Test 1

BIO 1M03 up to midterm

logically equivalent

logically equivalent

statements that express same fact in different words; if one is true other has to be true as well

How to test logical equivalence

example where one is true and one is false, what would it take for both to be true, what would it take to falsify each statement, parallel example to relate to?

Cell

highly organized compartment bounded by membrane

Genes

made up of DNA, hereditary; passed down from parents to offspring to determine characteristics

DNA

Double helix that carries information in forms of nucleotides in the cell nucleus

Proteins

Macromolecules made up of amino acids in a polypeptide chain

Amino Acids

Building blocks of proteins

Where do cells come from?

Come from other cells by growing

Maggot Experiment

three jars. One is sealed, one has mesh, one is open. sealed and mesh did not grow maggots, open did. sealed jar was a control. Some concerns of this are that: maybe not identical meat, increase sample size (not just three jars)

Hypothesis

proposed explanations of facts

falsify

tests to try and prove hypothesis is false. most hypothesis cannot be proven to be true so we attempt this and if we fail, then the hypothesis is supported

Mice and Vitamin C experiment

one mouse raised on a vitamin c diet. issue with this is that it is only one mouse, not enough replication to test if this works, also no control group

controlled

two or more groups that differ only in some factor we want to study, this factor must be as small as possible

replication

each treatment has more than one replicate (unit which is subjected to experiment)

independent

replicates in one group should not share ANYTHING in common that they don’t share with other group other than factor being studied

randomized

units are assigned to treatments randomly

observational studies

look for ways to collect data that will support or challenge hypothesis, don’t make conclusions off of this. we only do them to: see if it’s worth the experiment, what experiments must be done, and if it is even ethical to do so

Dinosaurs

we can’t say for sure what killed the dinosaurs as we cannot do it as an experiment again. we would need 10 earths, with the same species on each one, 10 meteors; its just impossible to replicate

evolution

species have changed through time, replaced the idea of special creation

special creation

each species is unique and was made by god

fossil

physical trace of organism that lived in the past, can be dated using radiographical equipment, they have information about history of life

fossil record

collection of all known fossils

extinction

fossils left by organisms that are no longer around, evidence that species are changing

transitional forms

when one species disappears from fossil records, another often emerges, often happens in same geographical area. (fish → salamander)

vestigial traits

trait that has no function but is similar to functional traits in related species: wisdom teeth, tailbone, tonsils, wings of flightless birds, appendix

examples of directly observed evolution

ground finches → beak change right away populations diverging

TB → treatment worked well in labs but not irl because some became resistant

TB evolution

by the time tb disease becomes apparant, there are usually many millions bacteria in the lung

resistant

pathogens, especially bacteria that no longer responds to the treatment negatively, and if there are many they will replace the sensitive population

sensitive

pathogens, especially bacteria that cannot withstand treatment and die

relationships bw species

if we all evolved from one ancestor, we expect to see evidence that they are related to each other (mammals, flowering plants, etc.), geographic patterns, homology

geographic relatedness

species that seem to be closely related that live very close by, we expect this with species that evolved independently

homology

similarity that is due to common ancestry

genetic homology

homology on the level of genetic coding, pretty convincing, genetic code is shared bw all living organisms

developmental homlogy

homology in traits of embryos, embryos of all vertebrates show similarities

structural homology

homology at level of developed organisms: very similar build of limbs bw organisms that look nothing alike

identifying homologies

homologies can assume evolution, and explain many other observed patterns. when two similar organisms don’t tell the same story, they’re probably not homologous

natural selection

the way adaptive evolution occurs, evolution will occur if there is heritable variation, and selection

adaptation

organisms evolving to become better suited to their environment (tricky as environments keep changing) physical and biological environment

darwins theory in four steps

variation, heritability, differential reproductive success, selection

variation

individuals that make a pop vary in traits they possess (size, shape, physiological details)

heritability

differences inherited by offspring (tall parents more likely to produce tall offpring)

differential reproductive success

in every gen, some organisms leave more offspring than others, fecundity

selection

reproductive success is not random, influenced by differences in traits, including heritable traits

fitness

in biology, it means the ability to do well under natural selection, average reproductive success. 3 basic components: survival, growth, reproduction

inheritance of acquired characterisitics

idea that individuals change in response to their environment and changes pass to their offspring (giraffes reaching for food) but this is not possible

goal-directed evolution

idea that organisms evolve towards specific goals, complex multicellular organisms “with a purpose” “the destination”. some evidence against this is vestigial traits, bidirectional evolution: finch beaks get larger then smaller then again. some gain complexity then lose it

acclimation

ability of organisms to respond directly to environment, does not affect offspring. eg: temperature at birth decides how many sweat glands you would acclimate

why do we acclimate

better chance of survival means better chance of offspring, evolved bc its beneficial, so in a way it’s adaptation. we were programemd to do it bc it’s usually beneficial

tradeoff

compromise bw conflicting goals. brightly coloured birds more attractive to mates, but more visible to predators

historical constranits

small steps, vestigial traits, humans not designed to stand upright as we evolved from 4 legs, blind spot in the eye is just so complex that it would take too long to take it away

where does heritable variation come from?

genetics

genes

basic traits determined by this (A1A1, A2A2, A1A2)

locus

location where a gene can occur. usually 2 alleles at each one, same or different

allele

particular version of gene (A1, A2)

heterozygous

organism with different alleles at particular locus

homozygous

organism with two copies of same allele at particular locus

evolution

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

genotype

collection of individuals genes

phenotype

collection of physiological and physical traits caused by genes

peppered moths

individuals w A1A1 phenotype are light coloured, A2A2 are dark coloured, so A1A2 must be either dark due to dominance or codominant and be grey

dominant allele

usually darker, will take over traits

reccessive allele

will let itself be taken over but will “lurk” in the background of genetics until possibility to show up

simple dominance

dominant allele takes over recessive allele

complex dominance

anything that isn’t close to simple dominance (red and white make pink)

expected frequencies

calculated frequencies based on assumptions, average of what is expected under assumptions, conceptual average over what would happen if we did the same experiment many times

observed frequencies

measured frequencies in population

handy weinberg distribution

distribution expected if alleles work like coins, A1A1=p², A2A2=q², A1A2=2pq

Hardy weinberg equilibrium

alleles selected at random from prev gens: random mating, closed pop, no genetic mutations, no diff in fitness, if held exactly, we get this. no change in allele frequencies from gen to gen. this NEVER happens so we look at values when very close

Differences from HWE

If we observe large differences from HWE, this is usually sign that mating is not random and that NS is operating, tells us that something but not what is going on.

null model

HWE is an example of one; tells us what to expect if complicating effects are absent. w/out it we couldn’t ask how do observations differ from expectations

Human blood groups example

MN blood groups in different human pops are very close to HWE; does not mean it is happening, just that it is a small population

Human HLA genes

these genes are used by immune system, to recognize disease-causing organisms. researchers hypothesized that heterozygous individuals may recognize more pathogens. data shows that more ppl are heterezygous for HLA genes than would be expected under HWE (bc it’s not random)

Types of natural selection

trait level and allele level

Trait level NS

directional selection, multi-directional selection, stabilizing selection, disruptive selection

directional selection

type of trait-level ns, tends to move pop in particular direction: complex human brains are the target, so we moved in that direction

multi-directional selection

type of trait-level ns, can change through time with the environment, need to know whether changes are heritable: finch beaks get thicker when food is scarce, smaller when abundant. Small beaked have advantage bc they can process seeds faster, reach smaller spaces, less energy to produce small beak

stabilizing selection

type of trait-level ns, tends to keep population where it is because usually pop is already adapter: mortality rates for differently sized babies vs the “mean” value of baby size survival

disruptive selection

type of trait-level ns, favours phenotypes different from the average value, can lead to speciation: black-bellied seedcrackers have different types w different bill sizes, not many medium-sized beaks

speciation

the formation of a new species, can happen due to disruptive selection

frequency dependence

type of trait-level ns, closely related to disruptive selection, idea that some trait types do relatively better if they are rare

Allele-level NS

positive/negative, balancing

positive selection

type of allele-level ns, allele that has greater fitness than others in particular context will tend to increase

advantageous

allele w greater fitness than others in particular context

negative selection

type of allele-level ns, allele that has less fitness than others in particular context will tend to decrease

deleterious

allele w less fitness than others in a particular context

Balancing selection

tends to maintain allele diversity when there is no best allele. disruptive selection at trait level will always cause some of this. can be caused by heterozygous advantage when they have higher fitness bc XY + XY = XX + YY + 2XY

Sickle Cell Phenotype

blood cells that can lose their shape and kill malaria parasites, ppl heterozygous for this trait get less sick w malaria, ppl homozygous have too much instability and severe anemia: heterozygous advantage

alleles and traits

most measured traits depend on many alleles from many loci, changes at one locus can affect selection at another

Other evolutionary mechanisms

genetic drift (small pop (founder effect, bottleneck), fixation and loss), gene flow, mutation, mating patterns

Genetic drift

type of evolutionary mechanism. change in allele frequencies due to random sampling, some individuals have more offspring than others due to chance events (nothing to do w heritability), offspring get some parental alleles but not others. these factors can lead accumulation of random changes in allele frequencies. likely reason why human pop has different MN frequencies

Small populations

type of genetic drift in evolutionary mechanisms. drift is much stronger in small pops than large ones, even if large now, was probably small in the past. Founder effects and bottlenecks

founder effects

type of small pop genetic drift in evolutionary mechanisms. new populations started by small number of individuals: tiny moth population flies over the hill and begins a population there by breeding withing new pop

bottlenecks

type of small pop genetic drift in evolutionary mechanisms. population becomes small (could be due to natural disaster) and then big again, frequency of alleles changes. also when beneficial genetic mutation takes over population, variation is lost bc new gene is better, directional selection on trait

fixation and loss

type of genetic drift in evolutionary mechanisms. may drift to frequency 0 (lost) or 1 (fixed)

Fixed

type of genetic drift in evolutionary mechanisms. advantageous are often this, and are positive selection

lost

type of genetic drift in evolutionary mechanisms. disadvantageous are often this, and are negative selection

neutral differences

alleles with this will be fixed or lost at random, true for alleles w small effects

Gene flow

type of evolutionary mechanism, movements of alleles from one pop to another, begs the question “how do we define a population?”. happens when individuals move from one pop to another to breed, helps keep populations similar, obstacle to speciation.

mutations

type of evolutionary mechanism. heritable errors in DNA replication, rare by themselves and don’t cause much evolution. mutations are extremely important bc they provide the variation in which ns acts, the only source of new alleles

types of mutations

DNA base change, chunks of DNA added or subtracted, whole genes duplicated, copying errors, lateral gene transfer