Biology 101: Introduction to Life and Scientific Principles – Study Notes

What is Biology?

• Biology is the study of living organisms and their interactions with one another and their environments.
• Science can be defined as knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method.
• The scientific method is a method of research with defined steps that include experiments and careful observation.
• Biology studies organisms from microscopic cells to global ecosystems; it includes exploration of structure, function, growth, interactions, and evolution.
• Clarifying questions about life: Is a rock alive? Is a tree alive? Is a virus alive? These questions motivate defining life.

Key themes to structure your thinking about biology

• Life is cellular (first unifying idea).
• Life evolves (second unifying idea).
• Life processes information (third unifying idea).
• The tree of life and the process of doing biology link these ideas together.
• The three greatest unifying ideas structure how we think about biology: cellular life, evolutionary change, and information flow in biology.

Life and the question of being alive

• Living things display a set of distinct properties that distinguish them from non-living matter.
• Major properties: order, response to stimuli, reproduction, adaptation, growth and development, regulation/homeostasis, energy processing, evolution.
• Life is organized at multiple levels from cellular to global scales.

Properties of life: overview of the eight key characteristics

• CHARACTERISTIC 1: ORDER
  • Living organisms are highly organized; structures range from atoms to molecules, organelles, cells, tissues, organs, systems, and beyond.
• CHARACTERISTIC 2: RESPONSE TO STIMULI
  • Organisms react to environmental changes; examples include plants growing toward light and bacteria moving away from toxins (phototrophism as an instance).
• CHARACTERISTIC 3: REPRODUCTION
  • All organisms are capable of reproduction; can be asexual or sexual; ensures continuation of the species.
• CHARACTERISTIC 4: ADAPTATION
  • Traits that evolve in organisms improve survival and reproductive success in a given environment (examples: stick insect, chameleon).
• CHARACTERISTIC 5: GROWTH AND DEVELOPMENT
  • Organisms increase in size and complexity; growth and development are guided by genetic instructions; regulated cell division and differentiation (tadpole developing into a frog as an example).
• CHARACTERISTIC 6: REGULATION/HOMEOSTASIS
  • Organisms maintain stable internal conditions (e.g., body temperature, glucose levels) via feedback mechanisms.
• CHARACTERISTIC 7: ENERGY PROCESSING
  • Metabolism: the sum of all chemical reactions that sustain life; includes energy capture, storage, and use; autotrophs (producers) vs heterotrophs (consumers).
• CHARACTERISTIC 8: EVOLUTION
  • The genetic makeup of populations changes over time, shaping biodiversity.

The science of biology: organization of life, continuity, unity

• Three core themes:
  • Organization of Life: Cell Theory
  • Continuity of Life: Chromosomal Theory of Inheritance
  • Diversity and Unity of Life: Theory of Evolution
• Each theme provides a framework that connects cellular structure, genetic information, and evolutionary history.

Hierarchy of biological organization (levels)

• Levels from smallest to largest:
  • Atoms → Molecules → Macromolecules → Organelles → Cells → Tissues → Organs and organ systems → Organisms, populations, and communities → Ecosystems → Biosphere
• Organized from smallest to most complex.

Atoms, molecules, macromolecules, organelles, and cells

• 1. Atoms: smallest unit of an element that retains properties of the element.
• 2. Molecules: chemical structures made of one or more atoms.
• 3. Macromolecules: very large, complex molecules.
• 4. Organelles: compartments and large molecular machines within cells that perform functions.
• 5. Cells: smallest collection of matter that performs all characteristics of life; basic unit of life.
• 6. Tissues: group of similar cells performing a function.
• 7. Organs: body parts consisting of two or more tissues performing a function.
• 8. Organ Systems: two or more organs functioning together for a system.
• 9. Organisms: an individual living thing.
• 10. Populations: all individuals of a given species in a region.
• 11. Communities: all living things in an ecosystem.
• 12. Ecosystem: living and non-living things in an area.
• 13. Biosphere: all land, water, and atmosphere on Earth.

Hierarchy of biological organization: examples and explanations

• Organelles example: the nucleus observed in onion cells.
• Organisms, populations, and communities: a forest example: a pine tree is an organism; many trees form a population; all plant and animal species form a community.
• Cells: examples include human blood cells.
• Tissues: e.g., human skin tissue.
• Organs and organ systems: stomach and intestine form the digestive system.
• Ecosystems: coastal ecosystem with living organisms and environment.
• The Biosphere: encompasses all ecosystems on Earth.

Linnaeus’s taxonomic system of classification (binomial nomenclature)

• In 1735, Carolus Linnaeus established a two-part scientific naming system still used today.
• Each organism is given a unique two-part name consisting of genus and species:
  • Genus: a closely related group of species.
  • Species: individuals that regularly breed together or share distinct characteristics from other species.
• Example:
  • Homo sapiens

Rules of nomenclature (scientific naming conventions)

• A organism’s genus and species designation is called its scientific name or Latin name.
• Scientific names are italicized.
• Genus names are always capitalized; species names are not capitalized.
• Example:
  • • Homo sapiens

Taxonomy and the domains/kingdoms

• Taxonomy is the effort to name and classify organisms.
• A taxon is a named group.
• The most inclusive grouping is the Domain, which consists of three taxa: Bacteria, Archaea, and Eukarya.
• The next most inclusive grouping is the Kingdoms; Domain Eukarya consists of four Kingdoms: Protista, Fungi, Plantae, and Animalia.
• Aside from Protists, the other three Kingdoms can be distinguished by shared characteristics.

Taxonomic ranks (continuation) and the order of classification

• After Kingdom, groups become increasingly exclusive based on shared characteristics.
• Taxonomic rank order: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species.
• Mnemonic (classic): King Philip Came Over For Good Soup.
• Example illustration: Domain Eukarya; Kingdom Animalia; Phylum Chordata; Class Mammalia; Order Carnivora; Family Canidae; Genus Vulpes; Species Vulpes vulpes (red fox).

The diversity of life and the phylogenetic tree

• Phylogenetic Tree of Life represents relationships among organisms.
• You are here in the tree; major domains: Bacteria, Archaea, Eukarya.
• Eukarya branches into major kingdoms and lineages such as Animals, Fungi, Plants, Protists, etc.
• The tree reflects both diversity and unity of life: DNA as a shared genetic code and common ancestry across organisms.

The three theories that form the framework of modern biology

• 1. The Cell Theory: What are organisms made of?
• 2. The Theory of Evolution: Where do organisms come from?
• 3. The Chromosome Theory of Inheritance: How is hereditary information transmitted from one generation to the next?

What is a theory? (scientific vs everyday use)

• A theory is an explanation for a very general class of phenomena or observations that is supported by a wide body of evidence.
• This usage differs from everyday language where theory may imply guesswork or speculation.

Core themes in biology

• Organization of Life: Cell Theory.
• Continuity of Life: Chromosomal Theory of Inheritance.
• Diversity and Unity of Life: Theory of Evolution.
• These themes connect cellular structure, genetic information, and evolutionary history.

The Cell Theory in detail

• Historical note: In the late 1660s, Robert Hooke and Anton van Leeuwenhoek were the first to observe cells.
• A cell is a highly organized compartment bounded by a plasma membrane and containing concentrated chemicals in an aqueous solution.
• The cell theory states that:
  • All organisms are made of cells.
  • All cells come from preexisting cells.

Implications of the Cell Theory

• All cells in a population of single-celled organisms are related by common ancestry.
• In multicellular organisms, all cells present descended from preexisting cells and are connected by common ancestry.

Core themes in biology (cont.): Evolution and unity

• Evolution by natural selection explains how adaptation leads to diversity.
• DNA as the heritable molecule and a common genetic code among all organisms explains unity across life.
• Question: What is the mechanism of evolution proposed by Charles Darwin? (Descent with modification)

The Theory of Evolution by Natural Selection

• In 1858, Darwin and Wallace proposed two claims:
  • All species are related by common ancestry.
  • Characteristics of species can be modified generation to generation.
• Darwin called this descent with modification.

Evolutionary concepts

• Evolution: a change in the characteristics of a population over time; populations, not individuals, evolve.
• A population is a group of individuals of the same species living in the same area at the same time.

Natural selection and populations

• Natural selection explains how evolution occurs.
• Two conditions for natural selection:
  1) Individuals vary in heritable characteristics that can be passed on.
  2) In a given environment, certain heritable variants promote greater reproductive success than others.

Evolutionary change and speciation

• If heritable traits increase reproductive success, they become more common in the population over time.
• Evolutionary change occurs in populations, not individuals.
• Speciation occurs when populations diverge to form new species.
• Fitness and adaptation drive natural selection:
  • Fitness: the ability of an individual to produce offspring.
  • Adaptation: a trait that increases fitness in a given environment.

The Chromosome Theory of Inheritance: Life processes information

• Key questions: What is the source of heritable variation? How is information stored and transmitted across generations?
• Chromosome theory of inheritance provides a foundation to answer these questions and is the third unifying idea of biology.

Life processes information: history and core concepts

• Proposed in 1902 by Walter Sutton and Theodor Boveri.
• Hereditary information is encoded in genes.
• Genes are units located on chromosomes.
• In the 1950s, chromosomes were identified as molecules of DNA.
• DNA is the hereditary material.
• Genes are segments of DNA that code for cellular products.

The DNA double helix and its components

• James Watson and Francis Crick proposed that DNA is a double-stranded helix.
• Each strand is composed of four building blocks: A, T, C, and G.
• The sequence of these bases encodes information needed for growth, development, and reproduction; DNA is the blueprint molecule.
• Base pairing: A pairs with T; C pairs with G.
• The two strands are held together by base pairing; this pairing allows DNA to be copied and preserves encoded information.

The Central Dogma of molecular biology

• Flow of information: DNA codes for RNA, which codes for proteins.
• DNA → RNA → Protein
• RNA is copied from DNA; the RNA copy is read to determine the building blocks used to make a protein.
• Proteins determine an organism’s traits; thus, genetic information ultimately influences phenotype.

DNA replication and variation

• DNA is copied to pass genetic information from cell to cell or from one organism to offspring.
• Copying DNA is highly accurate, but mistakes can occur.
• DNA sequence changes may lead to changes in proteins and, consequently, outward appearance.
• At the individual level, changes in DNA sequence can increase or decrease fitness; at the population level, heritable variation underlies diversity and makes evolution possible.

The diversity of life and the phylogenetic tree (continued)

• The phylogenetic tree shows relationships among life forms, with bacteria, archaea, and eukarya as primary domains.
• Within eukaryotes, major lineages include animals, plants, fungi, and various protists.
• The tree reflects both diversity and unity: a common genetic code and shared ancestry across life.

The process of doing biology: the nature of science

• Scientists ask questions that can be answered by measuring and collecting data.
• Science involves formulating hypotheses and gathering evidence that supports or conflicts with those hypotheses.
• Biologists test ideas about the natural world by testing predictions made by alternative hypotheses.

The scientific method: two modes of inquiry

• Discovery or Descriptive Science (inductive): describing natural phenomena through observation and data analysis; moves from specific observations to general conclusions.
• Hypothesis-based Science (deductive): uses induction from discovery to formulate a hypothesis; then uses premises to test a hypothesis via testable predictions.
• The combination of discovery and hypothesis-based science drives biological inquiry.

Scientific reasoning: induction and deduction

• Inductive reasoning: using related observations to arrive at a general conclusion.
• Deductive reasoning: using a general principle to forecast specific results.
• In practice, conclusions from induction often become premises for deduction in further testing.

The scientific method: steps and hypothesis testing

• The method consists of a series of well-defined steps:
  • Make an observation
  • Ask a question
  • Form a hypothesis that answers the question
  • Make a prediction based on the hypothesis
  • Do an experiment to test the prediction
  • Analyze the results
  • Determine whether the hypothesis is supported or not
  • Report results and repeat or refine as needed
• A hypothesis is a testable explanation based on past experience, data, and observations.
• A hypothesis can be falsified but never absolutely proven.

Pasteur’s experiment: key demonstration for cell theory

• Pasteur proposed that cells arise from pre-existing cells, not by spontaneous generation.
• The experiment compared straight-necked and swan-necked flasks with nutrient broth, boiled to sterilize, then observed growth of cells.
• In straight-necked flasks, cells entered from air and growth occurred; in swan-necked flasks, condensed air prevented cells from entering and growth was prevented.
• Conclusion: Cells come from pre-existing cells, not from spontaneous generation.

Hypothesis testing: design and interpretation

• Hypothesis testing is a two-step process:
  1. State the hypothesis precisely and list predictions.
  2. Design observational or experimental studies capable of testing those predictions.

Examples of hypothesis testing in biology

• Why do giraffes have long necks?
  • Food competition hypothesis: long necks evolved to access high foliage.
  • Predictions: neck length varies; neck length is heritable; giraffes feed high in trees. Tests by Simmons and Scheepers found predictions not all supported, prompting alternative hypotheses.
• The Sexual Competition hypothesis: long necks provide advantages in male combat and mating.
  • Data supported this hypothesis; the food-competition hypothesis was not fully supported; other hypotheses may better explain neck length.
• Experimental design—how do ants navigate?
  • Desert ants travel far to forage and return in a straight line; researchers tested how they navigate back to the nest.
  • The pedometer hypothesis proposed ants count stride number or length to estimate distance from nest.
  • Experimental setup involved manipulating leg length (stumps, normal, stilts) and measuring return paths.
  • Results showed: ants used stride information to estimate distance; manipulations affected return behavior, supporting pedometer-based navigation.

Experimental design and interpretation: key elements

• A well-designed experiment includes:
  • A control group to check for other effects (e.g., normal ants).
  • Controlled experimental conditions to eliminate confounding variables.
  • Repetition to reduce distortion from small sample sizes.

Summary of principles of experimental design

• Biologists practice evidence-based decision making:
  • Ask questions about how organisms work.
  • Pose hypotheses to answer those questions.
  • Use observational or experimental evidence to decide which hypotheses are correct.

Basic versus applied science

• Basic science (pure science) aims to expand knowledge regardless of immediate applications.
• Applied science aims to use science to solve current problems defined by the researcher.

Peer review and scientific publication

• Scientific progress often occurs through peer-reviewed literature.
• Peer review is a blind process where researchers submit experiments, results, and interpretations; reviewers assess the validity and merit for publication.
• Papers typically follow a format: Abstract, Introduction, Methods, Results, Discussion, Literature Cited.

Closing learning objectives recap

• By studying this section, you should be able to:
  • Identify and describe the properties of life.
  • Describe the levels of organization among living things.
  • Describe the three theories that form the framework for modern biological science.
  • Summarize the steps of the scientific method.
  • Compare inductive reasoning with deductive reasoning.

Observed and expressed equations and formulas

• Unit conversion example:
  • One micrometer is the scale for cells: 1~\mu\mathrm{m} = 10^{-6}\mathrm{m}
• DNA base pairing (conceptual): A pairs with T, C pairs with G; this is the underlying rule of DNA structure.
• Central Dogma (flow of information): \text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}
• DNA as the blueprint and matrix for inheritance; the coding sequence determines cellular products and phenotype.

Connections to real-world relevance

• Understanding life’s properties helps in fields from medicine to ecology.
• The tree of life informs phylogenetics and our understanding of biodiversity.
• The scientific method underpins evidence-based decision making in science and policy.
• The ethical and practical implications of biotechnology, genetics, and evolution are central to biology as a discipline.