Bio 1M03 midterm 1

logically equivalent

statements are logically equivalent if they express the same fact in different words in other words if either one is true the other one must be true

the cell theory

all living organisms are composed of cells

cell

highly organised compartment bounded by a membrane

genes

made of DNA

proteins

made of amino acids

what about viruses

no cells, not defined as livivng orgaisms

where do cells come from

theory of spontaneous generation, do they come from other cells? then where did first cell come from? origin of early cells is a big research topic

where do flies come from

thought came from meat ( 3 jars experiment)

where do microbes come from

boiled broth in swan neck and straight neck only grew in straight neck, the contrast is whats convincing

hypotheses

we purpose science by evaluating hypotheses these are propose explanation of facts

how do we use hypotheses

to make predictions, and use experiments and observations to attempt to falsify hypotheses most cannot be proved to be true, if we fail to falsify them we say that they are supported if a hypothese explains many facts and survives attempts at falsification we tend to believe it

control

good experiments are controlled; we have two or more groups that differ only some factor that we want to study, groups should be as similar as possible

replicated

good experiments are replicated each treatment groups has more than one replicate

replicate

a unit that is subject to a chosen treatment

randomized

units are assigned to treatments randomly

observational studies

look for ways to collect data that will support or challenge hypotheses scientists are cautious about making conclusion from observational studies b/c its hard to know if you’ve taken everything into account as experiments are more reliable we do them because of time practicality and ethics

why did dinos go extinct

probably a meteor, no replication no control

special creation

the theory of special creation asserts that each species is a unique type created by god

theory of evolution

asserts that species have changed through time (evolved)

fossil

physical trace of an organisms that lived in the past can be dated using complicated radiometric and geological techniques fossils provide info about the history of life

fossil record

refers to the collection of all known fossils

extinction

many fossils left by organism who are no longer around, so extinct

one piece of evidence that species are changing in a very limited way

transitional forms

when species disappears from the fossil record, a similar species often appears often happens in the same geological are consistent with species evolving or changing through time

vestigial trait

a structure that has no function but is similar to functioning structure in related species

directly observed evolution

some kinds of evolution can be and have been observed on faster time scale

tuberculosis

by the time TB disease becomes apparent there are usually many millions of bacteria in the lungs

if you treat with single drug some bacteria will become reistant

these bacteria multiply and replace the sensitive bacteria and cause the disease again

relationship between species

if species from common ancestor we expect to see evidence that they are related to each other, species fall naturally into groups, geographic patterns of relatedness, homology

geographic relatedness

species in same geo area often seem to be closely related, what we expect is species evolved independently starting from common ansestor in the region, support evolution

evolution + similarities

almost identicla developmmental genes in fruit flies and people

similar limb bone structure in turtles and people

similiarties as homologies

homology

similarity that is due to common ancestry

due to homology similiarties are widespread, this is a strenght of the theory of evolution

genetic homology

homology at the level of genetic coding

ex: genetic code itself is shared with minor exceptions by all living organisms

some genes involved in development are very similar all the way from insects to mammals genes from mice can cause frogs to grow eyes on their legs

developmental homology

is homology in the traits of embryos, all vertebrates

structural homology

homology at the level of developed organisms, tetrapod limbs

identifyfing homologies

how do we know whether similarities are due to common evolution? homologies assume evolution but can they be used for evidence?

the idea that many similarities are due to homology seems to explain many observed patterns

fall naturally into groups

genetic evidence and morphological evidence often agree

tetrapod evolution, whales and hippos

natrual selection

darwin’s big idea was this

natrual selection is the way adaptive evolution occurs

adaptation

organisms evolving to become better suited to their environment

includes physical environment and biological environment (competing, eating and not being eaten)

Darwin’s theory can be explained using 4 logical steps

variation, heritability, differential reproductive success, selection

if all 4 hold we expect evolution to occur

variation

the individuals that make a population vary in the traits they possess like size shape and physiological details

heritability

some of these differences can be inherited by offspring, tall people more likely to have tall offspring

differential reproductive success

in each generation some organisms leave more offspring than others

selection

reproductive success isnt random but is influenced by differences in traits like heritable traits

natrual selection

evolution by natrual selection will occur if there is

heritable variation in traits

selection(differential reproductive sucess) based on traits

fitness

darwinian fitness means an ability to do well under natrual selection, defined as average reproductive success given a suite of heritable traits components of fitness survival growth reproduction

two other models for how adaptive evolution could occur

goal directed evolution

inheritance of acquired characteristics (lamarck)

inheritance of acquired characteristics and ex

idea that individuals change in response to their environment and pass those changes onto their offspring

-giraffes reaching for food antelope running away from lions

now known that while indidvuals do often change in response to their environment such changes are not usually passed onto offspring

-sometimes this can happen but its not main wya that evolution proceeds

goal directed evolution

idea that organisms evolve towards specific goal complex multicellular organisms big brained human

if the organism is moving toward a goal it should move more or less in that direction all the time

inheritance of acquired characteristics

chop off mice tails, tails of further gen dont get shorter

evidence against goal directed evolution

vestigal traits

bidirectional evolution

finch beaks get larger then smaller birds gain then lose flying ability some organism gain complexity then lose it again

acclimation

is the ability or organisms to respond directly to their environment

DOES NOT affect the traits of their offspring

adaptation

genetic change that increases the fitness of organisms

doesn’t occur as a direct response to the environment and very slow, passed onto offsprings and dorm the basis of evolutionary change

why do we acclimate

evolved as an adaptive response because acclimation is beneficial

are responses to changed conditions always good

no, usually have been good system responses (some form of altitude sickeness due to acclimation systems going off track we do it because were programed to do it since its usually beneficial

much of adaptation is ___ between conflicting goals

compromise, brightly colored individuals are more attractive to mates and to predators larger individuals compete more effectively but are less efficient at reproducing

historial constraints

evolution proceeds by small steps

vestigial traits are often things evolution cant easily get rid of

blind spot in vertebrate eye

humans are not well designed to be upright

what evidence that species have evolved through time

fossil record, patterns of relatedness, homologies

evidence that this change is driven by natrual selection

Darwin’s logical postulates heritable variation in traits differential reproductive success based on traits

direct observations of natrual selection ( TB, finches)

experiments with artificial selection and other manipulations

natrual selection by (gradual) evolution imposes important constraints

species are not perfectly adapted

are basic traits are determined by…

genes

locus

loci, a location where a gene can occur

allele

a particular version of a gene

complex organisms usually have two alleles at each locus (can be same or different)

loci

complex organisms usually have two alleles at each locus

can be the same or different

heterozygous

an organisms with different alleles at a particular locus

homozygous

an organisms will with two copies of the same allele at a particular locus

evolution- in gene terms

heritable changes in species traits over time, driven by changes in allele frequencies

genotype

is the collection of an individuals genes

phenotype

collection of an individuals physiological and physical traits what we can observe about an individual phenotype is largely (but no means entirely) determined by genotype

simple dominance

dominat allele completely masks recessive

allele interactions

not worry about co dominance or incomplete dominance because well use complex dominance for anything thats not very close to simple dominance

analyzing genotype frequencies

make simple assumptions about how frequencies work

calculate expected frequencies under our assumptions

measure observed frequencies in the population

look for evidence of systematic not random difference between expected and observed frequencies

simple assumptions

expected frequencies are usually calculated by assuming that alleles assort randomly and independently like flipping two coins or rolling two dice

hardy Weinberg distribution

distribution expected if alleles work like coins (random and independent) p is dominant q is recessive its 2 for hetero cause you could get a from mom and A from dad or visa versa two ways to do it.

how do we know if coin is perfectly fair

you can never be sure that a coin is perfectly fair you can only evaulate your evidence that its more or less close to fair, never have evidence that a population is actually in HWE we can only evaulate how close or far it is from it

when do we expect genotype frequencies to act like coins

alleles selected at random from the previous gen

random mating within closed population

no differences in fitness between genotypes

no mutation no drift

if these hold then HWE with no change in allele frequency from gen to gen NEVER HAPPENS

Harvey Weinberg is a _____

null model it tells us what to expect if complicating effects are absent without a null model we couldn’t ask how do observation differ from expectations

if we observe large diffrences from HWE this is a sign that____

mating isn’t random or that natrual selection is operating, the analysis tells us tat something is going on but not what

Human blood groups

very close to HWE

no evidence fro non random mating or for fitness differences,, doesn’t mean its not happening but probably means that its small especially when we observe the same thing many times

at global level more homozygotes than HWE predicts cause mating isn’t random

human HLA genes

used by immune system to recognize disease causing organisms thought that heterozygous individuals would be able to recognize more bacteria and virus heterozygous levels are higher than HWE predicts

directional selection

tends to move a population in a particular direction ( giraffe necks and human brains)

multi directional selection

directional selection can change through time and with environment

swallows may get bigger during extreme old then small again through normal weather finch beaks get thicker when food is scre and smaller when abundant

stabilizing selection

tends to keep the population where it is, usually because population is already adapted, MODERATE ALLELE FORWARD

what happens if the target of directional selection stays the same for a long time

the population arrives at the target and directional selection becomes stabilizing selection (giraffe necks and human brains)

disruptive selection

favors phenotypes different from the average value

big bills may be good for big seeds and small for small in black bellied seedcrackers

prey might want to look different from there peers so predators don’t find them as easily

speciation

disruptive selection can lead to this, formation of new species

frequency dependence

disruptive selection is closely related, frequency dependence is the idea that some trait types do relatively better if they are rare

advantageous

an allele that has greater fitness than others in a particular context is called advantageous tend to increase due to positive natrual selection

deleterious

an allele that has less fitness than others in a particular context is called deleterious it will tend to decrease due to negative natrual selection

balancing selection

maintain allele diversity, when no single best allele, disruptive selection at the trait level will always cause some balancing selection

sickle cell phenotype

blood cells that can loose their shape and squash malaria paraistes

hetero get less sick with malaria

homo get too much instability and server anemia

genetic drift

change in allele frequency due to random sampling some individuals have more offspring than others due to chance events offspring receives certain parental alleles and not others

lead to accumulation of random changes in allele frequencies

likley reason why human populations have different MN allele frequencies

small populations and genetic drift

stronger than in large populations (law of averages) even if pop is big now might have been small in the past

founder effect

occurs when a new population is started by a small number of individuals

bottlenecks occur when a population becomes small then large again or when a benefits genetic mutation takes over a population

variation will be lost at that locus because the new gene is better

it can be lost at other loci at random because the whole future population is descended from individuals with the new mutations

an alle may drift to a frequency of ____ if its lost or ____ if its dixed

0 or 1

disadvantageous alleles are often but not always fixed

advantageous alleles are often not always fixed

alleles with neutral differences no selective difference will be fixed or lost at random

also true for alleles with small effects

drift tends to reduce genetic variation

gene flow

movement of alleles from one population to another

happens when individual move from one population to another and breed

how we think about gene flow depends on how we choose to define a population

gene flow can be an obstacle to speciation, helps keep population similar

mutations

heritable errors in copying DNA, by themselves don’t cause much evolution

where do new genetic sequences come from

copying errors

other organisms (lateral gene transfer)

deleterious mutations

most mutations are this, and bad for fitness

beneficial mutations

rarely, good for fitness

can complex organisms arise through random mutations

a central question of biology

large scale evolution takes a long time

benefits changes can accumulate gradually

much evidence of intermediate forms

what about sex?

doesn’t directly change allele frequencies

does bring alleles together and split them apart called recombination

not source of new alleles (depending on how we define allele but is a ource of new combo)