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                            <span class="section-heading-upper">E: Elucidate the Hypothesis</span>
                            <span class="section-heading-lower"> Elucidate the Hypothesis for Each Experiment</span>
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                            <p>Every experiment in a paper is trying to answer a different part of the overarching research question. Let's figure out what the research question is and how it is being answered.</p>
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                                        <a data-toggle="modal" data-target="#step-1-1-info" href="#"><img src="{{ '/img/e_overall_research_question.png' | absolute_url }}" class="card-img" alt="Abstract representation of overall research question."></a>
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                                            <h3>Identify the Overall Research Question</h3>
                                            <p>On a separate sheet of paper or in the margins of the article, <strong>write down the overall research question(s) that the paper is trying to answer.</strong></p>

                                            <p> Here are a few tips:</p>
                                            <ul>
                                                <li>The research question can often be found in or inferred from the introduction section.</li>
                                                <li>The concept map you made in C can also provide clues about the research question.</li>
                                                <li>Make sure the research question includes specific details.</li>
                                            </ul>
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                                        <a data-toggle="modal" data-target="#step-1-2-info" href="#"><img src="{{ '/img/e_type_of_study.png' | absolute_url }}" class="card-img" alt="Abstract representation of list of experiments with type of study."></a>
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                                            <h3>Determine the Type of Study for Each Experiment</h3>
                                            <ol>
                                                <li><strong>Identify all the experiments in your paper: </strong>Looking at the figures, make a list of all the experiments that the researchers conducted. Most of the time, each figure presents one experiment. However, some figures present multiple experiments side-by-side.</li>
                                                <li><strong>Write down whether each experiment presents a descriptive study, experimental test, or other study: </strong>A descriptive study looks at existing conditions, while an experimental test involves an experiment. It’s also possible that your figure doesn’t present a descriptive study or an experimental test.</li>
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                                            <h3>Identify the Hypothesis for Each Experiment</h3>
                                            <p>Each experiment in the paper is an attempt to answer part of the research question.</p>
                                            <p>On a separate sheet of paper or in the margins of the article, <strong>write a “Since, If, Then” statement for each experiment.</strong> A “Since, If, Then” statement is a way of formulating the hypothesis. It helps you discover…</p>
                                            <ul>
                                                <li>why the researchers did the experiment</li>
                                                <li>what question they were trying to answer</li>
                                                <li>what they expected the outcome of the experiment to be</li>
                                            </ul>
                                            <p>Here's how to do it:</p>
                                            <ol>
                                                <li><strong>Since:</strong> Identify the observation or rationale that led the researchers to conduct this experiment. This can often be inferred from the introduction or beginning of the results section. Turn this into a phrase that begins with the word “since”, e.g. <em>Since previous studies show that fungi have high cellulolytic activity….</em></li>
                                                <li><strong>If:</strong> Identify the specific question or hypothesis that the researchers are trying to answer through this experiment. You can also think of this as the observation that the researchers are trying to explain. Turn it into a phrase that begins with “if”, e.g. <em>if there is cellulolytic activity in leaf litter….</em></li>
                                                <li><strong>Then:</strong> Predict the expected outcome of the experiment, and turn it into a phrase that begins with the word “then”, e.g. <em>then most of cellulolytic potential (genes coding for cellulases) will be from fungi.</em></li>
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                                            <p>Some descriptive studies might not have clearly testable “If” statements because they may be exploratory. In those cases the "If, Then" part of the hypothesis may be more like the following:</p>
                                            <ol>
                                                <li>Since…</li>
                                                <li>If x and y are compared…</li>
                                                <li>Then we will observe…</li>
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                        <span class="section-heading-upper">What makes a successful "Since, If, Then" statement?</span>
                        <span class="section-heading-lower">Real student hypotheses</span>
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                                <h3 class="text-center">Example 1: <a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0225-7?sap-outbound-id=59B4908C4DD66E2B3E14234738AF54E708A355BF " target="_blank">Microbial Transfer Therapy</a></h3>

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                                                                    <th scope="row" class="text-right">SINCE</th>
                                                                    <td>there is a correlation between Autism Spectrum Disorders (ASD) severity and Gastrointestinal (GI) problems, and since GI symptoms can be attributed to dysbiotic gut microbiota,</td>
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                                                                    <td>Microbial Transfer Therapy (MTT) can effectively rebalance the microbiome and alleviate autism and GI symptoms,</td>
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                                                                    <th scope="row" class="text-right">THEN</th>
                                                                    <td>there will be a change in the composition of the gut microbiome and there will be improvements in GI and ASD severity.</td>
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                                                        <ul>
                                                            <li class="mt-3"><strong>SINCE</strong> includes the rationale for the entire study.</li>
                                                            <li class="mt-3"><strong>IF</strong> is the big picture hypothesis.</li>
                                                            <li class="mt-3"><strong>THEN</strong> is the expected outcome for the whole study</li>
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                                                <h4>Experiment 1</h4>
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                                                                    <th scope="row" class="text-right">SINCE</th>
                                                                    <td>alterations to the gut microbiome can correct dysbiosis and rebalance the community,</td>
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                                                                    <td>MTT is effective in shifting the gut community in ASD children,</td>
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                                                                    <td>there will be similar compositions between post-MTT microbial communities and donor communities.</td>
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                                                        <h5 class="text-center">Instructor Feedback</h5>
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                                                            <li class="mt-3"><strong>SINCE</strong> includes the rationale for this specific experiment.</li>
                                                            <li class="mt-3"><strong>IF</strong> is the idea being tested.</li>
                                                            <li class="mt-3"><strong>THEN</strong> is the observable expected result.</li>
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                                                <h4>Experiment 2</h4>
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                                                                    <th scope="row" class="text-right">SINCE</th>
                                                                    <td>the gut microbiome also includes viruses and <strong>SINCE</strong> the virome is dependent on the bacterial population,</td>
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                                                                    <th scope="row" class="text-right">IF</th>
                                                                    <td>MTT alters the bacterial population and composition,</td>
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                                                                    <td>there will be a corresponding change in the virome composition after MTT treatment.</td>
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                                                        <h5 class="text-center">Instructor Feedback</h5>
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                                                            <li class="mt-3">The second hypothesis in <strong>SINCE</strong> ("the virome is dependent on the bacterial population") leads logically from the first hypothesis ("the gut microbiome also includes viruses").</li>
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                                                <h4>Experiment 3</h4>
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                                                                    <td>antibiotic treatment leads to temporary improvements in ASD-related and GI symptoms/severity,</td>
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                                                                    <td>MTT is effective in treating children with ASD and GI problems with lasting benefits,</td>
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                                                                    <td>there will be long-term improvements in GI symptoms and autism severity.</td>
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                                                        <h5 class="text-center">Instructor Feedback</h5>
                                                        <ul>
                                                            <li class="mt-3">This hypothesis needs a bit of work.</li>
                                                            <li class="mt-3">It isn't clear how the <strong>SINCE</strong> rationale (antibiotic treatment) is related to MTT or the expected outcomes.</li>
                                                            <li class="mt-3"><strong>IF</strong> and <strong>THEN</strong> statements are circular ("if X is true, then X will be true"). This could be improved by changing the <strong>THEN</strong> to be more specific. What long-term changes would you expect to observe?</li>
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                                <h3 class="text-center mt-5">Example 2: <a href="https://link.springer.com/article/10.1186/s40168-016-0213-y" target="_blank">Infant Gut Microbiota</a></h3>

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                                                <h4>Figure 1</h4>
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                                                                    <td>birth mode has a significant effect on the nascent neonatal gut microbiota,</td>
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                                                                    <td>we characterize the gut microbiota at different developmental time points,</td>
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                                                                    <th scope="row" class="text-right">THEN</th>
                                                                    <td>they will have significantly different compositions.</td>
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                                                        <h5 class="text-center">Instructor Feedback</h5>
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                                                            <li class="mt-3">Good hypothesis overall!</li>
                                                            <li class="mt-3">It's clear that this is a descriptive study.</li>
                                                            <li class="mt-3">The <strong>IF</strong> statement is describing the comparison being done, while <strong>THEN</strong> is the expected result of the comparison.</li>
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                                                <footer class="citation-footer"><a href="https://link.springer.com/article/10.1186/s40168-016-0213-y#Fig1" target="_blank">Link to Figure</a></footer>
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                                                <h4>Figure 2</h4>
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                                                                    <td>metabolites are excreted through urine,</td>
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                                                                    <th scope="row" class="text-right">IF</th>
                                                                    <td>urine samples are taken as well as faecal samples,</td>
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                                                                    <td>there will be metabolites present that mirror the microbiota composition.</td>
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                                                        <h5 class="text-center">Instructor Feedback</h5>
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                                                            <li class="mt-3">This is a descriptive study.</li>
                                                            <li class="mt-3"><strong>IF</strong> and <strong>THEN</strong> here could be improved to better describe what is actually being compared and the specific expected outcome.</li>
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                                                <footer class="citation-footer"><a href="https://link.springer.com/article/10.1186/s40168-016-0213-y#Fig2" target="_blank">Link to Figure</a></footer>
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                                                <h4>Figure 4</h4>
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                                                                    <td>Caesarian section infants lack the natural inoculum of bacteria obtained through the birth canal,</td>
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                                                                    <th scope="row" class="text-right">IF</th>
                                                                    <td>urine samples are taken as well as faecal samples,</td>
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                                                                    <th scope="row" class="text-right">THEN</th>
                                                                    <td>there will be metabolites present that mirror the microbiota composition.</td>
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                                                        <h5 class="text-center">Instructor Feedback</h5>
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                                                            <li class="mt-3">This is an experimental study.</li>
                                                            <li class="mt-3">Good hypothesis overall, but&#8230;</li>
                                                            <li class="mt-3"><strong>IF</strong> could be improved: "<strong>IF</strong> bacteria can be transferred via breastfeeding, <strong>THEN</strong>&#8230;"</li>
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                                                <footer class="citation-footer"><a href="https://link.springer.com/article/10.1186/s40168-016-0213-y#Fig4" target="_blank">Link to Figure</a></footer>
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                                                <h4>Figure 8</h4>
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                                                                    <td>Bifidobacterium and Lactobacillus are known natural inhabitants of the healthy infant microbiota,</td>
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                                                                    <td>we use culture-independent methods to isolate these two bacteria from each birth mode,</td>
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                                                                    <th scope="row" class="text-right">THEN</th>
                                                                    <td>we will be able to test for their presence over time.</td>
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                                                        <h5 class="text-center">Instructor Feedback</h5>
                                                        <ul>
                                                            <li class="mt-3">This is an experimental study.</li>
                                                            <li class="mt-3">This hypothesis could be improved.</li>
                                                            <li class="mt-3"><strong>IF</strong> and <strong>THEN</strong> are both describing the method used in the experiment, not the scientific question being tested and expected outcome.</li>
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                                                <footer class="citation-footer"><a href="https://link.springer.com/article/10.1186/s40168-016-0213-y#Fig8" target="_blank">Link to Figure</a></footer>
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                  <h3>Tips &amp; Strategies</h3>
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                                            <h3>Tips &amp; Strategies</h3>
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                                                <li>When identifying the hypothesis for each experiment, it's helpful to think back to the experimental results you identified in R. <i>If this was your experiment, what hypothesis would you be testing?</i></li>
                                                <li>"If" and "Then" are often mixed up. Think of it in the following way, "If x is true, then I will observe y."</li>
                                                <li>"Since" is based on a more widely accepted rationale or a previous finding, while "If" is specific to the researchers' experiment.</li>
                                                <li>Be careful when making your list of experiments. Some papers have multiple experiments in one figure, while others have multiple figures that are about the same experiment.</li>
                                                <li>Take care that the "If, Then" statement isn't circular. For example: "If x is true, then x will be true."</li>
                                            </ul>
                                            <h3>Ready?</h3>
                                            <p>Now you are ready to elucidate the hypothesis! When you finish, use this checklist to double-check your work:</p>
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