Understanding the Basic Science Hypothesis and Writing Techniques
Exploring the concept of the basic science hypothesis, its importance in research, and tips for effective hypothesis writing. The scientific method, historical perspectives from Karl Popper to Paul Feyerabend, and the role of serendipity in scientific discoveries are discussed.
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The Basic Science Hypothesis What It Is and How to Write One
The Basic Science Hypothesis Outline History lesson: scientific method and the basic-science hypothesis Dos and Don ts of hypothesis writing and specific examples Goals Appreciate utility of a clear hypothesis in your research Help you communicate your hypothesis clearly to funding agencies and in the literature
Back to Basics: The Scientific Method Hypothesis Scientific method The process by which science is carried out Observation Prediction Or Experiment A continuous (never-ending?!) process of making observations, forming hypotheses, making predictions, and performing experiments Term gained use in the 20th century
Back to Basics: The Scientific Method Some historical perspective fabiusmaximus.com Karl Popper: There is a universal scientific method that separates science from pseudoscience
Back to Basics: The Scientific Method Some historical perspective fabiusmaximus.com Karl Popper: There is a universal scientific method that separates science from pseudoscience Probaway.wordpress.com Paul Feyerabend: Rejected a universal scientific method; argued that the operation of science by a fixed, universal rule was unrealistic and detrimental to science---that science is not necessarily a methodological process Feyerabend. Against Method. 1975
Back to Basics: The Scientific Method Some historical perspective Kerry: Whether or not there should be a universal scientific method, it is a useful tool for organizing research questions and clearly stating hypotheses
Back to Basics: The Scientific Method Serendipity vs. Scientific Method Serendipity = Unexpected good luck; happy accident Psychologist Kevin Dunbar estimates that 30%-50% of scientific discoveries are serendipitous Dunbar and Fugelsgang, 2005
Back to Basics: The Scientific Method Serendipity vs. Scientific Method Louis Pasteur: Chance favors the prepared mind Dunbar suggests that the scientific method prepares the mind to identify the unexpected (serendipitous) Artist: Robert Thom Dunbar and Fugelsgang, 2005
The Hypothesis in Basic Science Some definitions An unproven theory or statement (American Heritage Dictionary) A tentative assumption made in order to draw out and test its logical or empirical consequences (Merriam-Webster) A supposition or proposed explanation made on the basis of limited evidence as a starting point for further investigation (Oxford English Dictionary) An idea or explanation for something that is based on known facts but has not yet been proven (Cambridge Dictionary) An idea which is suggested as a possible explanation for a particular situation or condition, but which has not yet been proved to be correct (Collins English Dictionary)
The Hypothesis in Basic Science Some definitions An unproven theory or statement (American Heritage Dictionary) A tentative assumption made in order to draw out and test its logical or empirical consequences (Merriam-Webster) A supposition or proposed explanation made on the basis of limited evidence as a starting point for further investigation (Oxford English Dictionary) An idea or explanation for something that is based on known facts but has not yet been proven (Cambridge Dictionary) An idea which is suggested as a possible explanation for a particular situation or condition, but which has not yet been proved to be correct (Collins English Dictionary) An explanation for an observation
The Hypothesis in Basic Science Key features Hypothesis should be testable Based on sound logic Technology exists to perform the experiment Hypothesis should be falsifiable Evidence can be collected that proves the hypothesis incorrect Experimental support for a hypothesis does not mean it is true; falsification means it is definitely not true
The Hypothesis in Basic Science Recipe for hypothesis writing Hypothesis Observation Prediction Let s say you make these observations: - Bacterium X makes mice sick - Many genes in bacterium X appear to make toxins Experiment Hypothesis = Toxins made by bacterium X make mice sick
The Hypothesis in Basic Science Hypothesis Recipe for hypothesis writing With additional observations, the hypothesis can be made more specific and testable Observation Prediction Observation: Gene A in bacterium X is a suspected toxin gene Experiment Hypothesis: Gene A in bacterium X produces a toxin that makes mice sick Prediction: In the absence of gene A, bacterium X will not make mice sick Experiment: Infect mice with bacterium X that lacks gene A
Its Not a Prediction Hypothesis You make predictions and perform experiments based Observation Prediction on a hypothesis, which is based on observations Experiment
Its Not a Prediction When writing, don t phrase your hypothesis as a prediction Example We hypothesized that deleting gene A would attenuate the virulence of bacterium X in mice (predicts an experimental outcome) We hypothesized that gene A produces a toxin that contributes to the virulence of bacterium X in mice (gives an explanation for an observation)
Its Not a Prediction Example from the Journal of Bacteriology The pleiotropic effects of ybeY loss on cellular RNAs have been well documented in other bacteria [refs], and as such, we hypothesized that deletion of ybeY would lead to changes in mRNA levels in B. abortus. Therefore, we employed microarray technology to identify mRNAs that are influenced by YbeY. Budnick et al, 2018
Its Not a Prediction Example from the Journal of Bacteriology Observation The pleiotropic effects of ybeY loss on cellular RNAs have been well documented in other bacteria [refs], and as such, we hypothesized that deletion of ybeY would lead to changes in mRNA levels in B. abortus. Therefore, we employed microarray technology to identify mRNAs that are influenced by YbeY. Budnick et al, 2018
Its Not a Prediction Example from the Journal of Bacteriology Prediction The pleiotropic effects of ybeY loss on cellular RNAs have been well documented in other bacteria [refs], and as such, we hypothesized that deletion of ybeY would lead to changes in mRNA levels in B. abortus. Therefore, we employed microarray technology to identify mRNAs that are influenced by YbeY. Budnick et al, 2018
Its Not a Prediction Example from the Journal of Bacteriology The pleiotropic effects of ybeY loss on cellular RNAs have been well documented in other bacteria [refs], and as such, we hypothesized that deletion of ybeY would lead to changes in mRNA levels in B. abortus. Therefore, we employed microarray technology to identify mRNAs that are influenced by YbeY. Experimental approach Budnick et al, 2018
Its Not a Prediction Let s revise to state a hypothesis
Its Not a Prediction The pleiotropic effects of ybeY loss on cellular RNAs have been well documented in other bacteria [refs], and as such, we hypothesized that deletion of ybeY would lead to changes in mRNA levels in B. abortus. Therefore, we employed microarray technology to identify mRNAs that are influenced by YbeY. Revised to include a hypothesis The pleiotropic effects of ybeY loss on cellular RNAs have been well documented in other bacteria [refs], and as such, we hypothesized that YbeY modulates mRNA levels in B. abortus. Therefore, we employed microarray technology to identify mRNAs that are influenced by YbeY. Budnick et al, 2018
Its Not a Prediction Example from Free Radical Biology and Medicine We hypothesized that the AS52DKO cells, which lack the ability to repair oxidative lesions, would be more sensitive to PQ [paraquat] exposure. Tajai et al, 2018
Its Not a Prediction Example from Free Radical Biology and Medicine We hypothesized that the AS52DKO cells, which lack the ability to repair oxidative lesions, would be more sensitive to PQ [paraquat] exposure. Observation Tajai et al, 2018
Its Not a Prediction Example from Free Radical Biology and Medicine We hypothesized that the AS52DKO cells, which lack the ability to repair oxidative lesions, would be more sensitive to PQ [paraquat] exposure. Prediction Tajai et al, 2018
Its Not a Prediction Example from Free Radical Biology and Medicine We hypothesized that the AS52DKO cells, which lack the ability to repair oxidative lesions, would be more sensitive to PQ [paraquat] exposure. Experimental approach Tajai et al, 2018
Its Not a Prediction Example from Free Radical Biology and Medicine We hypothesized that the AS52DKO cells, which lack the ability to repair oxidative lesions, would be more sensitive to PQ [paraquat] exposure. the hypothesis that the PQ mutagenesis is dependent on the generation of ROS and oxidative-stress induced DNA damage. Hypothesis Tajai et al, 2018
Its Not a Prediction We hypothesized that the AS52DKO cells, which lack the ability to repair oxidative lesions, would be more sensitive to PQ [paraquat] exposure. the hypothesis that the PQ mutagenesis is dependent on the generation of ROS and oxidative-stress induced DNA damage. We hypothesized that PQ-induced mutagenesis depends on the generation of ROS and oxidative-stress--induced DNA damage. Revised to clearly state the hypothesis Therefore, we predicted that the AS52DKO cells, which lack the ability to repair oxidative lesions, would be more sensitive to PQ exposure. Tajai et al, 2018
Take Home Hypothesis Researchers make predictions and perform experiments based Observation Prediction on a hypothesis, which is based on observations Experiment
Write in Present Tense Write your hypothesis in the present tense A hypothesis explains an observation---something that is occurring here and now (even if describing a past experiment) Described by Francois Jacob as the invention of a possible world. Jacob. The Statue Within. 1987
Write in Present Tense Write your hypothesis in the present tense We hypothesized that gene A produced a toxin that contributed to the virulence of bacterium X in mice We hypothesized that gene A produces a toxin that contributes to the virulence of bacterium X in mice
Write in Present Tense 1) Good example from the Journal of Bacteriology We hypothesized that S. aureus utilizes fatty acids present within lipoprotein particles. To test this hypothesis, we monitored the sensitivity of S. aureus cultured in the presence of human LDL to the FASII inhibitor triclosan. Delekta et al, 2018
Write in Present Tense Hypothesis 1) Good example from the Journal of Bacteriology We hypothesized that S. aureus utilizes fatty acids present within lipoprotein particles. To test this hypothesis, we monitored the sensitivity of S. aureus cultured in the presence of human LDL to the FASII inhibitor triclosan. Experimental approach Delekta et al, 2018
Write in Present Tense 2) Good example from the Journal of Bacteriology Analysis of the known SpoVG-binding sites has not revealed any obvious consensus sequence; therefore, we hypothesize that SpoVG may interact with certain nucleic acid structural motifs rather than a particular nucleotide sequence. Savage et al, 2018
Write in Present Tense Observation 2) Good example from the Journal of Bacteriology Analysis of the known SpoVG-binding sites has not revealed any obvious consensus sequence; therefore, we hypothesize that SpoVG may interact with certain nucleic acid structural motifs rather than a particular nucleotide sequence. Hypothesis Savage et al, 2018
Take Home A hypothesis explains an observation---something that is occurring here and now (even if describing a past experiment) So, write in the present tense! Described by Francois Jacob as the invention of a possible world.
Be Confident Write with confidence! Be confident about your hypothesis (regardless of the potential experimental outcome) A hypothesis is made to be tested (and falsified) it s okay to be wrong!
Be Confident We hypothesized that gene A might produce a toxin that contributes to the virulence of bacterium X in mice We hypothesized that gene A produces a toxin that contributes to the virulence of bacterium X in mice
Be Confident Previous example from Journal of Bacteriology Analysis of the known SpoVG-binding sites has not revealed any obvious consensus sequence; therefore, we hypothesize that SpoVG may interact with certain nucleic acid structural motifs rather than a particular nucleotide sequence. Authors probably intend to express the possibility of this occurring But comes across as lacking confidence Savage et al, 2018
Be Confident Previous example from Journal of Bacteriology Analysis of the known SpoVG-binding sites has not revealed any obvious consensus sequence; therefore, we hypothesize that SpoVG may interact with certain nucleic acid structural motifs rather than a particular nucleotide sequence. interacts Savage et al, 2018
Be Confident From PLOS Pathogens Given that neutrophil recruitment is a major effect of IL-17, we hypothesize that the role of this cytokine in host defence against a particular pneumococcal strain may critically depend on the resistance of the strain to neutrophil phagocytosis, and hence on its degree of encapsulation. Ritchie et al, 2018
Be Confident FromPLOS Pathogens Given that neutrophil recruitment is a major effect of IL-17, we hypothesize that the role of this cytokine in host defence against a particular pneumococcal strain may critically depend on the resistance of the strain to neutrophil phagocytosis, and hence on its degree of encapsulation. depends critically Ritchie et al, 2018
Be Confident FromPNAS More specifically, we hypothesize that the altered firing patterns observed in Trpc5- deficient Th+ARC neurons should influence dopamine release at the median eminence and that the hypoprolactinemia phenotype may result primarily from these effects. Blum et al, 2019
Be Confident FromPNAS More specifically, we hypothesize that the altered firing patterns observed in Trpc5- deficient Th+ARC neurons should influence dopamine release at the median eminence and that the hypoprolactinemia phenotype may result primarily from these effects. influence results Blum et al, 2019
Take Home Take-home message When authors tell a story with confidence, the reader has more confidence in them and their data---and in how they interpret their results.
