#+TITLE: Cognitive and Comp Neuroscience
#+OPTIONS: num:nil ^:nil toc:3
#+STARTUP: hideblocks

* Meta
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
- ListServe with reading material before classes, go to
  http://mail.cs.unm.edu and sign up for =comp-cog-neurosci=
- file:data/calendar-of-speakers.pdf

* Notes
** 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
- self-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

*** 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)
:        |
:      birds
:        |
:     parakeet
:        |
: 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
- functionalism :: 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

     types of facts which can be appealed to through functional
     - 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
- 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

|          | $[S]o$ | $[S]i$ |
| $Na+$ | 145mm     | 12mm      |
| $K^{+}$  | 4mm       | 155mm     |

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

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

  V\alpha = Voe-\frac{length}{\lambda}

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 
:         --------===-------------===------------
:         --------   -------------   ------------
:                ||                               
:                ||h
:                ||

De-polarization -- firing
| m | open  |
| n | open  |
| h | close |

Re-polarization -- resting/recharging
| m | close |
| n | close |
| h | open  |

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 nerves | 120 m/s |
| pain fibers                      | ~1 m/s  |
| transduction along a synapse     | ~1 ms   |
| aka (absolute refractory period) |         |

*** Fernando Valenzuela -- learning and memory
- hippocampus :: 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

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.
- cooperativity :: critical number of pre-synaptic fibers must be
- input specificity :: restricted to input that recieves tetanic
- associativity :: 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
   :ID:       de820990-8743-4770-b09c-24bec12c1ee4
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
- psychology :: study human behavior
- neuroscience :: understand behavior as an /emergent/ property of the
     physical structure of the brain
- anatomy :: template for structure-function relationships
- neuroimaging :: non-invasive measuring of the brain

- can observe correlation and try to determine /criticallity/
- 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

- EEG :: 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

     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.

- MEG :: 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) \rightarrow *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

- 10 minutes of induced change can lead to ~1 hour of persistent
- 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
   :ID:       ada46e98-49dc-4b3f-b62c-4c2b08f14bef
*** 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
   :ID:       7f5be9e8-15cc-4145-b619-9065557b9ebc
*** 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

**** 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

**** 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
$h2=2(rMZ-rDZ)$, in which $h2=0.6$ 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

**** Genetic Factors
- autosomal :: the relevant genes are /not/ located on sex chromosomes
- pleiotropic :: of course, the related genes do plenty of other
     things as well
- polygenic :: 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
- 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

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

** 2011-04-06 Wed -- psychology and neuroscience
   :ID:       7299d4ff-1fea-45ae-8c1e-cadb50b6751f
*** Akaysha Tang
(see http://atlab.unm.edu/index.php/Main_Page)

- 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
    :ID:       b3efacb5-a4b9-4355-9603-78e2bcbad7da
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

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

- Genie :: neglected child
  - did acquire negation plural progressive
  - did not acquire pronouns, movement rules, auxiliaries

- Homesign :: 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
- 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

**** 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
   :ID:       020f9474-b30a-4225-950b-8aa7bcd1143d
on the relationship between intelligence and creativity

- genius is required for creativity
- mental illness is required for creativity

modes and domains
| processing \ domain | emotional | cognitive |
| deliberate          |           |           |
| spontaneous         |           |           |

/good/ ideas require /many/ ideas

study over a number of subjects
- high IQ subjects had a negative correlation between naa and
- low IQ subjects had a positive correlation between naa and

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

* Final Paper -- Thomas Metzinger
ego-machine.pdf (code, video)

** Meta
- 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

* Footnotes
[fn:1] http://www.prnewswire.com/news-releases/apache-innovation-bolsters-ibms-smartest-machine-on-earth-in-first-ever-man-vs-machine-competition-on-jeopardy-quiz-show-116151274.html

[fn:2] http://blog.reddit.com/2011/02/ibm-watson-research-team-answers-your.html

[fn:3] http://www.apache.org/