ICB - Expanded Table of Contents

ICB - Expanded Table of Contents

Campbell, Heyer, and Paradise Integrated Concepts in Biology

Integrating Concepts in Biology
by A. Malcolm Campbell, Laurie J. Heyer, and Christopher J. Paradise

Table of Contents (TOC)

Although we want students to see the connections between “big biology” and “small biology,” we recognize that many year-long introductory biology course sequences divide content by size. Integrating Concepts in Biology (ICB) is organized along that traditional divide, with the first 15 chapters focusing on topics at the organismal level and below, and the last 15 chapters focusing on the organismal and above.

The thirty chapters are divided evenly between small and big biology. The 15 chapters are distributed evenly among the 5 Big Ideas. Each chapter within a big idea focuses on a particular level of the biological hierarchy: molecular, cellular, and organismal for the small biology chapters 1 - 15, and organismal, population and ecological system for the big biology chapters 16 - 30. Thus, the organismal level appears in each set, but the case studies in each section focus on traditional small or big biology cases, respectively. The text easily fits two fifteen-week semesters, with 1 chapter per week, or about 42-45 case studies in each semester. ICB also fits three quarters spanning the traditional academic year and would work equally well for an extended approach that spans three semesters.

In the TOC below, we have listed the questions posed and answered in each chapter. Answers to the questions often require multiple cases but the cases are not redundant. Following the questions, we have listed familiar concepts or topics addressed within the chapters.

Fall Semester/ First half
Big Idea 1: Information
Living systems have multiple mechanisms to store, retrieve, and transmit information.
Main ideas to integrate throughout the Big Idea
 Heritable information provides for continuity of life.
 Imperfect information transfer produces variation.
 Information can be expressed and regulated without loss of content.
 Non-heritable information is transmitted within and between biological systems.
Chapter 1: Heritable Material / Concept/Topic
1.1 / What is biological information?
1.2 / What is the heritable material? / DNA as Heritable Material
BME 1.1 / Why do amino acids make a better code than nucleotides? / Multiplication Principle
1.3 / Can you prove protein is NOT the heritable material? / Proteins Not Heritable Material
ELSI 1.1 / Who owns your DNA? / Bioethics
1.4 / How does DNA’s shape affect its function? / DNA Structure
BME 1.2 / How much DNA is in each band? / Quantifying Bands
BME 1.3 / How are generations measured on a log scale? / Logarithms
1.5 / Is all genetic information encoded linearly in the DNA sequence? / Epigenetics
Chapter 2: Central Dogma / Concept/Topic
2.1 / How does DNA communicate information to the cell? / Transcription
ELSI 2.1 / Choose your words carefully / Precision of Words
2.2 / How is gene transcription regulated? / Gene Regulation
BME 2.1 / How can you measure the strength and speed of gene induction? / Quantifying Rates
BME 2.2 / How can you quantify a sequence pattern? / Position Weight Matrix
2.3 / How do cells make proteins? / Translation
2.4 / Can cells pick and choose information? / RNA Splicing
ELSI 2.2 / Is science possible if you are uncertain about what is true? / Uncertainty in Science
Chapter 3: Reproduction and Cell Division / Concept/Topic
3.1 / How can traits disappear and reappear in a later generation? / Mendelian Genetics
BME 3.1 / How much variation is there in random mating outcomes? / Histogram and Variable Data
BME 3.2 / Probability rules for genetics / Probability
3.2 / What happens when you follow two traits at once? / Mendelian Genetics
ELSI 3.1 / ‘Was that totally random?’ / Concept of Randomness
3.3 / How do prokaryotes communicate their identity to the next generation? / Cell Division
BME 3.3 / A mathematical model of cell growth / Modeling
3.4 / Do eukaryotes produce new cells the same way as bacteria? / Mitosis
3.5 / How can two parents produce non-identical offspring? / Meiosis
ELSI 3.2 / Should we engineer better babies? / Bioethics
Big Idea 2: Evolution
The diversity and unity of life can be explained by the process of evolution.
Main ideas to integrate throughout the Big Idea
 The origin of living systems occurred by natural processes, and life continues to evolve within a changing environment.
 Organisms can be linked by lines of descent from common ancestry.
 Natural selection is a mechanism of evolution that accounts for adaptation.
 Human activity can alter the course of evolution.
Chapter 4: Evolution and Origin of Cells / Concept/Topic
4.1 / What is evolution? / Definition and Mechanisms
ELSI 4.1 / Are evolution and religion compatible? / Science Defined
4.2 / Could abiotic molecules form biologically important molecules before life evolved? / Abiotic Synthesis of Organic Molecules
BME 4.1 / What is the significance of sequence and base pair conservation? / Rules for Computing Probabilities
4.3 / Can non-living objects compete and grow? / Vesicle Formation, Division & Competition
BME 4.2 / How fast is the vesicle size changing? / Fitting Exponential function
4.4 / Can non-living objects harvest and store energy? / Hydrogen Gradient
BME 4.3 / Logarithms: The power of pH / Logarithms
Chapter 5: Applied Evolution / Concept/Topic
5.1 / How do genetic diseases arise? / DNA Mutations
5.2 / How are new species formed? / Mutations; Formation of New Unicellular Species
BME 5.1 / What biological information is in a dot plot? / From Results of One of the IQs Using a BLAST Search
ELSI 5.1 / Are GMOs safe? / Misconceptions and Applications
5.3 / Why do my allergies get worse each year? / Clonal B Cells and Somatic Hypermutation
ELSI 5.2 / Banning PB&J: How far should a society go to protect the rights of an individual? / Risk Assessment
Chapter 6: Evolution of Eukaryotes / Concept/Topic
6.1 / How did the first nucleus come into being? / Fusion of Archaea and Eubacteria Cells
6.2 / How does a whole genome fit inside a tiny nucleus? / Nucleosomes and Histones
ELSI 6.1 / What are the ethical guidelines for scientific research? / Ethics
6.3 / How did mitochondria and chloroplasts originate? / Multiple Genomes within a Species
6.4 / How did multicellular organisms evolve? / Evolution of Complexity
BME 6.1 / How do you find average cell and colony sizes? / Relative Frequency Distribution
BME 6.2 / How can you count cells when you can’t see them all? / Sampling, Scaling Up
Big Idea 3: Cells
Cells are a fundamental structural and functional unit of life.
Main ideas to integrate throughout the Big Idea
 All cells come from preexisting cells.
 Cells maintain internal environments that differ from their external environments.
 Cell structure defines cell function.
 Cells communicate with other cells.
Chapter 7: Molecular Structure and Function / Concept/Topic
7.1 / What role does molecular structure play in a cell’s function? / Structure/Function
7.2 / How do cells respond to fear? / Signal Transduction
ELSI 7.1 / Can’t we speed up drug discovery and get products to the market quicker? / Clinical Trials
7.3 / Why are some membranes wavy? / Surface Area to Volume
Chapter 8: Cell Structure and Function / Concept/Topic
8.1 / What is a cell? / Diversity of Life
8.2 / Why aren’t there giant cells? / Diffusional Constraints
BME 8.1 / How can geometry help predict the optimal cell size? / Modeling Energy Supply and Demand
BME 8.2 / How do you quantify diffusion in a FRAP experiment? / Modeling Movement with Percentages
ELSI 8.1 / Does basic biology have any impact on the real world? / Applications of Research
8.3 / Are viruses alive? / Defining Life and exceptions to the Rule
Chapter 9: Neurons and Muscles / Concept/Topic
9.1 / How do I tell my muscles to move? / Nerve Action Potential and Exocytosis
BME 9.1 / What is the optimal amount of myelin for an axon? / Optimization
9.2 / How do muscles respond to exercise? / Muscle Contraction and Growth
ELSI 9.1 / What are the consequences of performance-enhancing drugs? / Steroids and Fair Play
9.3 / How do brain cells store memories? / Short Term and Long Term Memory Formation
ELSI 9.2 / If pills could make you remember or forget, would you take them? / What is Real vs. Artificial?
Big Idea 4: Homeostasis
Biological systems maintain homeostasis.
Main ideas to integrate throughout the Big Idea
 Biological systems utilize feedback mechanisms to regulate and maintain optimal conditions.
 Time-dependent processes regulate biological systems.
 Life requires organization, which is energy dependent.
 A biological system’s size and environment influences how it addresses physical and chemical challenges.
Chapter 10: Cellular Respiration / Concept/Topic
10.1 / How do biological molecules carry energy? / Second Law of Thermodynamics
10.2 / How does food get converted to molecular energy? / Digestion of Lipids, Proteins and Sugars
ELSI 10.1 / Should I memorize all these steps? / Retention of Information
10.3 / How is energy extracted from 2-carbon intermediates? / Cellular Respiration
10.4 / How is ATP produced? / Chemiosmosis
BME 10.1 / How do you measure the concentration of molecules in air? / PPM
ELSI 10.2 / Why should I eat vegetables? / Nutrition
Chapter 11: Photosynthesis / Concept/Topic
11.1 / Why is paraquat used in American but illegal in Europe? / Light Cycle of Photosynthesis
11.2 / How does Brazil’s rainforest affect Greenland’s glaciers? / Carbon Fixation, Carbon Sources and Sinks
ELSI 11.1 / How do you compromise when a policy hurts one country but helps another? / Borders vs. Biology
11.3 / Is there anywhere on earth devoid of life? / Extremophiles
BME 11.1 / Does it matter how you present your data? / Data Visualization
Chapter 12: Plant Physiology / Concept/Topic
12.1 / How do plants respond to changes when they can’t move? / Larger Genomes and contingencies
12.2 / How can changes in two cells affect an entire plant? / Stomata and Gas Exchange
BME 12.1 / Can localized context produce organismal response? / Cellular Automata
12.3 / How does a Venus flytrap catch its prey? / Ion Fluxes and Depolarization
ELSI 12.1 / How can you help someone correct a misconception? / Knowledge vs. Understanding
Big Idea 5: Emergent Properties
Interdependent relationships characterize biological systems, and these interactions give rise to emergent properties.
Main ideas to integrate throughout the Big Idea
 Biological systems require resources, which results in competition or cooperation.
 Biological systems exceed the sum of their parts.
 Randomness within a biological system provides flexibility of response.
Chapter 13 Molecular Switches / Concept/Topic
13.1 / What are emergent properties? / Definition
13.2 / How does blood carry oxygen? / Hemoglobin Cooperativity
BME 13.1 / How can you quantify cooperativity? / Predicting Using Fitted Models
13.3 / When does a virus kill its host? / Lambda Phage & Bistable Toggle Switches
13.4 / Does the genome allow random actions by cells? / Stochastic Events
ELSI 13.1 / Should synthetic biology be curtailed? / Scientific Limits
Chapter 14 Cell Networks / Concept/Topic
14.1 / How do single-celled organisms communicate with one another? / Quorum Sensing in Microbes
ELSI 14.1 / How can 90% of your body’s cells be non-human? / Microbiome
14.2 / Do unicellular species have to work solo? / Biofilms and Slime Mold Sporulation
BME 14.1 / Can emergent properties be modeled mathematically? / Agent Based Models
14.3 / Can cells tell time? / Circadian Rhythms of Non-mammals
Chapter 15 Animal Physiology / Concept/Topic
15.1 / How do mammals tell time? / Circadian Rhythms in Mammals
ELSI 15.1 / Is your sleep cycle affected by age? / Function of Sleep & Sleep Maladies
15.2 / How can a mother tolerate her fetus? / Cell-mediated Immunity (T cells)
15.3 / How do we maintain our weight? / Leptin and Weigh Regulation
ELSI 15.2 / Should the US have a public health strategy to deal with the obesity epidemic? / Incentives for Better Health
BME 15.1 / How correlated are leptin levels and body fat? / Correlation Coefficient
BME 15.2 / How accurately can you predict an outcome? / Confidence Intervals
15.4 / Why do individuals age and die? / Senescence and Aging
ELSI 15.3 / Should we alter the timing of death? / Ethics of Decisions About Death
Spring Semester/ Second half
Big Idea 1: Information
Living systems have multiple mechanisms to store, retrieve, and transmit information.
Main ideas to integrate throughout the Big Idea
 Heritable information provides for continuity of life.
 Imperfect information transfer produces variation.
 Information can be expressed and regulated without loss of content.
 Non-heritable information is transmitted within and between biological systems.
Chapter 16: Variation and Population Genetics / Concept/Topic
16.1 / What causes individual variation? / Variability & Variation Among Individuals
BME 16.1 / How does linear regression work? / Best Fit Lines and Regression
16.2 / How can population genetics information be used to predict evolution? / Pop Gen and Data Testing HW
BME 16.2 / How can you predict Hardy-Weinberg equilibrium? / Apply H-W equation
16.3 / Non-Mendelian genetics: Why do we need annual flu vaccines? / Viral genetics
ELSI 16.1 / Why do people refuse the flu vaccine for themselves and their children? / Misuse, Misconceptions of Science
Chapter 17: Behavior / Concept/Topic
17.1 / What is information at the population level? / Population Concept
17.2 / How is information transmitted between members of animal species? / Animal Behavior and Communication
BME 17.1 / How can observations be adjusted for varying conditions? / Regression, Variation
BME 17.2 / Are two situations significantly different? / Statistics and p-values
ELSI 17.1 / What causes love at first sight, and are there ethical and social consequences? / Physical and Chemical Attraction
17.3 / Does group living require more derived mechanisms of information transfer? / Social Behavior, Eusociality
BME 17.3 / What can you learn from a boxplot? / Plots
17.4 / How do plants of the same species recognize one another? / Pollen-pistil Interactions
Chapter 18: Information in the Environment / Concept/Topic
18.1 / Have organisms evolved to exploit communication between individuals of other species? / Prey Detection
18.2 / How do organisms assess their environment when searching for resources? / Foraging, Optimal Foraging
BME 18.1 / How do you predict foraging results? / Modeling Foraging
BME 18.2 / Is this the perfect time to leave? / Marginal Value Theorem
18.3 / Is chemical communication used to block competition or defend self? / Oviposition Deterrents, Competition
18.4 / How does change in number of species affect information content of an ecological system? / Biodiversity as Information
BME 18.3 / How do you measure biodiversity? / Shannon Diversity Index
ELSI 18.1 / Do we have an obligation to preserve biodiversity? / Ethics/Stewardship
Big Idea 2: Evolution
The diversity and unity of life can be explained by the process of evolution.
Main ideas to integrate throughout the Big Idea
 The origin of living systems occurred by natural processes, and life continues to evolve within a changing environment.
 Organisms can be linked by lines of descent from common ancestry.
 Natural selection is a mechanism of evolution that accounts for adaptation.
 Human activity can alter the course of evolution.
Chapter 19: Mechanisms of Evolution / Concept/Topic
19.1 / How does selection act on individuals with variable characteristics? / Natural Selection
BME 19.1 / Do females really prefer bold males? / Preference Testing
19.2 / How will communities respond to climate change? / Adaptation to Changing Environment
ELSI 19.1 / When do we have enough data to act and formulate policy? / Science Policy
19.3 / When are two isolated populations not isolated? / Gene Flow
BME 19.2 / Why is a relative frequency distribution useful? / Analyzing Frequency Distributions
BME 19.3 / How genetically different are two populations? / Measuring Genetic Variation
19.4 / Do populations evolve in the absence of natural selection? / Genetic Drift
BME 19.4 / How confident can you be in your observations? / Confidence Intervals
Chapter 20: Evolutionary History / Concept/Topic
20.1 / Can you observe descent with modification? / Evolutionary Histories; Rapid Diversification
BME 20.1 / How do you build an evolutionary tree? / Building Phylogenies
20.2 / When and how did plants colonize land? / Major Transitions in Evolutionary History
20.3 / Where, when, and from what ancestors did humans evolve? / Common Ancestors, Evolution of Humans
ELSI 20.1 / What is prejudice vs. good science? Eugenics yesterday and today / Eugenics
ELSI 20.2 / Has evolution reached its peak? Are humans still evolving? / Evolution is Not Goal Directed
20.4 / Can you observe evolution in your lifetime? / Rates of Evolution, Evolution of Resistance
ELSI 20.3 / When is there too much of a good thing? Overuse of chemicals. / Ethics
Chapter 21: Evolution of Interactions in Communities / Concept/Topic
21.1 / How have species evolved as a consequence of their interactions with other species? / Co-evolution
BME 21.1 / What does that equation mean? (And is it really necessary?) / Use of Equations in Science
21.2 / Why are corals dying around the world? / Symbiosis
BME 21.2 / Can you predict future coral bleaching? / Extrapolation
21.3 / How does the amount of light affect the distribution of photosynthesizing organisms? / Environmental Gradients, Variability Among Species
21.4 / How have ecological communities adapted to disturbance? / Disturbance as a Selective Factor
BME 21.3 / How fast did the trees grow? / Rates of Growth
ELSI 21.1 / Should we act to prevent forest fires? / Cost-benefit Analysis
Big Idea 3: Cells
Cells are a fundamental structural and functional unit of life.
Main ideas to integrate throughout the Big Idea
 All cells come from preexisting cells.
 Cells maintain internal environments that differ from their external environments.
 Cell structure defines cell function.
 Cells communicate with other cells.
Chapter 22: Disease / Concept/Topic
22.1 / How do genetic diseases affect cells and organisms? / Mutations, Disease
BME 22.1 / What is in the mixture? / Area Under the Curve
ELSI 22.1 / What is normal? What would we lose if everyone were perfect? / Ethics and Diversity
22.2 / How do pathogens affect cells and organisms? / Co-evolution, Cellular Effects of Pathogens
ELSI 22.2 / What are the issues with using animals in research? / Ethics of Animal Research
22.3 / Can parasites survive in more than one host species? / Life History Strategies, Complex Life Cycles
22.4 / How do diseases spread? / Propagule Transmission
Chapter 23: Cells in Tissues / Concept/Topic
23.1 / How do you break down and absorb nutrients from the food you eat? / Digestion
BME 23.1 / Are two sample means significantly different? / T-Test
23.2 / How do populations of cells in animals affect the whole organism? / Endocrine System