Themes and Concepts of Biology - Flashcards
Themes and Concepts of Biology
Biology Defined: Biology is the science dedicated to the study of life.
Defining Life's Complexity: While seemingly obvious, precisely defining life is challenging. Viruses, for example, exhibit some characteristics of living entities (like attacking organisms, causing diseases, and reproducing) but lack others, thus not meeting all biological criteria for life.
Fundamental Questions in Biology: Biology fundamentally addresses four core questions:
What are the common properties that make something "alive"?
How do various living organisms function?
How can we organize the remarkable diversity of life for better understanding?
How did this diversity originate and how does it continue to evolve?
Learning Objectives: By the end of this discussion, one should be able to:
Identify and describe the fundamental properties of life.
Describe the hierarchical levels of organization in living things.
List examples of various sub-disciplines within biology.
Properties of Life
All living organisms share eight key characteristics or functions that collectively define life:
Order:
Organisms are highly organized structures, composed of one or more cells.
Even single-celled organisms are complex, with atoms forming molecules, which in turn form cell components (organelles).
Multicellular organisms, with millions of cells, benefit from cellular specialization, allowing cells to perform specific functions and even be sacrificed for the organism's overall good.
Example: A toad represents a highly organized structure, from cells to tissues, organs, and organ systems.
Sensitivity or Response to Stimuli:
Organisms react to diverse stimuli from their environment.
Examples:
Plants bend towards light or respond to touch (e.g., Mimosa pudica leaves droop when touched, returning to normal after a few minutes).
Bacteria exhibit chemotaxis (movement towards or away from chemicals) or phototaxis (movement towards or away from light).
Movement towards a stimulus is a positive response, while movement away is a negative response.
Reproduction:
Single-celelled organisms: Reproduce by replicating their DNA (genetic material) and then dividing equally to form two new cells.
Multicellular organisms: Produce specialized reproductive cells that form new individuals.
During reproduction, genes (segments of DNA) are passed from parent to offspring, ensuring the offspring belongs to the same species and inherits similar characteristics (e.g., fur color, blood type).
Adaptation:
All living organisms demonstrate a "fit" to their environment, known as adaptation.
Adaptation is a direct consequence of evolution by natural selection, a process operating in all reproducing lineages.
Adaptations enhance an individual's reproductive potential, including their ability to survive and reproduce.
Examples:
Heat-resistant Archaea thriving in boiling hot springs.
The tongue length of a nectar-feeding moth precisely matching the size of the flower it feeds from.
Adaptations are not static; as environments change, natural selection drives corresponding changes in population characteristics.
Growth and Development:
Organisms grow and develop based on specific instructions encoded in their genes.
Genes direct cellular growth and development, ensuring offspring exhibit characteristics similar to their parents (e.g., kittens inheriting traits from both parents).
Regulation:
Complex organisms require multiple regulatory mechanisms to coordinate internal functions.
These include nutrient transport, response to stimuli, and coping with environmental stresses.
Examples:
Organ systems like the digestive or circulatory systems perform specific functions (e.g., carrying oxygen, removing wastes, delivering nutrients, cooling the body).
Polar bears regulate body temperature in cold environments by generating heat and reducing heat loss via thick fur and fat.
Homeostasis: (Implicitly covered under Regulation, though not explicitly listed as a separate bullet in the PDF, it aligns with regulating internal functions).
Energy Processing:
All organisms utilize a source of energy for their metabolic activities.
Some capture solar energy to convert it into chemical energy (food) via photosynthesis.
Others obtain chemical energy from molecules they consume.
Example: California condors use chemical energy derived from food to power flight.
Levels of Organization of Living Things
Living organisms are organized hierarchically from smallest to largest:
Atom: The smallest, most fundamental unit of matter, consisting of a nucleus surrounded by electrons.
Molecule: A chemical structure formed by at least two atoms held together by chemical bonds.
Macromolecule: Large, biologically important molecules formed by combining smaller units called monomers (e.g., deoxyribonucleic acid (DNA), which carries genetic instructions).
Organelle: Aggregates of macromolecules surrounded by membranes within cells, performing specialized functions (e.g., mitochondria, chloroplasts).
Cell: The smallest fundamental unit of structure and function in living organisms. (Viruses are not considered living because they are not made of cells and require a host cell to reproduce).
Prokaryotic cells: Single-celled organisms lacking membrane-bound organelles and a nucleus (e.g., bacteria, archaea).
Eukaryotic cells: Possess membrane-bound organelles and a nucleus (e.g., plant cells, animal cells).
Tissue: Groups of similar cells that work together to perform the same specific function (e.g., muscle tissue, nervous tissue).
Organ: Collections of different tissues grouped together based on a common function (e.g., heart, lung, skin in animals; leaves, stems in plants).
Organ System: A higher level of organization comprising functionally related organs (e.g., the circulatory system with the heart and blood vessels).
Organism: An individual living entity (e.g., a tree, a single-celled prokaryote or eukaryote). Single-celled organisms are often called microorganisms.
Population: All individuals of a single species living within a specific area (e.g., all white pine trees in a forest).
Community: The collection of different populations inhabiting a particular area (e.g., all trees, flowers, insects, and microbial populations in a forest).
Ecosystem: Consists of all the living things (community) in a particular area, along with its abiotic (non-living) parts (e.g., nitrogen in soil, rainwater).
Biosphere: The highest level of organization; the collection of all ecosystems, representing all zones of life on Earth, including land, water, and portions of the atmosphere.
Diversity of Life and Classification
Carl Linnaeus and Hierarchical Taxonomy: In the 18th century, Carl Linnaeus proposed a hierarchical system for organizing known species, classifying them based on similarities.
Taxonomic Hierarchy (from lowest to highest): The current system has eight levels:
Species: The most specific grouping, organisms capable of interbreeding and producing fertile offspring.
Genus: A grouping of closely related species.
Family: A grouping of similar genera.
Order: A grouping of similar families.
Class: A grouping of similar orders.
Phylum: A grouping of similar classes.
Kingdom: A grouping of similar phyla.
Domain: The highest and broadest level, a relatively new addition since the 1990s.
Three Domains of Life: Scientists now recognize three domains, proposed by Carl Woese:
Eukarya: Contains organisms with cells possessing nuclei. Includes kingdoms such as Fungi, Plants, Animals, and several kingdoms of Protists.
Archaea: Single-celled organisms without nuclei (prokaryotes). Many are extremophiles, living in harsh environments.
Bacteria: Another distinct group of single-celled organisms without nuclei (prokaryotes).
Prokaryotes: An informal name for cells without nuclei, encompassing both Archaea and Bacteria.
Evolution of Classification: The recognition in the 1990s that Archaea are genetically and biochemically as different from other bacteria as they are from eukaryotes led to the three-domain system, demonstrating that classifications evolve with new scientific information.
Binomial Naming System:
Linnaeus also introduced the binomial naming system, using two unique names for each organism.
Consists of the genus name (capitalized) and the species name (lowercase), both italicized.
Each species has a unique binomial name universally recognized (e.g., North American blue jay is Cyanocitta cristata, humans are Homo sapiens).
Evolution Connection: Carl Woese and the Phylogenetic Tree:
Phylogenetic tree: A diagram illustrating the evolutionary relationships among biological species based on genetic or physical similarities/differences.
Components: Composed of branch points (nodes) representing ancestral divergences and branches representing evolutionary lineages.
Woese's Contribution: Challenged the previous five-kingdom classification by showing life evolved along three lineages: Bacteria, Archaea, and Eukarya. He proposed the domain as a new taxonomic level based on genetic relationships (comparative sequencing of universally distributed, conserved genes of appropriate length), rather than solely on morphology (shape).
Example: The tree shows Bacteria and Archaea as prokaryotes (without nuclei) and Eukarya as organisms with nuclei.
Branches of Biological Study
Biology has a broad scope with many sub-disciplines:
Molecular Biology: Studies biological processes at the molecular level, including interactions of DNA, RNA, and proteins, and their regulation.
Microbiology: Studies the structure and function of microorganisms (can be further specialized into microbial physiologists, ecologists, geneticists, etc.).
Neurobiology: Studies the biology of the nervous system; an interdisciplinary field (neuroscience) using molecular, cellular, developmental, medical, and computational approaches.
Paleontology: Uses fossils to study Earth's history of life (e.g., excavating dinosaur fossils).
Zoology: The study of animals.
Botany: The study of plants.
Biotechnologists: Apply biological knowledge to create useful products.
Ecologists: Study the interactions of organisms with their environments.
Physiologists: Study the workings of cells, tissues, and organs.
The Nature of Science
Science Defined: From Latin "scientia" meaning "knowledge," science is a specific way of acquiring knowledge about the natural world, focusing on material phenomena (matter and energy).
Scientific Endeavor: Like other sciences, biology gathers knowledge through careful observation, record keeping, logical and mathematical reasoning, experimentation, and peer scrutiny.
Imagination and Creativity: Science also requires imagination and creativity; well-designed experiments are often described as elegant.
Practical & Curiosity-Driven: Science can be motivated by practical applications (e.g., disease prevention) or by pure curiosity.
Limitations of Science: Science cannot address purely moral, aesthetic, or spiritual questions because these are outside the realm of observable and measurable material phenomena.
Scientific Method: A defined method of research including experiments and careful observation, with hypothesis testing as a central aspect.
Hypothesis: A suggested explanation for an event that is testable and falsifiable (can be disproven by experimental results).
Scientific Theory: A generally accepted, thoroughly tested, and confirmed explanation for a set of observations or phenomena; the foundation of scientific knowledge.
Scientific Law: Concise descriptions, often mathematical (E=mc^2), of how elements of nature behave under specific conditions, without explaining why. Laws do not represent a higher level of certainty than theories; they are distinct types of scientific statements.
Scientific Inquiry
Goal: The ultimate goal of all science is "to know," driven by curiosity and inquiry.
Two Methods of Logical Thinking:
Inductive Reasoning (Descriptive Science): Uses related observations to arrive at a general conclusion.
Common in descriptive science, where scientists make and record observations (qualitative or quantitative data, supplemented by visuals).
Generalizations are inferred from many observations and large data analysis (e.g., observing many brains activated during a task to conclude a brain part controls that response).
Deductive Reasoning (Hypothesis-Based Science): Uses a general principle or law to forecast specific results (moving from general to specific).
Predictions are made (e.g., "If the climate warms in a region, plant and animal distributions should change").
Specific results are tested to see if they are consistent with the general principle, providing evidence for its validity.
Two Pathways of Scientific Study:
Descriptive (or Discovery) Science: Aims to observe, explore, and discover.
Hypothesis-Based Science: Starts with a specific question or problem and proposes a testable potential answer or solution.
Interplay: The boundary between these is often blurred; most scientific endeavors combine both. Observations lead to questions, which lead to hypotheses, which are then tested, forming a continuous dialogue.
Hypothesis Testing (The Scientific Method in Practice)
Origins: First documented by Sir Francis Bacon (1561–1626) for inductive scientific inquiry, though used in ancient times.
Steps: Not always rigid and linear, but typically involves:
Observation / Problem: Noticing something (e.g., classroom is too warm).
Question: Asking why the observation occurred (e.g., "Why is the classroom so warm?").
Hypothesis: A suggested, testable, and falsifiable explanation (e.g., "The classroom is warm because no one turned on the air conditioning.").
Testable: Can be investigated through experimentation.
Falsifiable: Can be disproven by experimental results (e.g., "Botticelli's Birth of Venus is beautiful" is unfalsifiable).
Prediction: An "If… then…" statement based on the hypothesis (e.g., "If the student turns on the air conditioning, then the classroom will no longer be too warm.").
Experiment: Designed to test predictions and eliminate hypotheses.
Variables: Parts of the experiment that can vary or change.
Controls: Parts of the experiment that remain constant for comparison.
Example: Testing if phosphate limits algae growth. Variable: phosphate presence/absence. Experimental cases: ponds with added phosphate. Control ponds: ponds with inert salt added.
Results and Conclusion:
If experimental data supports the prediction, the hypothesis gains support.
If data contradicts the prediction, the hypothesis is rejected.
Important: Experiments can disprove or eliminate a hypothesis, but they can never definitively prove one. Science deals in support and rejection, acknowledging that better explanations might emerge later.
Rejecting one hypothesis does not automatically accept others; it simply removes an invalid explanation.
Modern Approaches: Exponential growth of data in databases has led to "data research" or "in silico" research, using computer algorithms and statistical analyses, increasing demand for specialists in biology and computer science.
Example Application:
Observation/Problem: Toaster doesn't toast bread.
Question: Why doesn't the toaster work?
Hypothesis: Something is wrong with the electrical outlet.
Prediction: If something is wrong with the outlet, my coffee maker also won't work when plugged into it.
Experiment: Plug coffee maker into the outlet.
Result: Coffee maker works.
Conclusion: The hypothesis ("Something is wrong with the electrical outlet") is not supported.
Alternative Hypotheses: (e.g., "The toaster itself is broken"; "The circuit breaker for that outlet is tripped").
Basic and Applied Sciences
Debate: The scientific community debates the value of pursuing knowledge for its own sake versus applying knowledge to solve specific problems.
Basic Science ("Pure" Science):
Seeks to expand knowledge without immediate concern for short-term application.
Goal: knowledge for knowledge's sake.
Often leads to unexpected applications later.
Applied Science ("Technology"):
Aims to use science to solve real-world problems.
Focuses on improving crop yields, curing diseases, saving endangered animals, etc.
The problem is typically defined for the researcher.
Interdependence: Many scientists believe basic understanding is a prerequisite for application; applied science relies heavily on basic science discoveries.
Example 1 (DNA): Basic science discovery of DNA structure led to understanding replication mechanisms. This enabled applied science applications like identifying genetic diseases, forensic identification, and paternity testing.
Example 2 (Human Genome Project): A massive applied research effort to map human chromosomes, building on basic research from non-human organisms, with the ultimate goal of finding cures for genetically related diseases.
Serendipity (Fortunate Accidents): Some significant discoveries are made by accidental observation combined with a curious mind.
Example: Alexander Fleming's discovery of penicillin when mold accidentally grew on a Staphylococcus petri dish, killing the bacteria.
Reporting Scientific Work
Importance of Sharing: Scientists must share findings for others to expand and build upon discoveries; communication and collaboration are crucial.
Methods of Dissemination:
Scientific meetings/conferences: Reach a limited audience.
Peer-reviewed articles: The primary method for publishing results in scientific journals.
Reviewed anonymously by qualified colleagues (peers), often experts in the same field.
Ensures research originality, significance, logical rigor, and thoroughness.
Grant proposals (requests for funding) also undergo peer review.
Reproducibility: Publication allows other scientists to reproduce experiments under similar or different conditions, verifying and expanding on findings.
Reliability: Results in forums without rigorous peer review (e.g., some online open-access journals, popular press) are not reliable and should not form the basis for scientific work.
Exceptions: Personal communications from other researchers about unpublished results may be cited with the author's permission.
Career Connection: Forensic Scientist
Role: Applies scientific principles to answer questions related to the law.
Multidisciplinary: Biologists, chemists, and biochemists can pursue careers as forensic scientists.
Activities:
Provides scientific evidence for court use.
Examines trace materials associated with crimes (primarily against people: murder, rape, assault).
Analyzes samples like hair, blood, other body fluids, and processes DNA from various environments.
Analyzes other biological evidence such as insect parts or pollen grains.
Growing Field: Increased interest due to popular TV shows and advancements in molecular techniques (e.g., DNA databases).
Required Education: Students pursuing forensic science usually need chemistry and biology courses, plus intensive math courses.