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Fall Semester Lectures: Biological Sciences
Spring Semester Lectures: Physics
Sample Oral Examination Questions
Lecture Schedule
Fall 2007 Lectures: Biological Sciences
Read the full Syllabus for the Biological Sciences semester. The summary of topics and readings follows.
Segment B1: Introduction and the World of the Small [Prof. Wildman]
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Week 0 |
Introduction to the course. The World of the Small (elementary particle physics; periodic table). Housekeeping discussion of pedagogical philosophy for the biology section. |
Segment B2: Chemistry [Dr. Naidenko]
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Week 1 |
Introduction to quantum chemistry, periodic table; intro to the chemistry class next week. Vote on mascot. Setting up goals for the class/semester. Students with prior chemistry background sign up for presentations in weeks 2 and 3. Handout – Paolo Freire Pedagogy of the Oppressed (5-6 pages) and Parker Palmer The Courage to Teach (Ch.2, A Culture of Fear: Education and the Disconnected Life, pp. 35-47) |
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Week 2 |
General chemistry. This is the most uphill session, because a lot of abstract concepts are introduced rapidly, only to be supplanted immediately with “by the way, this is not how the world of the ‘small’ really works, so don’t get attached to the idea.” This reminds all of us to look for convincing upfront reasons for why the hard work of reviewing many semesters of chemistry in a three-hour lecture may be meaningful and necessary. Freeman Ch. 2 The atoms and molecules of the Ancient world. Handout for discussion on week 3 –Roald Hoffmann, The Same and Not the Same |
Segment B3: Biochemistry and Cell Biology [Dr. Naidenko]
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Week 3 |
Origin of organic molecules and life on Earth. Intro to sugars, lipids, proteins, and nucleic acids – structural and biochemical perspective. Discussion of “natural” and “artificial” organic molecules. Everybody signs up for homework project – using PDB and Swissprot databases (and any others you like), prepare a presentation about structure/function of a recently crystallized macromolecule. Freeman Ch. 3 Macromolecules and the RNA world |
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Week 4 |
From biochemistry to cell biology. Presentation of macromolecular structures from PDB. Sign up for homework project – presentation of cellular organelle photographs. Students with prior biology background – sign up for presentation on altered cell cycle in cancer. Freeman Ch. 4 Membranes and the first cells. Ch. 5 Cell structure and function. |
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Week 5 |
Processes of cell division. Introduction to energy and metabolism. Presentation of organelle structures. Sign up for homework project – presentation of a metabolic pathway. (prior biology background – sign up for presenting book review of chapters 1-3 from James Watson’s DNA: the Secret of Life which you can cautiously view as blatant propaganda, but it is written by one of the more colorful and eccentric founders of the field, so a great read). Freeman Ch. 8 Cell Division. Ch. 6 Respiration and Fermentation. |
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Week 6 |
Molecular biology and gene->protein information flow. Discussion of key terms related to energy (from website quiz) Presentation of metabolic pathways. Presentation of J.Watson’s book. Review of format for the midterm meeting. Freeman Ch. 11 How do genes work? Ch. 13 Transcription and translation. |
Oral Examination of Material in Segments B1, B2, B3
Segment B4: Evolutionary Biology [Dr. Naidenko]
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Week 7 |
Genes, Genomes and Evolution – Part I. Discussion of Freire and Palmer texts (copies from week 1) Watch multimedia presentations from the NIH human genome website www.genome.gov. “How to Sequence a Genome” and “Genes, Variation, and Human History” (possible) presentations from students with prior biology background - Freeman Chapters 12, 14, and 15. Tutorial on using genome databases - sign up for next week’s presentations. Discuss potential final projects. Final hour of the class - visiting a genetics lab (BU campus). Readings - Freeman Ch. 16, pp. 317-321 and pp. 324-328. |
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Week 8 |
Genes, Genomes and Evolution – Part II, evolution of protein domains Meiosis and Mendelian genetics – Freeman Chapters 9-10 as a reference. Mini-lecture on recombinant DNA methods. Freeman Ch 17 pp 336-339 as a reference. Sign up for projects on protein databases. |
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Week 9 |
Evolutionary patterns and processes Part I Sign-up for next week presentations of material from Freeman chapters 21-24. Presentation of protein database projects Informal update/progress report on final projects. |
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Week 10 |
Evolutionary patterns and processes Part II Presentation of material from Freeman Chapters 21-24. Sign-up for next week presentations from M. Kirschner and J. Gerhart, The Plausibility of Life (2005) or from any book on intelligent design. |
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Nov 23 |
No Class: Thanksgiving Recess |
Segment B5: Developmental Biology and the Evolutionary of Social Behavior [Dr. Naidenko]
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Week 11 |
Developmental biology and stem cell research. Discussion of contemporary arguments in evolutionary theory Sign up for presentation of research papers on sociogenomics, stem cells, or human sexuality for weeks 12 and 13. Handout – Q. Rahman, The neurodevelopment of human sexual orientation, (2004) Neurosci and Behav Rev 29: 1057-1066 (and 2007 papers). Freeman Ch. 18 An introduction to development. |
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Week 12 |
Current research in evolution of social behavior. Presentation of research papers on stem cells. Freeman Ch. 47 Behavior. G. E. Robinson, C. M. Grozinger, & C. W. Whitfield, Sociogenomics: Social life in molecular terms (2005) Nature Reviews Genetics, 6: 257-270; T.R. Insel & L.J. Young, Neurobiology of Human Attachment (2001) Nature Reviews Neuroscience, 2: 129-136; R.M. Sapolsky, Mothering Style and Methylation (2004) Nature Neuroscience, 7: 791-792. |
Oral Examination of Material in Segments B4, B5
Spring 2008 Lectures: Physics
Segment P1: Electromagnetism [Prof. Wildman]
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Week 1 |
Basic laws of electrostatics (Coulomb, Ampere, and Faraday) |
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Week 2 |
Maxwell’s equations (including theorems of Gauss and Stokes) |
Oral Examination of Material in Segment P1
Segment P2: Special Theory of Relativity [Prof. Wildman]
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Week 3 |
Conceptual Basics (classical mechanics; Galilean transformation; inertial frames of reference; motivation for a new mechanics; Lorentz transformation) |
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Week 4 |
Relativistic Mechanics (postulates of STR; relativity of simultaneity; length contraction; time dilation; addition of velocities; twin paradox; experimental evidence) |
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Week 5 |
Relativistic Dynamics (mass-energy equivalence), Electrodynamics and relativity (Maxwell’s equations in tensor notation) |
Oral Examination of Material in Segment P2
Segment P3: General Theory of Relativity [Prof. Wildman]
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Week 6 |
Conceptual Basics (theory of gravity or general theory of relativity?), Space-Time Tells Matter-Energy how to Move (geometric point of view; the equation of geodesic deviation; Riemann tensor; analogy with electromagnetism and Newtonian physics; calculating Riemann components) |
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Week 7 |
Matter-Energy Tells Space-Time how to Curve (calculating with equation of geodesic deviation; Einstein tensor; stress-energy tensor) |
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Week 8 |
Einstein’s Field Equations (approximation methods for solving Einstein’s field equations for entire universe; the closed universe; cosmological constant; other applications of GTR) |
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Mar 14 |
No Class: Spring Recess |
Segment P4: Cosmology [Prof. Wildman]
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Week 9 |
Early Cosmology (ancient and medieval concepts, planetary system debates, Galileo, Kepler) |
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Week 10 |
Big Bang cosmology (basic observations and theoretical model), Quantum cosmologies (competing models of the early universe) |
Oral Examination of Material in Segments P3, P4
Segment P5: Quantum Mechanics [Prof. Wildman]
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Week 12 |
Basic Experiments and Theoretical Moves (Plank’s postulate; photoelectric effect; Compton effect; atomic spectra; DeBroglie’s postulate; scattering experiments; low-intensity polarization; double-slit experiment; uncertainty principle) |
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Week 13 |
Formalism (Stern-Gerlach experiment; prediction versus explanation; wave functions; states, properties, and measurements; quantum electrodynamics) |
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Week 14 |
Non-Locality (Bohr versus Einstein; Einstein-Podolsky-Rosen thought experiment; Bell’s inequalities) |
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Week 15 |
Interpretations of Formalism (basic problems from the measurement problem to quantum chaos; Copenhagen “interpretation”; theories of measurement from DeBroglie, Bohm, and Popper to von Neumann, Wigner, and Everett) |
Oral Examination of Material in Segment P5
Mathematics Schedule
Fall 2007 Mathematics
Segment M1: One-Dimensional Calculus [Prof. Wildman]
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Week 1 |
Introduction (mathematical notation; number system; functions; continuity) |
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Week 2 |
Differentiation I (from first principles; geometrical interpretation of the derivative; circles, sine and cosine functions) |
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Week 3 |
Differentiation II (basic derivatives; basic rules of differentiation; differential equations) |
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Week 4 |
Integration I (from first principles; geometric interpretation of integral; sine and cosine functions revisited) |
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Week 5 |
Integration II (definite versus indefinite integrals; basic integration rules and techniques) |
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Week 6 |
Fundamental Theorem of Calculus (relation between areas under curves and anti-derivatives) |
Oral Examination of Material in Segment M1
Segment M2: Vector Spaces and Basic Linear Algebra [Prof. Wildman]
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Week 7 |
Vectors (geometrical interpretation; basic operations; length; angle), Bases (linear combinations; linear independence; dimensionality) |
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Week 8 |
Vector Spaces (definition; functions) |
Segment M3: Vector Calculus (for Physics Segment P1) [Prof. Wildman]
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Week 9 |
Generalizing the Derivative (directional derivative; gradient; divergence; curl; notation) |
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Week 10 |
Generalizing the Integral (path integral; surface integral; volume integral) |
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Week 11 |
Amazing Theorems (divergence theorem; Stoke’s theorem) |
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Nov 21 |
No Class: Thanksgiving Recess |
| Nov 28 | Review and practice |
| Dec 5 | Review and practice |
| Dec 12 | Review and practice |
Oral Examination of Material in Segments M2, M3
Spring 2008 Mathematics
Segment M3 (continued): Vector Calculus (for Physics Segment P1) [Prof. Wildman]
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Week 1 |
Vector Calculus Applications (electrostatics) |
Segment M4: More Linear Algebra (for Physics Segment P2) [Prof. Wildman]
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Week 2 |
Basis Change (coordinate systems; bases; basis change functions) |
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Week 3 |
Matrices (definition; matrix algebra; solving simple simultaneous equations; basis change functions represented as matrices; Galilean transformation; Lorentz transformation) |
Segment M5: Tensor Calculus (for Physics Segments P3, P4) [Prof. Wildman]
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Week 4 |
Understanding the Metric Tensor and the Polarization Tensor (building physical intuition for tensors; creating mathematical notation for describing the physics) |
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Week 5 |
Tensors in General Form (multi-linear functions; linear functionals; contravariant and covariant indices; partial derivatives) |
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Week 6 |
Examples (electromagnetic tensor; Riemann curvature tensor; stress-energy tensor) |
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Week 7 |
Breaking Down the Einstein Field Equations (Riemann curvature tensor; Ricci tensor; connections; Christoffel symbols; Einstein tensor) |
Segment M6: Hilbert Spaces (for Physics Segment P5) [Prof. Wildman]
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Week 8 |
Hilbert Spaces (definition; bases; orthonormal bases; basis change) |
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Mar 12 |
No Class: Spring Recess |
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Week 9 |
Functions on Hilbert Spaces (functions; operators), Application to Quantum Mechanics (wave functions, observables, and measurements) |
Segment M7: Complex Analysis (for Physics Segment P5) [Prof. Wildman]
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Week 10 |
Complex Number System (numbers, operations, converting between polar and Cartesian coordinates) |
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Week 11 |
Complex Functions (examples of complex functions, complex exponential function, application to wave functions, wave equation) |
Segment M8: Chaos Theory [Prof. Wildman]
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Week 12 |
The Logistic Mapping (understanding iteration; exploring bifurcation diagram using computer software; identifying regimes) |
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Week 13 |
Chaos (definitions; controversies; philosophical issues from modeling to meaning) |
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Apr 23 |
No Class: BU Monday Schedule |
| Apr 30 | Review and practice |
Sample Oral Examination Questions
These questions merely indicate the content of oral examinations. Exams are not limited to these questions. In general, and throughout the exams where appropriate, be prepared to speak about the relevance of the scientific material to philosophical, ethics, metaphysical, and theological questions (we call these “boundary issues”).
Examination of Biology Segments B1, B2, B3: Chemistry and Biochemsitry
What are fermions (leptons and quarks), bosons? What do they do, make, interact?
Explain why the periodic table arranged the way it is.
What is electron configuration for a given element? valence number? group? Calculate chemical formula for simple ionically bonded compounds based on valence numbers.
Describe the various types of chemical bonds and their relative strengths (ionic bonds, covalent bonds, hydrogen bonds, Van der Waal’s forces)
How does a chemical reaction work? What role does a catalyst play in a chemical reaction? What is a favorable reaction? How do you run reactions in unfavorable directions? Draw reaction energy diagrams.
Describe the four main macromolecules, their monomers, differences in their structure.
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Lipids: glycerol backbone with fatty acid tails
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Carbohydrates: glucose ring; forms long polymers
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Proteins: amino acid structure, twenty amino acids, peptide bond, polypeptide polymer
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Nucleic acids: nucleotide structure, four nucleotides, purines vs. pyrimidines
Describe the role of H+ bonding in macromolecular structure. Give two examples in:
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Protein structure
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DNA structure
Describe the cellular process of protein synthesis and where in the cell each step is occurring.
Examination of Biology Segments B4, B5: Cell Biology and Evolutionary Biology
Describe the types of cell. Describe the various parts of the cell (cell membrane, nucleus, mitochondrian, chloroplast, vesicular network, cytoskeleton) and give details about processes within each.
Distinguish between meiosis and mitosis. Outline the steps in each and the final outcome regarding the amount of cellular DNA present.
Describe cells in a functional context (either the immune system of the nervous system, depending on what was covered in class).
Summarize the work of Gregor Mendel. What two main principles of genetics were derived from his work (Independent Assortment and Segregation)? What is the molecular biological basis for these principles? What is an allele?
In mice there are two separate alleles for coat color and hair length. The dominant alleles are gray coat with short hair and the recessive alleles are tan coat with long hair. Work out a cross between a homozygous dominant mouse with a homozygous recessive mouse in the P generation and predict the allelic distribution in the F1 and F2 generations.
Summarize Darwin’s theory of natural selection. What evidence did Darwin adduce in support of it? What were its major flaws? What is the Modern Synthesis?
How does speciation occur? What are the factors relevant to population and evolutionary change?
Examination of Mathematics Segments M1: One-Dimensional Calculus
What is a function? Continuous function? Graph of a function? Tangent to a graph? Slope of a tangent?
How do the sine and cosine functions relate to the geometry of a circle? What are exponential and logarithmic functions and how do you calculate with them?
Define the derivative (from first principles). Describe the geometric meaning of a derivative and of the approximation method used to calculate it.
What are basic rules of differentiation? Basic derivatives? Differential equations?
Define the integral (from first principles). Describe the geometric meaning of an integral and of the approximation method used to calculate it. Distinguish definite from indefinite integrals. Explain area functions and their use in calculating definite integrals.
What are basic rules of integration? Basic integrals? Basic integration techniques?
What is an anti-derivative? State the fundamental theorem of calculus. Describe the relation between anti-derivatives and areas under curves.
Examination of Mathematics Segments M2, M3: Vector Calculus
What is a vector space? linear combination? linear dependence and independence? basis? dimension?
How do we define a metric on a vector space? Examples of metrics on R2, including graphs of length-1 vectors in Euclidean and Lorentzian metrics.
How do we use a metric to speak of length of vectors and angle between vectors? What is an orthonormal basis? coordinate system? How do we represent the same vectors in more than one coordinate system?
What is scalar (dot) product? vector (cross) product? linearity of an operation? test for orthogonality? right-hand rule? geometric and coordinate representation of dot product and cross product?
What are examples of functions with a variety of vector-space domains and ranges? vector fields and scalar fields? component scalar fields of a vector field?
What is directional derivative? partial derivative relative to a basis?
What is gradient? del? divergence? curl?
What is integral over a curve? a surface? a volume?
What is flux? circulation?
What is Gauss's theorem (divergence theorem)? Stokes’ Theorem?
Examination of Physics Segments P1: Electromagnetism
State Maxwell’s equations in differential and integral form. Show how to derive the integral from the differential form, and vice versa.
Explain the connection between Maxwell’s equations and the basic results of electrostatics. Derive Coulomb’s law from Maxwell I and Ampere’s Law from Maxwell II.
Write down the field equation for Electromagnetic radiation. (Bonus: derive it from Maxwell’s equations!) Explain the velocity of electromagnetic radiation from the field equation.
How do Maxwell’s equations establish the unification of light and electromagnetism? What is the significance of this result?
Examination of Physics Segments P2: Special Theory of Relativity
What is an inertial frame of reference? Principle of relativity? Galilean transformation?
State the postulates of STR. Describe the Lorentz transformation and its significance.
State the mechanical consequences of STR: relativity of simultaneity (via thought experiment), length contraction and time dilation (write up formulas), addition of velocities (write up formula).
State the dynamical consequences of STR: mass-energy equivalence (explain the energy triangle).
Describe experiments confirming STR.
What is a space-time diagram? Use one to explain the Lorentz Metric versus the Euclidean metric. Use one to explain the twin paradox.
What is the philosophical significance of STR for understanding space and time?
Examination of Physics Segments P3, P4: General Theory of Relativity and Cosmology
1. About tensors:
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Tensor in general form
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Coordinate language verus "object" language
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Einstein summation convention
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Examples of tensors (metric tensor, Riemann)
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Differentiation of tensors
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Parallel transport, geodesics, and curvature
2. About the General Theory of Relativity:
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Why the name GTR rather than "theory of gravity"?
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Geometric point of view (unconstained motion defines a geodesic in a curved space)
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Global versus local point of view
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Equation of geodesic deviation for a sphere (derive and interpret)
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Equation of geodesic deviation generally (state and interpret)
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Riemann curvature tensor (calculate Reimann components near the earth and inside the earth)
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Definition of Einstein Tensor and its constitutive tensors
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Einstein's field equations (state and interpret)
3. Big-Bang Cosmology
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Basic assumptions: homogeneity and isotropy
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Meaning of t,t component of field equations when density is constant
[ (a'')2=(8πρa2)/3 -1 ] -
interpretation as dynamic universe; Einstein's reaction (introduced cosmological constant)
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Evidence (Hubble, CBR, nuclear abundance, dark night sky,...)
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Narrative of early universe, including connections between high-energy particle physics and cosmology
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Inflation used to explain problems (such as flatness of universe and variations in CBR)
4. Quantum Cosmologies
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The overriding purpose of quantum cosmologies
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The connection between high-energy particle physics and quantum cosmologies
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Various quantum cosmologies—qualitatively describe and compare
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The metaphysical significance of quantum cosmologies
Examination of Physics Segments P5: Quantum Machanics
1. Early discoveries
1.1 Energy quantization of radiation
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Plank (1901) Black Body
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Einstein (1905) Photoelectric Effect
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Bohr (1913) Atomic Spectra
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Compton (1923) Scattering Xrays from foil
1.2 Interference effects of particles
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DeBroglie's (1924) postulate of wavelength tied to momentum
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Davisson-Germer (1927) and Thompson (1928) crystal scattering and transmission of electrons
1.3 Double-slit experiment (illustrates Heisenberg Uncertainty Principle)
1.4 Stern-Gerlach experiment (illustrates probabilities nature of measurement outcomes)
2. Formalism
2.1 Mathematical interpretation of systems, states, observables, measurement
2.2 von Neumann's Hilbert Space approach
2.3 Born's Projection Postulate
2.4 Schrödinger's Equation
3. Non-locality
3.1 Einstein-Podolsky-Rosen thought experiment (1935): locality entails violation of uncertainty principle, which implies incompleteness of quantum mechanics
3.2 Bell's inequalities: locality entails that statistics from experiments on correlated particles pairs should conform to specific inequalities (but Aspect's experiments show they do not, thus demonstrating non-locality)
3.3 Non-locality and faster-than-light information transfer
4. Philosophical Interpretation
4.1 Three levels of interpretation
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Correspondence rules and associated principles connecting formalism to observable phenomena
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Creating conceptually unifying, semi-pictorial models
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Adjustments to theory on the basis of appealing models
4.2 Major interpretations
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Standard (Copenhagen) interpretation (distinguish from Bohr)
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Many Worlds and Many Minds interpretations
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Hidden Variables interpretations (esp. Bohm)
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Continuous Spontaneous Localization theories
4.3 Significance for theology (optional)
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Freedom versus determinism
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Locus for natural-law-conforming action of divine being
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Entanglement and unity of divine creation
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