Understanding the Foundations of Scientific Reasoning

1. Mid Term #1 Study Guide 1

2. Empirical Science Observational, descriptive Science Detecting patterns, or departures from patterns Theoretical Science Generating and testing models (hypothesis testing) Concerned with explaining observations and making predictions Technological Science Generating new methods and processes Troubleshooting Basic Assumptions/ Beliefs Materialism and Naturalism Operate in a closed system Nothing interferes with the system All events are totally dependent on the whole system Natural explanation for all phenomena Scientific Knowledge is based on methodology Observation Hypothesis Experimentation Dynamic, not static Lecture 1 What is Science

3. Inductive Logic Reasoning from Experiences Knowledge Expanding Contains more information than premise Deductive Logic Start with general knowledge and predict a specific observation Truth preserving Contains less information than premises Scientific Reasoning(Propositional Logic) Key Terms • Postulate • Premise • Principle • Theory • Hypothesis • Test

4. Principles of Inductivism The number of observations forming the basis of a generalization must be large Observations must be repeated under a variety of conditions No observations should conflict with universal laws, principles, or theories Problems with Inductivism Appeals to logic Appeals to experience How many observations are required? What constitutes significant variation Must retreat to probability Theory: dependent on inductivism Inductivism fails to throw new light on science Recognize an example of inductive reasoning

5. Process Statement of problem Hypothesis as to the cause of the problem Experimental tests for each hypothesis Predict results (how to accept or reject the hypothesis Observe results Draw conclusions from the results (accept or reject the hypothesis) Premis Fundamental Assumptions Must be both valid and true Good tests Prediction is logically deducible Prediction is improbable Prediction is verifiable Deduction

6. Deductive Process Class is too large Problem If I make this confusing, then some students will drop Hypothesis Deliver miserable Lecture about logic Test Accept Reject Some people will get confused and drop Prediction Observation? Observation No Drops Loads-O-Drops Conclusion Accept Reject Was This a Good Example?

7. Deduction Premis, Fundamental Assumptions Must be both valid and true Good tests Prediction is logically deducible Prediction is improbable Prediction is verifiable

8. Hypothetico-Deductive Method Laws and theories Deduction Induction Facts acquired through observation Predictions and explanations

9. Deductive Falsification(Conjectures and Refutations) • Positivist- • Only has supporting evidence • Ignores evidence against

10. Falsification science: The process of developing a set of hypotheses, tentatively proposed, to as accurately as possible describe an aspect of the natural world. Hypotheses must be falsifiable: One develops logically possible observations which, if established, would falsify the H0. Problems with Falsification: Complexity of any realistic test of most modern theories is often extremely difficult. Theory underlying hypotesis may be false. The premise behind hypothesis is false. The Process of Popperian Falsification • Example of Falsification from Induction • Many lectures on the philosophy of science are boring • This is a lecture on the philosophy of science • Therefore, this class is boring • What is the experiment that would falsify or disprove our hypothesis?

11. Role of the Scientist Understanding whether science and scientists are objective or subjective is important in understanding what science is. These are not models but definitions of how science is practiced. Science Values Scientific Knowledge is not good or bad…Its Goodness or Badness depends on how it’s used and by what standard you grade it. Is science and are scientists objective? Subjectivism holds that man is not objective, but subjected to his surroundings, training, personal experience, etc. Objectivism is the belief that mankind can be removed from or independent of his surroundings and experiences while making observations. Objectivism vs. Subjectivism

12. Objectivism and Subjectivism result in at least three concurrent views of science • 1- Scientific Imperialism • Science is the Truth Arbiter • Therefore, anything goes if scientists say so • Objectivism is the belief that a scientist can be removed from or independent of his surroundings and experiences while making observations, conclusions and recommendations. • 2- Postmodern Relativism • Plurality of Truths • Science is only one form of Subjective Truth • Science has made errors in the past, • Therefore, science and scientists should be: • Questioned, Evaluated and Regulated • Subjectivism holds that science and scientists are not objective, but antecedents to surroundings, training, personal experience, etc. • 3- Godisms • Mankind is created and ultimately Truth is God Revealed. • Science is a product of mankind, therefore science must be carefully evaluated for its potential good and/or bad outcomes. • Since truth is ultimately Revealed and science is error prone, science is subjective and an ethical society must take care to evaluate and judge science’s pursuits and products carefully.

13. Science: Research programs • Hard core theory, often not easily challenged • Generates lots of Hypotheses Progress Degenerate Problems: 1) Politically influenced, 2) Special interest influenced, 3) Dictate large expenditures of public funds, 4) Redirect or sometimes misdirect science thrusts and 5) Often ideologically driven or oriented. Examples: Genomics, NASA, Aids Research, Cancer Research, Human Genome Project, etc.

14. Kuhn’s Scientific Revolution Normal Science Crisis Revolution Prescience A Scientific Theory is likea pitcher of water. Scientific knowledge is dynamic and changeswith new discoveries and additions of newinformation When one Theory fails its components often flow into another Theory.

15. Lecture 1: What is Science wrap-up • Human endeavor dependent on the scientific community and society. • Not infallible, often guided by scientific fads, yet the best we have. • There are at least 4 ways of describing Science: Inductivism, Falsification, Science Programs & Kuhnian Revolutions. • Based on presuppositions about how the world is, & many if not all, of these presuppositions are not scientifically testable.

16. Lecture 2: Outline • What is life • Characteristics- Definition- • Properties- Dynamic changing • Components- building blocks • Minimal life- simplest life forms • Organizing Life • Taxonomy • Functions of Life • Metabolism • Plant • Animal • Carbon, nitrogen and water cycling • Origin of Life • Where did it come from • Current Models • Introduction to Biological Chemistry

17. Properties of Life Dynamic = changing Adaptability Contain Information (DNA) Ordered Structure Uniformity of class Definition of Life An organismic state characterized by the capacity for metabolism, growth, reaction to stimuli, and reproduction. A principle or force that underlies the distinctive quality of animate beings. The quality that distinguishes a vital and functional organism from inanimate objects. Characteristics of Death Absence of life Total and permanent cessation of all vital (living) function Absence of the characteristics of life Key Terms in “Life” Definition Metabolism Acquires and expends “energy” Growth Makes what it needs Reaction Senses Environment Reproduction A population of one and only one is going to run into trouble sooner than later Smallest Components of Life Elements (atoms) Molecules Macromolecules Information carriers Enzymes, proteins Functional capacity Membranes and walls Boundaries, and containers What Is Life

18. Categories of life’s components Atoms, Amino Acids, Macromolecules, Organelles, Cells, Cells, Organ, Systems, Symbiotic organisms, Individual, Populations Life Quantitatively Complexity High Low How Biologists Measure Size: Metrics Assignment: Learn the metric measuring system and life sizes

19. How simple can life be? • Phytoplasma and Mycoplasma = simplest cell, lack a cell wall, DNA for 200 functions (walking pneumonia, STD’s) • Not Cells • Virus = RNA or DNA wrapped in protein coat (HIV, poliomyellitis) • Viroid = Tightly wound DNA or RNA (coconut cadang cadang, bunchy top) • Prions = 1/100 to 1/1000 the size of a virus, composed of proteins (Scapies, Multiple Sclerosis, Lou Gehrig’s disease) Is each of these really alive? Are they independent? Can they reproduce or metabolize on their own? Pneumonia mycoplasma HIV

20. Systematics Taxonomy Cladistics Phylogenics Methods of Classification Based on some relevant distinguishing characteristic It should be meaningful It should not be arbitrary Basis of Classifications Morphological characteristics Types of structures, Size, Diet, Reproduction Molecular characteristics Mitochondrial DNA Nuclear DNA Classification Kingdom Phylum Class Order Family Genus Species Classification The Kingdoms Animalia- multicelluar, consumers Plantae- multicellular, producers Fungi- mostly decomposers Protista- One-celled, producers and consumers Eubacteria- Normal, true bacteria, consumers… Archaebacteria- Extreme bacteria, consumers… Organizing Life Basic Premis (assumption) of taxonomy “Natura non facit saltum” (Nature does not make leaps).

21. So Who’s Related Classification schemes generate different trees based on which sorting criteria is used. Trees based on physical characteristics or reproductive characteristics are often different from trees made from comparisons of DNA. The specific DNA used also generates different trees. Mitochondrial DNA, or different nuclear genes encoding common proteins can each generate different trees. DNA sequences provide a direct record of the genealogy of extant species. surprising changes have recently been proposed for The tree of mammalian orders. These range from grouping whales with hippos, to placing African golden moles closer to elephants than to their fellow insectivores. Molecules remodel the mammalian treeWilfried W. de JongTrends in Ecology & Evolution 1998, 13:270-275

22. Metabolism Storing and releasing energy Converting light energy into chemical energy Plants fix carbon from the air Animals release carbon from storage moleclues Growth Using the stored energy Incorporating acquired materials Catabolic processes- breaking down Anabolic processes- building up Reaction Sensing environment Receptors andMetabolic changes Reacting to changing environment Examples from Bacteria, Plants and Animals Reacting to internal environment: Homeostasis Reproduction Sexual Reproduction: Cell Process: Meiosis and Mixing Genes Replication, Division: Cell Process: Mitosis and High fidelity copies Adaptation and Selection Functions of LifeFour categories for organizing the characteristic of life: Metabolism, Growth, Reaction, Reproduction

23. Three Models Neo-Darwinian Macro Evolutionary Process Cosmic Inoculation Panspermia Divine Creation The Standard Story The Big Bang 12-15 billion years ago all matter was compressed into a space the size of our sun Sudden instantaneous distribution of matter and energy throughout the known universe Planet Formation About 4.6 and 4.5 billion years ago The Earth formed and conditions were just right The right kinds of molecules formed The right molecules assembled Is Life is a property of matter and energy? Abiogenesis Origin (Neo-Darwinian) Macro Evolutionary Process Chance, Necessity, and Self Organization Chemical processes generated life precursors Precursors assembled into proto cells Extraterrestrial deposition (Panspermia) Organisms came from somewhere else Chemistry came from somewhere else Presuppositions Do Presuppositions Matter? Naturalism and Materialism Life is a property of matter and energy Chance, Necessity, and Self Organization Of course it works, we’re here aren’t we? Where does life come from?Objectivism and Subjectivism result in different views of science. These views and their assumptions affect fundamental questions of science

24. New ideas, new questions Matter, Energy, and Information Where does the information come from? Identifying LifeDoes Life Exist Elsewhere in the Universe? Are terrestrial biochemistry and molecular biology the only such phenomena that can support life? With only one example, we don’t know which properties of life are general and necessary, and which are the result of specific circumstances or historical accident. Normal Science Crisis Revolution Prescience Its life Jim, but not as we know it Origin of LifeWhere did it come from? Summary Definitions Properties Characteristics Organization Life and Energy Measuring Life Forms of Simple Life Origin of Life

25. Lecture 3: Chemistry of Life

26. Chemical Bonds

27. Fundamental forms of matter Can’t be broken apart by normal means Most Common Elements in Living Organisms: Oxygen, Hydrogen, Carbon, and Nitrogen What Are Atoms? Smallest particles that retain properties of an element Made up of subatomic particles: Protons (+) Electrons (-) Neutrons (no charge) Atomic Number Atomic Mass Isotopes and Radioisotopes Uses of Radioisotopes Tracers, Imaging, Radiation therapy HYDROGEN Elements

28. Electrons Carry a negative charge Repel one another Are attracted to protons in the nucleus Move in orbitals - volumes of space that surround the nucleus Electron Vacancies Unfilled shells make atoms likely to react Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells Chemical Bonds, Molecules, & Compounds Bond is union between electron structures of atoms Atoms bond to form molecules Molecules may contain atoms of only one element - O2 Molecules of compounds contain more than one element - H2O What Determines Whether Atoms Will Interact?

29. Electrostatic Covalent Chemical Bonds • 1. Ionic Bonding • One atom loses electrons and becomes a positively charged ion • Another atom gains an electron and becomes a negatively charged ion • Charge difference attracts the two ions to each other Ion Formation Atom has equal number of electrons and protons - no net charge Atom loses electron(s), becomes positively charged ion Atom gains electron(s), becomes negatively charged ion SODIUM ATOM 11 p+ 11 e- CHLORINE ATOM 17 p+ 17 e- electron transfer SODIUM ION 11 p+ 10 e- CHLORINE ION 17 p+ 18 e-

30. 2. Covalent Bonding Atoms share a pair or pairs of electrons to fill outermost shell High energy bonds hold together tightly. Require high levels of energy to break covalent bonds Two Flavors of Covalent Bonds Non-polar Covalent Atoms share electrons equally Nuclei of atoms have same number of protons Example: Hydrogen gas (H-H) Polar Covalent Number of protons in nuclei of participating atoms is NOT equal Molecule held together by polar covalent bonds has no NET charge Electrons spend more time near nucleus with most protons Example: Water Electrons more attracted to O nucleus than to H nuclei Electrostatic Covalent Chemical Bonds

31. + KEEP YOUR EYE ON THE ELECTRONS Example slight negative charge at this end molecule has no net charge ( + and - balance each other) O H H slight positive charge at this end

32. Hydrogen Bonding A bond by Hydrogen between two atoms • Important for O and N • Lets two electronegative atoms interact • The H gives one a net + and the other one that is still – is attracted to it. • The H proton becomes “naked” because its electron gets pulled away.

33. - - - + - Hydrogen bond figure KEEP YOUR EYE ON THE ELECTRONS Like Charge Atoms Repel Each Other Opposite Charge Atoms Attract Each Other

34. Hydrogen bonds are the most physiologically relevant chemical bond in all of nature!!!! one large molecule Hydrogen bonds hold DNA strands together and allow them to come apart and reform! another large molecule Hydrogen bonds take place between different parts of a polypeptide chain and give the molecule the glue it needs to fold correctly a large molecule twisted back on itself

35. Properties of Water Polarity Temperature-Stabilizing Cohesive Solvent Molecule has no net charge Water Is a Polar Covalent Molecule Oxygen end has a slight negative charge Hydrogen end has a slight positive charge Hydrophilic & Hydrophobic Hydrophilic substances Polar Hydrogen bond with water Example: sugar Hydrophobic substances Nonpolar Repelled by water Example: oil Water Is a Good Solvent Ions and polar molecules dissolve easily in water When solute dissolves, water molecules cluster around its ions or molecules and keep them separated Solvent- polar Keeps ions in solution Doesn’t dissolve membranes Water

36. The pH Scale and pH in general Measures H+ concentration of fluid Change of 1 on scale means 10X change in H+ concentration Highest H+ Lowest H+ 0---------------------7-------------------14 Acidic Neutral Basic The problem with water is a static view H3O+↔H2O↔OH- Draino and battery acid are really bad for your skin. Understanding pH, the basis of protein structure and formation of peptide bonds help you to understand why • Hydrogen Ions: H+ • Unbound protons • Have important biological effects • Form when water ionizes • Acids • Donate H+ when dissolved in water • Acidic solutions have pH < 7 • Strong acids forcefully give up H+ • Bases • Accept H+ when dissolved in water • Acidic solutions have pH > 7 • Strong bases forcefully take H+

37. Organic Compounds Hydrogen and other elements covalently bonded to carbon: Carbohydrates, Lipids, Proteins, Nucleic Acids Carbon’s Bonding Behavior • Outer shell of carbon has 4 electrons; can hold 8 • Each carbon atom can form covalent bonds with up to four atoms • Carbon atoms can form chains or rings • Other atoms project from the carbon backbone Functional Groups • Atoms or clusters of atoms that are covalently bonded to carbon backbone • Give organic compounds their different properties Examples of Functional Groups Hydroxyl group - OH Amino group - NH3+ Carboxyl group - COOH- Phosphate group - PO3- Sulfhydryl group - SH

38. Functional group transfer, Electron transfer, Rearrangement, Condensation, Cleavage Condensation Reactions Form polymers from subunits Enzymes remove -OH from one molecule, H from another, form bond between two molecules Discarded atoms can join to form water Hydrolysis A type of cleavage reaction Breaks polymers into smaller units Enzymes split molecules into two or more parts An -OH group and an H atom derived from water are attached at exposed sites Types of Reactions

39. Carbohydrates Monosaccharides (simple sugars) Oligosaccharides (short-chain carbohydrates) Polysaccharides (complex carbohydrates) Monosaccharides Simplest carbohydrates Most are sweet tasting, water soluble Most have 5- or 6-carbon backbone Glucose (6 C) Fructose (6 C) Ribose (5 C) Deoxyribose (5 C) Polysaccharides Straight or branched chains of many sugar monomers Most common are composed entirely of glucose Cellulose Starch (such as amylose) Glycogen Cellulose & Starch Differ in bonding patterns between monomers Cellulose - tough, indigestible, structural material in plants Starch - easily digested, storage form in plants Glycogen Sugar storage form in animals Large stores in muscle and liver cells When blood sugar decreases, liver cells degrade glycogen, release glucose Chitin Polysaccharide Nitrogen-containing groups attached to glucose monomers Structural material for hard parts of invertebrates, cell walls of many fungi THE MACRO MOLECULES

40. glucose fructose + H2O sucrose glucose fructose

41. stearic acid oleic acid linolenic acid THE MACRO MOLECULES Fatty acid(s) Lipids • Most include fatty acids • Fats • Phospholipids • Waxes • Sterols and their derivatives have no fatty acids • Tend to be insoluble in water Fatty Acids • Carboxyl group (-COOH) at one end • Carbon backbone (up to 36 C atoms) • Saturated - Single bonds between carbons • Unsaturated - One or more double bonds Triglycerides

42. Phospholipids • Main components of cell membranes

43. Sterols and Derivatives • No fatty acids • Rigid backbone of four fused-together carbon rings • Cholesterol - most common type in animals

44. Waxes • Long-chain fatty acids linked to long chain alcohols or carbon rings • Firm consistency, repel water • Important in water-proofing

45. Amino Acids Properties of Amino Acids Determined by the “R group” Amino acids may be: Non-polar Uncharged, polar Positively charged, polar Negatively charged, polar Protein Synthesis Protein is a chain of amino acids linked by peptide bonds Peptide bond Type of covalent bond Links amino group of one amino acid with carboxyl group of next Forms through condensation reaction Polyamino Acids = polypeptide = protein THE MACRO MOLECULES

46. Protein Protein Shapes Fibrous proteins Polypeptide chains arranged as strands or sheets Globular proteins Polypeptide chains folded into compact, rounded shapes Protein Structure Primary- just the sequence (1D) Secondary- interactions on the chain (2D) Tertiary- interactions between parts of the chain the chain. (3D) Quaternary- interactions with other chains Primary Structure & Protein Shape Sequence of amino acids Primary structure influences shape in two main ways: Allows hydrogen bonds to form between different amino acids along length of chain Puts R groups in positions that allow them to interact Secondary Structure Hydrogen bonds form between different parts of polypeptide chain These bonds give rise to coiled or extended pattern Helix or pleated sheet Tertiary Structure Folding as a result of interactions between R groups The 3D structure of a protein Quaternary Structure Some proteins are made up of more than one polypeptide chain Structure of a protein when it is folded with other polypeptides Polypeptides With Attached Organic Compounds Lipoproteins Proteins combined with cholesterol, triglycerides, phospholipids Glycoproteins Proteins combined with oligosaccharides THE MACRO MOLECULES

47. Examples of Secondary Structure

48. heme group coiled and twisted polypeptide chain of one globin molecule Hemoglobin

49. Denaturation • Disruption of three-dimensional shape • Breakage of weak bonds • Causes of denaturation: • pH • Temperature • Destroying protein shape disrupts function

50. A Permanent Wave hair’s cuticle coiled keratin polypeptide chain keratin macrofibril one hair cell microfibril (three chains coiled into one strand) different bridges form bridges broken hair wrapped around cuticles