Biology and Molecules of Life

The Study of Life and Earth’s Biodiversity

• Biology Defined: The scientific study of life.

• Current State of Biological Discovery:     - Scientists have identified only a fraction of the total organisms inhabiting Earth.     - New species are being discovered at a constant rate.     - Extinction Rates: Extinction is currently occurring at an accelerating pace.     - Example: New Guinea’s Foja Mountains serve as a specific site where new species are frequently discovered.

Levels of Organization in Nature

• Component Foundation: Both living and nonliving things consist of the same basic components.

• Hierarchy of Complexity:     1. Atom: The fundamental building block of all matter.     2. Molecule: An association consisting of two or more atoms. Life’s unique properties emerge from the specific interactions of these molecular components.     3. Cell: The smallest unit of life.     4. Organism: An individual consisting of one or more cells.     5. Population: A group of individuals belonging to the same species residing in a specific, given area.     6. Community: The collective of all populations of all species residing in a given area.     7. Ecosystem: A community of organisms interacting with their physical environment.     8. Biosphere: All regions of Earth that support and hold life.

Universal Characteristics of Living Things

• Shared Traits: All organisms share specific fundamental characteristics:     - Requirement for ongoing inputs of energy and raw materials.     - Ability to sense and respond to internal and external change.     - Capacity to pass DNA (genetic information) to offspring.

• Energy and Nutrients:     - Life’s organization is sustained through a one-way flow of energy through the biosphere and the cycling of nutrients among organisms.     - Energy: Defined as the capacity to do work.     - Nutrient: A substance necessary for survival that an organism is unable to produce for itself.

• Organisms and Energy Sources:     - Producers: Organisms that manufacture their own food using energy and simple raw materials obtained from nonbiological sources.         - Example: Plants utilizing photosynthesis.     - Consumers: Organisms that obtain both energy and nutrients by feeding on other organisms.         - Example: Mammals.

• Homeostasis: The process by which an organism maintains its internal conditions within a specific range that supports survival by sensing and responding to environmental or internal changes.

• Growth and Development:     - Growth: An increase in dimensions such as size, volume, and the number of cells within multicelled species.     - Development: The process through which the first cell of a new individual progresses to become a multicelled adult.

• Reproduction and Inheritance:     - Reproduction: The process by which individuals generate offspring.     - Inheritance: The transmission of DNA to offspring.     - DNA (Deoxyribonucleic Acid): The molecule that carries hereditary (genetic) information guiding development and biological activities; it is the primary source of the diversity of life.

Biological Classification and Diversity

• Biodiversity: The scope of variation among living organisms.

• Classification Schemes: Schemes known as taxonomy help scientists organize biological knowledge.

• Nucleus: A saclike structure that contains a cell's DNA. Organisms are broadly grouped based on the presence or absence of this structure.

• Prokaryotes: Single-celled organisms where the DNA is not enclosed in a nucleus.     - Bacteria: The most numerous organisms currently found on Earth.     - Archaea: Single-celled organisms that are evolutionarily more closely related to eukaryotes than to bacteria.

• Eukaryotes: Organisms whose DNA is contained within a defined nucleus. This group includes:     - Protists: The simplest eukaryotes, categorized by great diversity.     - Fungi: Eukaryotic consumers that break down food externally.     - Plants: Typically multicelled, photosynthetic producers.     - Animals: Multicelled consumers that ingest other organisms or their juices.

Taxonomy and the Species Concept

• Taxonomy Naming System: Developed by Linnaeus, this practice involves naming and classifying species.     - Genus: A group of species sharing a set of unique traits.     - Scientific Naming: Each species receives a two-part scientific name consisting of its genus and species identifier.         - Example: Humans are classified as Homo sapiens.

• Taxon: A group of organisms sharing a unique set of traits. The hierarchy of taxa (from most inclusive to least inclusive) is:     1. Domain     2. Kingdom     3. Phylum     4. Class     5. Order     6. Family     7. Genus     8. Species

• Determining Species Lines:     - Early naturalists used morphological (appearance) and geographical data.     - Modern biologists utilize biochemical traits, such as DNA sequences.

• Biological Species Concept: Defined by Ernst Mayr as one or more groups of individuals that can potentially interbreed and produce fertile offspring, while being unable to interbreed with other groups.

The Scientific Method and Critical Thinking

• Critical Thinking: The deliberate process of evaluating the quality of information before accepting it.

• Science: The systematic study of the observable world.

• Pseudoscience: Beliefs, theories, or practices presented as scientific but lacking scientific evidence or testability.

• Scientific Method Steps:     1. Observe an aspect of nature.     2. Formulate a Hypothesis: A testable explanation for a natural phenomenon.     3. Test the hypothesis:         a. Formulate a Prediction: A statement about a condition that should exist if the hypothesis is correct.         b. Test the prediction through experiments or surveys. A Model (an analogous system) may be used.         c. Analyze the Data: The test results from the experiment or research.     4. Form a conclusion regarding whether the results support the hypothesis.     5. Report the results to the scientific community.

• Experimental Terms:     - Variable: A characteristic that differs among individuals or over time.     - Experimental Group: Individuals possessing a specific characteristic or receiving a specific treatment.     - Control Group: A group not exposed to the independent variable being tested.     - Experiment: A test designed specifically to support or falsify a prediction.

Case Study: Peacock Butterfly Experiment

• Objective: To determine how wing spots and sound affect predation by birds.

• Experimental Data:     - Wing spots concealed: $5$ of $10$ eaten ($50\%$).     - Wings silenced: $0$ of $8$ eaten ($0\%$).     - Wing spots concealed and wings silenced: $8$ of $10$ eaten ($80\%$).     - No treatment (Control): $0$ of $9$ eaten ($0\%$).

Analyzing Experimental Results

• Sampling Error: The difference between results obtained from a small subset (sample) and the results from the whole population.

• Probability: The chance that a specific outcome will occur.

• Statistically Significant: A result that is highly unlikely to have occurred by chance alone.

• Quantitative Results: Science prioritizes data that can be measured or gathered objectively.

Scientific Theories and Laws

• Scientific Theory: A hypothesis that has resisted disproval after many years of rigorous testing.     - Theories can be consistent with all gathered data and help predict other phenomena.     - They can never be proven absolute, but a single inconsistent observation can disprove them.     - Example: Theory of Evolution.

• Major Scientific Theories:     - Atomic Theory: All matter consists of atoms and subatomic particles.     - Big Bang: The universe began expanding from a hot, high-density state.     - Cell Theory: All organisms consist of cells; the cell is the basic unit of life; all cells come from preexisting cells.     - Evolution by Natural Selection: Environmental pressures drive changes in inherited traits.     - Plate Tectonics: Earth's lithosphere is cracked into moving pieces.

• Law of Nature: A phenomenon observed to occur in every circumstance without fail, though it may lack a complete scientific explanation.     - Example: Laws of Thermodynamics.

• Scope of Science: Science is an objective description of the natural world. It does not address subjective questions, moral standards, aesthetics, philosophy, or the supernatural.

Distinguishing Science from Pseudoscience

• Observable Phenomena: Science involves only the natural world; pseudoscience may involve the supernatural or mysterious.

• Testability: Science is testable via predictions and designed to reveal flaws; pseudoscience is often untestable or resists flaw-detection.

• Evidence: Science relies on systematic data; pseudoscience relies on unverified info, anecdotes, or rhetoric.

• Inconsistent Evidence: In science, inconsistent evidence prompts hypothesis revision; in pseudoscience, it is ignored or denied.

Basic Atomic Structure

• Atom: The fundamental building block of all matter (solid, liquid, gas, and plasma).

• Subatomic Particles:     - Proton ($p^+$): Positively charged; found in the nucleus of all atoms.     - Electron ($e^-$): Negatively charged; occupies orbitals surrounding the nucleus.     - Neutron: Uncharged (neutral); found in the nucleus.

• Charge: An electrical property where opposite charges attract and like charges repel.

• Element: A pure substance consisting only of atoms with the same number of protons.     - Example: Phosphorus ($P$) has an atomic number of $15$.

• Isotopes: Forms of an element with different numbers of neutrons. This changes the mass number but not the electrical charge.     - Example: Carbon-12.

Molecules and Chemical Bonds

• Chemical Bond: An attractive force arising between two atoms when their electrons interact. Atoms typically fill vacancies by sharing electrons.

• Molecule: A group of two or more atoms joined by chemical bonds.

• Compound: A molecule consisting of atoms of more than one element.

Acids, Bases, and pH

• Water Dissociation: Water separates into hydrogen ions ($H^+$) and hydroxide ions ($OH^-$).

• pH Scale: A measure of the concentration of $H^+$ in a solution.     - Inversely Proportional: The higher the concentration of $H^+$ ions, the lower the pH value.     - Neutral pH: Pure water has a pH of $7$, where the number of $H^+$ ions equals the number of $OH^-$ ions.

• Acids: Substances that release $H^+$ ions; pH is less than $7$.

• Bases: Substances that release $OH^-$ ions; pH is greater than $7$.

• Buffer Systems: Chemical systems that help resist changes in pH.     - Bicarbonate Buffer System:         - Carbon dioxide forms carbonic acid in water: $CO_2 + H_2O \rightarrow H_2CO_3$         - Excess $H^+$ combines with bicarbonate: $H^+ + HCO_3^- \rightleftharpoons H_2CO_3$