Why does Cog Sci exist?

-Not traditional discipline

Interdisciplinary
-Tradtion vs reality
Pragmatics: Diversity of ideas/approaches
What’s Cognitive Science?
What is Cognition? (According to Wikipedia)
The scientific, interdisciplinary study of MINDS, and all of the processes, functions, and
products of minds
What do we mean by “mind?”
Two Tricky issues (among others)
- Kinds of minds: Human, non-human (animal/artificial)?
- c.elegans/icub
- Can communities act as “minds?”
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History of Comp Sci/AI
History of Anthropology/Linguistics

● Ethnographic methods: ways to study cultural methods

● Chomsky: Everyone is born with innate language structure development
○ Language Acquisition Device: Innate syntax-inferring ability (Kantian)
● Study the cognitive/conceptual traits of language

Where do we see modern Cog Sci?

● Brain Games - for elderly people

● Schools - to improve educational practices
● Corporate realm - manufacturing
● Medicine - MRIs/Neuroimaging tech
● Individuals w/Mobility Disabilities
● Robotics
● Understanding complex social groups - flight navigation groups, work groups in
company, Starbucks baristas (learn to minimize error rate)
● Understanding animal minds
● Image recognition
● Understanding human interaction

Central Nervous System - Brain/Spinal Cord

● PNS - Peripheral
 ● Main components
○ Brain
■ Forebrain: Cerebrum/Diencephalon
■ Midbrain (small)
■ Hindbrain: Pons/Cerebellum/Medulla
○ Spinal Cord
● Brain Features
○ Size
○ Contents
■ Glial: Word for blue
○ Surface Structure
■ Lateral view (bottom right):
■ Left: front/anterior
■ Right: back/posterior
■ Superior view (top left)
■ Inferior view
○ Interior Structure
■ Medial (Lateral) view of right hemisphere
○ Cerebral Cortex
■ Cortex means “bark”
■ Laminar structure (layered structure)
○ Gray vs white matter
■ Gray matter: Cell bodies
■ White matter: ​Connections b/t cell bodies​ Myelinated fibers (fiber
tracts)
■ Myelin: Covers axons, improving electric conduction
○ Cerebrum Function?
■ Receiving information from all other structures
■ Sending info (directly or indirectly)/ receiving info (see slides)
■ Efferent - Effect: Send motor or secretory command
■ Afferent - Accept: Receive info or command
○ Thalamus: Important structure within Diencephalon
■ “Grand Central Station” of CNS
○ Olfaction - smell
○ Pons
■ Somantic functions: Groups of cell bodies

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COGS 1 Lecture
● Not all neurons are created equal
○ Each neuron has a unique:
■ Location (area, layer)
■ Connections (inputs/outputs)
■ Electrical and chemical responses
● How do cells acquire, maintain, and adjust their diverse characters?
○ Brain development: tightly orchestrated process
● Puzzle: Different cells, same genome
● Levels of organization in the genome
○ DNA is wrapped around a histone particle
● Modifications to DNA are epigenetic “punctuation marks”
● EPIGENETICS: PUNCTUATION IS KEY
● The genome as a computational network
○ Encode: Encyclopedia of DNA elements
● Epigenetic regulation in insects
○ Queen/female worker bees
● Plants
○ Epimutation: Two forms of the toadflax plant w/ identical genotype but different inherited DNA
methylation patterns
● Mammals
○ Nutrients supporting healthy methylation
■ Folic acid
■ B-vitamins
■ SAM (S-adenosyl methionine)
○ Especially important for pregnant mothers/infants
● Epigenetic patterns in humans: Twins drift apart
● Can memories be inherited?
○ Mice trained to detect odor developed larger olfactory receptors for that odor
○ Offspring also had enlarged receptor neurons
● Role of computation
○ Testing the cognitive role of epigenetic modifications requires genome scale, base-resolution
neuronal epigenome profiling
● Studying gene networks: Shotgun sequencing
● Shotgun bisulfite sequencing
○ Methyl cytosine is protected from bisulfite conversion
● Two DNA sequence contexts for methylation
○ CG: Highly methylated in all cell types
○ non-CG (CH): Generally unmethylated after differentiation
● Surprise: Substantial non-CG methylation in neurons
● Non-CG methylation accumulates throughout childhood and adolescence
● Non-CG methylation increases during years 0-16, coinciding with synaptogeneisis and pruning
● Does DNA methylation contribute to brain cell diversity?
● Cell types have unique DNA methylation fingerprints
 ○ Transcription factor MEF2C:
■ Implicated in neurogenesis and cortical development
■ Hypermethylated (i.e. repressed) in glia
■ Methylation is repressive
● mCH is a characteristic feature of neurons, not astrocytes
● Non-CG DNA methylation is a specific feature of mature neurons
● Identifying gene methylation patterns is a “Big Data” challenge
● Unbiased clustering or methylation profiles identifies distinct gene sets
○ Principal component (PC) analysis of genome-wide methylation patterns
● Sub-types of neurons: Excitatory and inhibitory cells create balance
● What is the DNA methylation landscape in major neuron cell types?
● Data dimensionality
○ A data set…
● Dimensionality reduction by Principal Components Analysis (PCA)
○ Ex: Projection of 3D global geography onto 2D maps
● tSNE (t-Stochastic Neighbor Embedding)
○ Visualizing cells in high-dimensional space
● Linear/Non-linear dimensional reduction
○ Principal component analysis
○ t-Distributed stochastic neighbor embedding
● How many cell types are there? Lumpers vs. Splitters
○ Darwin says it’s good to have both
● Determining cell types through the integration of multi-modal datasets
○ Cell type
● Multi-omics data integration requires imputation
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Profanity
● Males/Females have increased heart rate when they swear
● Produced more sweat when they swore
● Swearing helps reduce pain/suffering for people
● Helps to increase strength
● Adrenaline - System that helps w/ flight/fight response
● Not much profane words in religion for American English compared to Canadian French
● Offensiveness of English Profanity is divided into 4 categories: Religion, Copulation,
Body (Functions), and Slurs
● Slurs are the most offensive
● Word structures/sounds may determine how offensive a word is
● 4 letter words w/ one syllable tend to be the most profane
● Syllable Structure
○ Open (Ends w/ vowel)
■ See, spy, rue
 ■Only abt. 5% of profane English monosyllabic words
○ Closed (Ends w/ consonant)
■ Sass, spit, runt
■ Abt. 95% of profane English monosyllabic words
● Stops: Sounds that make a 'pop' sound (puh, tuh, kuh)
● Some languages/cultures have been reported to not have any equivalent to profanity
● Blasphemy is a capital crime in parts of Afghanistan
● In France, ​gros mots​ "big words" aren't so bad that they need to be bleeped
● What makes profanity?
○ A cultural belief that some words are bad (in some contexts)
○ That belief applied to specific words
■ That are likely to be drawn from certain semantic fields
■ That may pattern together in sound
○ Cultural structures for reinforcing those norms (punishment, censorship, etc.
● Speech Errors
○ Speech is peppered w/ errors
○ Errors may reflect otherwise unstated and repressed thought (Freud, 1901)
○ If these repressed thoughts are more likely to be about taboo topics than not, then
speech errors should be more likely to result in taboo language than not
● Right inferior frontal gyrus - implicated in inhibitory control
● Picture-Word Interference
○ Taboo word is slower at responding
● Laterization: Function is passed from one side of brain to the other
● Predominant language functions are in the left-hemisphere of brain
● Jacques Lordat - Physician; Suffered a stroke
○ Only knew how to say 'I' and f-word in French
● E.C. - Expletives and curses were well articulated and clearly understandable
● Automatic Aphasia - "Could not provide the correct expletive for situations described to
him nor could he complete a curse"
● Basal Ganglia - Selecting and suppressing actions based on strong emotional states
● We're using a different part of the brain for swearing
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Midterm 1 Review
● Diversity of Traits: Genetics, Epigenetics, and Adaptive Phenotypes
● Genetic Diversity Ex: Allelic variations matter
○ One neurotransmitter is called serotonin (5-HT: 5-hydrotryptamine)
■ Modulates effects of other neurotransmitters
■ Affects anxiety, appetite, cognition, memory, mood, sleep, attention, etc.
○ Many cell types react, including various types of neurons
 Key difference across neurons: ​what​ kind of NT they respond to!
■
○ In humans 14 known types of 5-HT receptor proteins
○ Some types have alternate allelic variants = slightly different base sequences
■ Some variations of the receptor protein have been studied
■ Well-distributed in the healthy populations (or in this room)
● Shotgun sequencing: scalable (whole genome at once)
○ Fragment genome into chunks
○ Sequence each chunk
○ Do several times, each time the chunks will be a little different
○ Use sequences of identical bases to find overlap
● What else affects cognitive phenotypes?
○ Experience:
■ Learning, memory, practice effects, fear conditioning
■ These involve changes in gene expression but not changes to the genome
(sequence of DNA)
○ DNA is not the only factor in gene expression
○ Epigenetic variation
○ Principal component analysis
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Alien Intelligences: The Minds of Other Animals
● Cognition - Adaptive Engagement with the world
● To study cognition in nonhuman animals
○ Begin by assessing species-specific sensory-motor constraints
■ "Visible Light"
■ Some species do not distinguish colors
■ Match to Sample
 ● Not taking such constraints into account…
● Dolphins see black and white, so they fail at color-related tests
● Dolphin Vision: Sensitive to Motion and High Contrast
● Consider general learning principles
● Include ecological demands on cognition
● Examine implications for understanding human cognition
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HCI and Design at UCSD
● UCSD is a special place w/ a long history in Cog Sci and Human-Computer Interaction
(HCI)
● Early Days: Institute for Cog Sci, Parallel Distributed Processing, User-Centered System
Design (UCSD)
● Today: New Design Lab Focus
● Cog Sci 10: Cognitive Consequences of Technology
● Thinking w/ Computers
○ For far too long we have conceived of thinking as something that happens
exclusively in the head
○ Thinking happens in the world as well as in the head
○ We think with things, our bodies,…
● Computers are special - in that they provide a new kind of stuff, a new medium, out of
which to fashion dynamic interactive systems to assist thought communication,
collaboration, and social interaction
● Xerox Parc and the Alto
○ Xerox CEO decided Xerox should become "the architect of information"
○ Parc becomes…
● Computers are Special
○ Computation provides the most plastic medium for representation, interaction,
and communication we have ever known
■ Mimic existing media
■ Create new media and modify the form of existing media
■ Create models that represent, with ever increasing fidelity, the physical
world
■ Provide virtual worlds
■ Combine the real and the virtual
● Computers are also changing form
○ Monolithic computer is coming apart and being reassembled in myriad new forms
○ New device ecologies and ways of interacting
○ Already today a billion google searches; each using the equivalent of all of the
computing of he Apollo Project that landed the first human on the moon
 ○ For good and for ill, our activities are increasingly mediated by computers
● New types of computers: smartphones
○ Increasingly we have multiple and we don't think of many of them as computers
○ iPhone introduced in 2007
○ Internet: Connected computers, sensors, and people all…
● Boundary between physical and digital
● ObjecTop
● Data Revolution - We don’t know nearly enough about what people really do
○ Inexpensive digital recording devices, sensors, and storage facilities are
revolutionizing data…
● Data collection using Kinect
● Long Interested in Capturing Activity History
○ Activity Histories
■ Edit Wear and Read Wear
■ History-Enriched Digital Objects
● Intelligent Driver Support System
● Summary
○ Computers are special: New media for representation, communication, and
collaboration
○ Increasingly we think with computers
○ Moving beyond the desktop: onto the desk, into the world, and mobile
○ Increasingly permeable boundary between physical and digital
○ Important data revolution: Capture real-world activity for scientific scrutiny (We
don’t know enough about what people really do)
○ Activity Histories: read/wear, edit/wear
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○ Objective Truth: Yes/No Questions
○ Contextual Truth: "Modern Poems"
○ Peer review - Widely used today
○ When you design something, you're creating a potential future
○ Biggest Error: We know stuff, but it is wrong
○ Design Definition
■ Not oriented around a specific type of artifact, but the process/course of
action
○ Prototyping is a question
■ Then find the fastest way to answer that question
○ People do a much better job peer reviewing when they see things side-by-side
○ Wisdom of the crowds depend on the people's mistakes being evenly distributed
about the correct answer
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● Uncanny Valley: The more human-like and less-machine like something seems, the
easier it is for humans to respond to it emotionally; Except when something looks almost
life-like but is off by tiny bit, causing our emotional response to decrease and thinks its
creepy