Bio lecture 3 8/26 Scientific Method and Basic Chemistry Concepts

The Scientific Theory vs Hypothesis

• In science, a theory is an overarching explanation with overwhelming evidence for a phenomenon, not a guess or conjecture.
• A theory summarizes and ties together a wide range of data into a coherent framework (e.g., the theory of gravity, germ theory, atomic theory, theory of evolution).
• In ordinary language, people often say “theory” when they mean a guess; in science, a theory implies a well-supported explanation.
• Examples and nuances:
  • The theory of gravity is a modern explanation that includes Einstein’s relativity as a more complete framework; Newton’s law is still useful as a good approximation at slow speeds and everyday masses.
  • Newtonian physics is valid under certain conditions but breaks down at high speeds or extreme masses; Einsteinian relativity provides a more accurate description in those regimes.
  • The theory of evolution is supported by evidence across immunology, molecular biology, comparative anatomy, biogeography, etc., and uses a single genetic code across organisms as part of the overarching explanation.
• Scientific language about gravity and evolution emphasizes that these are well-established explanations, not merely conjectures about occurrence.
• The term “theory” in science signals a mature, evidence-based framework, not a mere hypothesis.

The Hypothesis and Testability

• A hypothesis is a narrowly focused conjecture about a specific phenomenon, testable and falsifiable, not an overarching theory.
• A hypothesis must be testable; if it cannot be tested or data cannot be gathered, it is not science (could be religion or a belief).
• Intelligent Design is presented as a theory by some, but it is not testable in the scientific sense, because it invokes existence of an intelligent designer (often equated with God) which cannot be empirically tested.
• Science and religion are described as serving different functions in society; science explains physical processes, while religion concerns purpose and meaning.

The Scientific Method: Five Steps (as presented)

• Step 1: Observation
  • Start with an observation about the natural world (e.g., a light doesn’t turn on when flipping a switch).
• Step 2: Develop a testable hypothesis
  • Propose a testable explanation for the observation (e.g., the bulb, the filament, the circuit).
• Step 3: Design an experiment and collect data
  • Create an experiment to test the hypothesis; include an experimental group and a control group; control all variables except the one being tested.
  • Define the independent variable (the factor you manipulate) and the dependent variable (the response you measure).
• Step 4: Analyze data statistically
  • Use statistical tests to compare the experimental treatment to the control.
  • If data do not support the hypothesis, reject it as a possible explanation.
  • If data support the hypothesis, do not claim proof; the hypothesis remains a tentative explanation that could be revised with new data.
• Step 5: Publish results
  • Publish so others can replicate or extend the work; science relies on open, repeatable processes and peer review.
  • The publication process involves critique by reviewers and editors; papers are revised before publication.

A Simple Everyday Example: Light Switch vs. Bulb

• Observation: The light doesn’t come on when you flip the switch.
• Hypothesis 1 (low effort): The switch is faulty.
• Hypothesis 2: The bulb/filament is faulty; test by replacing the bulb.
• Hypothesis 3: The circuit is faulty; test by checking wiring, breakers, etc.
• This illustrates iterative hypothesis testing in daily life as a micro-scale scientific method.

A Formal Experimental Example: Plant Growth under Leaf Litter vs Open Field

• Observation: A uniform wildflower grows taller under leaf litter than in an open field.
• Hypothesis: The taller growth under leaf litter is due to extra nutrients released by decomposing leaves (nitrogen release acts as fertilizer).
• Experimental design:
  • Setup: 100 seedlings in a plot with added nitrogen fertilizer (experimental), and 100 seedlings in a control plot without added nitrogen.
  • Independent variable: soil nitrogen concentration (e.g., 1% control vs 5% fertilizer).
  • Dependent variable: plant height after three months (in centimeters).
  • Controls: sunlight, water, temperature, and plant genotype (to ensure differences are due to nitrogen, not other factors).
• Reason for controls:
  • If everything else is held constant, a difference in height can be attributed to the nitrogen treatment.
  • Genotype can be used as a control factor because different genotypes may grow at different rates.
• Experimental setup details:
  • A plot with fertilized soil (nitrogen added) and a control plot (no nitrogen).
  • Documentation of sample sizes and environment variables to ensure comparability.
• Independent vs. dependent variables recap:
  • Independent variable: soil nitrogen concentration (x-axis in graphs).
  • Dependent variable: plant height after three months (y-axis in graphs).
• Graphing and data interpretation:
  • Use bar graphs with error bars representing a measure of variability (e.g., 95% confidence limits or standard deviation).
  • Example: control mean height around 25 cm with variability 20–30 cm; fertilized mean height around 50–55 cm with smaller variability.
  • Non-overlapping error bars suggest a statistically significant difference; overlapping bars suggest no clear difference.
  • If error bars overlap extensively, no strong evidence for a difference; a larger sample size may be needed.
• Concept of statistical difference:
  • If the error bars do not overlap, there is likely a statistical difference between treatments, supporting the hypothesis as consistent with the data.
  • If they do overlap, nitrogen may not be the cause; other factors or sampling variability could explain the difference.
• What does it mean to “prove” a hypothesis?
  • In science, nothing is ever proven beyond all doubt; results may be consistent with a hypothesis but could be revised with new data.
• Etiolation/edelation and phenotypic plasticity:
  • Phenotypically plastic organisms can allocate biomass differently in response to environmental cues.
  • Under shade or limited light, plants may elongate growth (etoliation/edelation) to reach light, a form of adaptive growth.
  • The observed taller growth under leaf litter could be due to ideation/biomass allocation responses in addition to nitrogen effects.

Key Terminology: Variables, Controls, and Graphs

• Independent variable: the variable deliberately changed or controlled in the experiment to test its effects.
• Dependent variable: the variable measured to assess the effect of the independent variable.
• Control group: a baseline group that does not receive the experimental treatment, used for comparison.
• Experimental group: the group that receives the treatment being tested.
• Random sampling: selecting individuals randomly to avoid bias in estimating population values.
• Error bars: graphical representation of variability in the data (can indicate standard deviation, variance, or 95% confidence limits).
• 95% confidence interval (CI): the range within which, if the experiment were repeated many times, the true mean would lie 95% of the time.
• Statistical significance vs. practical significance: non-overlapping error bars suggest significance; lack of significance does not prove the absence of an effect.
• Phenotypic plasticity: the ability of an organism to change its phenotype in response to environmental conditions.

Mass, Weight, and Matter

• Matter: anything that occupies space and has volume and mass.
• Mass vs. weight:
  • Mass is a measure of the amount of matter; it is constant in all environments.
  • Weight depends on gravitational field strength and can vary with location (Earth vs. Moon).
• How mass is measured:
  • Mass is typically measured with a balance or a scale, but in everyday language these terms are sometimes conflated.
• On the Moon vs Earth:
  • An astronaut’s mass remains the same, but weight is about one-sixth due to weaker gravity.
  • For objects like a fish, the scale reading changes with gravity, demonstrating that weight is not constant.

Atoms, Elements, Molecules, and Compounds

• Elements: basic substances that cannot be broken down chemically into simpler substances.
• Naturally occurring elements: about 92; others are artificially created in laboratories.
• Atom: the basic unit of an element; can exist as a single atom or combine to form molecules.
• Molecule: two or more atoms bound together; can be the same element (e.g., O2, N2) or different elements (e.g., H2O, CH4).
• Compound: a substance composed of atoms of two or more elements (e.g., H2O, CH4).
• Chemical formulas:
  • H2: diatomic hydrogen
  • O2: diatomic oxygen
  • H2O: water (two hydrogens, one oxygen)
  • CH4: methane (one carbon, four hydrogens)
• Notes on naming and symbols:
  • Element symbols are derived from traditional names or Latin names (e.g., Fe for iron from ferro, Pb for lead from plumbum, Na for natrium).

Subatomic Particles: Protons, Neutrons, and Electrons

• The three main subatomic particles:
  • Proton: charge +1; symbol p; superscript + (p^+)
  • Neutron: charge 0; symbol n; superscript 0 (n^0)
  • Electron: charge –1; symbol e; superscript - (e^-)
• Mass contributions:
  • Protons and neutrons contribute most of the atomic mass.
  • Electrons have negligible mass compared to protons and neutrons, but they determine chemical behavior and charge balance.
• Atomic structure: electrons orbit the nucleus composed of protons and neutrons.

Periodic Table and Carbon: A Detailed Example

• Carbon: symbol C; atomic number Z = 6; the number of protons equals 6 for all carbon atoms.
• Atomic mass number A: total number of protons and neutrons in the nucleus (A = Z + N).
• Carbon-12 example:
  • Carbon-12 has A = 12, Z = 6, N = A − Z = 6.
  • Neutral carbon has 6 electrons; electron count equals proton count to balance charge.
• Isotopes:
  • Carbon-13: Z = 6, N = 7 (A = 13)
  • Carbon-14: Z = 6, N = 8 (A = 14), a radioactive isotope used in dating and other studies.
• Atomic mass vs. atomic number:
  • The atomic mass number A roughly reflects the total mass contributed by nucleons (protons + neutrons).
  • Electron mass is negligible in determining atomic mass, but electrons balance the positive nuclear charge to yield a neutral atom.
• Nuclear charge and neutrality:
  • The nucleus has a +6 charge for carbon (six protons).
  • Neutral carbon atoms require six electrons to balance the +6 charge of the nucleus.
• Notation and interpretation:
  • The atomic number tells both the identity of the element and the number of electrons in a neutral atom.
  • Isotopes differ in neutron number while keeping the same number of protons.

Quick Recap: Key Takeaways

• In science, a theory represents a well-supported explanation, not a guess; hypotheses are narrower and testable conjectures.
• The scientific method involves observation, hypothesis, experimentation, data analysis, and publication with replication and peer review.
• Experiments require controlled variables, clear independent and dependent variables, and appropriate data interpretation using statistics and graphs.
• Negative results are common in science but are less likely to be published, highlighting the need for robust experimental design and reproducibility.
• Matter comprises atoms; elements are the simplest pure substances; molecules are bonded atoms; compounds are molecules with two or more elements.
• Subatomic particles (protons, neutrons, electrons) define atoms; the nucleus determines mass, while electrons determine charge and chemical behavior.
• The periodic table organizes elements by atomic number; carbon serves as a central example for understanding mass, isotopes, and electron configuration.
• Distinctions between mass and weight are important in understanding measurements and how gravity affects weight but not mass.
• The integration of physics (gravity, relativity), biology (evolution, germ theory), and chemistry (atom structure, bonding) illustrates how science builds comprehensive explanations from observations to theory.
• Philosophy and ethics:
  • Science operates within testable, repeatable frameworks.
  • Religion and science serve different functions; science does not address ultimate purposes, only physical explanations of phenomena.