BIOL 1001 STUDY NOTES
Test #1
Persephone Greco-Otto
Nature of Science:
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Science = a process for understanding the world, learn about universe (understand the
natural/observable world), evidence, based on critical thinking (kriticos = discerning judgment,
kriterion =standards)
o Developed through reasoning (inferences = logical conclusions based on observable
facts), test explanations against observations of the natural world (empirical = info
gained through observation or experimentation), more than 1 scientific method,
question-hypothsis-procedure-data-conclusions, never proves/method is flexible
Superstitions  do the actions influence the outcome? Incorrect ideas, animals become
superstitious (push lever and delay before food delivered, develop strange behaviours during
the lag that they repeat and associate w/food, self-association/conditioning)
Limitations  only natural phenomena, can’t deal w/belief/faith, no moral/aesthetic
Method  observe phenomenon, propose explanation, test through series of explanation 
accurate/valid (if explanation matches what’s observed, reproduction) OR revised/alternative
explanation proposed
Pseudoscience = individuals make scientific-sounding claims not supported by trustworthy,
methodical scientific studies (statement may be true, but relationship isn’t)
Anecdotal Evidence = based on only 1/few observations, not rigorously studied, not large
enough sample size
Theory and Hypothesis  Hypothesis = proposed explanation for a phenomenon, must clearly
establish mutually exclusive alternative explanations for a phenomenon, generate testable
predictions, test empirically (rational, testable, repeatable)  self-correcting
o Alternative Hypotheses  use evidence to determine which alternatives
stronger/weaker, all ideas open to scrutiny (modify ideas as new evidence appears)
o Theory = hypothesis for natural phenomena that is exceptionally well-supported by the
data, broad explanations for a wide range of phenomena
Logical Fallacies  post hoc, ergo propter hoc (it happened after, so it was caused by…),
confusion of correlation/causation
Evidence and Proof  hypotheses and theories may be supported by evidence but not proven
Believe and Accept  subject to peer review/replication, science based on inferences based on
evidence
Function and Purpose  designed tools have purposes, structures/behaviours of living things
have functions
Primitive/Less Evolved and Advanced/More Evolved  more highly specialized seen as more
advanced, but actually based on how well they’re adapted to their environment
Cause and Chance  chance isn’t meaningless, cause is the “why explanation”
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Fact  statements that we know to be true through direct observation
Law  generalization about data and is a compact way of describing what we’d expect to
happen in a particular situation
Observation  directly made w/our own sense or indirectly through use of tools
Falsifiable  a conceivable test that might produce evidence proving the idea false
Uncertainty  uncertainty in measurement is range of values within which the true value falls
Error  difference between a measurement and the true value
Prediction  what we would expect to happen or what we expect to observe if this idea were
accurate
“Theory of Intelligent Design”  “life is too complex for everything to have developed step by
step,” became popular when “creationism” was deemed unconstitutional to be taught, all living
things best explained by an intelligent cause and not an environmental cause (no evolution)
since world is fantastical, statistical improbabilities
o Can’t identify designer, make observations, run experiments, make predictions, make
hypotheses (doesn’t fit scientific method), only end products can be observed (no
hypotheses), can’t be tested (no predictions/hypothesis, not tested/can’t be falsified),
isn’t iterative (either the universe was created or it wasn’t, clergy letter project
Evolution, Phylogenetics, History of Evolutionary Thought
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Biological Evolution = doesn’t happen among individuals (only grow + change), but over
generations (genetic change), different species share common ancestors
Mosaic Evolution = different organisms/parts of organisms don’t evolve at the same rate
Theory of Evolution:
o 2 Types of Biological Evolution
 Microevolution = changes in genetic characteristics over time, changes in gene
frequency (how common an allele is in a pop), population over several
generations + changes in gene frequency in pop, thought that it leads to
macroevolution, eg. genealogy
 Macroevolution = descent of diff species from a common ancestor, much larger
scale, more generation, derivation of new species  biodiversity, eg. phylogeny
 *if characteristic is not genetic, then it isn’t evolution (many traits
environmentally and genetically determined)
o Biodiversity = the richness of living systems as reflected in genetic variability within and
among species, the number of species living on earth, and the variety of communities
and ecosystems
 Biosphere = all regions of earth’s crust, waters and atm that sustain life
 Ecosystem = group of communities interacting w/ their shared physical
environment (biotic and abiotic)
 Community = pop of all species that occupy the same area
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Population = group of individuals of the same kind/species that occupy the same
area
 Multicellular organism = individual consisting of independent cells
 Cell = smallest unit of life
Unity/Diversity of Life: don’t know how many species on earth  little, hard to
observe/live in harsh environments that we cannot reach
 Opportunities for Diversification  movement into new environments, eg.
extinction of dinosaurs allowed for diversification (more mammals), Galapagos
finches (moved into vacated island to avoid predators/more food)
 *Intracompetition (within a species) intercompetition (between species)
 1. Large changes in environment or evolution of key adaptation
 2. Release from competition or vacated niches eg. Cambrian
explosion/radiation (soft bodied to hard bodied)  1st representatives
of current phylum
 3. Specialization  different species descended from same species take
advantage of environmental changes eg. cichlids have diff. feeding
patterns which lead to different anatomical structures
 Ecological Opportunity = key adaptations that can be exploited
 Evolution of photosynthesis  production of O2  aerobic respiration
 development of ozone layer  organisms could live closer to water
surface  movement from water to land?
 Water-Land
 Originally partly aquatic/terrestrial  preexisting traits beneficial for life
on land (developed in organisms in water)
 To avoid predation?
 Approx. 370 mill years ago
 Challenges/adaptations  no support (buoyancy in water) to gravity,
conservation of water (skin maintains water), protection against UV,
waste excretion, reproduction (external fertilization in water  eggs
developed a membrane/shell to keep from drying out), food (plants on
earth), respiratory surfaces (gills to lungs  internal to keep from drying
out, fluid to allow diffusion of gas)
 Intermediary/transition fossil of fishapod to tetrapod (Tiktaalik)
changes in structure allowed life on land (more robust joints/digits),
exaggeration of already present features, flat skull like crocodile
 Selection pressures  those better at dealing w/pressures passed on
traits
Modes of Nutrition:
 Chemoautotroph  oxidize CO2, some bacteria/archaeans, no eukaryotes
 Chemoheterotroph  oxidize organic molecule, some bacteria/archaeans,
proteins, fungi, animals, plants
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Photoautotroph  light and CO2, some photosynthetic bacteria, proteins and
plants
 Photoheterotroph  lights and organic mlcs, some photosynthetic bacteria
o Populations = same species, individuals, reproduction
o Characteristics of Model Organisms: easy to culture/grow, small, reproduce quickly,
short lifespan, mature quickly, many offspring, kept in small space, invertebrates (ethical
approval)
Phylogenetics (represent hypotheses of relationships): informative/practical, oomycetes,
identify source pops of invasive organisms, infections (trace the source)
o Systematics = branch of biology that studies the diversity of life
+ its evolutionary relationships
o Phylogeny = classification organisms based on differences and
similarities (morphology, habitat, mode of nutrition,
locomotion, DNA/protein sequence, reproduction) *not to
scale so can’t tell how closely related/time
o Taxonomy = classification of organisms into an ordered system that indicates natural
relationships
o Classification = an arrangement of organisms into
hierarchical groups that reflect their relatedness
o Taxonomic Hierarchy: kingdom, phylum, class, order,
family, genus, species
o Taxon = a name designating a group of organisms
included within a category in the Linnaean taxonomic
hierarchy
o Common Ancestor = an ancestral organism shared by 2 or more descendant organisms,
DNA testing
o Monophyletic Taxa: an ancestral species and all of its
descendants
o Paraphyletic Taxa: an ancestral species and only some
of its descendants
o Polyphyletic Taxa: species from different evolutionary
lineages
o Principle/Assumption of Parsimony: simplest
explanation is likely the best
o Linnaean System of Classification: **degree of
inclusion, relative # of organisms
 Phyla
 Family
 Genus
 Species
 Domain
o Phylogenetic Trees (show patterns of descent):
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Speciation (nodes)  point in time where ancestral group split into 2 or more
descendant groups
 Termina  ends of branches, species can be extant/extinct
 Common Ancestors  shared common ancestor at bottom (most inclusive end)
 Unique vs. Shared History
 How Parsimony is used to construct phylogenetic trees  most optimal
phylogeny is the one that requires the least evolutionary change to explain the
data
History of Evolutionary Thought:
o Biogeography = the study of geographic distributions of plants/animals
o Plato  perfect creatures already exist (no evolution)
o Aristotle  scala naturae (no vacancies, no evolution, ladder of life)
o Linnaeus  binomial nomenclature, study nature to better understand Creator’s plan
o Cuvier  fossil evidence
o Catastrophism = theory that Earth has been affected by sudden, violent events that
were sometimes world-wide in scope
o Wallace  used biotas (all organisms living in a region) to define 6 biogeographic
regions
o Darwin’s Development of Evolutionary Hypothesis:
 Influences:
 Buffon  organismal differences related to environments inhabited
 Lamarck  species change through time, life evolved “upward into
higher” forms, simplest life forms, use and disuse (larger/stronger
w/use) – “inheritance of acquired characteristics”
 **both suggested populations are changing, importance of variation in
natural populations
 Lyell (Uniformitarianism)  geologic processes that shaped Earth’s
surface over long periods of time are the same processes as today 
led to idea that species are gradually and constantly changing
 Hutton (Gradualism)  Earth and its living systems changed slowly over
its history
 Thomas Malthus  economist, pop grow geometrically (exponentially),
but food supplies grow arithmetically *scarcity of food = competition
 ***competition for resources means that not everyone
survives  those w/FAVOURABLE TRAITS SURVIVE
 **Variation within populations is important
 **BIG changes can occur very gradually over long periods of time (accumulation
of changes)
 5 Observations
 Most organisms produce more than ½ offspring
 Populations do not increase in size indefinitely
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Food/resources limited for most populations
Individuals within populations exhibit variability in many characteristics
Many variations have genetic basis that is inherited by subsequence
generations
 2 Inferences
 Individuals within a population compete for limited resources
 Hereditary characteristics may allow some individuals to survive longer
and reproduce more than others
o ***a population’s characteristics will change over the
generations as advantageous, heritable characteristics become
more common
 Observations/explanations of phenotype/morphology on islands compared to
mainland
 2 ways that evolution can be observed today
o Natural Selection and Cell Theory (2 unifying concepts of evolution):
 Theory of Evolution by Natural Selection = characteristics of a pop change over
time, spp related by common ancestry (descent w/modification), individuals
w/certain heritable traits produce more offspring than those without traits *all
spp related by descent from a common ancestor and come from pre-existing
spp.
 Cell Theory = all organisms made up of cells, all cells come from pre-existing
cells *all single-cell organisms in a pop related to 1 common ancestor, all cells in
multicellular organisms descend from 1 ancestral cell
 **both have patterns, both are 2 unifying concepts of biology, all species are
related through descent to a common ancestor
Evidence for Evolution
o Fossil (any trace of an organism that lived in the past)  show extinction, spp change
over time; descent w/ modification (eg. finches on Galapagos islands, all diff spp very
closely resembled the 1 spp on mainland)
o Island Chains = spp disperses from mainland to new island (if
succeeds may give rise to several new spp as pop spread to
neighbouring islands)
 How?  rapidly buried by sediment which slows decomposition (if no
decomposition = intact/compression fossils, if decomposed =
cast/permineralized fossils)
 Incomplete, 2 Bias  only represents a fraction, needs the right conditions at
right time for fossilization
 Limitations  habitat (organisms that burrow, swampy areas),
taxonomic (hard bodied more likely, pollen), temporal (more recent
more common, plate tectonics [cause deformation]), abundance (higher
pop, more widespread, older species)
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 Certain locations of fossils make them more likely to be found
Transitional Fossil  fossils show intermediary species
Vestigial Traits = an anatomical feature of living organisms that no longer retains its
function
Radiometric Dating = dating method that uses measurements of certain radioactive
isotopes to calculate the absolute ages in years of rocks and minerals
Continental Drift/Plate Tectonics 
Background Extinction = ongoing standard
rate of extinction
Mass Extinction  99% of all species that
have ever existed are now extinct, caused by
catastrophic events (continental drift
[originally 1 continent “Pangaea” that split]
convergent boundaries)
 Breakup led to speciation/diversity
Endemic Species = a species that occurs in
only one place of earth
Dispersal = the movement of organisms away
from their place of origin
Homology vs. Convergent Evolution
 Convergent Evolution = evolution of
similar adaptations in distantly related organisms that occupy similar
environments
 Homology = characters that are similar as a result of common ancestry
 3 levels of homology:
 Structural (anatomical similarities)
 Developmental (developing embryos go through similar stages)
 Genetic (molecular homologies, DNA sequence similarity of genes from
different spp, developmental sequences + adult structures CAN’T be
homologous in diff spp UNLESS their genes are similar)
 Descent with Modification + Homology
 Nested pattern of homology
o Genetic code = homology shared by all species
o More recent homologies  shared by smaller groups of
organisms
o Anatomical homologies are reflected in mlc homologies
 Homoplasious Traits = characteristics shared by a set of spp, b/c they live in
similar environments, but not present in their common ancestor; often the
product of convergent evolution
Artificial Selection = selective breeding of plants/animals to ensure that certain desirable
traits appear at higher frequency in successive generations
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Evolutionary Developmental Biology (evo-devo) = field of biology that compares the
genes controlling the developmental processes of different animals to determine the
evolutionary origin of morphological novelties and developmental processes; how
evolutionary changes in genes regulating embryonic development can lead to changes
in body shape/form
o Genetic Tool-Kit (homeotic genes) = regulatory genes that code for transcription factors
that bind regulatory sites on DNA  activating/repressing the expression of genes that
contribute to an organism’s form
 All living animals inherited them from a common ancestor alive then
 Hox genes control overall body plan
 Pax-6 gene triggers formation of light-sensing organs
o Developmental Regulatory Genes/Genetic Switch Between Different Morphologies
 Small genetic changes account for large changes in characteristics of organisms
that lead to different/new morphologies
*****GENE SWITCHES?
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