Lecture 1 and 2: Syllabus Introduction to Biology AND Chemical Biology

What is Science?

• Question prompts from Page 5:
  • YOUR definition of Science?
  • Closest definition among options:
  • A) A large body of knowledge
  • B) A proven set of facts
  • C) Set of laws, properties, formulas, equations, and relationships
  • D) A practice of methodically pursuing answers to questions
• Answer emphasized: Science is a PROCESS and the knowledge collected through that process. This is often called “research.”

The Nature of Science

• Four Modalities of Scientific Research (Page 6):
  • 1. Experimentation
  • 2. Description
  • 3. Comparison
  • 4. Modeling

1. Description (Page 7)

• Involves the systematic observation and cataloging of components of a natural system in a manner that can be utilized, replicated (and verified) by other scientists.
• Commonly used to explain:
  • Unique natural systems (ecology, chemistry)
  • Large-scale phenomena (astronomy)
  • Past events (geology, forensic science)

2. Comparison (Page 8)

• Used to determine/quantify relationships between 2+ variables by observing different groups exposed to different treatments/conditions.
• Includes both retrospective (examine past events) and prospective studies (examine from present forward).
• Similar to experimentation in that:
  • Involves comparing a treatment group to a control, BUT the treatment is observed rather than imposed (due to ethical reasons or feasibility).
• Limitations and caveats:
  • Sampling error, correlation vs. causality, cause vs. effect

3. Modeling (Page 10)

• Involves developing a representation of a system:
  • Physical, conceptual, or computer-based.
• Purposes:
  • To replicate systems in the real world through simplification.
  • To perform an experiment that cannot be done in the real world.
  • To assemble several known ideas into a coherent whole to build and test hypotheses.
• Computer modeling is a relatively new scientific research method but is based on the same principles as physical and conceptual modeling.

4. Experimentation (Page 12)

• A research method in which 1+ variables are manipulated, and the effect of that manipulation is observed.
• Purpose: to determine causal relationships or to quantify the magnitude of response of a variable.
• Experimental designs should involve “controls”:
  • To provide a measure of variability within a system and a check for sources of error.

Page 9 Example: Lung Health Study (data visualization description)

• Figure: Loss of Lung Function in Lung Health Study Participants over 11 years.
  • Groups: Sustained quitters (blue circles), intermittent quitters (gray circles), continuous smokers (red circles).
  • Metric: Post-bronchodilator FEV expressed as a percentage of predicted value.
  • Source note: Anthonisen NR, et al. AJ Respir Crit Care Med. 2002 (figure reproduced with permission).
• This example illustrates description/descriptional data of health outcomes across exposure groups over time.

The Scientific Method and Research Design (Pages 27-29)

• The Scientific Method (Page 27):
  • Observation → Question → Hypothesis → Experiment → Conclusion
  • Note: This model is short, linear, and overly simplistic; descriptive science is not well captured by a strictly linear path.
  • Nevertheless, formulating hypotheses to explain observations and testing them with data is central to science.
• Theory Development (Page 28):
  • Induction vs Deduction diagram (Portney Foundations of Clinical Research, 4th ed., 2020):
  • Induction: Empirical Observations → Empirical Generalizations → Research Hypotheses
  • Deduction: Theory/Conceptual Framework → Predicted Relationships → Theory Testing
  • The model shows a circular relationship between empirical observations and theory, integrating inductive and deductive reasoning.
• Data Collection Standards (Page 29-30):
  • Reliability vs Validity (illustration: center true score):
  • A) Reliable but not valid: systematic error present
  • B) Random error but valid on average
  • C) Neither reliable nor valid
  • D) High reliability and validity
  • Emphasizes the distinction between getting consistent measurements (reliability) and measuring what you intend to measure (validity).

Ethics and Quality Assurance in Research (Pages 31-33)

• Ethics in Experimental Design (Page 31):

  • Experimental Controls:
  • Positive control: known to produce a result/effect (e.g., discovered soup suppositions)
  • Negative control: known NOT to produce a result/effect (e.g., sealed soup)
  • Experimental Variables:
  • Independent variable: new conditions being tested
  • Dependent variable: measurements taken from the new conditions
  • Replication: ensures results are consistent and repeatable
  • Verification: ensures results can be replicated by others/under other conditions
  • Discussion: why + and – controls are important

• Peer Review (Page 32):

  • Ensures claims are scrutinized by the scientific community
  • Experiments/observations/data must be thorough and rigorous
  • Study must be free of bias and subjectivity
  • Confidence and error must be reported
  • Any hypothesis must be replicated/independently verified
  • New ideas/theories are tentative until broad consensus is reached
  • Historical examples cited: ozone layer depletion (CFCs), Evolution and Natural Selection, DNA as genetic material, Global Climate Change

• Skepticism (Page 33):

  • Scientific skepticism: only systematic investigation yielding empirical (measurable) evidence can evaluate the correctness of a claim
  • “Skeptic” is not the same as a doubter or negative person
  • Claims not testable by empirical means are not scientific

Basic Biology and Life (Pages 34-37)

• All Living Organisms:

  • Have one or more cells
  • Require energy
  • Metabolize
  • Grow
  • Respond to stimuli
  • Adapt
  • Reproduce

• Cells are the basic units of life (Page 35):

  • Prokaryotic vs Eukaryotic cells (illustrated): nucleus, membrane-bound organelles, cytoplasm, etc.
  • Size references: 1 μm scale (illustration on page 35).

• Biological Classification is hierarchical (Page 36):

  • Domains: Bacteria, Archaea, Eukarya
  • Example kingdom placement: Plantae, Fungi, Animalia, Protists
  • Visual scale references: various organism sizes (e.g., 2 μm, 100 μm) shown in diagrams

• Review: Themes in Biology (Page 37):

  • The cell is the fundamental unit of life
  • Evolution by natural selection accounts for diversity of life
  • Science is a PROCESS that can CHANGE through research

Chemistry and Life: Biology is Chemistry (Pages 38-39)

• Matter, Mass, Weight, Elements, and Compounds:

  • Matter: anything that takes up space
  • Mass: amount of matter
  • Weight: force of gravity on matter
  • Element: pure substance of a single type of atom; 92 naturally occurring elements; 25 essential to life; ~96% of biomass is made of O, C, H, N
  • Compound: two or more different elements chemically combined in fixed ratios

• Elements in Life (illustration of NaCl, Sodium chloride) (Page 39)

Atomic Structure and Electron Configuration (Pages 40-43)

• Atomic Structure:

  • Atom: smallest unit of matter retaining element properties
  • Subatomic particles:
  • Proton: positive charge; mass = 1 Da
  • Neutron: neutral; mass = 1 Da
  • Electron: negative charge; mass ≈ 0 Da
  • Atomic number (Z): number of protons
  • Mass number (A): number of protons + neutrons
  • Example: Helium (He): Z = 2, A = 4

• Electron Configuration:

  • Electron energy levels (shells) and orbitals determine chemical properties
  • Valence electrons: outermost shell electrons determine properties
  • Energy states and flow: electrons move from high (unstable) to low (stable) energy states
  • Shell capacities:
  • First shell capacity: $2$ electrons
  • Second shell capacity: $8$ electrons
  • Third shell capacity: $18$, but is typically filled to $8$ in common bonding scenarios
  • Atoms prefer to have a full valence shell (2 or 8 electrons)

• Electron Shell Diagrams and Bonding visuals (Pages 43):

  • Representations: Lewis structures, space-filling models, and distribution diagrams for various elements (e.g., H, He, C, O, N, etc.)

Chemical Bonding (Pages 44-50)

• Covalent Bonding:

  • Atoms share valence electrons to form a molecule
  • If atoms are different, the result is a compound
  • Electrons are shared in pairs; single bond = one pair; double bond = two pairs
  • Shapes and 3D arrangement depend on electron pair geometry

• Ionic Bonding:

  • Transfer of electrons from one atom to another
  • Results in ions with full valence shells
  • Cation: positively charged ion; Anion: negatively charged ion
  • Ionic bonds form salts through electrostatic attraction between oppositely charged ions

• Electronegativity and Bond Polarity (Pages 47-48):

  • Electronegativity increases toward the right on the periodic table
  • If bonding electrons are not shared equally due to differing electronegativities, the bond is polar
  • polarity and molecular shape determine partial charges and dipole moments

• Polar vs Non-polar Molecules (Page 48):

  • Examples include polar molecules like H2O and non-polar molecules like O2, depending on symmetry and electronegativity differences

• Ionic Bonds and Salt Formation (Page 49):

  • Picture of electron transfer creating ions; salts form from complementary ions (cation + anion)

• Periodic Table and Salts (Page 50):

  • Visual reference for predicting salts and element interactions (illustrative periodic table section)

• Weak Chemical Bonds (Pages 51-52):

  • Hydrogen bonds: attraction between a slightly positive hydrogen and a slightly negative electronegative atom (e.g., O, N)
  • Van der Waals forces: transient attractions due to momentary dipoles as electrons move
  • These bonds are weaker than covalent/ionic bonds but are crucial for molecular interactions and structures

• The Shape of Molecules (Page 53):

  • 3D shapes are determined by electron orbitals
  • Hybridization changes orbital shapes during bonding

• Electronegativity Deep Dive (Page 54):

  • Atoms to the RIGHT are more electronegative than atoms on the left
  • More electronegative atoms pull electrons toward themselves, creating partial negative charges

• Hydrogen Bonding in Water (Page 55):

  • Oxygen is more electronegative than hydrogen; O pulls electrons toward itself
  • Water molecules form hydrogen bonds: each H2O molecule can form up to four H-bonds

• Biochemistry and Enzymes (Pages 56-57):

  • Living systems perform many chemical reactions by making and breaking bonds
  • Enzymes act as catalysts for chemical reactions in living systems
  • Water composition in life:
  • 70-75% of Earth's surface is water
  • 70-95% of all cells are water
  • Water’s polarity enables hydrogen bonding
  • Four central properties of water that enable life:
  • Cohesion
  • Moderation of Temperature
  • Ice Floats
  • Polar Solvent

• Review: Hydrogen Bonding (Page 58):

  • Oxygen is more electronegative than hydrogen, pulling electrons toward O
  • Oxygen bears partial negative charge; hydrogens bear partial positive charge
  • This causes weak, temporary attractions between molecules (hydrogen bonds)

Evolution by Natural Selection (Pages 21-23)

• Charles Darwin described how living things evolve
• Descent with modification: organisms become adapted to their environment over time
• Explains unity and diversity of life
• Method of Natural Selection:
  1) Variation in populations due to genetic (DNA) differences
  2) Differences affect survival and reproduction (feeding, escaping predators, etc.)
  3) Most fit individuals are more likely to survive and reproduce
  4) Offspring inherit adaptive traits from fit parents
  5) Over time, adaptive traits lead to genetic evolution of populations

Theories, Hypotheses, and Laws (Pages 18-26)

• Key terms:

  • Hypothesis: a tentative explanation for an observed phenomenon; a reasoned proposal predicting a possible causal correlation among multiple phenomena
  • Theory: explanations based on observations/data from many fields; grand in scale and unify many observations
  • Law/Principle: expressions of mathematical (law) or physical (principle) relationships

• Examples:

  • Theories: Newton’s Theory, Theory of Relativity, Theory of Evolution, Cell Theory
  • Laws/Principles: Ideal Gas Law, Newton’s laws of motion, Law of gravity (inverse square law), Mendel’s laws of inheritance

• Hypotheses vs Theories (Page 24):

  • Similarities: both must be testable/falsifiable, based on observations and data, make testable predictions
  • Differences: hypotheses are narrow/specific; theories are broad and give rise to many testable hypotheses; theories are refined over time as data accumulates

• Theory vs Law (Page 25):

  • Similarities: both are large unifying explanations; often related and build on one another
  • Differences: a law describes a mathematical relationship; a theory provides a scientific explanation
  • Examples of interplay: Mendel’s Laws and Cell Theory; conservation laws refined by Einstein’s Special Relativity

• Standard vs Non-Standard Language (Pages 13-15):

  • Science relies on standard language to avoid misinterpretation
  • Overly simplified analogies can lead to misunderstanding or fake news (the Babel Tower metaphor)
  • Non-standard language examples show how language can misrepresent science (shown as visual slides and provocative text)

• The Scientific Method (Page 27) and its Limits:

  • Observation → Question → Hypothesis → Experiment → Conclusion
  • Acknowledges that this model is simplistic and not strictly linear; especially limited for descriptive science

The Foundations of Research (Page 28-31)

• Induction and Deduction in scientific reasoning (Figure 4-1):

  • Induction: Empirical Observations → Empirical Generalizations → Research Hypotheses
  • Deduction: Theory/Explanations → Predicted Relationships → Theory Testing
  • Shows circular integration of observations and theory in scientific thought

• Data Collection Standards (Figure 10-1):

  • Reliability vs Validity in data collection
  • Valid score is accurate for the true value in the concept being measured; Reliability relates to consistency across measurements
  • Visual interpretation includes four scenarios (A-D) mapping reliability and validity

• Ethics in Research: Experimental Design (Page 31)

  • Experimental controls (positive/negative)
  • Experimental variables (independent/dependent)
  • Replication and verification
  • Discussion prompts on the importance of controls

• Ethics in Research: Peer Review (Page 32)

  • Ensures scientific claims are scrutinized by the scientific community
  • Emphasizes rigor, lack of bias, reporting of errors, replication, and verification
  • Historical examples cited: ozone layer depletion, evolution, DNA as genetic material, climate change

• Ethics in Research: Skepticism (Page 33)

  • Systematic investigation yielding empirical evidence is required to evaluate scientific claims
  • “Skeptic” is not simply a doubter; untestable claims do not qualify as scientific

The Nature of Life: Cellular Biology (Pages 34-37)

• All Living Organisms:\

  • Have one or more cells
  • Require energy
  • Metabolize
  • Grow
  • Respond to stimuli
  • Adapt
  • Reproduce

• Cells are the basic units of life (Page 35):

  • Prokaryotic vs Eukaryotic cells summary in diagram form
  • Nucleus present in eukaryotes; DNA distribution

• Biological Classification is hierarchical (Page 36):

  • Domain-based view: Bacteria, Archaea, Eukarya
  • Within Eukarya: Kingdoms such as Plantae, Fungi, Animalia, Protists

Quick Themes to Remember (Page 37)

• The cell is the fundamental unit of life
• Evolution by natural selection explains life’s diversity
• Science is a PROCESS that evolves with continuing research

Biology is Chemistry (Pages 38-39)

• Key chemical concepts for life:
  • Matter, mass, weight, elements, and compounds
  • 92 naturally occurring elements; 25 essential to life
  • About 96% of biomass composed of O, C, H, N
  • Compound: two or more elements bonded in fixed ratios to form new properties

Atomic Structure and Bonding: Summary Points (Pages 40-50)

• Atoms and subatomic particles; nucleus; electron orbitals; charges and masses
• Atomic number Z (#protons) and Mass number A (protons + neutrons)
• Electron shells and valence electrons determine chemical properties
• Covalent bonds: sharing electrons; single/double bonds; formation of molecules/compounds
• Ionic bonds: transfer of electrons; formation of ions; salts
• Electronegativity and polarity: rightward trend; polar vs non-polar bonds
• Hydrogen bonding and van der Waals forces as weak interactions that underpin structure and interactions
• Three-dimensional shapes arising from orbital hybridization and bond geometry
• Water as a life-enabling solvent due to polarity and hydrogen bonding

Water, Life, and Biochemistry (Pages 56-58)

• Water’s four central properties enabling life:

  • Cohesion
  • Moderation of temperature
  • Ice floats (factors into ocean and climate stability)
  • Polar solvent capability

• Hydrogen bonding underpins water’s properties and molecular interactions

Connections to Real-World Relevance

• The Nature of Science as a process underpins how scientific knowledge is built, tested, and revised in light of new evidence.
• Experimental design, controls, replication, verification, and peer review ensure credibility and reliability of findings.
• Understanding the difference between hypotheses, theories, and laws helps evaluate scientific claims and their robustness.
• The chemistry of life (elements, bonding, water) provides the molecular basis for biological processes and ecosystem function.
• Evolution explains the unity and diversity of life, guiding interpretations in biology, medicine, ecology, and conservation.

Ethical, Philosophical, and Practical Implications

• The need for clear scientific language to avoid misinterpretation and spread of misinformation (standard language vs. pseudo-science).
• The role of skepticism and empirical evidence in evaluating claims.
• The balance between simplification for communication and precision in scientific reasoning.
• The impact of human activity on science topics (e.g., climate change, ozone depletion) and the importance of robust evidence in policy discussion.

Key Formulas and Conventions

• Electron shell capacities (as a guide):
  • First shell: $2$ electrons
  • Second shell: $8$ electrons
  • Third shell: $18$ electrons (often observed to fill to $8$ in common bonding contexts)
• Hydrogen bonding and polar covalent interactions are described qualitatively; quantitative descriptors include dipole moments, bond energies, and electronegativity differences (notated in standard chemistry textbooks).

Note on Figures and Diagrams Mentioned

• Lung Health Study diagram (Page 9): illustrates FEV % predicted over 11-year follow-up with groups of quitters and smokers.
• River cross-section (Page 11): geometric/geographic example used to discuss description and modeling.
• Figure 4-1 (Page 28): model of scientific thought showing circular relationship between empirical observations and theory.
• Figure 10-1 (Page 29): reliability vs validity diagram for data collection.