BISC 1008: UNDERSTANDING ORGANISMS THROUGH SERVICE PROF. SCULLY
MIDTERM 1 NOTES
IMPORTANT NAMES IMPORTANT TERMS IMPORTANT CONCEPTS
The Nature of Science and the Characteristics of Life:
1. Science is a collection of facts.
a. Science is a search for explanations about the natural world.
b. Science is fluid.
c. Scientists rely on 3 pillars: order, explain, achieve.
2. Scientists are always right and are unbiased.
a. Scientists are limited by the current technology (human error).
3. Science is a foreign language.
a. Hypothesis: an educated guess
b. Theory: supported, very hard for a hypothesis to become a theory. It takes many years of work to make a hypothesis a theory.
If you want to learn more check out English reformation is a series of what?
i. Scientific terminology is used in a different context in common language. ii. The media often mixes up words.
iii. Public often comes up with their own terminology which conflicts with the scientific definition.
Andrew Wakefield: British medical researcher. His study, based on 12 children, linked childhood vaccines to autism, which ‘caused’ the public opinion that vaccines cause autism. He is accused of fraud and lost his license.
What is another reasonable explanation for an increase in autism rates? • 1990s: a new scheme of autism (before you were either autistic or not) • New definition:
o A range of complex neurodevelopment disorders characterized by
▪ Social impairments
We also discuss several other topics like In astronomy, the sun is a star at the center of which system?
▪ Communication difficulties
▪ Restricted, repetitive, and stereotyped patterns of behavior
Why should biology matter?
• Awareness and appreciation of other organisms (we couldn't survive without them) • Important decisions of life (issues dealing with biology arise daily)
• Allows for creation of new technology
The Scientific Method:
• Purpose -> Research -> Hypothesis -> Experiment -> Analysis -> Conclusion
A hypothesis can be tested; Don't forget about the age old question of What is the definition of lithification?
• Through observational studies.
• Scientists use statistics to estimate the
reliability of data.
• Through experimental studies.
• Experimental/treatment group:
o Dependent variable: the variable
being tested. It depends on the
o Independent variable:
the variable that is changed or
controlled in a scientific
experiment to test the effects on
the dependent variable.
• Control group: the group that does not receive treatment by the researchers and is then used as a benchmark to measure how the other tested subjects do. Don't forget about the age old question of How does the market overcome shortages and surpluses?
Why do different studies conflict with one another?
• Very commonly occurs
• Too many variables
o Genetics, Age, Environmental conditions, past heath issues, current health issues, stress, life, etc.
Limits to the Scientific Method:
• Useful for studying the natural world
• Scientific analysis cannot:
o Make moral judgements: Although information leading to those judgements may be based on scientific information.
o Prove or disprove faith-based beliefs
o Determine personal aesthetic values
Characteristics of Life: Don't forget about the age old question of What is the function of a slope?
What is the unit of life?
• Organism: An individual unit which contain all the characteristics of life.
All of life contains DNA (some viruses only have RNA.) From that DNA, we can reproduce, develop, and grow.
Cellular and Utilize DNA:
• Organisms are composed of cells.
o First organisms were single cells.
o Prokaryotes are single cells.
• Cell is the basic unit of life.
o Self-contained units.
o Multicellular organisms made of different, specialized cells.
• Living organisms reproduce or replicate themselves.
• Single-celled organisms
o Produce two genetically identical cells.
• Multicellular organisms
o Variety of ways.
o Both asexual and sexual. If you want to learn more check out In the human variation, what is heritability?
• Genetic material
o Passed from parents to offspring
o DNA: deoxyribonucleic acid
▪ DNA as a blueprint:
• Organisms grow and propagate themselves.
• Organisms develop and grow in complexity.
Reproduce, Develop, and Grow:
Acorn -> Seeding -> Sapling -> Oak Tree
Capture, Storage, and Use of Energy:
Collect energy form their environment, use energy to grow and develop. • Producers: use sunlight to create their own food
o Capture suns energy via photosynthesis
o Convert sunlight to chemical via photosynthesis
• Consumers: use chemical energy form other living organisms
o Consume plants or animals
Sense and Respond
Maintain Internal Conditions:
Sense and respond to internal conditions.
Homeostasis: the ability to maintain a constant internal environment in response to environmental changes.
• Maintaining internal conditions (ex: drinking water)
• Humans maintain body temperature (98.5°F)
Every Organism Evolves:
Individual organisms change rapidly
• Growth of individual
o A seed becomes a tree
Groups of organisms change slowly
o Group of interbreeding organisms
o Produce fertile offspring
• Evolution: one does not matter if they don’t reproduce
o Characteristics of a species/ group changing over time
History of Life:
Big Bang: The Big Bang occurred
approximately 13.7 billion years ago. The
universe started out as an atom. Followed
by an explosion, it has been expanding
• Earth formed 4.6 b years ago.
• Life on earth formed 3.8 b years
The 24-hour model of the geologic time:
Notice the evolution of humans at 1 min
17 sec before midnight. Oldest known
rocks contain carbon (organic matter)
hinting at life = 3.8bya but cell-like
structures called stromatolytes 3.5bya
Life is grouped: grouped based on characteristics
• Broad levels: general features are similar
o Domains of life (above kingdoms)
• Narrow groupings: all features are similar
o Species, genes, class
• Evolutionary trees depict these relationships and the progression of evolution over time.
3 Domains of Life:
Prokaryotes: (cell structure) Informal label for Bacteria and Archaea. (organisms that are not in the domain Eukarya)
• Single celled
• Reproduce asexually only
• Resemble the more ancient forms of
• Have many nutritional strategies (both
producers and consumers) (can use
CO2 to make food or light energy etc.)
• Pathogenic relationships
• More advanced cell feature
• Not pathogenic
• Extremophiles (extremely strange
habitats, for example, super
• Weird metabolism
• Roughly 2.8 bya, a group of bacteria evolved a type of photosynthesis that releases oxygen as a by-product.
• Use of O2 = complex cells called Eukaryotes
• Complex cells + more O2 = multicellular life
o Organelles formed within these cells (little cells within bigger cells, each have a different purpose e.g. protein function)
• More oxygen= extinction!! Many of the organisms that lived by that time were not exposed to O2. Unlike us, the O2 in the air caused these organisms to go extinct.
• Prokaryotes: Bacteria, Archaea
• Eukaryotes: Protists, Plants, Fungi, Animals
In the old way, organisms were classified based on appearance. That is why the classification of protists is wrong!
• Larger cells - more complex cells
• Eukaryotic, which means they have a nucleus.
• Build more sophisticated molecules
• Asexual and sexual reproduction - chosen based on the environment • More complex energy production
o Zooplankton (consumers)
o Phytoplankton (producers)
o Plasmodium (pathogens)
The Protista is not a natural grouping; it is a catchall label for groups whose evolutionary relationships are still being sorted out.
The first multicellular organisms: 650 mya in the oceans.
540-490 mya: major increase in fossils b/c of Cambrian exp. (Extinction allows for species to form new organisms) (Adaptation- sexual rep.)
Colonization of Land:
1. Green algae
2. Fungi - could have a relationship with algae, very resilient cells.
3. Amphibians – the first definite fossils of terrestrial animals are of spiders and millipedes and date from about 410 mya. We don't see animals until enough resources (plants) made it to the land. About 500 mya, descendants of green algae were the first organisms to colonize barren land. These early terrestrial colonists had few cells and a simple body plan, but from them land plants evolved and diversified greatly by the end of the Devonian.
• Multicellular with some exceptions
• Producers with some exceptions
• Asexual and sexual reproduction
o CO2 build up
o Runoff - agricultural issues
• Single-celled or multicellular
• Rigid cells:
o Chitin is made of glucose and very strong to help protect the cell
o Allows the threads of fungi to easily penetrate the ground.
• Naturally produce antibiotics
• Consumers: fungi are absorptive heterotrophs that digest organic material outside the body and absorbs the released molecules.
• Fungi are more closely related to humans than to plants.
• Fungi are the key decomposers on land.
o Fungi recycling nutrients by breaking down leaf litter and dead organisms into inorganic chemicals, which are used by other organisms to produce food. o About a hundred different species of fungi live on and in the average person. The richest fungal gardens? Our feet. Researchers found 60 different species in toe clippings and 40 in swabs between the toes. The great majority are harmless. • Fungi infections are difficult to treat. Not all are harmful.
Animals: The most plentiful group of animals is Arthropods.
• Super diverse
• No cell wall - more flexible cells
• Ingestive consumers
• Body plans
o Making something big
▪ Organ system
o Specialized areas
Levels of body organization: cell -> tissue -> organ -> organ system Animals can be organized into groups based on body plans.
What forms of life existed at this point?
There were many attempts and many failures/ Success has common features.
History of Evolutionary Thought:
Charles Darwin: (1809-1882)
He dropped out of med school and traveled to the Galápagos Islands (Voyage of the Beagle.) He collected many kinds of birds from the islands. Galapagos birds that Darwin brought back, were, in fact, twelve separate species of finches.
• All life is linked through a common ancestor (Descents with modification) • Populations of living things change with time
• The environment influences this change
• So that advantageous traits are selected over less-advantageous traits (natural selection)
Alfred Wallace: (1823-1913) Darwin’s compatriot Alfred Wallace had been studying the diversity of related species living on the many different islands of the Malaysian archipelago, and he independently arrived at the same conclusions as Darwin.
Natural Selection: How does it work?
Observation 1. Fertility and exponential growth,
Observation 2. Stable with seasonal fluctuations,
Observation 3. Environmental resources are limited,
Inference 1. Struggle to survive, few do,
Observation 4. No two individuals are exactly alike,
Observation 5. These differences are heritable,
Inference 2. Heritable traits give better reproductive and survival success, Inference 3. Populations change over time.
Mechanism of Evolution:
What is changing?
DNA is changing within a population
• Physical/ behavioral characteristics = gene
• Genetic Variation:
o Increase, decrease, appear, disappear
▪ New allele can be brought into a population from another and disappear: mutation can generate new allele, and natural selection.
Evolution fundamentally involves genetic change in the population.
• All the variation in the population = gene pool
o Presence and proportion (%) of characteristics within a population.
▪ Due to individuals bringing alleles into a population from another and disappear, mutation can generate new allele, and natural selection
Genetic Basis of Evolution:
• a1, a2, a4
• Dark skin
• Light skin
• All the genetic variation that exist in the
Many genes can produce a trait such as body coloration, and each gene often has many alleles or variants. Each individual in a population, however, can possess only two alleles for each gene, one allele inherited from its mother and one inherited from its father. The two frogs in the figure both have maternal and paternal copies of chromosome 3 that house genes for coloration. The chromosomes of the two frogs will differ, however, in the allelic variants they have of these genes. For example, the frog with dark coloration may possess alleles a1 and a2 of a chromosome-3 gene that codes for coloration, whereas the light-colored frog may possess alleles a2 and a4 of this same gene.
• increase light skin
• increase dark skin
(a) The change in environment divides the single
frog population into two populations, separated
by the barren terrain. The two frog populations
now have different environmental pressures,
such as the kinds of predators each faces, and
they no longer interbreed; after many
generations their coloration diverges as they
adapt to the different pressures.
Four Mechanisms for Evolution:
Evolution causes change in allele frequencies in four ways, all of which can occur during overlapping time periods.
o Mutations are random events.
o Ultimately, all variation comes from mutations/genetic recombination. o Mutations can be harmful, beneficial, or neutral.
▪ Ex: DDT being sprayed on a NY beach in the 40s to kill mosquitos.
Resistance to DDT in mosquitos is caused by single mutation.
2. Gene flow:
o Gene flow exchanges alleles between two different populations
▪ New alleles being introduced
▪ Alleles being removed
• Ex: migration of an Aa bird to a population that only has AA type birds. 3. Genetic drift:
o Chance events leading to differences between individuals in reproduction or survival within the population
▪ Not based upon any characteristics of individuals
▪ Due to;
▪ Ex: First Generation Flowers: AA, aa, AA, Aa, aa
Second Generation Flowers: AA
▪ Ex: The disappearance of a pink flower through
generations because of chance events, only some plants
are able to produce offspring. This causes the frequency of
an allele to reach 100% in two generations.
o Establishing a new population:
▪ Ex: Founder Effect: the reduced genetic diversity that
results when a population is descended from a small
number of colonizing ancestors.
▪ Ex: Bottleneck Effect: Population bottlenecks occur when a
population's size is reduced for at least one generation.
▪ May reduce genetic variation. (larger effect on small
▪ Fixation: neutral, harmful, or beneficial
▪ Increase extinction
4. Natural selection:
o When individuals with favorable traits have a higher reproductive rate. o Three types:
1. Directional selection: When an extreme phenotype is favored over other phenotypes, causing the allele frequency to shift over time in the direction of that phenotype.
2. Stabilizing selection: when genetic diversity decreases and the population mean stabilizes on a particular trait value.
3. Disruptive selection: when extreme values for a trait are favored over intermediate values. In this case, the variance of the trait increases and the population is divided into two distinct groups.
Natural Selection Can Act on Any Trait That Has A Genetic Basis:
• Behavioral Adaptations: Weaver ants collaborate to pull nest leaves together. • Developmental Adaptations: Nemoria arizonaria. N. arizonaria caterpillars differ in appearance depending on what they feed on—the flowers or leaves of oak trees, but they are the same species of moth.
• Structural Adaptations: The flowers of some orchids have evolved to look strikingly like the females of a wasp species that can be found flying in the area. The match is so good that the orchids can achieve pollination by being “mated” by a fooled male wasp.
Sexual Selection: (a form of natural selection)
■ Sexual dimorphism
■ Females place selective pressure on males
– Peacock’s feathers: The peacocks with the showier feathers are able to attract mates, so they are the ones that have offspring.
– Lion’s mane: Mane darkness indicates nutrition and testosterone and influences both female choice and male-male competition. Mane length signals fighting success and only appears to influence male-male assessment.
Human Mate Selection:
What do men look for in a female mate?
(Makeup and facial reconstruction)
What do women look for in a male mate?
o Large jaws
o Prominent brows
o Indicative of health
Evolution Does Not Craft Perfect Organisms!
What constraints exist?
• Survival and reproductive trade-offs
Natural extinction is the result of a specie's inability to adapt to adverse changes in the environment.
Evidence Supporting Evolution:
Six lines of evidence provide compelling support for biological evolution:
• The earliest horses had four toes.
2. Traces of evolutionary history
o Pharyngeal slits exist in sea lamprey, pond turtle, chicken, domestic cat, and humans.
• Homologous: Of or referring to a characteristic shared by two groups of organisms because of their descent from a common ancestor
o Humans, whales, and bats have bones from the same origin.
• If no utility then selection may work against characteristic. Vestigial organs are reduced or degenerate parts whose function is no longer needed
• Convergent Evolution: Similar environmental pressures led to similar adaptations.
• Analogous vs. homologous: Analogous is the wings of two animals. Homologous is the bone structure in those wings.
3. Similarities and divergences in DNA
o Humans are more similar to rhesus monkeys than to moths, but all descended from a common ancestor.
▪ Ex: Darwin’s Birds
4. Direct observations of genetic change in populations
o Artificial selection is the process by which only individuals with certain inherited characteristics are allowed to breed e.g. dog breeds.
o Artificial Selection: selecting for our needs e.g. farming crops and domesticated animals.
5. Geographic distribution of organisms and fossils
• Continental Drift: Portions of the supercontinent Pangaea began to drift apart about 200 million years ago.
o The lungfish existed before the break up of Pangaea.
o Representatives of the lungfish are all over the worl.d
6. The present-day formation of new species
o Rapid evolutionary change due to environmental conditions
o Harsh conditions drive changes in the population
o Changes can be seen in our time
• Evolution in Action:
o Medium ground finch in the Galapagos
o Changes in beak and body size correlate with rainfall over time
The “Ever-Changing” Tree of Life:
Domain Bacteria = Kingdom bacteria
Domain Archaea = Kingdom archaea
Domain Eukarya = Kingdom Protista, Plantae, Fungi, Animalia
How do prokaryotes evolve?
• Sex: exchange of genetic information
• Conjugation: connection and exchange between living bacteria
• Transformation: DNA taken up from environment o Can produce
▪ Pathogenic strains
▪ Antibiotic resistant strains!
• They can have mutations but they also can have sex…
• Transduction: exchange of DNA through infection by phages (viruses)
Name a human intervention that is affecting the formation of species around the globe. • Deforestation, air and water pollution, etc.
What are species?
The word is commonly applied to members of a group that can mate with each other to produce fertile offspring, not all species can be defined by their ability to interbreed. (For example, many species, including all bacteria, reproduce asexually.)
Classification: identifying the group to which an organism belongs (relative through evolution). Based upon homology (features evolving in a common ancestor).
Identifying is very important!
Morphological species concept: is separate and distinct group of organisms by the unique set of morphological characteristics.
• Have the same physical traits you are grouped together. Moths and butterflies. Biological species concept: is a group of populations that can interbreed with one another but are reproductively isolated from other such groups. (any individual that can reproduce is considered in that group, and cannot reproduce with an individual form another group) Those who asexually reproduce are not included.
Genetic Species Concept: Group of organisms that may inherit characters from each other (sex), has a common gene pool (similar DNA composition), is a reproductive community that forms a genetic unit.
How to study the evolution of groups of organisms?
• Developmental characteristics
• Physical characteristics
• Genetic characteristics
• Behavioral characteristics
What is their product?
• An evolutionary tree
o Ancestral lineages are shown to change along a line
o At each branching point (node) a group splits off
o Each ancestral lineage evolves new characteristics (shared derived features)
Speciation: Generating Biodiversity
Speciation is the process in which one species splits to form two or more species that are reproductively isolated from each other.
o Different selective pressures/mechanisms of evolution
o Reproductive isolation prevents gene flow
▪ Prezygotic barriers prevent fertilization or the formation of a zygote.
▪ Postzygotic barriers prevent zygotes from developing into healthy and fertile offspring.
Geographic Isolation: Easiest path to reproductive isolation/preventing gene flow. The distance required for geographic isolation to be effective, varies from species to species aka allopatric speciation (when two species change and if they are introduced to one another.) (e.g. rising sea levels)
Prezygotic Barrier: mating is prevented
1. Temporal isolation: mating, feeding, being active
2. Ecological isolation: your habitat will dictate whether you will interact or not survive. 3. Behavioral Isolation: different mating dances and sounds.
4. Mechanical isolation: when genitals don't fit together (snails).
5. Gametic isolation: sperm and egg can't get together to infuse to create a zygote.
Postzygotic Barrier: what offspring will do survive or die, prevents offspring form being healthy. Zygotic death: most hybrid offspring do not survive
• Hybrid is infertile
• Hybrid breakdown
A horse and a donkey may produce a hybrid, sterile offspring, a mule.
Pace of Evolution:
When does speciation occur?
Due to geographical isolation
• Allopatric speciation
o Ring species
Without geographic isolation
• Sympatric speciation
Under some circumstances, speciation can occur without separation!
Ring species: (result of geographic isolation) can develop when populations loop around a geographic barrier in which populations at the two ends of the loop are in contact with each other, yet individuals from these populations cannot interbreed.
Plants: Genetic tricks!
• Rapid change in chromosome number = polyploidy
Occurs in animal species as well!
Rates of Speciation:
• Rates vary in different organisms
• Speciation occurs when gene flow stops and reproductive isolation occurs
• Evolution doesn’t have a goal – no perfect being
Gradualism: small changes accumulate over long periods of time
resulting in large changes. (if occurring slowly)
• Evolution is a slow, gradual process.
• Many small changes accumulate over long periods of time
to give large changes.
Punctuated equilibrium: long periods of no change interrupted by
periods of fast changes.
When a group of organisms expands
• to take on new ecological roles
• to form new species
• reduction in competition (Elimination of species in the competition.) • new adaptation that enables it to use its environment in new ways
Microevolution: Small-scale changes
• Mutation: (process of producing something new.) any change in the DNA sequence • Gene Flow: allows for groups to become similar over time. migration of individuals which changes the genetic variation of the population
• Genetic Drift: not purposeful like catastrophes. random events that kill off individuals or allow individual to breed.
• Natural Selection: differential survival and reproduction of individuals with favorable traits.
Large-scale changes – new species!
• Is the variation that has occurred changed the population so that they can no longer mate with the original population?
• How can mating be prevented?
• Limitations: asexual organisms are not included in this description.
What is causing the reproductive isolation?
1. Ecological isolation: different habitats. Can live in different habitats over time. Frog species instead of blending into green leaves, blend into woods.
2. Temporal isolation: different timing of mating/eating/etc. Timing is different (applies to human reproduction too, not fertile forever)
3. Behavioral isolation: display/acts which attract a mate. Different mating calls.
4. Mechanical isolation: physical structures don’t fit. Had to be some crucial mutation and reproductive parts don’t fit together.
5. Gametic isolation: egg and sperm physically don’t fit. Cells cant fit together.
Zygote death: viability of the zygote. To form the zygote, you have to have identical DNA. Zygote can form but can die later (typically because DNA don't match)
Hybrid Performance: hybrid infertility and breakdown. When you have an offspring, even if they grow up to be an adult, they cant produce their own sperm/egg. Frist generation hybrids are fertile but their offspring cannot reproduce.
Outcome of Evolution:
• match-maker between populations and their environment
• relate to complex characteristics
• important functions
• Multi-drug resistant pathogens
• Overuse of antibiotics
• Not taking an entire prescription of antibiotics: Not using the full prescription causes not killing all the pathogen and could cause them to become immune to that antibiotic.
• Agricultural/industrial use
• Overuse of other substances
Coevolution: Interaction between two species strongly influences their survival so that they evolve in tandem.