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Midterm II
CS 107
186
Computer Science
Undergraduate 2
05/01/2010

Additional Computer Science Flashcards

 


 

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Term
federation
Definition
single self-replicating molecule is not as efficient as a federation-may not be good at everything nec. to create a complex organism
Term
copy fidelity in genes
Definition
DNA polymerase checks copying accuracy and cuts
out miscopies, redundant code, T replacing U eliminates common error
Term
longevity in gense
Definition
RNA less stable than DNA
Term
descent with modification
Definition
children inherit genes of parents, but not perfectly so
Term
differential reproduction
Definition
some genese are more equipped to be passed on than others
Term
mechanisms of evolution
Definition
inheritance, genetic variation, differential reproduction
Term
evolution algorithm
Definition
1) make mult copies of gene 2) introduce slight changes 3) test each copy, choose best 4) repeat
Term
selection pressure
Definition
rate of natural selection- how quickly do org. reproduce, how harsh is selection process
Term
niche
Definition
set of environmental conditions and
opportunities for survival. Habitat, food source, competitors
Term
speciation
Definition
process of forming new gene federations (species) which exploit niche
Term
punctuated equilibrium
Definition
stable situation to period of rapid change to another long stability, etc...
Term
how flying developed
Definition
feathers for warmth in dinosaurs, long feathers make gliding possible (exploitation of air as a niche)->flying
Term
prokaryotes
Definition
membrane w dna and other structures floating around. limited bc can't absorb much energy through membrane, can't get larger bc volume grows faster than surface area
Term
eukaryotes
Definition
1000X bigger than prok, have mitochondria. giant factory, organized
Term
mitochondria
Definition
produce ATP for cell. remnants of cellular invaders. still have own DNA (37 genes). leave free O2 (free radicals) which destroy structure
Term
apoptosis
Definition
cell chooses to die as result of damage induced on dna by mitoc. ->senescene is a deal the earliest eukaryotes made
Term
blandings turtle
Definition
no evidence senescence, grow more fertile
Term
genes for dying young
Definition
subject to stronger selection
Term
Michael Rose's flies
Definition
waits to let them reproduce until older- selects genes that are healthy for longer
Term
why mitoc. have uniparental inheritence
Definition
if mitoc. dna were allowed to be diverse, they would compete w each other, at expense of parent cell
Term
isogamous
Definition
algae and fungi, no obvious sex differences – two ‘mating types'
Term
examples of non-binary sex
Definition
‘split gill’ mushroom – 28,000 mating types   Slime mold – 13 sexes
Term
two leading theories of why there's sex
Definition
allows offspring w/out mutations even if parents had, keeps disease/parasites from adapting to specific niche
Term
topminnow
Definition
can choose asex. or sex. reproduction. sex. rep. ones are less infested w/ black spot worm parasites
Term
kin selection
Definition
a gene that can help other copies of itself will proliferate.
Term
relatedness
Definition
brother- 1/2. cousin- 1/8. aunt- 1/4. parents- 1/2. hamilton's rule- rB>C
Term
parental care
Definition
special case of kin selection- extreme relatedness, high reproduction potential
Term
herring gulls
Definition
don't recognize eggs, but do rec. chicks
Term
haplodiploid
Definition
fertilized->female->worker, unfertilized->male->drone. bees, wasps, ants. females share 3/4 genes with sisters, 1/2 with sons, so care more about helping queen than own young
Term
ability to predict future
Definition
adaptive trait, but only in some niches. defines human niche.
Term
dollar bill auction
Definition
winner gets it, but loser pays too- never ends. example of escalating selfishness
Term
game theory
Definition
A way of analyzing situations in which the outcome of your decision depends on both how you choose and your opponent chooses
Term
penny matching
Definition
example of no dominant strategy
Term
assumptions of game theory
Definition
everyone knows rules, everyone makes best response to others' actions, everything that effects decision is in game
Term
zero sum
Definition
fixed amount of winnings. von neumman proves there will always be a strategy that makes each player happiest
Term
non zero sum
Definition
bank pays out- diff bt what is good for the group and good for the individual
Term
Mr. Big & The Diamond
Definition
no one shows up bc that's better in both cases for each
Term
axelrod broadens prisoner's dilemma
Definition
iterated pd, players can identify each other
Term
tit for tat
Definition
cooperate, then copy last move
Term
nice; forgiving
Definition
never defect first; limit punishment
Term
vampire bats
Definition
donate blood to ones who didn't get any, remember who doesn't donate back
Term
pd in evolution
Definition
primary expansions of human brain: language, face recognition, emotional interaction. language:medium for expression, creating alliances, detecting lying and cheating. understanding each other: cognitive arms race
Term
prisoner's dilemma means
Definition
cooperation can evolve from selfish genes
Term
nash equilibrium
Definition
set of strategies that, when played by everyone, no one has incentive to change. essentially an ESS. for example, always defect.
Term
Polymerase Chain Reaction
Definition
make large # copies of specific DNA strand. Key point: in a very short time, test tube is filled with millions of copies of the particular DNA of interest. target sequences grow exponentially, so you get much more than superfluous.
Term
PCR uses
Definition
amplification, forensics, mummies, neanderthals, detection of hereditary diseases, paternity testing, cloning genes
Term
amplification
Definition
millions of copies of a portion of dna strand (specified by endpoints)
Term
primers
Definition
molecules that recognize start and end nucleotide sequences- guide polymerase to attach to strand
Term
short tandem repeat
Definition
repeated pattern of 4 nucleotides- don't code for anything useful we can identify- used in dna fingerprinting
Term
dna computing
Definition
huge memory capacity, dissipate little energy, essentially parallel
Term
DNA computing TSP
Definition
roads are complements of two city codes. Answer will be expressed as a DNA strand which is a combination of cities and roads. 1) generate all possible routes. 2) select itineraries that start/end with right cities (PCR) 3) select itineraries w/ right # cities (electrophoresis) 4) select itineraries that have all cities.
Term
affinity purification
Definition
Select strands that have affinity for each city. Result: set of strands that encode the problem solution
Term
why dna computing doesn't solve tsp
Definition
problem isn't time anymore, but supplies
Term
in computation, _ is always better
Definition
smaller
Term
sanger
Definition
studies bacteria-acttacking virus- ring DNA strand, mapped out locations of genes (sometimes overlapping) ->accelerating sequencing rate
Term
craig venter
Definition
advances in software/hardware-sequences bacterium. frustrated w/ slow hgp founds celera
Term
human gene #
Definition
21000. less than many plants. found by open reading frames.
Term
diploid
Definition
full genome, made of dna from both parents
Term
venter's genome
Definition
1st diploid- amazing heterogeneity (44% genes differ bt mother & father's contribution)
Term
watson's genome
Definition
cyp mutations, slow drug metabolizing, Not much effect from antipsychotics, antidpressants
Term
single nucleotide polymorphism; indel; inverstion
Definition
1 base pair variation; insertion or deletion; flips horizontally
Term
genomic high variability
Definition
little evolutionary pressure->drifting
Term
alignment; genetic distance
Definition
which sequences from diff genomes have common ancestor? process of finding which bases/amacids conserved after mutations; how far apart are two diff sequences?
Term
how can we tell 2 diff genes are 2 versions of same gene?
Definition
similar, but not identical.
Term
eyeless
Definition
pre-cambrian- controls 2000 other genes- contains homeobox. like aniridia & others, has HOX domain
Term
mrDNA mutation in as a tool
Definition
point mutations can be used to trace lineages in coding regions; fraction of bases changed can be used to trace lineages in D-Loop; assuming constant rate of change, gives time since most recent ancestor
Term
currently paleoanthropology theory
Definition
seems that there were five species of human, the last four of which migrated broadl
Term
out of africa
Definition
evolved there 150,000 years ago
Term
regional continuity
Definition
single large migration c. 2 Mil yrs ago followed by
evolution in place – African, European, and Asian populations evolved separately
Term
bioviruses
Definition
circular, linear, sealed ends- basically nucleic acid and protein coat. not alive- no metabolism or chem activity outside of host, don't self replicate (ie code for own structures)
Term
computer assisted biology
Definition
algorithms that easily let us do alignment
Term
viruses take over metabolism
Definition
hijack transcription/translation, use host dna polymerase by tricking cell into thinking its dividing. move in to nucleus
Term
rabies
Definition
fecundity: makes animal aggressive, bites, rabies spread through saliva
Term
toxoplasmosis gondii
Definition
Eucaryotic parasite- rats lose fear of cats when infected bc only completes life cycle in cats
Term
wolbachia
Definition
dead end in males so might: get sperm to only fertilize eggs of infected females, enable females to breed w/out males, kill male offspring. essential to african riverblindness nematoad
Term
retrovirus
Definition
copies info from rna to dna, releases viral rna and reverse transcriptase, cleaves to dna and starts to be transcripted
Term
drive
Definition
gene that outcompetes its alleles in next generation
Term
t haplotype
Definition
mouse w/ drive in males but normal in females. causes normal sperm to be dysfunctional.
Term
mobile genetic element
Definition
(transposon) carries message "copy me and put me back into DNA in new place"
Term
retrotransposon
Definition
produce dna from own rna and insert it at random
Term
alu
Definition
junk dna. mimics recognition site from LINE-1 to get copied. implicated in cancer.
Term
line-1
Definition
highly repetitive. 15% whole human genome. can ->hemophilia
Term
intron; exon
Definition
interspersed nonsense elements. spliced out before sent to ribosome. all have a few nucleotide sequences in common; separated parts of the same gene
Term
spliceosome
Definition
complex splicing molecule
Term
prions
Definition
misfolded protein, causes others to misfold. form of self replication. ->madcow, kuru
Term
for an information system to be hackable
Definition
has to have copying mechanism, be able to move info from place to place
Term
how prions, viruses and transposons cam about
Definition
random variation in the genome
Term
worms
Definition
don't require humans to propagate- do not live on harddrive, only running form
Term
electronic viruses
Definition
exist in code on document, requires human to spread
Term
first email viruses
Definition
melissa 1990- emails porn sites to friends; love bug 2000- sends passwords to author; mafiaboy 2000- denial of service attacks on cnn, yahoo, ebay, amazon; anna kornukova 2000- visual toolkits available
Term
2000 transition
Definition
mainly viruses to mainly worms
Term
Morris Worm
Definition
search for computers to break into, guess password
Term
how a worm works
Definition
find hosts on internet at random, target web sites, firewalls
Term
witty worm
Definition
march 2004- first destruction- deletes random part of harddrive
Term
assumptions of virus spreading
Definition
population is large, each encoumter has fixed probability will infect other (fixed virulence), constant probability people likely to meet each other
Term
number of infected
Definition
grows exponentially. N=# individuals infected per time unit
Term
degree
Definition
number of edges connecting a node
Term
clustering
Definition
if two people are friends, their friends are likely to know each other too
Term
clique
Definition
extreme clusering
Term
virus spreading on a lattice
Definition
n(t)=nt^2
Term
milgrim's experiment
Definition
wichita to cambridge- usually 6 degrees
Term
small world network
Definition
circle- distance bt people drops fast with only a few shortcuts
Term
innoculation
Definition
currently inoculating randomly, but most efective would be to inoculate high degree nodes
Term
kuru
Definition
cannibalistic societies- women/children eat last, get brains. nothing living associated with it so hard to treat
Term
toolkits; script kiddies
Definition
allows you to turn a crank and create new virus ; kids using these
Term
sapphire virus
Definition
virulence planes out bc no more computers to infect
Term
complex network
Definition
(small world) our network, somewhere between lattice and clique
Term
k
Definition
avg # connections to others (actors- 29)
Term
random mixing; lattice mixing
Definition
fast, exponential speed; slow, polynomial speed
Term
examples longevity, fecundity, copy-fidelity in memes
Definition
winston tastes good, citation count, dogma
Term
hub
Definition
frequently broadcasts infectious memes
Term
gladwell's ideas
Definition
law of the few, stickiness factor
Term
broken windows theory
Definition
disorder->more disorder
Term
immune systems
Definition
system that collects potential viruses, transports
them back to the central facility, where they are analyzed, and
updated virus defs distributed. This fact is true for either bio or electronic viruses.
Term
the more variable/chaotic the environment, the harder to survive w/out
Definition
memory, prediction abilities
Term
proximal purpose
Definition
brains control behavior (purposeful movement on short timescales)
Term
example info processing w/out neurons
Definition
e coli have receptors in cell walls, communicate chemically to flagella, e coli orient to gradients- kind of memory. 1 bit of info determines roll or tumble
Term
neuron function
Definition
integration, transmission information from one location in body to another. chemical coding in, electrical coding inside, chemical coding out
Term
soma
Definition
where information integrated
Term
sensory neurons; motor neurons
Definition
connect to sense organs, bring stimuli to cns; connect to muscles and glands, bring stimuli out of cns
Term
synapse
Definition
two neurons in close proximity- chemicals diffuse across gap quickly
Term
electrical coding in neuron
Definition
big development brought by neuron. allows for rapidity
Term
neural membrane
Definition
hydrophobic and hydrophilic sides. proteins embedded. allow certain things to pass through
Term
resting potential
Definition
at rest, neuron constantly pumping Na+ & K+ out of cell->negative inside. creates a voltage, or tendency for current to flow
Term
transmembrane protein
Definition
sticks all the way through cell
Term
action potential
Definition
movement of ions across membrane that propagates down axon. temporary, digital code,
Term
ion channels
Definition
proteins that change shape in presence of voltage. opening in one region is caused by loss of resting potential (depolarization) in another- dominoes
Term
synaptic transmission
Definition
AP in presynaptic neuron causes release of neurotransmitters->affects ion balance in postsynaptic neuron->excited or inhibited AP in postsyn.
Term
axon hillock
Definition
measures stimulation, decides whether to generate Action Potential. ie if sum of inputs above threshold, new ap generated
Term
firing rate
Definition
individual firings don't carry information, only the rate
Term
collections of neurons
Definition
individual neuron has too small range of activation levels. important encoding done by collections using combinatorial code, vectors
Term
nerve
Definition
bundle of axons
Term
vectors
Definition
when numbers used in combinatorial codes. natural isomorphism bt vectors and points in space. how our brain presented with info
Term
why is the brain so good at face recognition?
Definition
perhaps bc encoding in face space
Term
artifical neural network
Definition
computer simulations of simplified neurons. answer question, how can collections of neurons produce high level functions? activation level and synaptic weight.
Term
potential
Definition
X1W1+X2W2. if potential>threshold, X>0
Term
vector transformation
Definition
neural networks do this. input-set of #, output-diff. set of #. pattern of connections, weights determine transformation
Term
pattern matching
Definition
given particular input vector, network generates associated output vector
Term
categories
Definition
regions in vector space (facial subregion, male subregion, etc)
Term
distributed representation
Definition
correct classification not usually marred by failing of a few neurons
Term
ANN activation level; weight
Definition
number that represents neuron firing at specific rate; extent to which one neuron causes firing of another
Term
hidden layer
Definition
each cell connected to each input & each output cell, every connection has a weight- can't solve by hand like diagonal problem
Term
training the network
Definition
use examples to get network to pick right set of weights
Term
generalization
Definition
see whether testing the network worked on images never seen before
Term
seven features of consciousness
Definition
short-term memory, sensory inputs, steerable attention, capacity for alternative interpretations of data, disappears in deep sleep, reappears in dreaming, Places all sensory modalities into a single unified experience
Term
consciousness and sleep
Definition
program that brain turns on and off. recurrent neural network
Term
intralaminar nucleus
Definition
bagel-shaped structure in center of brain, connections to and from all parts of cortex. proposed by rudolfo llina as seat of consciousness. lesions to it ->vegetation
Term
mind reading
Definition
theoretically possible if we understand how brain encodes information. for ex, control electronic devices
Term
mouse mover patient
Definition
brain stem stroke, no motor control. probe emplanted, encourages surrounding neurons to grow. imagines moving hand, eventually understands hand->mouse->cursor & only needs to think about cursor. problem is we need to extract vectors, not just single values
Term
thinking about drinking
Definition
learn through computer relationship bt vector codes associated w/ certain activity. watch waves & decide whether to swing bar. eventually net adapts-rat only had to think about pressing bar to produce waves, get water
Term
cochlear implant
Definition
direct electrical stimulation of auditory nerve. required understanding of vector codes used in inner ear
Term
brain prosthesis
Definition
wire axons to computer, do associative experiments w/ many stimuli->upgradable hippocampus
Term
kevin warwick
Definition
microelectrode in wrist can control electronic devices
Term
two teams independently develop electronic computer
Definition
turing, england, 1943, for code-breaking; eckert & mauchly, upenn, 1943-4, to guide navy missles
Term
ENIGMA
Definition
german encoding that the polish broke in the 30s. turing invents machine that breaks it rapidly.
Term
colossus
Definition
turings gen. all purpose computing device, built just as war ending. all colossus info became constantly classified
Term
zimmerman telegram
Definition
warned of german/mexican alliance. germans were using very old encoding that eng solved easily
Term
eniac
Definition
stores 20 #, performs 5000 additions/second. made commercially available 1951 (aot england)
Term
moore's law
Definition
computing capabilities double every 18 months. exponential growth
Term
any computer needs to
Definition
store a set of symbols, perform simple operations on them, accept an arbitrary sequence of instructions
Term
why binary
Definition
engineering decision. only requires 2 symbols, easy to make devices that are bistable
Term
64 bits available means...
Definition
2^64 (16 quintillion) is the first # too big to represent
Term
adding in binary
Definition
1+1=0, carry the 1. 1+0=1. 0+0=0.
Term
binary digits; eight of them
Definition
bits. 8 bits=byte
Term
instruction set
Definition
set of operations hardware can perform
Term
the first network
Definition
telegraphy- uses 5-bit encoding of alphabet.
Term
paul baran
Definition
creating resilient systems (cold war) star
Term
why internet so successful
Definition
decentralized means no control. the more ppl connect, the more valuable to be connected. anyone can add nodes. packet-switching
Term
communications satelites
Definition
used for transmission of tv. geostationary (rotate same speed as earth)
Term
diff bt AI & cognitive science
Definition
AI-build apparently intelligent machines. cog sci- understand human intelligence by building programs
Term
turing test (imitation game)
Definition
room 1- human. room 2- computer. judge outside, determining who is responding to his messages
Term
first attempts at AI
Definition
conference at dartmouth 1951. try to make computers solve our hardest problems- checkers/chess/go, automatic language translation
Term
samuel's checkers program
Definition
"gold stars" the positions occurring in winning games. you can set up 2 to play against each other.
Term
eliza
Definition
simple syntax conversion to simulate conversation. ppl love eliza too much, made creator turn back on AI as waste of time
Term
short term solution to common sense problem
Definition
restrict domain of discourse- SHRDLU, TRIPS
Term
searle's view on ai
Definition
brains, fundamentally biological, cause minds. symbol manipulation does not -> understanding.
Term
creativity as recombination
Definition
david cope. Effective recombination requires extensive musical analysis and very careful recombination to be effective
Term
pons asinorum
Definition
comp realizes, just flip triangle over to prove congruence
Term
long term potentiation
Definition
adjustment of synaptic "weights" in true neural networks (infant development). production of additional synapses, change of synaptic strength
Term
exemplars
Definition
ANN training inputs
Term
feed forward; recurrent
Definition
no loops; connections in network that loop back- emergent effects: short term memory, interpretation ambiguous senses, limit cycles
Term
divisons of cortex
Definition
frontal lobe: higher level though functions, memory. parietal lobe: integrating sensory info, obj manipulation. temporal lobe: hearing, high level visual processes, declarative memory. occipital lobe: visual processing
Term
pop-out effect
Definition
evolutionary, preconscious. evidence of the kinds of
representations used in the hidden layers of our visual cortex
Term
distributed representation
Definition
meaning derived from connections bt networks. vector for face space more detailed when features added
Term
declarative memory
Definition
factual, depends on hippocampus
Term
working memory; procedural memory
Definition
stores small amnt #s, letters, function of cycling activity in brain, non-permanent change; skills, learned movt
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