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Life Science 2D03 - textbook & Lecture notes.docx

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Life Sciences
Rashid Khan

Life Science 2DD3 - Textbook Notes 9/7/2013 9:27:00 AM -Animals intricate part of society – many humans work with some animals such as cattle’s, chickens, turkeys, hogs, and sheep.  People manage animal behavior to accomplish a task. -Animals are also resourceful for research and medicinal purposes  Helps researchers understand more about sensory, motor and cognitive functioning.  For example: behavioral changes reflect effects of neurochemical agents, neurotoxins or hormonal changes (Animal tests can interpret results for humans) -Animals also used for entertainment purposes (zoo, circus, movies, etc.) Recognizing and Defining Behavior - Animal Behavior  Any internally coordinated, externally visible patterns of behavior that responds to changing external or internal conditions -Internally Coordinated  Refers to internal information processing (such as actions of neurotransmitters) o Internal actions are controlled (such as giraffes mating leading to aggressive behavior). -Externally Visible  Refers to patterns that we can observe and measure  Physical aspects that can be externally observed and measured such as changes in behavior in specific animals during certain times of the day, temperature, etc. (ex: desert lizards moving from the top of a hot rock to underneath it to physically reduce body temperature because as ectotherms they are internally unable to automatically do it).  (Internal aspects are not accounted like heart rate of lizard) Measuring Behavior: Elephant Ethograms -Behaviors must be measurable and such processes begin with a completion of an Ethogram  Formal description or inventory of animal’s behaviors (Definition)  It lists discrete behaviors that an animal exhibits  Researchers can measure o Frequency, duration, rate, intensity of behavior  Usually behaviors that occur over a period of time is recorded  This helps researchers quantify total and relative time animals engaged in each behavior  The overall time budget records total time and relative frequency of each behavior. The Scientific Method – Formalized Way of Knowing About the New World -Process of Science  Observing events, organizing knowledge, and providing explanations through the formulation and testing of hypotheses Hypotheses  Hypotheses are explanations that make predictions that can be tested. Scientists begin with formulating questions into hypotheses.  Less debate is brought about usually because these tests can be repeated by other scientists Scientific Method  The scientific method is a formalized process that involves the testing of hypotheses  It begins with an observation of a single event or pattern that requires an explanation which forms the basis of a research question o This a brief statement which we would like to understand Next Step …  Formulation of research hypotheses (an educated guess) -Research Hypotheses  An explanation based on assumptions that produces a testable prediction  Evaluated using two statistical hypotheses that reflect two possible outcomes o Alternate Hypothesis or H a  The observation does have a significant effect o Null Hypothesis or H o  The possible outcome does not have a significant effect Last Step … -Evaluate the research hypothesis by testing the prediction of the null hypothesis  One way to do this is … Make new observations by collecting data from many different resources (example: yards for robins example) o With this data, you can test the prediction of the null hypothesis -When you fail a hypothesis you develop a new research hypothesis to explain the original observation Correlation and Causality -Correlation  The collected data represent a correlation between the two variables measured (they co-vary or vary together predictably)  Correlation does not demonstrate causality (even if they are correlated) therefore further testing is necessary for hypothesis o And researchers have to rule out plausible alternative explanations Hypotheses & Theories -Scientific Theories  Hypotheses that make many predictions, have been tested many times by many different scientists and have not been rejected(DEF)  They explain various phenomena which are all supported by observations & experimental testing o Examples: cell theory of living organisms & germ theory of disease -Social Sciences & The Natural Sciences -Social scientists create scientific theories and test their hypotheses using the scientific method to study human behavior and societies  Methodology includes: collecting data (surveys, questionnaires, and public opinion polls) & conducting experiments to obtain information about human values, perception & behavior -Two ways to study human behavior  Directly  Indirectly (through the study of animals) Negative Results & Directional Hypotheses -Negative Result  A situation where one does not reject the null hypotheses (therefore rejecting the alternate hypothesis) [DEF]  This indicates that the alternative hypothesis does not explain behavior being examined  In this case, scientists need to develop a new alternate hypothesis to explain the observation -Directional Hypotheses  Predicts specifically how the variable under examination will affect a particular behavior (positively or negatively) -Nondirectional Hypotheses  Usually offers no specific prediction of how the variable will affect behavior  Researchers usually use this when they have no specific prediction of how the variable will affect behavior Hypotheses from Mathematical Models -Fitness  The relative survivorship and reproductive success (ability to produce viable offspring) of an individual -Another source of hypotheses and predictions are mathematical models -Resulting mathematical model generates predictions about which behaviors maximize and individuals fitness  Advantage of this model: allow scientists to easily manipulate their assumptions to produce new predictions about behavior Anthropomorphic Explanations of Behavior Assign Human Emotions To Animals and Can be Difficult to Test -Anthropomorphism  Tendency to attribute human motivations, characteristics, or emotions to animals (DEF) Scientific Knowledge is Generated & Communicated to the Scientific Community via Peer-Reviewed Research -Scientific Literacy  The ability to evaluate scientific information critically and ascertain its validity The Primary Literature -Primary Literature  The original source of scientific information, typically peer-reviewed scientific journals -Peer Review  A process in which editors of scientific journals use experts to help decide whether to accept or reject a paper for publication (DEF)  Reviewers evaluate the importance of the research question and the validity of the hypotheses, methodology, analyses, and conclusions  Also comment on how clearly and concisely is written The Secondary Literature -Secondary Literature  A report that summaries and interprets the primary literature (often reported in newspapers, books, and magazines) (DEF) Lecture – Chapter 1 9/7/2013 9:27:00 AM -Animals and behavior are part of human society  Animals have impact on way we function and live -Scientific method is a formalized way of knowing about the natural world  Starts off with an observation  Then to a research question based on observation  To a research hypothesis  Based on hypothesis, people make predictions  When making predictions, you need a methodology to test prediction  Using that method, you come up with some data  And from data and you have to come up with an analysis  And the significance of the analysis -Scientists test hypotheses to answer research question about behavior  2 categories of hypotheses -Anthropomorphic explanations of behavior assign human emotions to animals and can be difficult to test  Assuming animals behave same way as humans (emotions, etc.) -Scientific Knowledge is generated and communicated to the scientific community via peer-reviewed research Lascaux Cave Paintings  South-western France (*Unsure*)  Pictures – represent a clear concept o Anthropologists saw pictures of animals that were extant (species that were still around) Altamira Cave Paintings  People assume the pictures in cave paintings were symbolic  In the conceptual perceptive the concept is presented clearly -Agricultural Products – were connected to animals in some sense -Using animals in various industries – media, horse racing, pets, etc. Behavior  Any internally coordinated, externally visible pattern of activity that responds to changing external or internal conditions. (DEF)  Lizards – ectotherms o Change in body temperature occurs externally – behavioral changes are needed to be physically changed o Lizard – sitting on top of hot rock, then moves under rock because body temperature rises Internally Coordinated  Internal information processing (ex: neurochemical changes)  Information coming from the senses  Any internal changes  5 senses (visual, sensory, tactile, metabolic, etc.) Externally Visible  Observe & measure  We can see it and we can measure it -Behavioral responses to changing conditions  Mating season, testosterone increases, aggressive encounters over females  When mating season is over, testosterone decreases, aggression decreases Lecture 2 – Chapter 1 9/7/2013 9:27:00 AM -Animals and their behavior are an integral part of human society -The scientific method is a formalized way of knowing about the natural world -Scientists test hypotheses to answer research questions about behavior -Anthropomorphic explanations of behavior assign human emotions to individuals and can be difficult to test -Scientific knowledge is generated and communicated to the scientific community via peer-reviewed research *Animal Behavior, internally coordinated, externally visible* (know this !) Measuring Behavior: Elephant Ethograms -Ethograms  Behavior must be measurable  It’s an inventory -Different people need to be able to recognize these behaviors independently -Time Budget  Total time budget - records total time of each behavior  Relative - fraction of frequency of behavior -Both of these are raw numbers High frequency Behaviors & Low Frequency Behaviors  Table 1.1  Take one example and remember description -Stereotypical behaviors exhibited by animals kept in captivity and repeated over and over again  Repetitive  Ex: animal pacing back and forth  Doesn’t necessarily have a significance Negatively Correlated -Using space feeders slowly and at random times could reduce the frequency of stereotypic behavior -The scientific method is a formalized way of knowing about the natural world -Observation – research question – research hypothesis – prediction – methodology (test of prediction) – analysis of data  Analysis of data o 1) data does not match prediction (hypothesis rejected) o 2) data matches prediction (hypothesis supported) Research question  Any question we would like to further understand Research Hypothesis  Explanation based on assumptions that can lead to a testable prediction The Scientific Method 1) Formulate the research question based on a careful review of the literature 2) Generate hypotheses based on current observations/what is already known 3) Design an experiment using a paradigm and methods appropriate to the research question, incorporating carefully designed controls  Control is a good way to access that there isn’t any kind of bias in the study o Ex: the act of injecting needle in mice does not lead to aggression in the animal so control is necessary How do we advance knowledge in our field of research? Obtain ethics approval for the study Collect data with careful attention to random sampling and random assignment Analyze data and formulate interpretations using appropriate statistical tools Communicate results in the form of published articles and presentation at scientific conferences (peer review process) Replicate! Generate the next research question based on new results Primary Literature  Original study of publishing  Has gone through a peer-review process  Other people in the same field as me will read and critic it  Peer-review – people in the same level as you (same field, category, etc.) Secondary Literature  Someone else’s interpretation of the original primary literature  Summary of something that has already been published Impact factor is a measure and this measure reflects the average number of citation  Citation: referenced, used in other papers Lecture 3 – Chapter 1 9/7/2013 9:27:00 AM Peer review process  When you write an article and you submit it … other people in your field will critic and review your work (those whom are in the same level of as you) The Scientific Method  How do we advance knowledge in our field of research? o Primary Literature  The people who conducted that experiment, wrote it.  You find it in journals  Use information from other journals that have been published o Peer Review Process o Secondary Literature  Summarized versions of primary literature (in textbooks, magazines, etc.)  Someone else’s interpretation of primary literature  Impact factor is a measure and this measure reflects the average number of citation -Articles/database – McMaster library – peer reviewed articles -Another journal search source: Web of Knowledge The Nitty-Gritty  How do you know that the journal/paper is peer-reviewed? o Ulrichsweb o Look for quote “peer-reviewed” or “referee” The Scientific Method  What is a research hypothesis? o An explanation based on assumptions that produce a testable prediction o Based on previous observations or extensions of scientific theories o A provisional idea whose merit is to be evaluated o Must be testable and falsifiable o Use the word “support” instead of “prove”  How do we test hypotheses? o Descriptive: to develop description of phenomenon o You need to be able to define that behavior very clearly o Correlational: Is there an association between two variables? o Experimental  Independent Variable: manipulate  Ex: giraffe – testosterone level  Dependent Variable: measure  Ex: giraffe – behavior (result of the manipulation) Sampling From a Population  Sample – a small number of individuals that represent the population at large o Ex: Psych experiment The Scientific Method  What is a research hypothesis? o Research hypotheses are evaluated using two hypothesis reflecting two possible outcomes  Alternate Hypothesis (Ha)  The proposed explanation for the observation does have a significant effect  Null Hypothesis (Ho)  The proposed explanation for the observation does not have a significant effect  Scientific Process Table 1.1 o Research Question: Why is there variation in the number of robins feeding in yards? Hypothesis Testing In the Brush Legged Wolf Spider  Females: mate only once, but males mate multiple times  Research Question: How do male spiders find unmated females o One way to do that is that they look at the behavior of other males o Male spiders will have these vibrations (song & dance) to attract the females  Hypothesis: Male spiders use the behavior of nearby males to find receptive females  Prediction: The presence of rival males will result in the searching to orient toward the rival, search for female and begin courtship tapping  Ho = Male wolf spiders do not use the behavior of nearby males to find receptive females o Failed to reject null hypothesis  Ha = male wolf spider use the behavior of nearby males to find receptive females o Rejected alternate hypothesis  Visual Cues (one male) – Semismic Cue (the other male) – Semismic + Visual Cue (ways of courting)  Male will search for females rather slowly  Males will find other males who are courting Therefore…  Ho = Male wolf spiders do not use the behavior of nearby males to find receptive females o Failed to reject null hypothesis o Support for it.  Ha = male wolf spider use the behavior of nearby males to find receptive females o Rejected alternate hypothesis o Didn’t find any support, all the results were fairly the same -Whenever interpreting graph – always look at the conditions showed in graph itself -Bar graph  Pre exposure – prior to exposure of the three “keys”  Stimulus Exposure – exactly what you wanted to test  Post-exposure – everything goes away and behavior is again tested -Bout of activity  Short period of intense activity as a function of pre-exposure, stimulus exposure, and post-exposure. Negative Results & Bidirectional Hypothesis  What happens if the null hypothesis is not rejected? o Indicate that alternate hypothesis is not able to explain the research question o Negative results are formulated o Development of new alternate hypothesis  Hypotheses can be directional or non-directional o Non-directional – alternate hypothesis is non-directional because alternate hypothesis does not prove research question -Mathematical Models  Mate-guarding o When females have the ability to mate multiple times (in other kinds of species)  Challenge for the male  Sperm competition – multiple males deposit for sperm in female’s reproduction tract and not sure of which males are his  Mate-Guarding o After reproduction – male sticks around with female to protect his sperm for offspring. o So no other male has access to female.  How long should a male spend mate-guarding a female? -Kokko and Morrell (2005) constructed a model to understand variation in mate guarding behaviour Assumptions: (different categories of females in certain species)  1. Male fitness increases with number of eggs fertilized  2. Some males are more attractive to females than others  3. Once mated, some females sometimes/always/rarely mate with other males   Unattractive males working hard (prediction would be…) yet more females stay faithful. However, when more males are attractive … the females never stay faithful.  Mathematical models help us predict behavior of individual. Evolution & The Study of Animal Behavior 9/7/2013 9:27:00 AM Evolution by Natural Selection Favors Behavioral Adaptation that Enhance Fitness -Artificial Selection  Human breeders who allowed reproduction among individuals (dogs – in the example) that possessed different traits -Natural Selection  Discovered by Charles Darwin o A similar process to artificial selection, however occurs naturally  It is the differential reproduction and survivorship among individuals within a population (DEF)  This mechanism results in adaptive evolution  NS occurs because there are variations in traits among individuals in a population, and some traits provide individuals with greater reproductive success o Heritable  When heritable, these traits are passed from parents to offspring o Evolution  NS results in change in allele frequencies in a population over time -Three Conditions Needed for Evolution by NS  Variation exists among individuals in a population in the traits they possess  Individual traits are heritable o Traits can be passed from parents to offspring (resemblance to parents and traits they posses)  Fitness o Traits present differences in survivorship and reproduction o Individuals with certain traits will have a higher fitness, while those with a lower fitness will have a lower fitness relative to one another o Therefore fitness is based on traits Measures of Heritability Determining heritability of trait (2 methods used) – must be heritable for NS to occur  Parent-Offspring Regression o Statistical technique used to examine the similarity between parents and offspring in the traits they possess (DEF) o Should be positive relationship between offspring and parent trait values  Selection Experiment Method o Different groups of individuals are subjected to differential selection on the trait in question o If artificial selection acting on a trait results in changes in the trait value in future generations, the trait has a genetic basis Great Tit Exploratory Behavior  Observation & Previous Research: Indicated individuals exhibit differences in their exploratory behavior when placed in novel environments o Some are quick to explore new environment o Others may be more introverted and slow to explore environment -Exploratory Behavior is heritable  In Great Tits (bird), there is a genetic component o Conclusively based on two pieces of evidence  1) Offspring resemble parents in behavior  2) Artificial Selection on Exploratory behavior produced significant differences in two artificially selected lines Variation Within a Population -One point to remember is that individuals differ in their genetic composition. In each generation, new genetic variations in a population through gene recombination, the immigration of new alleles in a population and mutations -Because genetics of individuals vary, behavior also varies – this is because  1) Changes in environmental conditions change the fitness of different traits and so maintain variation in the frequencies of different alleles  2) Both genetic and environmental effects cause a change in behavior o Therefore even close relatives exhibit different behavior as adults when they are exposed to different environmental conditions as kids  3) Because complex behaviors require learning, behavior is modified with experience. Differences in behavior is exhibited as the individual becomes more exposed conditioned to it  4) There may be little or no variation in over a wide range of behaviors o Ex: Dispersal Behavior  Dispersal – the process of moving away from the natal area, or place of birth to find an adult breeding area or territory  The same fitness can be observed for many individuals whether what direction they go to. When this occurs, we expect variation in dispersal direction within a population  5) Fitness (behavior) of a trait may be related to its frequency in a population o Rare – behavior may yield high fitness o Common – may result in a lower fitness o These individuals can maintain different behaviors in a population  Ex: Male Fish – Defends territory to attract female  Other male fish – hide at the edge of the territories and attempt to fertilize eggs of females attracted to territory holder  Frequency dependent – called “sneaker” male behavior – results in high fitness – when most males defend territories – more opportunities to fertilize  Lower fitness when few males defend territories (fewer opportunities for reproduction) -Variations in size, nutritional status, health and other traits  This leads to differences in behavior Fitness & Adaptation -Some traits confer higher fitness (survivorship and reproduction) than others -Adaptations  A trait that enhances fitness. Also an evolutionary process that results in a population of individuals with traits best suited to the current environment (DEF)  Traits that confer selective advantage  Individuals with this trait tend to survive better and leave more offspring than with individuals without selective advantage -To measure the fitness of an individual, the number of progeny (that go on to reproduce) that is produces over its lifetime  This is time consuming and logistically difficult -Therefore indirect measures of fitness are used  Behavioral researchers often estimate fitness by quantifying parameters such as survivorship, number of mating’s, body size, growth rate, and feeding efficiency o Typically positively correlated with more direct fitness measurements Modes of Natural Selection Describe Population Changes -Evolutionary biologists identified three modes of natural selection which describe how populations change as a result of the relative fitness values of different traits  1) Directional Selection o When individuals with one extreme trait value posses the highest fitness  The frequency of the individuals will increase  2) Disruptive Selection o When individuals with either of two extreme trait values have the highest fitness  Ex: Red & White Individuals have a higher fitness than pink in the same environment. Therefore frequency of red & white will increase while pink will decrease  3) Stabilizing Selection o Occurs when individuals with intermediate trait values have the highest fitness in a particular environment  Ex: Pink has a higher fitness than red or white individuals Studying Adaptation – The Cost & Benefit Approach -Optimal Trait  The trait that confers the highest fitness in a population in a particular environment (DEF)  If trait under selection is heritable, and if the selection regime remains constant, then populations will evolve toward the optimal trait value (or values) over successive generations o Therefore natural selection is seen as an optimizing process -Cost-Benefit Approach  A method used to study behavioral adaptations in which the fitness benefits and costs of different traits are examined to determine which has the highest net benefit (benefit-cost) (DEF) -Individual Selection  Natural selection acting on individuals (DEF) -Group Selection  Selection that favors a particular group of individuals over other groups such groups of the same species (DEF) -Kin Selection  A form of natural selection in which individuals can increase their fitness by helping close relatives, because close relatives share the helper’s genes – used to explain altruism (DEF) -Inclusive Fitness  A combination of individual fitness and fitness obtained by helping close relatives -Multilevel Selection  A form of natural selection that involves both selection on groups and selection on individuals Sexual Selection is a Form of Natural Selection That Focuses on the Reproductive Fitness of Individuals -Sexual Selection  A form of natural selection that acts on heritable traits that affect reproduction o There is differential reproduction within a sex because individual differ in their ability to compete for mates or attract individuals of the opposite sex -Sexual Dimorphism Morphological differences between the sexes Chapter 2 – Lecture 1 9/7/2013 9:27:00 AM Learning Objectives -Evolution by natural selection favors adaptations that enhance fitness -Modes of natural selection describe population changes -Individual and group selection have been used to explain cooperation -Sexual selection is a form of natural selection that focuses on the reproductive fitness of individuals Artificial Selection  Dog breeders selected individuals with specific traits (qualities) associated with them and allowed mating  It is artificial selection because it was specifically selected and it is therefore unnatural o Ex: golden retrievers – good at hunting  Came into existence … because the mechanism is artificial selection Charles Robert Darwin & Alfred Russell Wallace  Started to think about if a similar process existed in nature o Started to think about the evolution of the different breeds of species Natural Selection  Differential reproduction and survivorship among individuals within a population  The key to natural selection: Differential reproductive success because of heritable variants; everyone has ancestors, but not everyone leaves descendants  Certain species survived whereas certain species became extinct and each species’ environment allowed for survivorship  Heritable o A genetically-based trait that can be passed from parents to their offspring  Evolution o Changes in allele frequency in a population over time  Allele – DNA sequence  Frequency has to do with number  Allele Frequency – has to do with number of DNA sequence -Darwin’s Book  On the Origin of Species  Published on 24th November 1859 -Darwin’s conditions required for evolution by natural selection  1. Variation exists among individuals in a population in the traits they possess  2. Individuals’ different traits are, at least in part, heritable o Mutation – random change in allele frequency or that DNA sequence  3. Traits confer differences in survivorship and reproduction, a measure we call fitness -Gene alleles (genotypes result in phenotypes) are the basis of phenotypic traits  Phenotypic – what your able to measure  Ex: an individual has the gene allele for brown hair, the phenotype is what your able to see (the brown hair) -Natural selection acts on heritable variation among individuals and can result in changes in allele frequencies and associated trait values in a population -Traits that confer high fitness increase over time, while those that confer low fitness decline  Low survivorship low reproduction…vice versa. Natural Selection Provided 3 Key Answers  1. Descent with modification o change over time  2. Adaptive function o if something is adaptive – its helping you survive and reproduce o What is the purpose of behav
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