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Chapter 01 Lecture Outline See separate PowerPoint slides for all figures and tables pre-inserted into PowerPoint without notes and animations. 1 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. **Important study hint** • Review the study hints at the end of the syllabus. • Multitasking does NOT work! Eliminate distractions while studying. – – – – – Don’t watch TV Don’t text or watch for texts. Turn off your phone. Don’t log in to social media. Don’t email or use social media in class. http://www.slate.com/articles/health_and_science/science/2013 /05/multitasking_while_studying_divided_attention_and_technol ogical_gadgets.html Follow link 2 The Science of Biology Chapter 1 3 The Science of Life • Biology unifies much of natural science • Life defies simple definition – Living systems are the most complex chemical systems on Earth – Life is constrained by the properties of chemistry and physics • Science is becoming more interdisciplinary – Combining multiple fields 4 The Science of Life 7 characteristics of all living organisms 1. 2. 3. 4. 5. 6. Cellular organization Ordered complexity Sensitivity Growth, development, and reproduction Energy utilization Homeostasis 7. Evolutionary adaptation – at population level 5 The Science of Life • Living systems show hierarchical organization – Cellular level – Organismal level – Populational level – Ecosystem level – Biosphere 6 http://iws.collin.edu/biopage/faculty/mcculloch/1406/outlines/chapter%201/chap01.html The Science of Life • Living systems show hierarchical organization – Cellular level • Atoms, molecules, organelles, cells • Cell is the basic unit of life CELLULAR LEVEL Atoms Molecule Macromolecule Organelle Cell O C H N O H N C O 0.2 µm 7 Cellular Level CELLULAR LEVEL Atoms Molecule Macromolecule Organelle Cell O C H N O H N C O 0.2 µm (organelle): © Dr. Donald Fawcett & Porter/Visuals Unlimited; (cell): © Steve Gschmeissner/Getty Images Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 8 The Science of Life • Living systems show hierarchical organization ORGANISMAL LEVEL Tissue Organ Organ system Organism – Organismal level • Tissues, organs, organ systems • individual organism 9 Organismal Level ORGANISMAL LEVEL Organ Tissue Organ system Organism 10 100 µm (tissue): © Ed Reschke; (organism): © Russell Illig/Getty Images RF Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. The Science of Life • Living systems show hierarchical organization – Populational level • Population (interbreeding) • Community (all populations within a habitat) POPULATIONAL LEVEL Population Species Community Ecosystem Biosphere – Ecosystem level – Biosphere • Earth is an ecosystem we call the biosphere 11 Populational Level POPULATIONAL LEVEL Population Species Community Ecosystem Biosphere (population): © George Ostertag/agefotostock; (species): © PhotoDisc/Volume 44 RF; (community): © Ryan McGinnis/Alamy; (ecosystem): © Robert and Jean Pollock; (biosphere): NASA Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 12 The Science of Life • Each level has emergent properties – Result from interaction of components – Cannot be deduced by looking at parts themselves – “whole is greater than the sum of the parts” – “Life” is an emergent property 13 The Nature of Science • Science aims to understand the natural world through observation and reasoning • Science begins with observations, therefore, much of science is purely descriptive – Classification of all life on Earth – Human genome sequencing 14 The Nature of Science • Science uses both deductive and inductive reasoning… Deductive reasoning uses general principles to make specific predictions (big idea specific situation) Inductive reasoning uses specific observations to develop general conclusions (specific observations big idea) 15 http://toknow-11.wikispaces.com/Inductive+Reasoning The Nature of Science • Scientists use a systematic approach to gain understanding of the natural world = Scientific Method – Observation – Hypothesis formation – Prediction – Experimentation – Conclusion 16 http://www.bcps.org/offices/lis/researchcourse/develop_writing_method_quantitative.html Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Observation Note the use of alternative hypotheses Question Potential hypotheses Hypothesis 1 Hypothesis 2 Hypothesis 3 Hypothesis 4 Hypothesis 5 Remaining possible hypotheses Hypothesis 2 Hypothesis 3 Hypothesis 5 Last remaining possible hypothesis Hypothesis 5 Experiment Reject hypotheses 1 and 4 Experiment Reject hypotheses 2 and 3 Modify hypothesis Predictions Experiment 1 Experiment 2 Experiment 3 Predictions confirmed Experiment 4 17 The Nature of Science • A hypothesis is a possible explanation for an observation – NOT just an “educated guess” • A hypothesis (the “if”) – Must be able to be tested to determine its validity – Allows for predictions to be made if hypothesis is true – Is often tested in many different ways • Iterative – Hypotheses can be changed and refined in light of new data 18 The Nature of Science • Predictions (the “then”) – Valid hypotheses must provide testable predictions – Predictions provide a way to test the validity of hypotheses, … – Hypothesis must be rejected if the experiment produces results inconsistent with the predictions – The more experimentally supported predictions a hypothesis makes, the more valid the hypothesis 19 http://www.bcps.org/offices/lis/researchcourse/develop_writing_method_quantitative.html The Nature of Science • Experiment – Tests the hypothesis thru predictions – Must be carefully designed to test only one variable at a time – Consists of a test treatment(s) and a control(s) – Must have replication – Results must be reproducible Control (0 mg drug) 1 mg drug 2 mg drug 4 mg drug 20 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. SCIENTIFIC THINKING Question: What is the source of contamination that occurs in a flask of nutrient broth left exposed to the air? Germ Hypothesis: Preexisting microorganisms present in the air contaminate nutrient broth. Prediction: Sterilized broth will remain sterile if microorganisms are prevented from entering flask. Spontaneous Generation Hypothesis: Living organisms will spontaneously generate from nonliving organic molecules in broth. Prediction: Organisms will spontaneously generate from organic molecules in broth after sterilization. Test: Use swan-necked flasks to prevent entry of microorganisms. To ensure that broth can still support life, break swan-neck after sterilization. Note that the alternative hypotheses have different (mutually exclusive) predictions Broken neck of flask Flask is sterilized by boiling the broth. Unbroken flask remains sterile. Broken flask becomes contaminated after exposure to germ-laden air. Result: No growth occurs in sterile swan-necked flasks. When the neck is broken off, and the broth is exposed to air, growth occurs. 21 Conclusion: Growth in broth is of preexisting microorganisms. The Nature of Science • Complimentary philosophical approaches to science – Reductionism • To break a complex process down to its simpler parts – Systems biology • Focus on emergent properties that can’t be understood by looking at simpler parts 22 http://likethedew.com/2013/03/23/sciences-sacred-cows-reductionism/ http://en.wikipedia.org/wiki/Graphical_model The Nature of Science • Models in science – Way to organize thought – Parts provided by reductionist approach – Model shows how they fit together – Suggest experiments to test the model – Mathematical, graphical, computer 23 http://www.treehugger.com/clean-technology/xmas-is-early-for-climate-scientists-new-cesm-modeling-software-is-out.html The Nature of Science • Scientific theory – more than “just a theory” – Body of interconnected concepts – Supported by much experimental evidence and scientific reasoning – Expresses ideas of which we are most certain • Compare to general meaning of theory – Implies a lack of knowledge or a guess 24 Darwin and Evolution • Example of how a scientist develops a hypothesis and a theory gains acceptance • Charles Darwin served as naturalist on mapping expedition around coastal South America • 30 years of observation and study before publishing On the Origin of Species by Means of Natural Selection Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 25 Voyage of the HMS Beagle Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. British Isles NORTH PACIFIC OCEAN NORTH AMERICA Galápagos Islands Western Isles NORTH ATLANTIC OCEAN Valparaiso Society Islands ASIA NORTH PACIFIC OCEAN Canary Islands Cape Verde Islands SOUTH AMERICA Bahia Marquesas EUROPE Philippine Islands AFRICA INDIAN OCEAN Ascension Madagascar St. Helena Rio de Janeiro Keeling Islands Mauritius Bourbon Island Equator AUSTRALIA Friendly Islands Sydney Montevideo Buenos Aires Port Desire Straits of Magellan Falkland Islands Cape Horn Tierra del Fuego Cape of Good Hope SOUTH ATLANTIC OCEAN King George’s Sound Hobart New Zealand 26 http://www.theguardian.com/science/blog/2012/jan/04/new-hms-beagle-2013 Darwin and Evolution • Darwin was not the first to propose evolution – It was known that living things have changed over time • Darwin’s contribution was a mechanism for evolution – Natural selection 27 https://en.wikipedia.org/wiki/Human_evolution Darwin and Evolution • On the Beagle, Darwin saw that characteristics of similar species varied from place to place • Galápagos Finches – 14 related species differ only slightly – “Descent with modification” or evolution Woodpecker Finch (Cactospiza pallida) Large Ground Finch (Geospiza magnirostris) Cactus Finch (Geospiza scandens) 28 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Darwin and Evolution • Darwin studied Thomas Malthus’s An Essay on the Principle of Population – Populations of plants and animals increase geometrically (multiplicative, example x3) – Humans can only increase their food supply arithmetically (additive, example +2) – Populations of species remain constant because death limits population numbers 29 Darwin and Evolution Darwin saw that: • Every organism has the potential to produce more offspring • But, only a limited number survive and reproduce themselves Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. geometric progression arithmetic progression 54 Human Growth is Geometric Human food production is Arithmetic 18 6 2 6 8 4 30 Darwin and Evolution Darwin made an important association: • Individuals with attributes that give them an advantage in their environment are more likely to survive and reproduce • Pass these characteristics on to their offspring • The population will gradually change over time • Darwin called this selection http://www.historyrv.com/blog/en/2012/01/broken-natural-selection/ Darwin and Evolution • Evidence supporting Darwin’s theory has only grown – Fossil record – Earth’s age – Mechanism for heredity – Comparative anatomy – Molecular evidence 32 http://itlaligarcia.blogspot.com/2011/02/why-is-fossil-record-hard-to-interpret.html Darwin and Evolution • Evidence supporting Darwin’s theory has only grown – Fossil record • Transitional forms have been found at predicted positions in time – Earth’s age 33 • Physicists of Darwin’s time were wrong • Earth is very old – 4.5 billion years old Image by B. Tyler Darwin and Evolution • Evidence supporting Darwin’s theory has only grown – Mechanism for heredity • Mendel’s laws of inheritance were unknown to Darwin • At time of Darwin there was no concept of “genes” or how heredity worked • Darwin could not completely explain how evolution worked • Now have detailed understanding of heredity 34 Darwin and Evolution • Evidence supporting Darwin’s theory has only grown – Comparative anatomy • Vertebrate forelimbs all share the same basic array of bones • Homologous – same evolutionary origin but now differ in structure and function (forelimbs of verts) • Analogous – structures of different origin used for the same purpose (butterfly and bird wings) 35 Human Cat Bat Porpoise Horse Darwin and Evolution Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Human Cat Bat Porpoise Horse Homologous – same evolutionary origin but now differ in structure and function 36 Darwin and Evolution Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • Evidence supporting Darwin’s theory has only grown – Molecular Evidence • Compare genomes or proteins of different organisms • Phylogenetic trees – based on tracing origin of particular nucleotide changes to reconstruct an evolutionary history Human 0 Rhesus 10 Dog 20 30 Frog Bird 40 50 60 70 Number of Amino Acid Differences in a Hemoglobin Polypeptide 37 Unifying Themes in Biology • Cell theory – All organisms composed of cells – Cells are life’s basic units – All cells come from preexisting cells Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a. b. 60 µm 500 µm a: © Dennis Kunkel/Phototake; b: © Karl E. Deckart/Phototake 38 Unifying Themes in Biology • Molecular basis of inheritance – Deoxyribonucleic acid (DNA) – Sequence of 4 nucleotides encode cell’s information – Gene – discrete unit of information – Genome – entire set of DNA instructions – Continuity of life depends on faithful copying of DNA into daughter cells 39 http://employees.csbsju.edu/hjakubowski/classes/ch331/dna/chromosome.gif Unifying Themes in Biology • Structure and function – Study structure to learn function – Know a function – look for that structure in other organisms – Example • Receptor on human cell for insulin known • Find similar molecule in a worm • Might conclude this molecule functions the same in the worm 40 http://www.nature.com/nrd/journal/v1/n10/images/nrd917-i1.gif Unifying Themes in Biology • Diversity of life arises by evolution – Underlying unity of biochemistry and genetics argues for life from the same origin event – Diversity due to evolutionary change over time – 3 domains of life • Bacteria – single-celled prokaryote • Archaea – single-celled prokaryote • Eukarya – single-celled or multicellular eukaryote 41 http://www.bacterialphylogeny.com/img/archaea/three_domain.jpg Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Domain Kingdoms Plantae Fungi Eukarya Animalia Protista (plantae middle): © David M. Dennis/Animals Animals; (plantae right): © Corbis/Volume 46 RF; (fungi left): © Royalty Free/Corbis; (fungi middle): © Mediscan/Corbis; (fungi right): © PhotoDisc BS/Volume 15 RF; (animalia left): © Royalty-Free/Corbis; (animalia middle): © Tom Brakefield/Corbis; (animalia right): © PhotoDisc/Volume 44 RF; (protista left): © Corbis/Volume 64 RF; (protista middle): © Tom Adams/Visuals Unlimited; (protista right): © Douglas P. Wilson/Frank Lane Picture Agency/Corbis 42 Unifying Themes in Biology • Evolutionary conservation – All organisms today descended from a simple creature 3.5 BYA – Many characteristics preserved – Ex: use of DNA Tree of Life – Conservation reflects that they have a fundamental role in life Evidence for evolution 43 http://learn.genetics.utah.edu/content/variation/tracktraits/ Unifying Themes in Biology • Cells are information-processing systems – Information in DNA used to direct synthesis of cellular components • Control of gene expression leads to different cells/ tissue types – Cells process environmental information • Glucose levels, presence of hormones – Cells in multicellular organisms must coordinate with each other 44 https://upload.wikimedia.org/wikipedia/commons/thumb/7/7f/Tet-ON_inducible_transgene_expression_cells.svg/500px-TetON_inducible_transgene_expression_cells.svg.png http://www.eoearth.org/files/115001_115100/115006/300px-Ecosystem_matter_energy.gif Unifying Themes in Biology • Nonequilibrium state – Living systems are open systems – Constant supply of energy needed – Self-organizing properties at different levels – Emergent properties from collections of molecules, cells, and individuals Cells to ecosystems are open 45 http://origin-ars.els-cdn.com/content/image/1-s2.0-S0005272899000651-gr1.gif