On Computing the Brain and Mind

Thinking about the mind? Or the brain?
Type it out and see what others think.
encode_decode
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On Computing the Brain and Mind

Post by encode_decode » Sat Sep 30, 2017 1:55 pm

    Abstract

    Here we look at many facets or aspects of the brain and mind to understand meta-information and regular information and any information as it relates to the brain and mind. We break the brain and mind up into disciplines, concepts and anything else that comes along. We are free in the Sea of Thoughts to explore the brain and the mind. Anything goes as long as we are making sense of working out the brain and mind . . .

    Image
    - Mind is an ever changing dimension that is bound to reality, logic and emotion. (2017) -

    encode_decode
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    Definitions

    Post by encode_decode » Sat Sep 30, 2017 1:58 pm

      When defining the title 'On Computing the Brain and Mind'

      It is important to have in mind some definitions of the three most important words in the title: Computing, Brain and Mind. I do not want to use any specific definition - by this I mean I want to keep flexibility in the conversation especially to begin with. The idea is that we are trying to make sense of how we work out the brain and mind. Everything in the definitions is valid to use.

      ≡ Computing and compute, from Google dictionary:
      • ► Computing as a noun is the use or operation of computers
        - in a sentence looks like this: "developments in mathematics and computing".
      • ► As a verb, compute is to reckon or calculate (a figure or amount)
        - in a sentence looks like this: "the hire charge is computed on a daily basis".
      • ► Informally, compute means to seem reasonable; make sense
        - in a sentence looks like this: "the idea of a woman alone in a pub did not compute".
      synonyms for compute: calculate, work out, reckon, figure, enumerate, determine, evaluate, assess, quantify, put a figure on; add up, add together, count up, tally, total, totalize; measure; tot up; cast

      Origin: early 17th century: from French computer or Latin computare, from com- ‘together’ + putare ‘to settle (an account)’.


      ≡ Brain, from Google dictionary:
      • ► an organ of soft nervous tissue contained in the skull of vertebrates, functioning as the coordinating centre of sensation and intellectual and nervous activity.
      ≡ Mind, from Google dictionary:
      • ► the element of a person that enables them to be aware of the world and their experiences, to think, and to feel; the faculty of consciousness and thought.
      - Mind is an ever changing dimension that is bound to reality, logic and emotion. (2017) -

      encode_decode
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      Initial Topic - Scanning

      Post by encode_decode » Sat Sep 30, 2017 2:00 pm

        Two of many questions

        How is it that we work out what the brain is doing?
        How is it that we work out what the mind is doing?

        We are not necessarily here to answer these two questions as there are many more questions . . .
        . . . these two questions set for us a theme to work with . . .

        Initial Topic - Scanning - A Dirty Intro

        Here a dirty intro is to be taken as an intro written on the fly with no hardcore thought put into it . . .

        Scanning the brain in order to understand its ability to process patterns of information.

        From Google dictionary: to scan is to look at all parts of (something) carefully in order to detect some feature.
        - in a sentence looks like this: "he raised his binoculars to scan the coast"

        First we must understand that scanning is not just about technology - in this context we are looking at something with care to detect a feature. Although previously I have mentioned flexibility, so any of Google's definitions will suffice. There is quite a bit of inference going on to say the least - to say this is done without errors is quite silly. The inference is made on the following: Cutting up the neocortex - delightful, brain scans(neuroimaging) - there are at least ten we could choose from. Interestingly the idea of neuroimaging goes back a long way and its life actually starts out in blood circulation over 120 years ago but anyway. PET and fMRI scans are very useful. EEG has added much data despite its spatial limitations - there is no substitute for cutting the brain up. Obviously microscopes(optical and electron based) give plenty of visual data.

        A little bit of psychological data can go a long way to get started.

        Philosophically we have been asking many questions about the brain and mind for a long time.

        By scanning data whether by computer or making sense with our minds we are able to make many conclusions by looking for correlations in available data.
        We are also able to create metadata that can be graphed for visual reference.

        Let the ambiguity begin . . .
        - Mind is an ever changing dimension that is bound to reality, logic and emotion. (2017) -

        encode_decode
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        Briefly covering PET

        Post by encode_decode » Sat Sep 30, 2017 2:05 pm

          Positron-emission tomography (PET) is a nuclear medicine functional imaging technique that is used to observe metabolic processes in the body. The system detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. Three-dimensional images of tracer concentration within the body are then constructed by computer analysis. In modern PET-CT scanners, three-dimensional imaging is often accomplished with the aid of a CT X-ray scan performed on the patient during the same session, in the same machine.

          Image
          Brain PET-MRI fusion image

          PET scans are increasingly read alongside CT or magnetic resonance imaging (MRI) scans, with the combination (called "co-registration") giving both anatomic and metabolic information (i.e., what the structure is, and what it is doing biochemically). Because PET imaging is most useful in combination with anatomical imaging, such as CT, modern PET scanners are now available with integrated high-end multi-detector-row CT scanners (so-called "PET-CT").

          Image
          PET scan of the human brain.
          - Mind is an ever changing dimension that is bound to reality, logic and emotion. (2017) -

          encode_decode
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          DTI

          Post by encode_decode » Sat Sep 30, 2017 2:09 pm

            Sneak preview . . .

            Image
            DTI Color Map

            The Synapse

            In the brain we need to look at synaptic connections. It is widely accepted that the synapse plays a role in the formation of memory.

            As neurotransmitters activate receptors across the synaptic cleft, the connection between the two neurons is strengthened when both neurons are active at the same time, as a result of the receptor's signaling mechanisms.

            fMRI

            Functional magnetic resonance imaging or functional MRI (fMRI) measures brain activity by detecting changes associated with blood flow. This technique relies on the fact that cerebral blood flow and neuronal activation are coupled. When an area of the brain is in use, blood flow to that region also increases.

            The primary form of fMRI uses the blood-oxygen-level dependent (BOLD) contrast, discovered by Seiji Ogawa.

            As we can now tell there are different forms of fMRI - we start at a low resolution:

            Image
            These fMRI images are from a study showing parts of the brain lighting up on seeing houses and other
            parts on seeing faces. The 'r' values are correlations, with higher positive or negative values
            indicating a better match.

            Statistics

            Now we wonder how we can get higher resolution and mathematics holds the key as usual: Statistical inference uses mathematics to draw conclusions in the presence of uncertainty. There is much uncertainty in low resolution imaging.

            Tensors

            When using Diffusion MRI as opposed to fMRI we can apply Diffusion tensor imaging (DTI) which is an MRI technique that enables the measurement of the restricted diffusion of water in tissue in order to produce neural tract images instead of using this data solely for the purpose of assigning contrast or colors to pixels in a cross sectional image.

            Lets start with low resolution DTI:

            Image
            Visualization of DTI data with ellipsoids.

            A more precise statement of the image acquisition process is that the image-intensities at each position are attenuated, depending on the strength (b-value) and direction of the so-called magnetic diffusion gradient, as well as on the local microstructure in which the water molecules diffuse.

            The principal application is in the imaging of white matter where the location, orientation, and anisotropy of the tracts can be measured. The architecture of the axons in parallel bundles, and their myelin sheaths, facilitate the diffusion of the water molecules preferentially along their main direction. Such preferentially oriented diffusion is called anisotropic diffusion.

            Image
            Tractographic reconstruction of neural connections via DTI
            - Diffusion MRI relies on the mathematics and physical
            interpretations of the geometric quantities known as tensors.

            Only a special case of the general mathematical notion is relevant to imaging, which is based on the concept of a symmetric matrix. Diffusion itself is tensorial, but in many cases the objective is not really about trying to study brain diffusion per se, but rather just trying to take advantage of diffusion anisotropy in white matter for the purpose of finding the orientation of the axons and the magnitude or degree of anisotropy.

            Matrices

            The following matrix displays the components of the diffusion tensor:

            Image

            Sources: Wikipedia
            - Mind is an ever changing dimension that is bound to reality, logic and emotion. (2017) -

            encode_decode
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            To process patterns of information . . .

            Post by encode_decode » Sat Sep 30, 2017 2:16 pm

              On scanning the brain, in order to understand its ability, to process patterns of information.

              Image
              • A gentle and relaxing introduction to the art and science of understanding
                - pattern matching as it pertains to the human brain and mind.
              To scan the brain is to look at all parts of the brain carefully in order to detect it's features.

              We should first remind ourselves that scanning is not just about the machines commonly referred to as scanners - in this context we are looking at the brain with a high degree of scrutiny to reveal its architecture. We have the intention of building a sophisticated mechanism with which to understand the brains ability to empower the mind with the capacity to perform pattern matching subconsciously. Extrapolations have been previously made to help us arrive at our current understanding of the brain. Philosophically, we have been asking many questions about the brain for a long time.

              Cognitive science seeks to unify neuroscience and psychology with other fields that concern themselves with the brain, such as computer science (artificial intelligence and similar fields) and philosophy. The oldest method of studying the brain is anatomical, and until the middle of the 20th century, much of the progress in neuroscience came from the development of better cell stains and better microscopes. Computational neuroscience encompasses two approaches: first, the use of computers to study the brain; second, the study of how brains perform computation.

              On one hand, it is possible to write a computer program to simulate the operation of a group of neurons by making use of systems of equations that describe their electrochemical activity; such simulations are known as biologically realistic neural networks. On the other hand, it is possible to study algorithms for neural computation by simulating, or mathematically analyzing, the operations of simplified "units" that have some of the properties of neurons but abstract out much of their biological complexity. The computational functions of the brain are studied both by computer scientists and neuroscientists.
              Hippocrates, On the Sacred Disease wrote:Men ought to know that from nothing else but the brain come joys, delights, laughter and sports, and sorrows, griefs, despondency, and lamentations. ... And by the same organ we become mad and delirious, and fears and terrors assail us, some by night, and some by day, and dreams and untimely wanderings, and cares that are not suitable, and ignorance of present circumstances, desuetude, and unskillfulness. All these things we endure from the brain, when it is not healthy...
              By using previous data, whether written or graphical in nature, we are able to enhance our exploration to uncover many of the brains still hidden secrets. We are able to make many conclusions by looking for correlations in available data against our own theories, ideas and thoughts. We are also able to create metadata that can be graphed for further visual reference(we can call these graphs, meta-graphs). The output from the machines that we refer to as scanners, and the meta-graphs that we create can be collectively referred to as scans.

              Andreas Vesalius (31 December 1514 – 15 October 1564) was a 16th-century Flemish/Netherlandish anatomist, physician, and author of one of the most influential books on human anatomy, De humani corporis fabrica (On the Fabric of the Human Body). Vesalius is often referred to as the founder of modern human anatomy.

              Image
              A quick scan(careful look) of these two images, reveals the basal ganglia and some history.

              In vertebrates, the reward-punishment system is implemented by a specific set of brain structures, at the heart of which lie the basal ganglia, a set of interconnected areas at the base of the forebrain. There is much reward for understanding how the brain gives the subconscious the ability for pattern matching even though somtimes the effort can be rather punishing. The subconscious I believe has an intimate connection to the brain . . .

              In the next part we will take a brief look at pattern matching.

              Information Source: Wikipedia.
              (2017)
              - Mind is an ever changing dimension that is bound to reality, logic and emotion. (2017) -

              encode_decode
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              The Neocortex

              Post by encode_decode » Sat Sep 30, 2017 2:19 pm

                What I know, I take for granted. Up until now I have been trying to illustrate an answer to a question which turns out has some difficulty associated with providing an answer. Hopefully I can further improve on this for the time being. Then I can add to it later.

                In the next part we will take a brief look at pattern matching but for now let us continue with this part . . .
                . . . This part is going to give us a few hints. This post is no exception . . .

                Image

                First let us quickly examine the neocortex. We are talking about scanning the brain and we must understand how we arrived at current day methods and why those methods are improving all of the time. Some of the methods currently not publicly available are quite sophisticated compared to those that are public.

                First we must understand that scanning is not just about technology - in this context we are looking at something with care to detect a feature. There is quite a bit of inference going on to say the least - to say this is done without errors is quite silly. I believe the inference is quite accurate and the computer models show this to be the case as I will demonstrate.

                This will take a little time to develop, sink in and make sense.

                The inference is made on the following: Cutting up the neocortex - delightful, brain scans(neuroimaging) - there are at least ten we could choose from. Interestingly the idea of neuroimaging goes back a long way and its life actually starts out in blood circulation over 120 years ago but anyway. PET and fMRI scans are very useful. EEG has added much data despite its spatial limitations - there is no substitute for cutting the brain up. Obviously microscopes(optical and electron based) give plenty of visual data.

                We were able to guess at what the brain was doing before we made many attempts at breaking it down further. With the results from our thoughts we started looking for things that may have not been there but in many cases were.

                Now we are able to get many high resolution photographs from microscopy.

                Microscopy is the technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye (objects that are not within the resolution range of the normal eye). There are three well-known branches of microscopy: optical, electron, and scanning probe microscopy.

                However we still find use of illustrations and diagrams ever important and perhaps . . .
                . . . these are more important for making guesses before developing the technology.

                Illustrations, diagrams, graphs and textual data. We will first take a look at a few illustrations . . .
                - Mind is an ever changing dimension that is bound to reality, logic and emotion. (2017) -

                encode_decode
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                Triune Brain

                Post by encode_decode » Sat Sep 30, 2017 2:49 pm

                  Using the Triune model of the Brain we come up with this illustration:

                  Image

                  Certainly we can use other models but this will suffice for this part of our discussion . . .
                  - Mind is an ever changing dimension that is bound to reality, logic and emotion. (2017) -

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                  Layers

                  Post by encode_decode » Sat Sep 30, 2017 2:50 pm

                    The neocortex, also called the neopallium and isocortex, is the part of the mammalian brain involved in higher-order brain functions such as sensory perception, cognition, generation of motor commands, spatial reasoning and language. This illustration is where we need to start paying attention:

                    Image

                    Here we are looking at the six layers of the neocortex that I mentioned before. The different cortical layers each contain a characteristic distribution of neuronal cell types and connections with other cortical and subcortical regions. There are direct connections between different cortical areas and indirect connections via the thalamus, for example. The thalamus has multiple functions. It may be thought of as a kind of hub of information.[clarification needed] It is generally believed to act as a relay between different subcortical areas and the cerebral cortex. The cerebral cortex can be classified into two parts, the large area of neocortex and the much smaller area of allocortex - we are examining the neocortex.

                    Thanks to Wikipedia for most of the information here . . .
                    - Mind is an ever changing dimension that is bound to reality, logic and emotion. (2017) -

                    encode_decode
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                    The Grid aka The Plane

                    Post by encode_decode » Sat Sep 30, 2017 2:52 pm

                      Next comes what I like to call the grid - we are looking at the columns from the top down:

                      Image

                      This illustration is convenient because we get to see the columns as well as the "grid".
                      - Mind is an ever changing dimension that is bound to reality, logic and emotion. (2017) -

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