilian complex, the brainstem

So in other words, the brain has three different complexes.


The reptilian complex – brainstem

The brainstem controls heart rate, respiration, basic sensory possessing, chemical environment in the blood (acidity – CO2). If you broke your brainstem you generally die.



The ventricles can be seen injecting air in the brain that stops x-rays so the ventricles with bubbles of air appear in x-ray images.




The limbic system

Between the two parts of the limbic system is the corpus callosum. Read more at wiki

The limbic system does many things. but one of the key things it does is core evaluation, it scans everything on the outside, hearing, sight, sounds, touches, feelings inside your body. It scans everything that you might want to pay attention to because it’s going to help you survive. So things like donuts, things like spiders, things like sexual partners. It warns so you for example go away from the spider. it creates a feeling of craving, like the feelings you want to go forward to something or feeling for terror or fear to move. 

These core evaluations are computations done at a very low level that scan the entire external or internal environment in order to give your cerebral contour, your cortex a signal to move towards things and move away from things, and those signals are experienced as feelings.

Another picture of the limbic system is this with the orbitofrontal cortex in front.



the amygdala in the limbic system activates when there is a danger you should move away from.

The neurologist Jill Bolte Taylor tells about one way the Amygdala can activate in her Ted


The ventral striatum is the pleasure area that makes you move toward things, like drugs, sexual partner


The images in this section are taken from the RI video with Eleanore MAguire RI seminar 2014 )

(Source: Eleanore MAguire RI seminar 2014 )

Behind the Amygdala and above the parahippocampus gyrus. The hippocampus was damaged in Henry Molaison when operated 1957 to help him get rid of Epilepsia.

Hippocampus memory function is confirmed by functional studies with MRI (FMRI). “Place cells” in the hippocampus embody memories for particular place memories.

Hippocampus is engaged in these functions:


Cortex – the thinking brain

The cortex manages all the computations that are required for higher cognition stuff, stuff like language, stuff like high order object recognition telling the difference between a Vag Gogh and a Rembrandt, consciousness being consciously aware of your thoughts, consciously aware of your feelings, all that fancy stuff we consider to be human, this tends to be computed and instantiated in the cerebral cortex

The orbitofrontal cortex

The orbitofrontal cortex is not part of the limbic system. But it is involved in evaluating the signals that are coming from the amygdala and from the ventral striatum in the limbic system. It adds context to those drives telling you to do things, e.g. by telling there is a cage around the spider ore by telling you should not take those drugs or donuts… it helps inhibit those drives that should be inhibited.

the orbital frontal cortex was damaged Phineas Gage. He got emotional amnesia (see below).



Cortex areas


Broca’s area

Broca’s area seems according to studies with patients with aphasia,  to be involved in vocalizing language. So they understand spoken language but have difficulties to generate spoken language. Broca’s area near the area that control’s lips and tongue.

Wernicke’s area

close to the auditory cortex for incoming sounds signals is the Wernicke’s area. A patient with damages in this area, don’t understand spoken language well but can talk fluently.



The cortex centers

The idea of centers is old and not applicable anymore.

There is no visual region

Susan Greenfield said that there are at least 30 regions related to vision, color, form, motion (video min 18:05)

As Dan Bennett explains confirms, visual  aspects, like motions, location, shape, colors are evaluated in different subareas as described with the image below, this image makes it looks like a detailed view of a visual center:

( Source: screenshot from Dan Bennetts video)



There is no consciousness area.

If anesthetic is given to a patient, a single area should shot down. This is not the case as this image shows: All areas are shot down.

( Source: screenshot Susan Greenfields video )


Another proof of the no consciousness area hypothesis is the hydrocephalus case I describe below. 

Axel Cleeremans (AC) is a cognitive psychologist at the Université Libre in Brussels. Learning from hydrocephalus cases, AC answers in an interview that There’s a second lesson perhaps if you’re interested in consciousness — that is the manner in which the biological activity of the brain produces awareness … One idea that I’m defending is the idea that awareness depends on the brain’s ability to learn.

SB (ed. interviewer): So, does that mean then that there is not one region of the brain responsible for consciousness?

AC: Precisely. These cases  are definitely a challenge for any theory of consciousness that depends on very specific neuro-anatomical assumptions.” Read more in


Three hierarchical / function levels

the brain is hierarchically organized. You do are not informed about lover levels as the limbic system and the brainstem. You only get aware when the brainstem has measured high acidity (high levels of CO2 ) in the blood (air) as you need to move away and eg open a window to get fresh air.


Functional specialization

different parts of the brain do different things. So damages in specific regions create specific impairments. This was not obvious 100 years ago. Both Gall and Flourens went to far in their conclusions (Gall: “every part has its own function so the bumps of the skull could tell about impairments” and Flourens “the size of brain damages decide the impairment.”



I studied this at University in Göteborg in the seventies. It is good to have a reminder of the electrical and chemical functions of neurons with Octavio Choi in his video.

Inside the axon, there are microtubules that transport neurotransmitters. They are involved in maintaining the structure of the cell and, together with microfilaments and intermediate filaments, they form the cytoskeleton. Microtubules are very important in a number of cellular processes. Microtubules damages cause Alzheimer’s. See below




image and information are taken from Susan Greenfields seminar in Australia. I shared in my consciousness page.

( Source: Susan Greenfields video  )

These are the main neurotransmitters in the brain. They go everywhere in the brain but acetylcholine seems to work as a modulator. As a modulator, it makes a cell more or less sensitive to a response opening or closing K+ channels


Neuronal assembly

Susan Geenfield talks about this

Neuronal assemblies” are defined here as coalitions within the brain of millions of neurons extending in space up to 1–2 mm, and lasting for hundreds of milliseconds: as such they could potentially link bottom-up, micro-scale with top-down, macro-scale events.” Read meanwhile about this in

Susan G says that the width of assemblies determines the depth of consciousness. Something you look at (e.g.a motorbike) trigger may be nothing for some, but a lot of memories in others.



A new born has 10 times more nervcells. Many inactive dies while others develop axons and synapses. These are developed during the whole life of the individual.

“Neuroplasticity allows the neurons (nerve cells) in the brain to compensate for injury and disease and to adjust their activities in response to new situations or to changes in their environment.

Brain reorganization takes place by mechanisms such as “axonal sprouting” in which undamaged axons grow new nerve endings to reconnect neurons whose links were injured or severed. Undamaged axons can also sprout nerve endings and connect with other undamaged nerve cells, forming new neural pathways to accomplish a needed function.” (Read more at )

It is known that a human that has had a stimulated brain since birth by e.g learning different languages and many years of schooling has higher probability to recover from strokes and less risc to develope dementia in higher age. Read more at .

Image from Susan Greenfields video )


Imaging techniques


Tau Pet imaging
read about this imaging technique in

Sincotrone Elegtra at Trieste Italy—Il-Sincrotone-Elettra-di-Trieste-2ef657c0-2316-4abd-848d-eab10107c4c2.html

These tools could maybe be used by neuroscientists. The Fermi lab is used to study the Photosynthesis. Read more at


CNS dysfunctions

  • Agnosia
    when not being able to recognize things. May think that a tool is something else.
    Broca’s area seems according to studies with patients with aphasia,  to be involved in vocalizing language. So they understand spoken language but have difficulties to generate spoken language. Broca’s area near the area that control’s lips and tongue.
  • Alzheimer 
    ! out of 9 in the USA suffer from Alzheimer’s. (Source: BBC Scienze “le meraviglie del cervello” p 82) Reading about prevention at it looks like this depends on bad lifestyles in the USA. (to big sugar intake and too little physics.)
    Tau proteins are important in “maintaining the stability of microtubules in axons. Microtubule transports neurotransmitters inside the axon. Tau protein are abundant in the neurons of the central nervous system (CNS).  When Tau protein hyperphosphorylates the microtubules do not work anymore causing axons and the neurons to die. The Tau proteins  “become hyperphosphorylated into insoluble aggregates called neurofibrillary tangles.
  • When this happens  you get  Alzheimer’s.    (read more in Wiki) ” 

With TAU PET  we can predict future atrophy and Alzheimer’s. (source: youtube ). In this disease, neurons die.
 Alzheimer’s can be prevented among others getting “plenty of omega-3 fats. Evidence suggests that the DHA found in these healthy fats may help prevent Alzheimer’s disease and dementia by reducing beta-amyloid plaques.” Read more at

  • Dementia  
  • Emotional amnesia

    Dr. Octoavio Choi said: People like Phineas Gage with orbitofrontal damages, can feel emotions but they just can not store these. They can not form the linkages between the context and the feeling in their body that ordinarily stops you from doing things like e.g. urinating in public o groping people. Damasio’s hypothesis is that the orbitofrontal cortex holds the linkages between the facts that compose a situation and the somatic markers, the emotions previously paired with it. That is a major part of where conscience is substantiated.

  • hydrocephalus
    Another curious case is the Frenchman that was missing 90% of his brain but could lead a normal life.
  • “When a 44-year-old man from France started experiencing weakness in his leg, he went to the hospital. That’s when doctors told him he was missing most of his brain. The man’s skull was full of liquid, with just a thin layer of brain tissue left. The condition is known as hydrocephalus. “He was living a normal life. He has a family. He works. His IQ was tested at the time of his complaint. This came out to be 84,”

these scans of a French man’s brain were published in The Lancet in 2007. Read more in  and in

  • prosopagnosia
    Like agnosia but can not recognize faces.



  • right and left hemisphere

  • Two present the two hemispheres, I use this video from 2008 where neuroanatomist Jill Bolte Taylor shares her neuroscience knowledge and experience of a stroke in her left hemisphere 1996.
  • She gives a new perspective on consciousness, that there is a left hemisphere consciousness.

( Image source: Jill Bolte Taylor in her video )

The two hemispheres
do communicate with one another
through the corpus callosum,

which is made up of some 300 million axonal fibers.

But other than that,
the two hemispheres are completely separate.
Because they process information differently,

each of our hemispheres thinks about different things,

they care about different things, and, dare I say,
they have very different personalities. (Source: video transcript.)

the right hemisphere

functions like a serial processor. ill Bolte said:

“Our right human hemisphere is all about this present moment.

It’s all about “right here, right now. Our right hemisphere thinks in pictures and it learns kinesthetically through the movement of our bodies. Information, in the form of energy, streams in simultaneously through all of our sensory systems.

And then it explodes into this enormous collage of what this present moment looks like, what this present moment smells like and tastes like,
what it feels like and what it sounds like. I am an energy being connected to the energy all around me through the consciousness of my right hemisphere.

(Source: video transcript.)


The left hemisphere

functions like a parallel processor. ill Bolte said:

“Our left hemisphere thinks linearly and methodically.
Our left hemisphere is all about the past and it’s all about the future.
Our left hemisphere is designed to take that enormous collage of the present moment (ed. shared by the right hemisphere) and start picking out details, and more details about those details. It then categorizes and organizes all that information, associates it with everything in the past we’ve ever learned and projects into the future all of our possibilities. And our left hemisphere thinks in language.
It’s that ongoing brain chatter that connects me and my internal world
to my external world.” (Source: video transcript.)




I have been hypnotized myself as I told about in the introduction. I wonder what neuroscience says about that state.

Albert Nerenberg explains in this Ted how hypnosis works and what happens during hypnosis.



After my last stroke (I got 6) my neurologist asked me after some cognitive tests “How many years have you studied?”, I explained my background with many years in school in different countries learning German, Latin, French, and Italian, and 5 years of University studies. She answered that she understood that. I had a relatively good recovery from those stroke thanks to good brain gymnastics during my life. In 2017 I was back teaching 100%.

I have found it very useful to learn more about the nervous system. About the Amygdala and brain plasticity, I have understood that I have to reprogram my amygdala. it is probably a cause of anxiety I suffered after my strokes in 2014. I am a lot better now and have found that mindfulness meditation is one way to reprogram and get new good memories in the hippocampus. I do not like it when people are fighting each other. I am probably not alone about that. But it is good to be able to keep calm in those situations and maybe go away to stop anxiety and stress.Jill Bolte’s experience gives an idea of how meditation works. With it, my consciousness self trains to observe my left hemisphere activity and probably also my limbic system. I dedicated pages about consciousness and meditation in:

Notebook of a pluralist

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