Integrative Biology Notes: Introduction to Life and the Biological Hierarchy

Welcome and Course Introduction

The course is titled Integrative Biology (APMED1-A, B) for the 1st Semester of the School Year 2026-2027 at the Far Eastern University – Dr. Nicanor Reyes Medical Foundation. The institutional branding emphasizes the motto: "Exploring Life. Understanding Health. Advancing Medicine." The course begins with a spiritual reflection from Jeremiah 29:11, stating: "For I know the plans I have for you, declares the LORD, plans to prosper you and not to harm you, plans to give you hope and a future."

The agenda for the introductory week, titled "WK 1: Life & Lens," includes a welcome and introduction, group discussions, course orientation, and laboratory activities. The laboratory focus involves an introduction to life and lenses, including laboratory safety, the history of the microscope, and microscope basics such as parts and functions.

Introductory Group Discussion and Icebreakers

Students are tasked with several introductory activities to foster a sense of community ("familEE"). In the "Getting to Know You" icebreaker, students must provide their first name or nickname, share their favorite living organism (excluding humans) and explain why, and describe their motivation for enrolling in the APMed program. Additionally, students are asked what they are most excited to learn in Integrative Biology this semester and may optionally share one fun fact about themselves.

A secondary group discussion (groups of 5–6 students) focuses on philosophical and scientific inquiries. This includes defining life from both a scientific and philosophical perspective, debating whether life can be defined in a single sentence, and explaining views on the origin of life (scientific, philosophical, or faith-based). The groups also identify the characteristics required for an organism to be considered living and discuss unique qualities that set humans apart from other organisms.

The Scientific Definition of Biology

Biology is derived from two Greek words: $bios$, meaning life, and $logos$, meaning to study. It is the scientific study of living organisms. This branch of science specifically deals with the origin, development, and interactions of living organisms with their environment.

Theories and Concepts Regarding the Origin of Life

The origin of life is explored through various scientific theories and conceptual frameworks:

1. Abiogenesis: This theory focuses on the origin of the first life from non-living matter through natural chemical processes involving organic molecules.

2. RNA World Hypothesis: This hypothesis suggests that RNA molecules were the first genetic material, preceding both DNA and proteins in the evolutionary timeline.

3. Endosymbiotic Theory: This theory explains the origin of organelles such as mitochondria and chloroplasts. It posits that one early eukaryotic cell engulfed another (likely a bacterium) and formed a permanent symbiotic relationship. For example, chloroplasts are thought to have evolved from cyanobacteria.

4. Microbial Life Theory: This identifies the first organisms on Earth as microorganisms, specifically bacteria and archaea, which dominated the planet during its early stages.

5. Cyanobacteria and Oxygenation: This concept highlights the role of cyanobacteria in shaping the Earth's atmosphere. Through photosynthesis, these microbes led to the rise of atmospheric oxygen.

Perspectives on Life's Origin and the Age of Earth

There are several views regarding how life began, partitioned by their acceptance of supernatural intervention and the geological age of the Earth:

• Biblical Creationism: Accepts supernatural divine creation. Rejects the scientific age of the Earth, positing it is approximately $6,000$ to $10,000$ years old. The mechanism is direct divine creation.

• Old Earth Creationism: Accepts supernatural intervention and the scientific age of the Earth (approximately $4.5 \times 10^9$ years). The mechanism is divine creation occurring over long periods.

• Intelligent Design: Implies a supernatural or intelligent cause and accepts the scientific age of the Earth.

• Abiogenesis / RNA World: Rejects supernatural intervention. Accepts the scientific age of the Earth. Mechanisms involve natural chemical processes and RNA-based self-replication.

• Hydrothermal Vents: Life originated from the unique chemistry found at deep-sea vents. Accepts the scientific age of the Earth.

• Panspermia: Life arrived on Earth from space. Supernatural involvement is not necessarily required, and it accepts the scientific age of the Earth.

Debunking Spontaneous Generation

Historically, the theory of spontaneous generation suggested life could arise from non-living matter. This was disproved by two landmark experiments:

1. Francesco Redi’s Experiment (1668): Redi used meat in three containers: one open, one sealed with a cork, and one covered with gauze (mesh). Maggots only appeared on the meat in the open container where flies could reach it. In the gauze-covered container, maggots were found on the gauze but not on the meat. This proved that maggots do not form spontaneously from meat.

2. Louis Pasteur’s Experiment: Pasteur used swan-neck flasks to show that "Omne vivum ex vivo" (Life only comes from life). He boiled broth to kill microorganisms. The curve of the flask's neck prevented outside air/microbes from entering, so no contamination occurred. When the neck was broken, bacteria reached the broth, and growth occurred. This demonstrated that microorganisms in the air, not the air itself, caused growth.

The Hierarchy of Biological Organization

Biological organization is a structured hierarchy where each level builds upon the one below it. The levels are categorized as follows:

• Subatomic Particles
• Atoms: The smallest units of matter.
• Molecules: Atoms bonded together to form compounds (e.g., $H_2O$).
• Macromolecules: Very large molecules such as proteins, fats (lipids), carbohydrates, and nucleic acids.
• Organelles: Structures made of macromolecules (e.g., Mitochondrion, Peroxisome, Golgi complex, Nucleus, Ribosomes, Endoplasmic reticulum).
• Cells: The basic unit of life, made up of macromolecules and organelles.
• Tissues: Groups of the same kind of cells working together (e.g., Red blood cells, cartilage cells, bone cells).
• Organs: Groups of the same kind of tissues working together (e.g., heart, lungs).
• Organ Systems: Multiple organs working together (e.g., respiratory system, circulatory system).
• Organism: The entire living thing, which may be a single cell or complex multicellular systems.
• Population: Localized groupings of organisms belonging to the same species.
• Community: Several populations of different species living and interacting together.
• Ecosystem: Formed when biological communities interact with their physical (abiotic) surroundings.
• Biome: A large naturally occurring community of flora and fauna occupying a major habitat.
• Biosphere: The global sum of all ecosystems, including the Atmosphere (air), Ecosphere, Hydrosphere (water), and Lithosphere (land).

Fundamental Characteristics of Living Things

1. Organization: Living organisms have a structured, hierarchical arrangement. Each level supports the next.

2. Cellular Structure: The cell is the basic unit of life. Organisms can be unicellular (one cell) or multicellular (trillions of cells).

3. Reproduction: This ensures the continuation of a species. It involves genetic transfer ($DNA$). Methods include sexual or asexual reproduction. On a smaller scale, genes replicate, and cells divide for growth and repair.

4. Possession of Genetic Code: $DNA$ (Deoxyribonucleic acid) is the heritable material directing cell activity. Genes are the units of information passing from parents to offspring. $DNA$ serves as a blueprint for proteins, with $RNA$ acting as an intermediate. "Gene expression" refers to converting genetic info into biological products.

5. Growth and Development: Growth is an increase in size and cell number. Development is the process of change and specialization throughout an organism's life.

6. Metabolism: The sum of all chemical reactions for energy conversion and building materials. This includes Anabolism (synthesizing complex molecules from smaller units, requiring energy) and Catabolism (breaking down complex molecules to produce energy).

7. Homeostasis: The ability to maintain a stable internal environment (e.g., temperature, $pH$, fluid balance) despite external changes.

8. Responsiveness to Stimuli: The ability to detect and react to internal or external changes. This is also called "irritability" at the cellular level.

9. Adaptation and Evolution: Successive genetic changes over generations allow species to adjust to their environments. Evolution explains both the unity and diversity of life.

10. Interaction: No organism lives in isolation. Interactions can be internal (between organs/systems) or external (with other organisms or the environment).

Ecosystem Interactions and Roles

Organisms play specific roles within feeding relationships in an ecosystem:

• Producers: Usually plants or microbes that produce their own food.
• Consumers: Organisms that rely on others for nutrients. These include Herbivores (eat plants), Carnivores (eat meat), and Omnivores (eat both).
• Scavengers: Break down dead organic matter into smaller particles.
• Decomposers: Consume the smaller particles further (e.g., fungi, bacteria).

Symbiotic relationships describe the close interactions between species:

• Mutualism: Both organisms benefit.
• Commensalism: One organism benefits, while the other is neither helped nor harmed.
• Parasitism: One organism benefits at the expense of the other (the host).

Questions and Discussion

Regarding the biological status of viruses, it is concluded that viruses are not living things. While they are complicated assemblies of molecules (proteins, nucleic acids, lipids, and carbohydrates), they lack their own biological machinery for metabolism or replication. They cannot multiply without entering a living cell.

Discussion questions for student groups include:

1. How did Pasteur’s experimental design allow air, but not microbes, to enter, and why was this important?
2. What was the control group in Pasteur’s experiment and what did it show?
3. What knowledge can we gain from Pasteur’s experiment that you can apply in your future profession as doctors?

Personal reflection prompts:

1. Which theory or belief about the origin of life do you personally find most convincing? Why?
2. Can religious beliefs and scientific theories coexist when it comes to explaining the origin of life? Why or why not?

Assignment: Cell Theory

Students are assigned to watch the video "The Wacky History of Cell Theory" and answer:

1. What does the cell theory state ($3$ parts)?
2. How does the cell theory disprove the theory of spontaneous generation?
3. How can you personally relate to the statement: "If something bores you, dig deeper."