Bio 110 Note Guide: Defining Life, Metabolism, Cellular Scale, and Evolutionary Principles

Defining Life and the Key Concepts of Biology

• The phenomenon of life lacks a simple definition; living entities are recognized primarily by their actions, processes, and functional characteristics.

• In the study of origin-of-life biogenesis theories (such as work documented by Noam Lahav), there exist at least 48 formal definitions of life.

• Life can be framed through six fundamental core concepts:

  • Chemistry

  • Organization

  • Energy Transfer

  • Information Transfer

  • Evolution

  • Emergent Properties

Chemical Foundations and Thermodynamic Principles

• Organisms are compositions of chemical components, including water, minerals, proteins, sugars, nucleic acids, and fats, yet living organisms remain fundamentally distinct from static chemical mixtures.

• Element abundance differs significantly between the non-living environment (such as Earth's crust) and living matter (such as the human body):

  • Composition of Earth's Crust:

  • Oxygen ($\text{O}$): $46.5\%$

  • Silicon ($\text{Si}$): $28\%$

  • Aluminum ($\text{Al}$): $8\%$

  • Iron ($\text{Fe}$): $5\%$

  • Calcium ($\text{Ca}$): $4\%$

  • Hydrogen ($\text{H}$): $0.14\%$

  • Phosphorus ($\text{P}$): $0.1\%$

  • Carbon ($\text{C}$): $0.09\%$

  • Other elements: $8.3\%$

  • Composition of the Human Body:

  • Oxygen ($\text{O}$): $65\%$

  • Carbon ($\text{C}$): $18\%$

  • Hydrogen ($\text{H}$): $10\%$

  • Nitrogen ($\text{N}$): $3\%$

  • Calcium ($\text{Ca}$): $1.5\%$

  • Phosphorus ($\text{P}$): $1\%$

  • Iron ($\text{Fe}$): $< 0.05\%$

  • Aluminum ($\text{Al}$): $< 0.001\%$

  • Other elements: $1.5\%$

  • Living cells are predominantly composed of oxygen, carbon, and hydrogen, with the majority of hydrogen and oxygen occurring in the form of water ($\text{H}_2\text{O}$).

• Thermodynamics in Biological Systems:

  • First Law of Thermodynamics: Energy cannot be created or destroyed. Organisms take up input energy in the form of sunlight or food chemical energy and convert it entirely into work and heat.

  • Second Law of Thermodynamics: Chemical reactions within a cell can increase internal order by harnessing energy, but excess energy is released into the surroundings as heat. This heat increases entropy (disorder) in the external environment, ensuring that the total disorder of the universe increases and the Second Law is maintained.

Biological Organization, Domains, and Cellular Structure

• Hierarchical Levels of Organization:

  • Molecule $\rightarrow$ Cell / Organ $\rightarrow$ Organism $\rightarrow$ Population $\rightarrow$ Community $\rightarrow$ Ecosystem $\rightarrow$ Biosphere.

• Domains of Life:

  • All known life forms descend from a single common ancestor and are classified into three primary domains: Bacteria, Archaea, and Eukarya.

  • Domain Bacteria: Unicellular prokaryotic organisms lacking a membrane-bound nucleus.

  • Domain Archaea: Unicellular prokaryotic organisms lacking a membrane-bound nucleus.

  • Domain Eukarya: Eukaryotic organisms containing membrane-bound nuclei and internal cellular compartmentalization; predominantly multicellular.

• Kingdoms of Domain Eukarya:

  • Kingdom Plantae: Multicellular organisms that synthesize their own sugars and organic nutrients via photosynthesis.

  • Kingdom Fungi: Multicellular or unicellular decomposers that absorb nutrients by digesting dead organisms and organic waste.

  • Kingdom Animalia: Multicellular organisms that obtain nutrients by ingesting and digesting other organisms.

  • Unique Nutritional Exceptions & Phenomena:

  • Carnivorous plants capture and digest animals to supplement nutrient acquisition in nutrient-poor environments.

  • Kleptoplasty occurs in specialized organisms, such as photosynthetic sea slugs or insects capable of sequestering chloroplasts to capture light energy.

• Biodiversity Metrics:

  • As of 2025, approximately $2.3\text{ million}$ species have been formally described on Earth (excluding extinct organisms).

• Cellular Foundation of Life:

  • All living organisms are composed of cells, bounded by a plasma membrane that regulates internal environments to maintain homeostasis.

  • Cells store and transmit genetic information, and acquire, convert, and utilize energy for cellular processes.

  • Eukaryotic cells possess compartmentalized, membrane-bound organelles to separate distinct biochemical environments.

Scale and Relative Dimensions of Biological Structures

• Biological structures span wide spatial dimensions measured on a logarithmic scale:

  • $0.1\,\text{nm}$: Single Atom

  • $1\,\text{nm}$: Protein molecule

  • $10\,\text{nm}$: Lipids / Cell Membrane thickness

  • $100\,\text{nm}$: Influenza Virus

  • $1\,\mu\text{m}$: Mitochondria, Typical Bacteria

  • $10\,\mu\text{m}$: Animal cell, Plant cell

  • $100\,\mu\text{m}$: Human egg cell

  • $1\,\text{mm}$: Frog egg

  • $10\,\text{mm}$: Chicken egg

  • $100\,\text{mm}$: Ostrich egg

  • $1\,\text{m}$: Adult human female

• Visual Limits of Scientific Instruments:

  • Electron Microscope: Resolves structures from $0.1\,\text{nm}$ up to approximately $100\,\mu\text{m}$.

  • Light Microscope: Resolves structures from $1\,\mu\text{m}$ up to approximately $1\,\text{mm}$.

  • Unaided Human Eye: Resolves structures from approximately $100\,\mu\text{m}$ up to $1\,\text{m}$ and beyond.

Energy Transfer, Metabolism, and Homeostasis

• Energy Requirements and Currency:

  • All organisms require energy to drive cellular functions, with ultimate energy inputs typically originating from solar radiation or chemical compounds.

  • Adenosine Triphosphate (ATP) serves as the universal energy currency across all life forms.

• Metabolism:

  • Defined as the sum total of all chemical reactions occurring within an organism.

  • Anabolism: Metabolic pathways that construct complex biological macromolecules from simpler biological precursors, requiring energy input.

  • Catabolism: Metabolic pathways that break down complex molecules into simpler units, releasing chemical energy.

• Homeostasis and Autopoiesis:

  • Autopoiesis describes the continuous self-maintenance and structural self-generation required for living systems to maintain structural stability.

  • Biochemical processes demand stringent conditions regarding temperature ($T^\circ$) and pH levels.

  • Homeostasis is the active regulation of internal biological conditions to maintain dynamic constancy, which is distinct from thermodynamic equilibrium.

Information Transfer and the Central Dogma

• Storage and Inheritance:

  • Nucleic acids (such as DNA) preserve and transmit the information required for cellular construction and functionality.

  • Specific base pairing within the double-helical structure of DNA ensures precision and fidelity during nucleic acid replication.

• Central Dogma of Molecular Biology:

  • Genomic sequences in DNA code for functional biological products.

  • Process flow: Genetic DNA sequences are transcribed into an RNA intermediate message, which is subsequently translated into functional protein products.

  • Natural exceptions to the traditional unidirectional flow of the Central Dogma exist in biological systems.

• Genotype and Phenotype Expression:

  • Genotype: The genetic instructions encoded within the genome.

  • Phenotype: The physical and functional realization of genetic instructions, categorized into:

  • Behavioral phenotypes

  • Morphological phenotypes

  • Biochemical phenotypes

  • Physiological phenotypes

• DNA is distinct from a mechanical or structural blueprint, as gene expression is dynamically mediated by physiological context and environment.

Evolution, Natural Selection, and Sexual Selection

• Key Drivers of Evolution:

  • Populations evolve over generations; individual organisms do not evolve within their lifetimes.

  • Natural selection functions through three required conditions:

  1. Variation: Individuals within a population possess phenotypic differences.

  2. Selection: Specific variation patterns influence an individual's survival and reproductive success.

  3. Inheritance: Variations are genetically based and passed to offspring.

• Misconceptions on Fitness:

  • Natural selection relies on differential reproductive success rather than physical dominance or simple survival.

  • Organisms produce more progeny than environmental carrying capacities can support, generating competitive pressure.

• Sources of Genetic Variation:

  • Random genetic mutations represent the primary origin of new genetic traits.

  • While mutations occur randomly, natural selection acts non-randomly on traits that impact survival and reproduction.

• Artificial Selection:

  • Human-driven selection in which specific phenotypic traits are intentionally favored for breeding in agricultural crops and domesticated animals.

  • Crop Evolution Example: Modern corn was selectively bred from the wild grass Teosinte by indigenous populations in Mesoamerica starting roughly $7{,}000\,\text{years}$ ago.

• Sexual Selection and Dimorphism:

  • Mate choice exercised by one sex exerts selective pressure on the traits, physical ornamentation, morphological structures, and behaviors of the opposite sex, generating sexual dimorphism.

• Structural Evolutionary Relationships:

  • Homology: Structural or genetic similarity resulting from shared evolutionary descent.

  • Analogy / Convergent Evolution: Structural similarities that evolve independently in unrelated lineages due to similar environmental pressures (e.g., body forms of Ichthyosaurs, Dolphins, and Sharks).

Emergent Properties and Boundary Cases of Life

• Emergent Properties:

  • Complex traits that arise from the interaction of simpler components, which do not exist within the individual elements themselves.

  • Chemical Example: Elemental Sodium ($\text{Na}$, a reactive metal) combines with Chlorine ($\text{Cl}$, a toxic gas) to form Sodium Chloride ($\text{NaCl}$, common edible salt).

• Challenging Boundary Cases in Biological Definitions:

  • Plant Seeds: Seeds (such as those from cantaloupe, okra, leek, lettuce, bell pepper, eggplant, broccoli, and tomato) remain metabolically dormant for extended durations before germination, challenging rigid criteria of continuous living processes.

  • Tardigrades (Water Bears): Microscopic animals capable of undergoing extreme dehydration into a dried powder state (cryptobiosis). In this state, metabolic activities cease entirely. Upon rehydration, tardigrades fully resume active cellular metabolism and life functions.

The Scientific Method and Principles of Biological Inquiry

• Definition of Biology: The systematic science investigating how biological systems function, ranging across:

  • Molecular and cellular mechanisms.

  • Integrated organ networks and individual organismal systems.

  • Ecological interactions among distinct organisms within natural ecosystems.

• Core Process of Scientific Investigation:

  • Observation & Questioning: Direct observation leads to specific biological inquiries.

  • Hypothesis Formulation: A hypothesis provides a tentative explanation that yields testable, falsifiable predictions regarding unknown phenomena or unperformed experiments (a prediction itself is distinct from a hypothesis).

  • Experimental Testing & Data Interpretation: Conducting experiments or collecting field observations to evaluate predictions.

  • Refinement of Understanding: Hypotheses are modified, accepted, or rejected based on observational data.

• Distinguishing Scientific Theories from Everyday Hypotheses:

  • In common language, a "theory" refers to a hunch or unproven speculation.

  • In scientific practice, a Theory represents an overarching explanation of natural phenomena backed by rigorous testing, consistent observational data, and extensive experimental validation (e.g., Theory of Gravity, Theory of Evolution).

• Mechanics of Scientific Inquiry:

  • Science is an iterative process rather than a rigid linear procedure.

  • Exploration: Making observations, engaging scientific literature, asking questions, maintaining curiosity.

  • Investigation: Constructing testable hypotheses and models, executing experiments, interpreting gathered data.

  • Loop & Revision: Inconsistent results require hypothesis modification or rejection. Broadly consistent results across diverse experimental conditions lead to the establishment of scientific theories.

  • Communication: Presenting results in peer-reviewed literature, discussing experimental findings, participating in conferences, informing public policy, and solving practical real-world problems.

• Historical Context and Analysis: Biological structure and origin studies draw upon fundamental conceptual frameworks detailed by researchers such as Cami and Farre (2003) as well as Goodsell (2005).