BSC 116 first three lectures
BSC 116 first three lectures BSC 116
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This 9 page Class Notes was uploaded by Ashley Bartolomeo on Sunday January 24, 2016. The Class Notes belongs to BSC 116 at University of Alabama - Tuscaloosa taught by Professor Harris in Spring 2016. Since its upload, it has received 80 views. For similar materials see Principles Biology II in Biological Sciences at University of Alabama - Tuscaloosa.
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Date Created: 01/24/16
Lecture 1 Review of the Scienti c Method The jobs of a scientist are to know things about the world and to explain them 0 Two phases of scientific research discovery and explanation 0 Both involve inquiry asking questions 0 Each phase informs the other 0 Pieces of information data plural singular datum 0 Quantitative countable measureable O Qualitative descriptive comparative 0 The same observations can be reported as either 0 Explanations are hypotheses plural singular hypothesis 0 Educated guess to explain a set of observations 0 Interesting hypotheses suggest where to look for new knowledge cyclic 0 Scientific knowledge is conditional the meaning of our data changes as we get more 0 There are two different kinds of reasoning applied 0 Inductive reasoning extrapolating from observations to a generalization O Deductive reasoning use a generalization to explain particular cases I Leads to predictions if then 0 We have to be willing to replace our explanations when they are shown to be wrong 0 For a hypothesis to be useful it must 0 Provide the best explanation 0 It must be falsifiable testable A Variety of Hypotheses Have Explained the Age of the Earth 0 Bishop James Ussher 15811656 Primate of Ireland 0 Used Genesis account traced all the so and so begat so and so 0 Determined that the Earth was created on 23 October 4004 BC 6000 years old 0 All the various landforms resulted from Noah s Flood catastrophism 0 Charles Lyell 17971875 English geologist O Looked at rates of erosion and thickness of rock formations O Assumed processes constant and slow uniformitarianism 0 Determined that Earth must be much older than 6000 years 0 William Thompson 18241907 Lord Kelvin O Assumed the Earth formed as a big molten blob cooling over time 0 From time needed to cool estimated the Earth to be 20400 million years old 0 20th century use radiometric dating to determine the age of rocks 0 Example radioactive uranium238 decays to lead206 at a known rate 0 Use proportion of elements to determine age 0 We now know the age of the Earth to be 46 billion years The Mechanism that Resulted in Present Biodiversity 0 Creation of life explained in Genesis 0 William Paley 17431805 Natural Theology 0 Observation of the natural world provides evidence of the Creator creationism I When Charles Darwin sailed around the world on the HMS Beagle he was a creationist 0 But he was also a scientist that asked questions If Special Creation is True Then I We wouldn t expect transitional forms I We wouldn t expect homology These Observations and many more Led Darwin to propose and Alternative 0 Darwin realized that his observations were not consistent with Creationism O The eVidence did not support each species being specially created 0 Proposed a new hypothesis transmutation 0 New species arise from changes to existing species descent with modification 0 Organisms are adapted to their environments by natural selection 0 The Origin of Species 1859 0 150 years of research has tested and refined Darwin s hypothesis now known as the Theory of Evolution A Few Concluding Words About the Scienti c Method 0 Scientific theories are 0 Hypotheses that have survived repeated tests 0 General incorporate many subhypotheses 0 Laws are even more general 0 It is unscientific to not abandon theories hypotheses when they lose their explanatory power I Separates science from philosophy theology I Hypotheses theories and laws are ways of organizing data using general explanations Lecture 2 History of Life on Earth Origin of Life 0 Life on Earth is at least 45 billion years old 0 How did it start 0 Chemical physical processes on early Earth may have produced simple cells in sequential stages I Abiotic synthesis of small organic molecules I Joining of these small molecules into macromolecules I Origin of selfreplicating molecules Synthesis of Organic Compounds 0 Earth ca 46 billion years old 0 Early atmosphere likely contained water vapor and chemicals released by volcanic eruptions nitrogen nitrogen oxides carbon dioxide methane ammonia hydrogen hydrogen sulfide O No oxygen MillerUrey Experiment 0 Atmosphere of early Earth was probably a reducing environment 0 Evidence for this hypothetical atmosphere is not entirely convincing 0 Another possibility first organic compounds were synthesized near submerged volcanoes and deepsea vents One Possible Scenario 0 Reducing environment gave rise to organic molecules amino and nucleic acids lipids etc 0 Catalytic RNA molecules ribozymes capable of self replication formed 0 Another RNA property information storage 0 Self assembly of lipids into spheres liposomes gave these molecules a protective environment Protobionts 0 Key properties of life replication and metabolism 0 Lipid bilayer could have provided compartmentalization for these tasks 0 Protobionts aggregates of abiotically produced molecules surrounded by a lipid membrane 0 Protobionts could have formed with simple metabolic activities Selfreplicating RNA amp the Dawn of Natural Selection 0 Ribozymes can catalyze many different reactions 0 Given enough time early protobionts and their simple machinery may have replicated mutated and eventually developed enough metabolic machinery to be considered life 0 RNA world could have given rise to DNAbased life more stable using RNA as an intermediate to protein synthesis How is the History of Life Studied 0 Fossils preserved remains of living organisms 0 Almost always in sedimentary rocks accumulation of layers of sand mud silt etc 0 Sediments and sedimentary rocks preserve the history of life youngest near the surface oldest deeper The Fossil Record 0 Fossil record is biased in favor of species that O Existed for a long time 0 Were abundant and widespread 0 Had hard parts fossilized easily Radiometric Dating 0 Inferring age of rocks and fossils based on amounts of radioactive elements 0 Mass spectrometer separates amp quantifies each isotope by mass 0 Example the mineral zircon as it forms contains uranium but not lead 0 U235 decays to Pb207 with a half life of 700 million years 0 Half life the time it takes for half of the parent element to decay to the daughter element 0 Analysis the sampled rock contains equal amounts of U235 and Pb207 0 Conclusion the rock is 1 half life 700 million years old Great Moments in the History of Life 0 46 billion years ago bya solar system forms 0 On a 24 hour clock 1201 am I 39 bya 300 am Earth cools stabilizes fewer volcanic eruptions O No free oxygen Reducing electrondonating atmosphere 0 Abiotic nonlife synthesis of small organic molecules amino acids bases etc and polymers I Replicated in lab I Recovered from meteorites Earth prior to life I 39 35 bya O The RNA world early pre and protolife probably depended on RNA which carries information and is catalytic 0 RNA enzymes ribozymes I RNA based life I DNA based DNA is more stable I 35 bya 400 am traces of first life The earliest living organisms 0 Earliest life prokaryotes 0 35 bya 400 am 0 Stromatolite fossilized bacterial mats identical in structure to extant bacterial mats Oxygen I Photosynthetic bacteria produce oxygen which increases in concentration starting about 27 bya I 3521 bya 400 am 100 pm only living forms are bacteria Oxygen Revolution 0 Posed a challenge for most life forms 0 Adaptations 0 Greater ability to harvest energy from sunlight 0 Cellular respiration O Drove evolution of multicellularity Eukaryotes 0 Origin of eukaryotes 100 pm 0 Hybrid cells 0 Mitochondria and plastids eg chloroplasts are of bacterial origin 0 Engulfed by protoeukaryote and establish symbiotic relationship I Symbiosis two organism live in proximity in a mutually beneficial arrangement 0 Endosymbiosis theory for the origin of eukaryotic cells 0 Eukaryotic cells originated by multiple rounds of intracellular incorporation of bacteria 0 Evidence for symbiosis O Mitochondrial plastids have bacteria like genomes 0 Current primitive eukaryotes that have bacterial symbionts Multicellular Organisms 0 12 bya 600 pm earliest multicellular organisms small algae 0 First animals 565mya 900 pm 0 535565 mya Ediacaran fauna I Found worldwide mysterious organisms unlike any known today lineages completely extinct 0 535525 mya Cambrian explosion Major groups of animals appear suddenly in fossil record First predators Ancestors of all known animal groups I Why an explosion ie why do these seem to appear suddenly I It s not really an explosion due to incomplete fossil record I It really is an explosion of body forms predation promotes rapid evolution exible developmental program Life on land I Aquatic organisms venture onto land and become primarily exclusively terrestrial I 1 bya bacteria 0 500 mya fungi plants and animals on land 0 420 mya arthropods I 365 mya tetrapod vertebrates 0 Land plants 952 pm 0 Dinosaurs 1056 pm 0 Mammals 1139 pm 0 Humans 1159 pm Lecture 3 The Pattern and Process of Evolution Descent with Modi cation 0 Darwin found that his observations were not consistent with the predictions of Creationism O E g geographical patterns transitional forms homology 0 Without a designer how do we get organisms that are so well adapted to their environments 0 Answer evolution Darwin s Four Observations 0 1 Members of a population vary in their traits 0 2 Traits are inherited from parents to offspring I 3 All species are capable of producing more offspring than their environment can support 0 4 There is competition for resources and many of these offspring do not survive the reproduce Darwin s Two Inferences 0 1 Individuals whose inherited traits give them a competitive edge to survive and reproduce leave more offspring than other individuals 0 2 This unequal ability of individuals to reproduce will lead to the accumulation of favorable traits in the population over generations Microevolution 0 Mutation selection and drift can lead to change in populations over time 0 The ultimate source of phenotypic variation is mutation 0 Genetic variation leads to phenotypic variation 0 Sexual reproduction recombination allows alleles to be shared among lineages 0 Mixes alleles creates new combinations 0 Population group of interbreeding individuals 0 Frequencies of alleles change in populations over time 0 Selection increase in the average fitness of a population 0 Drift result of random processes important in small populations 0 Populations gradually change over time As new traits that improve fitness arise thru mutation they eventually replace other traits Macroevolution 0 If populations become divided by a barrier the microevolutionary processes will operate in isolation O Populations will diverge acquire different traits 0 Eventually diverge to the point that they are no longer compatible 0 Cant survive in the other s environment 0 Cant reproduce with the other 0 Speciation the process by which two daughter species arise from an ancestral species 0 Analogous to cell division 0 It is the processes of change with time and speciation that resulted in the biodiversity we see today Evolutionary Time 0 Major innovations in the history of life 0 Formation of earth 0 Singlecelled prokaryotes O Photosynthesis O Singlecelled eukaryotes 0 Multicellular eukaryotes 0 Animals 0 History of diversification led to extinction O 5 major mass extinctions 0 This history is not mere speculation It is supported by an overwhelming amount of data from several lines of inquiry including the evolutionary relationships of living things Classi cation of Living Things 0 People like to classify things all things 0 Explanation hypothesis a way to make sense of individual observations things 0 Ex library card catalog 0 People have forever ie preEvolution discovered described named and classified living things 0 Natural Theology the goal was to understand the Creator 0 Group organisms based on shared characteristics I Ex robins and blue jays are both birds because they both have bird traits 0 By the mid 1700 s this caused problems 0 Proliferation of names same name for different organisms different organisms With multiple names 0 Too many species to keep track of Carolus Linnaeus amp Classi cation 0 1758 10th edition Systema Naturae introduced hierarchical classification system in use today 0 Taxa single Taxon are categories smaller nested in larger 0 Domain Kingdom Phylum Class Order Family Genus Species I Each level diagnosed by specific traits 0 Binomial nomenclature 39 Genus species 0 Intended as an information retrieval system 0 Evolution gave this system more meaning 0 Organisms share traits because they are more closely related to each other 0 Did King Phillip Come Qver Eor great paghetti Expressing Relationships as Trees 0 The process of evolution results in this hierarchical pattern 0 Traits arise in a species 0 Passed to daughter species speciation 0 Results in nested arrangement of traits 0 Can represent evolutionary history as a phylogenetic tree or phylogeny 0 Branch points represent ancestral species common ancestors 0 Sister taxa daughter lineages that diverge from common ancestor 0 Linnaean classification verbal description of a phylogeny O Often With more information How Do We Infer Phylogenetic Trees 0 If evolution occurs over long periods of time no one can observe it 0 Use the fossil record 0 Easy to determine age but difficult to determine ancestry 0 Very incomplete 0 Many groups have no fossils 0 Cladistics use the pattern of traits among living organisms Cladistics 0 Cladistics method for reconstructing phylogenies 0 Clade an ancestral species and all of its descendants O Monophyletic ancestor and all its descendants 0 A phylogeny is a nested hierarchy of clades just like a classification is a nested hierarchy of taxa 0 Clades are diagnosed by shared derived homologies 0 What are homologies 0 What are derived homologies Homology vs Analogy I We need to distinguish the traits that resulted from common ancestry from those that didn t I Homology trait shared by common descent O Organisms that share homologies inherited them from their common ancestor I Analogy natural selection can cause similar traits to appear in unrelated groups 0 Will lead us to incorrect relationships 0 How to distinguish homology from analogy O Corroborative characters 0 Fossil evidence 0 Character complexity Derived Characters vs Ancestral Characters 0 These are two kinds of homologies because species have many ancestors 0 Some homologies are shared with distant ancestors shared ancestral characters I Ex all mammals have vertebrae and jaws I These are not useful characters for diagnosing mammals 0 Some homologies are evolutionary novelties of particular clades shared derived characters I Ex mammals have hair and mammary glands I These characters suggest a clade of mammals exclusive of species that lack them 0 We rely only on shared derived characters in cladistics to infer evolutionary relationships 0 Synapomorphy shared derived characters Using Derived Characters to Infer Phylogenies 0 By looking at the distribution of characters among taxa we can infer a phylogeny I What is important we can use characters from living taxa to infer evolutionary history What is the Value of Knowing Evolutionary Relationships 0 We can use classification phylogeny to infer characters phylogenetic bracketing 0 Ex phylogeny of birds relatives 0 Birds and crocs share traits 4chambered hearts vocalize build nests 0 Acquired traits from common ancestor 0 Can predict that dinosaurs would have the same traits 0 Supported by the evidence I We can use characteristics of species we know well to make hypotheses about species we don t 0 The characters that organisms have are full of evolutionary information including their genomes The Revolution of Molecular Phylogenetics 0 DNA data can be used in the same way as morphology and behavior to infer phylogenies I Requires much less knowledge about the taxa you are studying 0 Apply standard lab methods polymerase chain reaction etc same for all taxa O O 0 Generate long strings of DNA Use complex computer algorithms to align sequences determine homologous base positions Alignment serves as character table 0 Gives us new kinds of information that morphology can t O 0 Molecular clocks Phylogenies among organisms with few obvious morphological characters Molecular Clocks 0 Morphological characters evolve at highly variable rates 0 Some taxa look the same as they did millions of years ago living fossils I Ex horseshoe crab 0 Molecular characters evolve at a relatively constant rate 0 O The more distantly related species are the more mutations will have accumulated between them If we have fossils to calibrate the mutation rate we can use this pattern to estimate time Use this to estimate ages of evolutionary events without fossils
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