BIOL 108 Introduction to Biological Diversity Lecture Notes PDF

BIOL 108 Introduction to Biological Diversity Topic 2: Scientific Methods Lecture A2 Yan-yin Wang Terminologies and definition # A Portray of Charles Robert Darwin. Evolution: Descend with modifications. Evolutionary theory: A coherent bod...

BIOL 108 Introduction to Biological Diversity Topic 2: Scientific Methods Lecture A2 Yan-yin Wang Terminologies and definition # A Portray of Charles Robert Darwin. Evolution: Descend with modifications. Evolutionary theory: A coherent body of knowledge that guides our exploration of biodiversity. Theory: A set of broad, comprehensive, and systematic explanation of an aspect of the natural world based on a body of evidence and repeated experiments. Characteristics of theories: Overarching and broad in scope. Supported by strong chains of evidence. Serve as framework and guide for research. Contain multiple hypotheses and other theories. By Julia Margaret Cameron/ Adam Cuerden - Alfred Steiglitz Collection reference 1949.881, Art Institute of Chicago, Public Domain, https://commons.wikimedia.org/w/index.php?curid=131628151 Terminologies and definition Facts: Indisputable observations of natural phenomenon. Data: Recorded observations of natural phenomenon. Qualitative data: discrete units of records (e.g. colour) Quantitative data: continuous, numerical records (e.g. body height) Hypothesis: A tentative explanation of certain natural phenomenon based on available factual data that leads to testable predictions. Characteristics of facts: Specific and narrow in scope. Supported by some evidence (e.g. previous research). Serve to propose a predictive explanation for testing. Hypotheses are ether true or false, meaning they are falsifiable. https://www.pinterest.com/pin/59743132529768263/  Oversimplified Illustration of Scientific Research Observe Ponder Hypothesise Experiment Write report https://www.dreamstime.com/illustratio https://gfycat.com/discover/bloody- https://imgflip.com/memegenerator/ https://imgflip.com/memegenerator/1838023 https://www.vectorstock.com/royalty-free- keyboard-guy-gifs n/stick-figure-magnifying-glass.html 4/monocle-guy 29404897/Challenge-Accepted vectors/dna-cartoon-vectors How to Observe Understand the type of questions “Mechanistic” question (e.g. identifying a species, and how a limb is developed in an embryo?) “Evolutionary” question (e.g. why do zebras have strips and horses do not, is it adaptive?) Establish a question (e.g. if swans are white). Clearly define the data to collect (e.g. colours of feathers). Observe and collect data. Good to ask questions (e.g. What am I seeing? How may I record this?) Formulate ideas and even hypothesis. Inductive reasoning! Inductive Reasoning Definition: the logical process to Observe Ponder Hypothesise reach a generalised conclusion by synthesising observations. Often require repeated observations by multiple researchers. Sometimes inductive reasoning is the only feasible approach. The mass extinction events in Earth’s history. https://www.dreamstime.com/illustratio https://imgflip.com/memegenerator/ https://imgflip.com/memegenerator/1838023 n/stick-figure-magnifying-glass.html 4/monocle-guy 29404897/Challenge-Accepted Example of Hypothesising with Inductive Reasoning # The sockeye salmon, Oncorhynchus nerka. Yum. https://www.fisheries.noaa.gov/species/sockeye-salmon Note that each hypothesis leads to a testable prediction! Note that hypothesis is never proven to be true. Deductive Reasoning Definition: a logical process to reach a conclusion from premises that are assumed to be true. Ponder The form of logical is rigorous such that if the premises are true, the conclusion must be true. Make highly specific predictions for testing in experiment. General syntax: Deduce If (Premise_1) and (Premise_2) are true, then (My_prediction). Example: If vertebrate animals require oxygen to survive and cats are vertebrate animals, then cats need oxygen to survive. https://imgflip.com/memegenerator/ https://imgflip.com/memegenerator 29404897/Challenge-Accepted /18380234/monocle-guy Hypothesis Testing Controlled experiment: scientific test with Experiment Write report one or several independent factors being modified while all remaining factors being the same. Control group: mice with intact tendon. Experimental group: mice with severed tendon. Necessity of control group: we cannot determine whether the modifications in the # limb of mice embryos. experiment are related to the observed results without comparison with the default condition in the control group. Experiments can lead to unexpected results, which may lead to new hypotheses. Blitz, E., Viukov, S., Sharir, A., Shwartz, Y., Galloway, J. L., Pryce, B. A.,... & Zelzer, E. (2009). Bone ridge patterning during musculoskeletal https://www.vectorstock.com/royalty-free- https://gfycat.com/discover/bloody- assembly is mediated through SCX regulation of Bmp4 at the tendon-skeleton junction. Developmental cell, 17(6), 861-873. vectors/dna-cartoon-vectors keyboard-guy-gifs Why Running Experiments? # Private Captain Hook, the most unclean. Correlation: Two things tend to progress and change together. Used to predict conditions and status. Appropriate example: Smoking and getting lung cancer are positively correlated. Inappropriate example: The number of privates at sea drops, and the global temperature rises. The two can be said to be correlated. Causation: Changes in one thing leads to changes in another. Used to understand the mechanisms. Appropriate example: Some bacteria (# Escherichia coli O157) causes diarrhea. Incorrect example: global warming reduces private activities. Experiments can conclude with correlation or causation. By F.D. Bedford - James Matthew Barrie, "Peter and Wendy", Charles Scribner's Sons, New York, 1912, page 188 , Public Domain, https://commons.wikimedia.org/w/index.php?curid=4210385 Inductive vs Deductive Reasoning Proposed idea: Scientific methods include both forms of reasoning. Inductive observations can formulate premises and hypotheses, and deductive reasoning can formulate predictions. Example: We observe a wall-like structure in cells from insects, humans, plants, and fungi. We inductively state that all organisms should have a wall-like structure in cells. We deduce that if all organisms have said structure, then we will find it in other organisms. We predict that sampling bacteria will result in observation of a wall-like structure (prediction). We design a controlled experiment to sample and observe cells from bacteria. We observe no wall-like structure in all sampled bacteria. We reject the hypothesis and conclude that not all organisms on Earth have a wall-like structure in the cells. … Repeat the controlled experiment and try to replicate the results. Synthesise and summary results from all experiments. Note the importance of observations for formulating hypothesis. Summary on Scientific Methods