geosci 110 - evolution and extinction

What are some of the fundamental questions about our physical world/universe that religions attempt to answer?

• What’s out there beyond self?

• What came before self?

• What comes after self?

• Questioned origins of the universe

What were some of the predictions of the Abrahamic biblical account of the world and how did religion help motivate the systematic study of nature?

• Prediction: finite age of Earth and universe - divinely created

• Nature as Reflection of Divine - influenced research to “further understand God’s creation”

How did Galileo’s approach to understanding the world differ from Bishop Ussher’s?

• Galileo: empirical evidence based - used observation and experimentation using telescopes

• Ussher: relied on dating of the bible - creationist

What observations did Galileo make that decentralized Earth as the vessel of creation?

• Jupiter’s moons - challenged geocentric model and provided evidence for heliocentric

• After Galileo: discovery of algebra, heliocentrism, planetary motion, astronomy, analytical geometry, mechanics, gravitation - all of which included God but also believed God’s plan to be accessible through observable phenomenon, natural laws, and REASON

What distinguishes a scientific theory?

• Testability 

• Use of empirical evidence to prove

What are Steno’s principles of stratigraphy?

• Principle of lateral continuity: strata originally deposited continuously unless interrupted by solid object; gaps in same strata indicate material has been removed after their formation

• Principle of original horizontality: strata are deposited on Earth’s surface horizontally or nearly so, departures indicate strata have been moved after they formed

• Principle of superposition: strata are arranged in temporal order - oldest at bottom

• Principle of cross-cutting relationships: any geological feature that cuts through another feature is younger than the feature it cuts through - relates to igneous rocks

What are “strata” and how do they form?

“Strata” - sedimentary layers

Deposition → tilting → erosion of layers → deposition again → erosion of canyon

How did Steno’s work challenge the notion that Noah’s flood washed fossils on mountains?

• Used empirical evidence

• Layers contradicted idea that they were all deposited at one time

What is uniformitarianism? What types of uniformity apply in this world view?

• Uniformitarianism: past recorded in rocks, processes operating and observable today help understand processes of the past - provides mechanism to arrive at rates and empirical age for geological features

Types of Uniformity:

1. Law: natural laws are invariant in space & time

2. Process: only processes operating today operated in the past

3. Rate: changes take place at constant rate or constant distribution of rates

4. State: dynamic equilibrium results in no net change - no directionality

What is the sedimentary cycle?

weathering/erosion → erosion transport → transient deposition → submarine deposition → long-term deposition → burial

• Steno’s stratigraphic principles orient ‘time’s arrow’ by identifying sequence of events in rock record

• Measured rates of erosion which makes new sediments

• Current state of Earth implies many cycles of erosion and deposition - demands very large amounts of time

What are the temporal implications of “angular unconformities?”

• Angular unconformities are geological features that represent a significant gap in the geological record, where tilted or folded strata are overlain by horizontal layers. Their temporal implications include:

Temporal implications:

1. Geological time gaps

2. Tectonic activity

3. Reconstruction of Earth’s history - provides history to help understand history

4. Relative dating 

• Uniformitarian principles → recognition of sedimentary cycle and importance of angular unconformities - showed Earth was much older than suggested by Bishop Ussher’s biblical chronology

What led Hutton to conclude that the Earth must be very old?

• Uniformitarianism 

• Additional about Hutton: Early discovery of sedimentary cycle and rock record

What is the old Scala Naturae and how does it differ from the Linnaean hierarchy?

The “Natural Ladder” (scala naturae)

• “Kinds” of life with obvious traits in common

• Life must therefore somehow be connected

• Humans were placed as top in position of dominance - seen as divinely created

• Simple life forms at bottom

Linnaean Hierarchy - becomes more exclusive as you proceed down

• Nested groups of relationships

• Links humans to animals - Homo sapiens, member of “Anthromorpha”

• Linnaeus built empirical classification scheme based on shared physical traits and reproductive continuity - still foundation for modern classification

What are the names of the ranks of the Linnaean hierarchy and their order?

The order: 

All Life

Kingdom

Phylum 

Class

Order

Family

Genus

Species 

Subspecies

Variety

individual

What was the most controversial aspect of Linnaeus’ classification scheme?

• Included humans in the scheme

What is a species?

Biological species concept: species are groups of natural, interbreeding populations that are reproductively isolated from other such groups

What observations pose problems for the definition of a species and ultimately caused Linnaeus to abandon the notion that species are “fixed in nature”?

1. Hybridization - ex: flowers

2. Morphological Variation

3. Geographical Variation

4. Extinct and Fossil Species: 

Typological species concept: fixed properties define species which reflect a divine plan - “as many as created in the beginning”

• Linnaeus’ view originally - empirical observations of hybridization and variation caused him to abandon

• “Fixity of species” rejected based on empirical evidence - opened door to questions about species changing over time

What is a cladogram?

Cladogram: diagram of hierarchy in similarity

• Not all traits are useful in defining groups - some may conflict

What are the three domains of life and what are some of the properties of those domains?

“Old modern” 3 domain classification of life:

• Eukarya

• Bacteria

• Archaea - more closely related to Eukaryotes than to Bacteria

Prokaryotes: cells lack nucleus

Ex: Bacteria and Archaea, but not Eukaryotes

Why was the organic interpretation of fossils not obvious in the early Renaissance?

• Misinterpretation of why fossils form

• Dominant philosophical view

• Early Renaissance - anything dug up from ground was considered a fossil (crystals, cave formations, rocks, etc.) - Inorganic “fossils” - early museum 

What were some of the conceptual problems posed by fossil objects?

• “Easy” fossils are one thing but what about fossils like nothing found alive today?

• Biologic origin of many fossils largely undeniable in 1669

• Possibility of extinction contradicted narrative shared in Bible

• Violated principles of plentitude (nature is as complete and possible and perfect according to God’s plan)

How did Nicholas Steno conclusively demonstrate that some fossil objects are the remains of once living things?

observed that many fossils resembled the teeth and bones of living animals. He examined fossils of sharks and recognized that some were identical in shape to the teeth of modern sharks. This led him to conclude that these objects were not merely geological formations but the remains of actual organisms.

Principle of Superposition: Steno established this principle, which states that in undisturbed sedimentary rock layers, older layers are found beneath younger layers. This helped him understand that fossils found in specific layers could be correlated to the time period when those organisms lived, providing a timeline for the existence of species.

Stratigraphy: Through his studies, Steno recognized that fossils were often found in specific strata, leading him to conclude that these layers represented different periods in Earth's history. This understanding of stratigraphy supported the idea that life has changed over time.

What are fossils in the modern sense of the word? Include the three types of fossils in your answer.

Fossils: the remains or traces of past life

1. Body fossils

2. Trace fossils

Molecular fossils (chemical compounds)

What are some properties of organisms that make them more likely to be preserved as fossils?

• Hard parts and large parts

Probability of fossilization:

• Low: soft parts, small parts (ex: skin)

• High: hard parts, big parts (ex: bones)

How was the common occurrence of fossils of ocean animals in the rocks of mountains first explained?

Early theories of Noah’s flood putting ocean animal fossils

• Later discovered to be development of mountains where seabeds rose thousands of feet in the air over time

What potential role did top-down, religiously-oriented explanations for fossil objects play in the development of science?

• Originally provided explanations for fossil discovery and limited thoughts about origins of fossils - attributed to Bible stories

• Later: used empirical evidence to really look into these claims and see if they were accurate - led to what we know about fossil origins today

How and why did William Smith go about studying fossils?

• On-site ‘foreman’ for canal digging projects during early Industrial Rev. in England

• Studied rocks and fossils for practical economic reasons - to predict how long it would take to complete any given canal project

• Field work: strictly empirical observation of fossils and strata in which they occur, focused on collection and documentation of fossils and their position in strata

• First large-scale geologic map in 1815

• Effects of map: demonstrated large-scale order of strata in geologic record, used field data to predict distribution of rock types both on surface and in subsurface

• Established whole new approach to studying and characterizing rock record: geologic mapping

What was the significance of the first geologic map, which was made by William Smith?

Making the map:

• Extensive descriptive/observational field work

• Measured physical orientations and thickness of strata

• Systematically collected fossils and noted order of occurrence in strata → key new insights

Fossils help identify strata:

• Rock type alone has little/no relative age 

• Same fossils can occur in many rock types but order of fossils is consistent and similarly repeated everywhere despite appearance of rock

What is “faunal succession” and how is it used to understand the rock record?

Fossils occur in regular temporal succession in strata - faunal succession

• Fossils alone can be used to determine relative position of sedimentary rock

• serves as predictive framework for correlation of strata (biostratigraphy)

• Relative aging tool

• Fact - important to note that it does not assume evolution 

• Importance: $$$, predictive framework for resource acquisition and infrastructure planning - still used today

What is biostratigraphy?

Biostratigraphy (based on principle of faunal succession): correlation of strata and determination of relative ages based on the index fossils that those strata contain

• Framework constantly revised as new data is assembled - working hypothesis

• Accurate tool of prediction for fossil fuel industry ($$$)

31. How was the geological time scale initially constructed and what are the two types of dating that can be applied to the rock record?

• Constructed through relative dating of strata

Two methods of dating:

1. Relative: age of events/rocks expressed in rank order relative to one another - primary means by which rock record is interpreted

2. Numerical: age of events/rocks expressed in units of real time

32. Are you familiar with the parts of the geological timescale that were identified in lecture as something to remember? (Note: this will be more important later in the course)

Eons: The largest time units, which include:

• Hadean: The earliest eon, starting from the formation of the Earth.

• Archean: When the first life forms appeared.

• Proterozoic: When more complex life forms began to develop.

• Phanerozoic: The current eon, which includes most of the history of visible life.

32. What are some of the large-scale trends (i.e., changes over time) that are observed in the fossil/rock records?

Evolution of Life Forms: The fossil record shows a clear progression from simple single-celled organisms to complex multicellular life. For example, the transition from prokaryotes to eukaryotes and the emergence of multicellular organisms mark significant evolutionary milestones.

Mass Extinctions: The fossil record identifies several mass extinction events, such as the Permian-Triassic extinction and the Cretaceous-Paleogene extinction. These events dramatically altered biodiversity and opened up ecological niches for the evolution of new species.

Geological Changes: The rock record documents major geological events, such as plate tectonics, continental drift, and the formation of mountain ranges. These changes have impacted habitats and influenced evolutionary pathways.

Fossils occur in regular temporal succession in strata - faunal succession

Biostratigraphy (based on principle of faunal succession): correlation of strata and determination of relative ages based on the index fossils that those strata contain

33. What were some of the conceptual problems posed by the possibility of extinction?

Conceptual problems: 

• Biologic origin of many “fossil objects” now undeniable

• Possibility of extinction contradicted Bible’s narrative

• Violated principle of plenitude (nature is as complete as possible according to God

Fossil Evidence: The presence of fossils of organisms that no longer existed presented difficulties in classification and understanding. Early scientists had to reconcile the existence of these remains with their beliefs about the continuity of life.

34. What is comparative anatomy and how is it useful in the study of fossils and living things?

Comparative Anatomy: systematic study of similarities and differences in morphology of living and fossil organisms, based on core principles..

1. Correlation of parts

2. Subordination of characters

Goals of comparative anatomy: 

• establish similarities between organisms that reflect patterns of affinity and true hierarchy of form in nature

• Reconstruct function from incomplete form

Importance of comparative anatomy: one of most fundamental approaches to vertebrate paleontology

• Helps identify key traits that can be used to classify organisms
  

Ohio animal”

• Example of use of comparative anatomy - calls mammoth (new type of elephant)

• Proved that fossils of mammoths were distinct from all living elephant species

35. What types of fossils did Cuvier study and how did they lead him to the conclusion that extinction is a real phenomenon?

Extinction is Real: proved by Cuvier

• Fossils of huge mammals challenged notion that these animals were still out there

• Proved reality of extinction beyond reasonable doubt - causes trying to be understood ever since by paleontologists - fossils were too big to be on Earth, humans would have known if they were still around

36. How did Cuvier explain the observation that fossils change between successive strata?

All extinction - there is no evolution

Cuvier’s explanation for changing fossil record & extinction:

• Fossils change in taxonomic composition and morphology between vertically stacked, physically distinct sedimentary rock strata

• Environments of deposition of sediments also change between successive strata - why strata appear distinct

• Extinction caused by “revolutionary” change in environment

• Thought new animals appear in successive strata at location observed due to migration after extinction not extinction itself

How did Lamarck explain the observation that fossils change between successive strata?

• All evolution - there is no extinction

• Inheritance of acquired characteristics

• Adaptation to environment

38. Can you describe Lamarck’s concept for how and why organisms change over time?

Lamarck’s Mechanism for Evolution:

• Individuals acquire characteristics most useful to mode of life

• Acquired traits passed on via inheritance

• Species constantly evolve instead of go extinct - so much evolution that extinction appears to happen but doesn’t

• Teleological notion of “progress” towards perfection

39. What are homologous, analogous, and vestigial structures in organisms, can you name some examples?

Homologous structures: shared similarities in structure that are not functionally necessary - serve as key morphological characteristics in comparative anatomy and classification

Analogous structures: anatomical parts with functionally similar forms that are constructed in different ways - can be hierarchical

Vestigial structures: features of organisms that have no apparent purpose or function - often resembling parts in use by other organisms

• Often greatly reduced in size and modified from original form

Ex: snake legs, human tail

40. Why was the development of an individual animal from an egg to an adult referred to as “evolution?”

• Sequential development and morphological similarities - despite the fact that it is the same individual in both stages - rather than comparing more than one organism

41. What are some features of developing animal embryos that suggest that changes have or can occur over time?’

Heterochrony: changes in timing of developmental events

• Think development of mickey mouse over time

Neoteny: retention of juvenile features to adulthood

• Vestigial structures 

42. What are cross cutting and enclosing relationships?

Principle of cross-cutting relationships: any geological feature that cuts through another feature is younger than the feature it cuts through - relates to igneous rocks

Molten nature of igneous rocks:

• cross-cutting and enclosing relationships

• Molten rock can intrude into pre-existing rocks or flow over them
  Therefore can enclose or contain pre-existing rocks

• Relative timing of rock formation can be determined by these relationships

44. The third chapter of the Origin of Species is titled “Struggle for Existence” (we are reading this in discussion sections). What fundamental fact about all organisms is central to Darwin’s assertion about a “struggle”? What led Darwin to the realization?

“Struggle for existence” - led to by fact that all species can overproduce at a level that will take over the entire environment and that this struggle for existence causes the need for evolution of species

Things that led Darwin to this idea:

Observations on the Beagle: Darwin's extensive observations during his voyage on the HMS Beagle, particularly in the Galápagos Islands, helped him notice variations among species and the adaptation to specific environments.

Breeding experiments: solidified idea of competition and selection in nature

45. We covered some math and used a simple model to describe the inherent potential of populations to grow. Can you qualitatively describe that model and identify its basic mathematical underpinnings?

net growth = (p-q) = r

exponential growth and decline of population equation

46. What are some important properties of a population?

Key characteristics of a population:

1. Geographic distribution (area, connectedness)

2. Population size (# individuals, density (individuals/area))

3. Growth rate: how population size changes - positive or negative growth 

• Found as slope of population graph over time 

• Often some kind of exponential growth

• Lower slope = lower growth rate

47. What are the parameters of a population that determine its characteristic growth rate? Does that growth rate always have to be positive? Why or why not?

1. Density-independent checks on population

2. Density-dependent checks on population

3. Food webs - provide positive or negative feedback on growth rate

4. Carrying capacity: K, point where growth rate r must drop due to limited resources and/or interactions with other species

48. Does the term “exponential growth” (aka “geometric growth”) apply to the human population? How do we know either way?

It does until we reach carrying capacity, K

49. The second chapter of the Origin of Species is titled “Variation under Nature.” Give some examples of how organisms vary in nature and describe why that is relevant to selection.

Morphological Differences: Organisms within the same species often exhibit differences in size, shape, color, and structure. 

For example, Darwin noted variations in the beak sizes and shapes of finches in the Galápagos Islands, which adapted to different food sources.

• Physiological Traits: Variations can also occur in physiological aspects, such as metabolic rates or tolerance to environmental conditions.

Example:  some plants can thrive in drought conditions while others cannot, demonstrating variability in water-use efficiency.

• Behavioral Differences: Animals may exhibit different behaviors that affect their survival and reproduction.

For example, variations in foraging strategies among bird species can influence their ability to find food and avoid predators.

• Reproductive Strategies: Some species may show variation in reproductive strategies, such as the number of offspring produced or the timing of reproduction, which can affect their success in different environments.

Relevance to Selection:

• Survival Advantage: Variations can lead to differences in survival and reproduction. Traits that confer advantages in a given environment—such as better camouflage, improved foraging ability, or increased resistance to disease—can lead to higher survival rates and greater reproductive success.

• Natural Selection: When certain variations prove beneficial, those individuals are more likely to survive and pass those traits on to the next generation. This process, known as natural selection, drives the evolution of species over time.

• Adaptation: The presence of variation within a population is crucial for adaptation. Without variation, there would be no raw material for natural selection to act upon, limiting the ability of populations to adapt to changing environments.

50. The first chapter of the Origin of Species is titled “Variation under Domestication.” What did Darwin seek to demonstrate in this chapter?

Darwin and domestic breeding - selection at work

• Opens Origin of Species with idea of artificial selection 

• Nature can create mass divergence by choosing which individuals breed

• Analogy between artificial selection and natural selection

• Discusses many other familiar products of domestication - cows, rabbits, sheep, etc.

51. What is “artificial selection” and how is it or is it not different from “natural selection?”

Breeding for one trait (artificial selection) often causes changes in other traits

Properties important for artificial selection

1. Heritable variation - more variable and heritable the trait - the easier it is to manipulate

2. Numbers - must be able to raise many individuals in each generation - directly related to variation

3. Generation time - more generations to work with = more change that can be affected

4. Breeding control - must be able to control reproductive patterns

Domestic pigeons figured prominently in Darwin’s first chapter. What are some general properties of domestic pigeons and how do they relate to the argument for the power of selection?

• High reproductive capacity

• Morphological variances like beak size

Process of Selection

• Two types of artificial selection on pigeons

1. Methodical “purposeful”

2. Unconscious “accidental”

52. Why did Darwin try to distinguish between methodical, purposeful selection and unconscious, accidental selection when considering domestic breeding? 

By contrasting these two types of selection, Darwin highlighted the role of human agency in breeding and how this can amplify variation. Methodical selection demonstrates how specific traits can be enhanced quickly, while unconscious selection shows that variation can also arise without direct human intervention.

53. What is allometric and isometric growth in organisms and what is the potential significance of this difference to breeders?

Allometric growth

• Allometry: Change in shape during ontogeny (growth and maturation) - ex: dogs

• Can result in very different morphologies (shapes) between juvenile and adult

• Large amount of allometry: big change from juvenile to adult

• Note: changing timing of adulthood can have huge effects

Isometric growth: pattern of growth in which an organism maintains a consistent shape as it increases in size. In this type of growth, the proportions of the body parts remain the same relative to each other as the organism grows, meaning that all dimensions scale uniformly.

Key difference: allometric growth → change in size while isometric does not

54. What is heterochrony? How is it relevant to the possible effects of selection?

Heterochrony: changes in timing of developmental events

Relation to possible effects of selection:

• Speciation: Changes in developmental timing can contribute to speciation, as populations may evolve different traits that enhance their survival and reproductive success in distinct environments.

55. What are some possible reasons for the differences in variability that exist between domestic dogs and cats?

• Dogs have more change as they age due to the change in their size compared to cats - allometric growth

56. What is meant by “heritability?”

Heritability: How parents pass on their traits to their offspring

Measuring heritability - look at correlation between parent traits and offspring traits 

What properties of organisms are most important to domestic breeders and why?

Properties important for artificial selection

1. Heritable variation - more variable and heritable the trait - the easier it is to manipulate

2. Numbers - must be able to raise many individuals in each generation - directly related to variation

3. Generation time - more generations to work with = more change that can be affected

4. Breeding control - must be able to control reproductive patterns

58. What were some key aspects of the “state of knowledge” surrounding geology and biology around 1850, just before Darwin published the Origin of Species?

Geology:

1. Uniformitarianism

2. Stratigraphy

3. Fossil Record

4. Chronology of Earth

Overall Context:

• Scientific Inquiry: The mid-19th century was marked by a growing emphasis on observation and evidence-based science. The scientific community was increasingly interested in understanding natural processes rather than relying solely on philosophical or religious explanations.

• Interdisciplinary Connections: There was an emerging connection between geology and biology. Understanding the Earth's history and the fossil record was crucial for developing ideas about the evolution of life.

This backdrop of scientific inquiry and evolving theories set the stage for Darwin's revolutionary ideas about natural selection and the evolution of species, fundamentally changing the understanding of biology and its relationship to the Earth's history.

How did Darwin explain coral reef atolls and what is the relationship, if any, between their mode of formation and his ideas about the origin of species?

He proposed that atolls form through a specific process involving the sinking of volcanic islands and the growth of coral around them

60. What were some of the key observations made during the voyage of the Beagle that contributed to Darwin’s ideas about the origin of species?

Key observations:

1. Distinctions between species and varieties of species are typically unclear

• Barnacles - dissected and studied thousands of individuals of the same species, impressed by large amount of variation in natural populations

2. Fossil animals are often similar to living species found in same area, but are also clearly different from species now extinct - ideas proved by Cuvier

3. Geographic variation in morphology and species replacement regionally

4. Populations of organisms isolated on different islands are typically classifiable as different varieties, “subspecies”, or species

5. Species on Galapagos Islands have South American affinities

• Island species characteristics - size often different from mainlands

• Dispersal ability often limited - ex: flightless

• Different behavior - unafraid of humans

• Increased individual variability

6. Species have highly effective & varied dispersal abilities - both purposeful & accidental, many terrestrial organisms found far out to sea

7. Small incremental changes can add up to have great effect - sedimentary deposits high on Andes mountains originally formed on beaches, earthquake, physical uplift of beach from tsunami

61. Why were the properties of organisms on islands, like the Galapagos, so important to the development of Darwin’s ideas?

Unique Adaptations:

• Ex: the finches had different beak shapes depending on their food sources

2. Variability Among Species:

• Darwin observed that closely related species on different islands often differed significantly from one another, yet shared common ancestors. This variability highlighted how isolation can lead to speciation and the development of distinct traits, supporting the idea that species are not fixed but can evolve over time.

3. Isolation and Speciation - separate species spread out over different islands 

62. Who was Alfred Russel Wallace and why was he important to the eventual publication of the idea of natural selection?

• “Wallace Line”: major division in biogeography

Scientific hypotheses depend on accumulation of fact & Darwin and Wallace built on same accumulated body of fact (lived in same place at same time) → both converging on mechanism for evolution

63. What is required in order for natural selection to occur? Do these requirements occur in nature?

Requirements for natural selection to occur:

1. Variability - offspring not exact copies of parents, individuals within populations are not identical

2. Heritability - parent traits → offspring

3. Differential reproductive success - individuals with favorable/advantageous traits will contribute more offspring than others with unfavorable or disadvantageous traits

• Result of these: morphology over time

64. In what sense, if any, is natural selection, or a natural selection-like process, “creative?” We saw a computer simulation in class. What did that simulation demonstrate?

• Innovation through variation

• Complex structures

• Ecosystem diversity

65. A common pattern when selection first occurs is for the population to change rapidly and then more slowly as time passes. Why might this be?

• Nears carrying capacity, logistic growth

66. What is “fitness” in the biological and natural selection sense of the word?

• Fitness: the relative ability of an individual to reproduce and contribute offspring to the next generation

• Combines both probability of survival and relative fecundity in population

67. What are the types of selection, or selection regimes, and how do they affect populations?

Types of selection

1. Directional selection: selection in favor of one end of the distribution of traits 

• Causes directional change in population morphology

• Need to no change in original variability of population

2. Stabilizing selection: selection against the extremes (end members) in a population

• Results in the maintenance of the status quo around an optimum

• May cause decreased variability in a population if rate of introduction of new variants is low relative to strength of stabilizing selection

3. disruptive selection: selection for the extremes in a population, results in divergence away from existing mode in all directions and the separation of population into 2 or more discrete modes

• Usually results in an increase in the variability of a population

• No selection (“drift”): no differential reproduction - all forms equally successful

• Expectation is no change in average morphology of population

• Often results in an increase in the variability of population 

68. Does natural selection always have to result in change over time? Why or why not?

In summary, while natural selection is a powerful mechanism for change in populations, it does not always lead to evolutionary change. The specific context, including environmental stability, existing adaptations, and genetic variation, plays a crucial role in determining whether natural selection results in significant changes over time.

• Ex: drift leads to no differential production

69. What is the “adaptive landscape” and how do populations respond to it?

The adaptive landscape provides a framework for understanding how populations navigate the complexities of evolutionary change. By moving toward fitness peaks, populations can adapt to their environments, and the landscape can change in response to various factors, including genetic variation and environmental shifts. This concept helps illustrate the dynamic nature of evolution and the processes that drive biodiversity.

70. We previously discussed homologous, analogous, and vestigial structures? How are each of these explained in light of Darwin’s hypothesis?

Homologous

• Homologous structures reflect common ancestry and descent with modification (evolution)

Analogous

• Analogous structures reflect independent derivations of morphologies in response to natural selection on the “adaptive landscape” - natural selection can “discover” specific solutions to problems from different starting points

Vestigial

• Vestigial structures reflect ancestry from organisms with those parts

71. How does Darwin’s mechanism explain changes in fossils over time? 

In summary, Darwin’s mechanism of natural selection explains changes in fossils over time by emphasizing gradual evolution, descent with modification, and adaptation to environmental changes. The fossil record provides tangible evidence of these processes, illustrating how species have evolved and diversified throughout Earth's history.

72. Darwin famously drew a diagram to illustrate what he thought was the outcome of natural selection and evolution. What are the key features of that diagram and why was it so impactful?  

Tree diagram

73. What were some of the gaping holes in Darwin’s understanding of natural selection (and evolution generally)?

Mechanism of Inheritance:

• Lacked understanding of how traits were passed to offspring.

• Proposed "blending inheritance," which diluted advantageous traits.

Source of Variation:

• Did not know the origins of genetic variation.

• Limited insight into the role of mutations.

Gradualism vs. Punctuated Equilibrium:

• Emphasized gradual change, ignoring instances of rapid speciation.

Environmental Influences:

• Recognized environmental impact but did not fully grasp rapid changes.

• Did not consider how environmental dynamics affect evolution.

74. Why must there be checks on population growth in nature?

Keeps any one species from producing at a rate at which the environment cannot sustain them

75. What are density dependent and density independent checks on population? Can you give some examples of each and explain them?

Density-dependent: dependent on amount of people there are

Density-dependent: change in growth rate is expected outcome of natural population growth

• Ex: housing 

• Ex: disease/bacteria - more dense, more opportunity for rapid spread of disease

• Ex: predator-prey interactions & food webs

Density-independent: don’t depend on how many people there are

• Only really effective when they happen often

• Ex: Natural disasters - one off events

• Note: drought conditions can cause dramatic drop in size of population

76. What are food webs and why might they matter to population sizes?

Food webs: complex ecological interactions result in many positive & negative feedbacks to population growth rate → resulting in dynamic equilibria in population sizes

• Physical and biological disturbances can tip system

• example of density-dependent checks on population 

77. What is a “carrying capacity” and what might determine it?

• The maximum amount of a species population an environment can handle

• Natural resources and food may determine it

78. What are the key, high-level components of the Central Dogma? How far down can you drill into each of those components and how well can you describe what is going on? What are the implications for evolution? [NOTE: this question encompasses pretty much everything that follows in this section!]

Central Dogma: DNA → RNA → proteins

Key Components of the Central Dogma

1. DNA (Deoxyribonucleic Acid):

   • Structure: Double helix composed of nucleotides (adenine, thymine, cytosine, guanine).

   • Function: Serves as the genetic blueprint for organisms, storing information necessary for the development, functioning, and reproduction of life.

   • Replication: DNA can replicate itself, ensuring that genetic information is passed on during cell division.

   • Drilling Down:

     • Genes: Segments of DNA that encode specific proteins or RNA molecules.

     • Regulatory Elements: Control when and how genes are expressed, influencing traits.

2. Transcription:

   • Process: The synthesis of RNA from a DNA template.

   • Types of RNA:

     • mRNA (messenger RNA): Carries the genetic code from DNA to the ribosome for protein synthesis.

     • tRNA (transfer RNA): Transfers specific amino acids to the growing polypeptide chain during translation.

     • rRNA (ribosomal RNA): Structural and functional components of the ribosome.

   • Drilling Down:

     • Initiation, Elongation, Termination: Steps involved in transcription.

     • Post-Transcriptional Modifications: Processes such as splicing, capping, and polyadenylation that modify mRNA before it exits the nucleus.

3. Translation:

   • Process: The synthesis of proteins based on the sequence of mRNA.

   • Ribosomes: The cellular machinery where translation occurs, composed of rRNA and proteins.

   • Amino Acids: Building blocks of proteins, linked by peptide bonds in a specific sequence dictated by mRNA.

   • Drilling Down:

     • Initiation, Elongation, Termination: Key stages of translation.

     • Genetic Code: The set of rules that dictate how mRNA sequences are translated into amino acids.

4. Proteins:

   • Structure: Composed of one or more polypeptide chains, folded into specific three-dimensional shapes.

   • Function: Serve as enzymes, structural components, signaling molecules, and more.

   • Drilling Down:

     • Post-Translational Modifications: Changes to proteins after translation that can affect their activity, stability, and localization.

Implications for Evolution

1. Variation and Mutation:

   • Genetic variation arises from mutations in DNA, which can affect the resulting RNA and proteins. Mutations can be beneficial, neutral, or harmful, influencing evolutionary fitness.

2. Natural Selection:

   • Variations in traits resulting from differences in proteins can lead to differential survival and reproduction. Natural selection acts on these variations, shaping the evolution of populations.

3. Gene Regulation:

   • Regulatory elements can lead to changes in gene expression, allowing organisms to adapt to different environments without altering the underlying DNA sequence. This flexibility can drive evolution.

4. Horizontal Gene Transfer:

   • In some organisms, particularly bacteria, genes can be transferred between individuals, allowing for rapid adaptation and evolution outside traditional vertical inheritance.

79. What are some of the important properties of the DNA molecule that allow it to store and convey information?

Double Helix Structure:

• Stability: The double helix structure provides stability and protection for the genetic code. The complementary base pairing (A with T, C with G) ensures accurate replication and transcription.

2. Nucleotide Sequence:

• Information Encoding: The sequence of nucleotides (adenine, thymine, cytosine, guanine) serves as a code that specifies the information necessary for the synthesis of proteins and the regulation of cellular functions. Variations in the sequence lead to different traits and functions.

3. Complementarity:

• Replication and Repair: The complementary nature of the DNA strands allows for precise replication during cell division. Each strand serves as a template for synthesizing a new complementary strand, ensuring the faithful transmission of genetic information.

4. Variable Length:

• Diversity of Information: DNA molecules can be of varying lengths, allowing for a vast range of genetic information. This variability supports the complexity of life forms, from simple bacteria to complex organisms.

5. Genetic Code:

• Codons: The genetic code is read in triplets (codons), with each triplet corresponding to a specific amino acid. This systematic encoding allows for the translation of the DNA sequence into functional proteins.

6. Regulatory Elements:

• Gene Expression Control: DNA contains regulatory sequences that control gene expression, determining when and how genes are turned on or off. This regulation is crucial for development, adaptation, and response to environmental changes.

7. Mutability:

• Adaptation and Evolution: DNA can undergo mutations, which introduce variations. Some mutations may be beneficial and can be acted upon by natural selection, contributing to the evolutionary process.

8. Packaging and Organization:

• Chromatin Structure: In eukaryotes, DNA is packaged into chromatin, which helps regulate access to the genetic material. The organization of DNA into chromosomes during cell division ensures proper segregation and distribution to daughter cells.

80. What are the nucleobases (aka “bases”) in DNA and how do they interact with one another?

• A-T pairs = 2 H bonds

• G-C pairs = 3 H bonds

Adenine, Guanine, Thymine, Cytosine

81. What is involved in DNA replication and what is the expected outcome of that process?

DNA replication - spontaneous coordination of multiple enzymes & ingredients

• Helicase unzips double strand DNA - replication fork

• Primase generates short strands of RNA that bind to the single-strand DNA to initiate DNA synthesis by DNA polymerase

• Note: DNA polymerase can only add new bases to the 3’ end of strand - replicates leading strand continuously

• Lagging-strand replication forms chunks that link together

82. How many base pairs are in our genome (i.e., single copy of our DNA)? Does the size of the genome convey anything important about the properties or complexities of organisms?

• approximately 3 billion base pairs in a single copy of DNA, organized into 23 pairs of chromosomes

• Little to no relationship between genome size and “complexity”

• Organisms with large genomes tend to have larger proportion of untranslated DNA - mostly in form of “transposable elements”

83. What are proteins and what roles do they play in life?

Function of DNA: store necessary code to make proteins

• Proteins: chemical compounds composed of single linear chain of amino acids, critical to every part and function of cell

• Interactions between amino acids as protein is formed causes folding configuration into globular forms 

• Function of protein seen by sequence of amino acids and folding configuration of the protein itself

84. What are amino acids? 

Amino Acids

• 20 have same basic structure - “rigid backbone” attached to 20 different R groups (interact with each other to determine protein shape and function)

• Have asymmetry and 2 forms of each - all life on earth uses one of the forms (“left-handed” versions)

• Bodies create 10 of them, must get the other 10 from food consumption

85. How is RNA similar to and different from DNA? What is mRNA, where does it come from, and what does it do? Are there other types of RNA?

Similarities: 

• Both RNA and DNA are composed of nucleotides, which are the building blocks of these molecules. Each nucleotide consists of a sugar, a phosphate group, and a nitrogenous base.

• Both RNA and DNA can store and convey genetic information. 

• Both molecules utilize base pairing to form structures. DNA and RNA can both form C and G pairs

Differences: 

• DNA serves as the long-term storage of genetic code, while RNA plays a key role in translating that code into proteins

• Bond: A with U in RNA and A with T in DNA

86. What are ribosomes and tRNA and how do they interact to build a protein?

tRNA: small ribonucleic acid - has both double and single stranded regions - “transfer” RNA

• Terminal 3’ single strand binds to specific amino acids based on the R group properties 
  

Ribosomes: coordinate mRNA and tRNA interactions to make proteins - result of translation of DNA code

• Consist of complex, folded framework of 65% rRNA and 35% ribosomal proteins

87. What is a codon? In what ways is redundancy built into the genetic code? What are some implications of that redundancy?

Codons: 3 base sequence identifying 1 of 20 amino acids

Genetic code: redundant 3-part info system

• RNA - U,C,A,G

• U and A paired and C and G paired

• DNA - T,C,A,G

• T and A paired and C and G paired

Implications: ability for mutations to occur

88. What are some of the mechanisms that lead to changes in the genome?

• Mutations: alterations of DNA base-pair sequences

• Some point mutations have no effect on genotype, some have dramatic effect on phenotype

• Point mutations: substitution errors made during DNA replication - become permanent once DNA is replicated

• Insertions and deletions: slippage of strand during replication can → addition or deletion of bases → longer or shorter daughter DNA strands

• Replication slippage: unstable heritable element, usually serial base pair repeat that gets worse as more copies are made

89. What is a “silent mutation?”

• Silent mutations: point mutations that cause no change in amino acid identity

90. What is a “gene”?

Genes: regions of DNA that are transcribed and translated or that are involved in these processes

91. Are all portions of an mRNA turned into protein?

1. Exons: determine the sequence of amino acids in proteins, are translated

2. Introns: un-translated pieces of DNA between exons - removed after making mRNA and before making protein, are not translated

92. About what percent of the human genome actually codes for proteins? What are the implications for/causes of that?

1-2% of DNA used to make proteins

23,000 protein-coding genes

93. What is reverse transcription and how do retroviruses work?

Reverse transcription: transfer of information from RNA back into DNA - strategy employed by retroviruses (HIV, etc.)

Human Endogenous retroviruses

• Use reverse transcription - host cell treats DNA of virus as its own

• If this happens in egg or sperm, becomes part of heritable genome

• 5-8% of our genome composed of transposons from retroviruses, the untranslated portions of the genome

94. What is the significance of the homology that is represented by the Central Dogma? How does that all relate to Darwin’s ideas?

The homology in the Central Dogma provides evidence for common ancestry and supports Darwin’s theory of evolution by explaining how genetic information drives the diversity of life.

95. How did Gregor Mendel go about determining the rules for what would come to be known as “Mendelian genetics?” What are those rules?

Gregor Mendel

• Raised lots of pea plants, controlled reproduction, detailed notes on plant traits generation by generation

Experiment: 1 pure-breeding lineage with long stems, 1 pure-breeding lineage with short stems, crossbred and resulted in all long-stemmed plants, 3:1 long:short phenotypic ratio

• Gene: two alleles, when combines define the genotype 

• Dominant: always expressed when present

• Recessive: must have copies to express

Homozygotes: two copies of the same allele (dominant or recessive) for a gene

Heterozygotes: 1 dominant and 1 recessive copy

“Germ plasm”

Principle of segregation - each parent contributes one randomly chosen allele from each gene to each offspring

Principle of independent assortment - Allele pairs (genes) behave independently of all other allele pairs

96. What is the difference between a phenotype and a genotype? Which is relevant to natural selection and why?

Phenotype: The observable traits of an organism (e.g., flower color).

Example of relevance to natural selection: In a population of moths, those with coloration that provides better camouflage against predators will survive longer and reproduce more, influencing the frequency of that phenotype in the population.

Genotype: The genetic makeup of an organism (e.g., the specific alleles it carries, such as AA, Aa, or aa).

Example of relevance to natural selection:  If a mutation in the genotype confers a beneficial trait (like increased resistance to disease), individuals with that genotype may produce more offspring, leading to an increase in that genotype in the population over generations.

Key distinction between relevance: natural selection acts on phenotypes, genotypes are fundamental for generating the variation on which natural selection operates

97. Can you predict the outcome of reproduction for any Mendelian case? For example, what are all of the predictions if you cross two individuals that are heterozygous for a Mendelian trait?

• Genotypic Ratio: 1 AA : 2 Aa : 1 aa

• Phenotypic Ratio: 3 dominant trait expressed: 1 recessive gene expressed

98. There are many examples of non-Mendelian behavior. Can you list several examples and explain them?

Non-Mendelian characteristics

1. Incomplete dominance of alleles

2. Co-dominance of alleles

3. Multiple alleles for one gene in a population

4. One gene, multiple effects 

5. One phenotype, multiple contributing genes

6. Gene-gene interaction

7. Gene-environment interaction
   

8. Ex: In snapdragon flowers, crossing red (RR) and white (WW) flowers produces pink (RW) flowers. The phenotype is a blend of the two parental traits.

9. Ex: Blood type - has three possible alleles instead of 2 - leads to 4 blood types 

99. What is the importance of identical twin studies and what do they demonstrate?

Twins

• Identical twins have exactly the same genotype

• “Twin studies” provide important information on genetic basis of complex, non-Medelian traits

• Allows for nature vs. nurture tests