Cognitive and Comp Neuroscience

Table of Contents



  1. 100-word summary after every class on either/any of the presenters
  2. 10 or so page research paper due at the end of the semester covering a topic related to the content of the course, include a bibliography, email either Prof. with any questions

Weekly Reading


2011-01-19 Wed – Introduction to the class

The content of this course will start with the philosophy of mind and end with sociology

2011-01-26 Wed – Phil o Mind and AI intro

philosophy and cognitive science constrain each other

Three historical views of consciousness

John Locke, self-reflection, continuity of identity, our most primary sensations are those "from the inside"
phenomenal experience
Thomas Nagel, there is something that it is like to be that organism – qualia
phenomenalogical foundation
Edmund Husserl – "the reflective study of the essence of consciousness as experienced from the first-person point of view" – extends beyond qualia to meaning and intentionality


  • perspectival – from a first person perspective
  • immediacy
  • privileged

(Descarts) Dualism – matter and consciousness are different kinds with different properties. Matter res extensa has size and shape and the mind res cogitans doesn't.

What do we want from cognitive science

  • explanation of why anything is conscious
  • definition and ability to distinguish
  • explanation for why or mapping of physical states to conscious states

AI foundations

artificial intelligence – creating intelligence through skilled (art) labor (ficial)

formally started in a 1957 conference

divide between the cognitive science and engineering approaches

Some early work in the cog sci camp. Associative memory hierarchy identified through analysis of reaction times for the answering of simple questions. Time to answer generally grew for concepts higher up the hierarchy, e.g.

    animals      (semantic network)
tweety the parakeet

cached out currently in object oriented programming.

Seminal paper by Alan Turing appeared in the Journal Mind, entitled "can computers think" – introduces the Turing test – with the goal of allowing intelligence to exist separate from human intelligence.

empiricists vs. rationalists – AI tends to cross this border

  • village law – can't keep your goldfish in a curved bowl
  • rationalists
    • pure forms
    • numbers really exist
  • empiricists – Rodney Brooks
    • you only have access to that which has been perceived
    • Hume induction has no foundation

2011-02-02 Wed – no class due to Freezing of New Mexico

2011-02-09 Wed – missed class

2011-02-16 Wed – Phil o Mind intro part two

proposed by Harry Putnam, the mind should be understood by what it does. how different from behaviorism?

analysis through functional decomposition – would this explicitly not investigate emergent properties of consciousness?

types of facts which can be appealed to through functional analysis

  • causal facts
  • structural
  • representational

three scenarios pre-qualia and anti-functionalism

  • zombie world is no different
  • cog scientist who lives in a world of black and white (like the bat argument) who knows everything about blue, she learns when she is allowed to see blue
  • McGinn 1989 – scientists announce tomorrow that they have found the cause or correlate of consciousness in the brain, then why should that set bring about consciousness. how can there be physical causes of the perspectival immediacy, phenomenal, and privileged access of consciousness

options seem to be Metzinger or dualism

100ms delay between action and conscious experience of action

grounding is the cognitive science term for bases of understanding

2011-02-23 Wed – Don Partridge and Fernando Valenzuela

Don Partridge – mechanics of neurons

  • Reflexes
               +-------------->|  transformer  |------------+
               |               +---------------+            |
    control +--+--+        +----------+     +--------+      | length
     ------>|  Σ  |------->|  force   |---->|  mass  |------+------>
            +-----+        +----------+     +--------+
  • Cell Composition
    Nerve cells are excitable cells meaning that they can change the potential across their surface – note: a cell is water on the inside, water on the outside, and a lipid bi-layer separating the two, this requires;
    ion channels
    protein molecules which form water-filled pores through the bi-lipid membrane of a cell, these are selective to specific ions (generally for \(Na^{-}\), \(Ca^{++}\), \(Cl^{-}\), \(K^{+}\)), these are gated meaning they can be open or closed
    concentration gradients
    or a pump which hydrolyzes at to "flip over" and move molecules from one side of the cell to the other, these require energy but can move ions up their concentration gradient, much slower than ion channels

    Cells swimming in a high-sodium low-potassium medium (as found in the ocean or in our bodies) with low-sodium high-potassium insides.

    These differentials in ions lead to voltages across the cell membrane, which the cell can control using its ion channels and concentration gradients.

    Potential along nerves falls off exponentially with a space constant λ as follows with \(\lambda \simeq 1mm\).

    \begin{equation} V_{\alpha} = V_{o}e^{-\frac{length}{\lambda}} \end{equation}

    Given how quickly the potential drops off it will need to be amplified along the way (say while traveling up a leg).

  • Firing of a neuron
    gates sense the voltage across the membrane of a cell, when they hit a certain threshold they will fly open releasing the potential in the cell in a burst of energy, the cell then requires some amount of time to recharge before it can be excited again (like a flush toilet)

    A membrane with three kinds of gates

                     m               n 
            --------   -------------   ------------

    De-polarization – firing


    Re-polarization – resting/recharging


    speed of gates

    fast                slow
      m ------- h ------- n
  • Amplitude to Frequency Encoding
    This recharge period is essential to "frequency encoding", a high potential will push the cell through it's hyper-polarized resting phase more quickly resulting in more frequent cell firing.
  • Movement of Action potential
    An action potential moves along a neuron by discharging a series of capacitors – as each capacitor (+,- pair) discharges it induces its neighbor to discharge.
     +   +   +   +   +   +   +
     -   -   -   -   -   -   -    
  • Synapse — clasp in greek
    the action potential releases neurotransmitters in the pre-synapse, which trigger an action potential in the post-synapse, thus the potential jumps from the dendrite of the first neuron to the axon of the second.
  • Speeds
    pain fibers are the slowest – reflexes pull you hand back, but pain is just to teach you not to do it again (not time sensitive)
    along mylenated long-term nerves120 m/s
    pain fibers~1 m/s
    transduction along a synapse~1 ms
    aka (absolute refractory period)

Fernando Valenzuela – learning and memory

the center in the brain for learning and memory

The famous H.M. Patient had intractable epilepsy, part of the hippocampus and the amygdala were removed and the patient lost no real intelligence or personality but did lose the ability to form new memories.

It is still not clear if the hippocampus is just required for forming memories which are stored elsewhere, or if the hippocampus does both forming and storage, and it was only partially damaged.

Cab drivers in London spend a year navigating the city in mopeds with the goal of memorizing the city. This changes the size of the hippocampus in these drivers to have a smaller anterior hippocampus and a larger posterior hippocampus.

long term potentiation (LTP)
persistent increase in synaptic strength that can be rapidly induced by brief neural activity

Applied current to a neuron over a couple of minutes can result in increased potentiation on the order of minutes, days, years, etc… the frequency intensity and duration of the stimulation affects the time.

critical number of pre-synaptic fibers must be activated
input specificity
restricted to input that recieves tetanic stimulation
stimulation of weak after stimulation of strong leads to potentiation of weak

"cells that fire together wire together"

Just a few seconds of calcium increase is sufficient to result in the formation of short-term memories in a neuron.

Dendrites on neurons can grow spines in response or as part of the formation of memories, these changes can happen visibly on the order of 25 minutes.

2011-03-02 Wed – missed class

2011-03-09 Wed – two psychology speakers

Basically this current induction is like drugs only without the whole-body whole-brain effects, and it is super-cheap ($300).

Imaging and Modulating Brain Dynamics

study human behavior
understand behavior as an emergent property of the physical structure of the brain
template for structure-function relationships
non-invasive measuring of the brain


  • can observe correlation and try to determine criticallity (necessary)
  • determine biological basis of many diseases and disorders (funding)

can be imaged

  • anatomy
  • connectivity
  • chemistry
  • metabolism – FMRI
  • neuronal dynamics


Diffusion Tensor Imaging DTI
trace the cables (mylenated neuronal arms) connecting parts of the brain
Transcranial Magnetic Stimulation (TMS)
apply changing magnetic field to the brain, induce electric pulse
attach electrodes to the brain, and can allow the subject to run around free of wires (e.g., dolphins, rats in a maze etc…). These are all about brain dynamics, with limited information on the sources of the activity – due to Maxwell's equation.

inversion algorithms are used to guess at sources of sensed activity

epilepsy was a big initial application of EEG (huge signals)

EEG is a direct measure of neuronal activity. Can see background oscillation as well as discrete events.

does not require direct attachment to the scalp, and can detect deep into the brain.

Fetal Alcohol Syndrome FASD – broken wiring in the cortex of the brain, due to drinking during pregnancy, can lead to premature hand-off of control from the back of the brain to the cerebellum before the cerebellum is mature enough to make good decisions (doesn't mature until 22-23) → stupid teenagers

This work is looking for abnormal cortico-cerebellar network dynamics in FASD affected children.

Similar technique can be used to speak to the brain, after listening to enough chatter between parts of the brain it should be possible to influence this conversation through external electrical stimulation with Transcranial magnetic and direct current stimulation TMS and TDCS respectively.

  • 10 minutes of induced change can lead to ~1 hour of persistent change
  • 10 minutes a day for 5 days could lead to a couple of months of effective change

could be used to cheaply change inhibitions, affect epilepsy, etc…

Using this technique to short out parts of the brain can be useful for detecting critical relations between.

Brain Stimulation and Imaging

Vincent P. Clark

Many of our cognitive abilities may have developed in response to natural camouflage of prey animals.

How the MIND network overcame financial problems through a DoD grant related to camouflage.

There are many tools for imaging at the MIND network.

People receiving tDCS during training were learning more than a control group.

2011-03-23 Wed – more class project discussion and neural nets

class project discussion

interesting topics

  • how does the mind cognitively represent space? physics and philosophy Heidegger
  • affordence, (e.g., a chair is always for sitting, how tall can a step be before we see it as a step)

more neural nets

Biological learning is entirely unsupervised. (what is the scope of the biological system?)

  • a winner take all neural network is the first element of a self organizing system, in this system only the single neuron closest to an input is trained (changed) by that input
  • Hebb's Rule: neurons that fire together wire together. Requires no teacher and requires no non-local interactions

An example showing how non-supervised learning can be used to identify poisonous foods.

2011-03-30 Wed – two more psychology speakers

Ron Yeo – human intelligence

  • general intelligence (g)
    the consensus perspective on intelligence, the hierarchical model
           +----+                            |
           |    |  General Intelligence (g)  +---+            Psychology
           |    |                            |   |                      
            \   +--------+------------+------+   |                      
            |            |            |          |                      
            |       +----+----+       |          |                      
       +----+----+  |         |  +----+---+  +---+----+                 
       |         |  |         |  |        |  |        |                 
       |  verbal |  | spatial |  | memory |  | etc... |                 
       |         |  |         |  |        |  |        |                 
       +-+--+-+--+  |         |  +--+-----+  +-----+--+                 
         |  | |     +---+-----+     |              |                    
         |  |  \        |           |               \         Cognitive           
        /   |  |        |          /                |         Neuroscience

    The mid-level elements of intelligence tend to be positively correlated.

  • Operational Definitions of g
    • first principal component of a large battery of cognitive tests
    • Wechsler Adult Intelligence Scale Full IQ
    • Ravens Progressive Matrices non-verbal test
  • The nature of g
    • a hypothetical construct
    • may or may not reflect a unitary physiological or psychological process
  • Well-founded suspicion of tests due to misuse
    • testers used to take English language tests out to Ellis Island and send back hopeful immigrants who fare poorly on said tests
    • society invests great importance in intelligence
      • all states but Texas won't execute stupid enough people
      • "would you rather your kids marry an ugly or a stupid person?"
    • well correlated with risks of Alzheimer's Disease, Schizophrenia, Dyslexia, ADHD, Depression, PTSD
    • including alcoholism, smoking, mortality (age at death), general health – much of this is even true among the top 1% of intelligence
  • Heritability
    \(h^{2}=2(r_{MZ}-r_{DZ})\), in which \(h^{2}=0.6\) meaning roughly 60% of an the variance of an individuals intelligence in a population can be explained by genetic factors, leaving 40% up to environmental factors.

    This sort of thing can be determined by comparing/contrasting shared and unique environmental features between genetically similar individuals.

  • Genetic Factors
    the relevant genes are not located on sex chromosomes
    of course, the related genes do plenty of other things as well
    with about 25,000 genes, 60-80% are expressed in the brain, with very little evidence for single-gene effects

    Ron's been looking into the hypothesized that personal mutation level in the genome could be related to intelligence.

    • symmetry is correlated with intelligence
    • beauty is weakly correlated with intelligence
    • both are weak indicators of if you are built to plan or somewhat mutated
    • the amount of deletion mutations in your genome is generally negatively correlated with your intelligence

    Given all this, no one has found specific genes which seem to be individually related to intelligence.

    87% of an infants energy budget is devoted to brain development.

  • Graph theoretic view of the brain
    • nodes are functional clusters in the brain
    • edges are connections between these centers, and the brain is a small world network

      the clustering coefficient doesn't seem to relate to general intelligence, rather the number of length (shorter is better) of inter-node connections is positively correlated with intelligence

Derek Hamilton – behavioral/neuro-biological constituents spatial navigation

  • space and navigation are ubiquitous

There is well defined circuitry in mammals supporting spatial navigation, and this shares many mechanisms with the structure supporting long-term memory, so it appears that spatial abilities have piggy backed on mechanisms originally developed to support long-term memory.

what is learned when an animal successfully navigates a maze.

  • it seems animals generally are better at learning spatial relations rather than directional relations, e.g. west instead of left
  • distal cues are used over other sources of navigation information
  • place cells in the hippocampus fire in relation to places, however many of these are also conditioned on the direction in which the animal is moving, as well as the place
  • the most important frame of reference is the local frame of reference

2011-04-06 Wed – psychology and neuroscience

Akaysha Tang


  • novelty detection should be parallel and distributed through the brain
  • how does Gabba (inhibitory neurotransmitter) affect novelty detection in a network

2011-04-27 Wed – sign language psycho-linguist

Jill Morford – Critical Period to Language Acquisition

ASL is not a signed form a English, but rather is its own language with its own lexicon and grammar.

French sign language is much more similar to American sign language than is British sign language.

conclusion: the critical period is critical for efficient and rapid processing of language, rather than the ability to construct complex linguistic constructs

  • critical period
    The idea of critical period is not unique to language

    The critical period

    • children begin stringing words together around the age of two
    • children cease to learn new linguistic constructs around puberty

    Evidence that the younger an individual at emigration into the US, the better their English proficiency, explanations

    • critical period
    • sociolinguistic factors
    • cognitive decline

    It seems that brain plasticity could be related to the critical period.

    Linguists believe that the hierarchical structuring of language is innate, and all that is required during the critical period is for these innate structures to be triggered through exposure.

  • linguistic isolation during the critical period
    Curious Monarchs
    at three times in recorded history, monarchs have isolated children from language to investigate the effects of growing up without language, in all cases the results were contaminated by language, or the children died
    neglected child
    • did acquire negation plural progressive
    • did not acquire pronouns, movement rules, auxiliaries
    when deaf children are raised in loving families but are not signed to (more common in the 60s and 70s), often these kids invented a way to communicate through gesture (ubiquitous)
    • points to reference nouns, and temporal points
    • iconic gestures (like visual onomatopoeia), are likely to function more like verbs, can be moved spatially to associate the verb with a noun
    • generally isolate alphabet of core motions which are re-purposed to a wide array of situations

    Homesigners generally produce language rather than perceive language as do normal children.

  • post-critical period language acquisition
    • outperformed by early learners
    • highly variable performance
    • late learners have incomplete grammatical knowledge although they tend to be able to learn every other part of the language

    Second language learners are better than post-critical period learners largely in their ability to recover when they've missed a sign or misunderstood a word.

Melanie Moses – Scalable RADAR

Talk from IEEE Alife April 2011

  • scales in ant colonies
    • Argentinian leaf cutters with millions of ants and ages ~50 years
    • small ant colonies inside of a single acorn with ~12 members
  • ants often don't use any pheromones but with rather often collect a pile of seeds by themselves without ever asking for help
  • immune system
    • like a distributed metabolic system with many little separate hearts (lymph-nodes) each of which is responsible for an area of enforcement
    • the immune system does not show the 3/4 power law shown in other biological systems, rather the speeds are generally equal across species sizes — makes sense, as there's great selective pressure
      • this could be due to the architecture of the lymphatic system, both the number and size of lymph-nodes scale with size (but not directly)
  • repeated sampling
    repeatedly searching until you find something
    • searching is a really effective way to search if you keep looking whenever you don't find anything
    • in ants this is like an ant stopping its search when it found some seeds, but not telling other ants about the seeds
    • in immune systems this is like T-cells never communicating back to the lymph-node, but continuing to circulate (search) until it runs into an inflamed region with an infection

2011-05-04 Wed – Rec E. Jung on Creativity

on the relationship between intelligence and creativity


  • genius is required for creativity
  • mental illness is required for creativity

modes and domains

processing \ domainemotionalcognitive

good ideas require many ideas

study over a number of subjects

  • high IQ subjects had a negative correlation between naa and creativity
  • low IQ subjects had a positive correlation between naa and creativity

Transient hyper-frontality: down-regulation of the frontal lobes to allow novel connections between disparate regions of the brain.

Final Paper – Thomas Metzinger


  • 8-10 pages including references (no longer than 10 pages)
  • due the Monday of finals week
  • would be good to get it in early
  • web references should include an access date

Notes: There is no Self – Metzinger

  • philosopher
  • theory of consciousness…
    • consciousness doesn't exist
    • rather is a trick the brain plays on itself to help in planning and communication
    • related to pre-frontal cortex
  • Rex Young, intelligence, related
  • Derek Parfit
  • read this Metzinger book The Ego Tunnel




Author: Eric Schulte

Date: 2011-05-17 10:26:02 MDT

HTML generated by org-mode 7.4 in emacs 24