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Lectures 1-3 Notes

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Biology (Biological Sciences)
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Biology 108 Notes January 7 , 2012 – Lecture 1:  Snippets of natural history are tied together by the theory of evolution o Natural History – documentation of appearance, behavior, distribution etc. of an organism o Theory – refers to a “body of knowledge” NOT a hypothesis  Mechanistic Question o E.g “what pigments make the spider pink?”  Proximate Question o Deals with mechanisms and does not always require evolutionary thinking  Ultimate Question o Are concerned with evolutionary origins and functions  Approaches to Science 1. Observation & Induction  Observation: Provides raw material for hypothesis testing  Induction: creation of generality from accumulated instances o Sometimes, this is the only way that we can make generalizations in biology since some things are not testable through experiments 2. Hypothesis-Based Science  Occurs after observation/induction has led to form a hypothesis o It is a tentative approach to a question o Uses words “if” and “then”  Must note vital interaction between observations and testing of hypothesis o Hypothesis is not formed, unless an observation suggests it o Experiment can also lead to different results and therefore a new hypothesis 3. Deductive approach  a particular outcome is predicted from a generalization o Often called hypothetico-deductive approach January 9, 2013 – Lecture 2 – Taxonomy & Systematics I  Etymology: the study of word origins o Studying the origin of the word  gives us a better understanding  Etymos = true sense  Logos = word  Taxonomy: the (theory and) practice of classifying organisms  taxo = arrange  nomos = knowledge/science of  Systematics: the theory (and practice) of classifying organisms  Nomenclature: a system of rules for naming things  Nomen= name  Ethnotaxonomy o Examines how different cultures classify plants and animals  Since, every society and language groups has developed its own way of classifying organisms  In some cltures, what biologists call one species is called something else depending on size, shape or utility - Ex) a certain tree is called a different name if it has more branches (growth) versus if it has less branches (allowing it to be made into a spear) o Ethonotaxonomic classification may lmp hundreds of ‘useless’ organisms by the same name  Ex) yolngu of Arnhem lan have one name for ALL butterflies and moths  Common Names o Common name differ among countries and languages o This can be a problem:  When there is a same name for different species  Common names might imply a relationships between species that does not exist  Linnaean System o Carl von Linné or Carolus Linnaeus in his serious Systema Naturae proposed:  Use of Latin as universal language of scientific nomenclature  Use of unique binomen as names for each species - Binomen has two part – genus name and specific name (aka specific epithet) - Together, (the genus and specific name) makes up the species name o Linnaen system involves nested subsets (taxonomic levels or ranks) containing groups of organisms (taxa)  All animals placed in one of the seven taxonomic levels: - Kingdom - Phylum - Class - Order - Family - Genus - Species  A recent higher taxonomic level = Domain - Domain = most basic divisions of life  Archaea, Bacteria, Eukarya  Spelling Conventions 1. Genus and specific epithet = italicizes 2. Taxon names (expect specific epithet) = capitalized 3. Genus name can be abbreviated, but no the specific epithet  International Codes  Determined by international meetings and written in the International Code of Zoological Nomenclature I (ICZN)  Rules – according to ICZN:  Determine how animal taxon names should be formed/ when they should be changed  January 1 , 1758 first day that published bionomials considered ‘official’  the oldest published name for a taxon is considered the correct one o i.e. it has priority and is called the senior synonym, whereas the more recent name is called junior synonym  the person who originally described the taxon is the taxon’s author (usually written beside the species name)  once a name for a taxon is published, event if it is used incorrectly, it can never be used for another taxon  if the same name is used for two different taxa, the oldest name wins (senior homonym)  same names from different codes are not homonyms o in other words, plants and animals can have the same genus name  specific epithets can be shared but not in the same genus  names MUST be in Latin  family names end in –idea  if a species is placed in a new genus (for some reason) this is indicated by parentheses around the authority o ex) Genus specific epithet (author name)  Exception to ICZN rules is made when there is a fear/ threat to stability o A generic example: it is found that a certain species was placed in the wrong genus, but if we were to change the name, it would cause enormous scientific confusion and the name change was not successful January 11, 2013 - Lecture 3 Taxonomy & Systematics II Considered the hardest material of the course *  Taxonomy : the (theory and) practice of classifying organisms o Taxo = arrange o Nomos = knowledge/ science of  Systematics: the theory (and practice) of classifying organisms  Nomenclature: a system of rules for naming things Changes in Systematics from 1960  Focus switches from adding new taxa to methods for determining relatedness among taxa  Desire for evolutionarily informative taxonomies means that old taxonomies are often changed Revelations from molecular systematics  Molecular systematics: using proteins, DNA and RNA o This accelerated rate of taxonomic change o Allows us to ‘see’ characteristics of organisms that were previously invisible ‘Old-style’ evolutionary systematics  Before 1960’s, systematics was relatively unstructured discipline  Few tools available: o Stratigraphy (temporal order in which fossils occur) o Expertise in the taxon – so experts in a certain taxon = ‘tool’ o ‘common sense’ about which aspects of morphology seemed more primitive vs. advanced  method was subjective and choosing which was the ‘best’ classification system was mainly due to preference  in 1960s, a new method arose that allowed objective classification: Hennigian Systematics Hennigian Systematics  invented by Willi Hennig in 1950’s  wanted classifcations that reflected ancestor-descendent relatipnships  also wanted methods to e objective and trasnarent o so these methods were available to everyons o tried to remove the ‘subjectivity’ of earlier classification  so, no more relying on ‘expert’s’ preference  ancestor-descendent relationships was to focu only on shared, derived characteristics o groups of organisms related in this way = clade  Henning’s approach called: cladistics or phylogenetics systematics o Clados = branch o Phylon = tribe or race o Gen = to create  Branching diagrams showing these relationships = cladograms Cladistic methods  To construct phylogenetic hypotheses, systematists collect info: o Such as morphology, behavior, DNA sequence and biochemistry  Info is found on the group whose relationships we are interested in untangling, this is called the ingroup  Each type of structure, behavior etc. is termed = character  the manifestation of the character in a given taxon = state o example: ‘eye color’ = character, Columba livia (a specific type of pigeon) has the state ‘orange’ (it’s eyes are orange)  also collect info on these characters for one or more taxa that are related to the ingroup, but have diverged from it at an earlier time o these are called outgroups  example: if you want to reconstruct the phyloheny of terrestrial vertebrates good place to look for outgroups is among aquatic vertebrates - because we know from fossils, that aquatic vertebrates were present long before terrestrial (they had diverged at an earlier time)  goal: construct a set of nested relationships that minimize the number of times a character has to change states o this is called: parsimony (in other words: minimizing ‘stuff’ or making it simple)  rationale: if one must postulate a number of unknowable events (in this case, changed in character states) the best hypothesis is the one requiring the fewest postulates  Principle of Parsimony aka Occam’s Razor Example  Enter information into a matrix o
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