% !TEX program = xelatex
\documentclass[11pt,letterpaper]{article}
\usepackage{hypothesis_generation}
\usepackage{natbib}

% Document metadata
\title{[Phenomenon Name]}
\author{Scientific Hypothesis Generation}
\date{\today}

\begin{document}

\maketitle

% ============================================================================
% EXECUTIVE SUMMARY
% ============================================================================
\section*{Executive Summary}
\addcontentsline{toc}{section}{Executive Summary}

\begin{summarybox}[Executive Summary]
\textbf{Phenomenon:} [Provide a clear, concise description of the phenomenon requiring explanation. What was observed? Why is it important?]

\vspace{0.3cm}
\textbf{Key Question:} [State the central question that these hypotheses address]

\vspace{0.3cm}
\textbf{Competing Hypotheses Overview:}
\begin{enumerate}
  \item \textbf{[Hypothesis 1 Title]:} [One sentence mechanistic summary]
  \item \textbf{[Hypothesis 2 Title]:} [One sentence mechanistic summary]
  \item \textbf{[Hypothesis 3 Title]:} [One sentence mechanistic summary]
  \item \textbf{[Add Hypothesis 4 \& 5 if applicable]}
\end{enumerate}

\vspace{0.3cm}
\textbf{Recommended Approach:} [Brief statement on which experiments should be prioritized and why. This provides readers with immediate guidance on the most promising path forward.]

\vspace{0.3cm}
\textbf{Expected Impact:} [Brief statement on what resolving this question would mean for the field]
\end{summarybox}

\vspace{0.5cm}

% ============================================================================
% COMPETING HYPOTHESES
% ============================================================================
\section{Competing Hypotheses}

This section presents [3-5] distinct mechanistic hypotheses that could explain the observed phenomenon. Each hypothesis is evaluated based on current evidence and provides testable predictions.

\subsection*{Hypothesis 1: [Concise Descriptive Title]}

\begin{hypothesisbox1}[Hypothesis 1: [Title]]

\textbf{Mechanistic Explanation:}

[Provide a detailed mechanistic explanation (2-3 paragraphs) of HOW and WHY this phenomenon occurs. Include:
\begin{itemize}
  \item Specific molecular, cellular, physiological, or population-level mechanisms
  \item Causal chain from initial trigger to observed outcome
  \item Key components, pathways, or factors involved
  \item The scale or level of explanation (molecular, cellular, organ, organism, population)
\end{itemize}

Example: "This hypothesis proposes that [mechanism X] operates through [pathway Y], resulting in [outcome Z]. The process initiates when [trigger], which activates [component A]. This activation subsequently leads to [downstream effect B], ultimately producing the observed [phenomenon]. This mechanism is supported by [brief reference to key evidence]."
]

\vspace{0.3cm}

\textbf{Key Supporting Evidence:}
\begin{itemize}
  \item [Evidence point 1 with citation \citep{author2023}]
  \item [Evidence point 2 with citation \citep{author2022}]
  \item [Evidence point 3 with citation \citep{author2021}]
  \item [Evidence point 4 - analogous mechanism in related system \citep{author2020}]
  \item [Evidence point 5 - theoretical framework support \citep{author2019}]
\end{itemize}

\vspace{0.3cm}

\textbf{Core Assumptions:}
\begin{enumerate}
  \item [Assumption 1: What must be true for this hypothesis to hold?]
  \item [Assumption 2: What conditions or contexts does it require?]
  \item [Assumption 3: Additional critical assumptions]
\end{enumerate}

\end{hypothesisbox1}

\vspace{0.5cm}

\subsection*{Hypothesis 2: [Concise Descriptive Title]}

\begin{hypothesisbox2}[Hypothesis 2: [Title]]

\textbf{Mechanistic Explanation:}

[Detailed mechanistic explanation distinct from Hypothesis 1. Follow the same structure as above, providing 2-3 paragraphs explaining the mechanism, causal chain, and key components. Ensure this hypothesis offers a genuinely different explanation, not just a variation on Hypothesis 1.]

\vspace{0.3cm}

\textbf{Key Supporting Evidence:}
\begin{itemize}
  \item [Evidence point 1 with citation]
  \item [Evidence point 2 with citation]
  \item [Evidence point 3 with citation]
  \item [Evidence point 4 with citation]
  \item [Evidence point 5 with citation]
\end{itemize}

\vspace{0.3cm}

\textbf{Core Assumptions:}
\begin{enumerate}
  \item [Assumption 1]
  \item [Assumption 2]
  \item [Assumption 3]
\end{enumerate}

\end{hypothesisbox2}

\vspace{0.5cm}

\subsection*{Hypothesis 3: [Concise Descriptive Title]}

\begin{hypothesisbox3}[Hypothesis 3: [Title]]

\textbf{Mechanistic Explanation:}

[Detailed mechanistic explanation distinct from previous hypotheses. Continue with same structure.]

\vspace{0.3cm}

\textbf{Key Supporting Evidence:}
\begin{itemize}
  \item [Evidence point 1 with citation]
  \item [Evidence point 2 with citation]
  \item [Evidence point 3 with citation]
  \item [Evidence point 4 with citation]
  \item [Evidence point 5 with citation]
\end{itemize}

\vspace{0.3cm}

\textbf{Core Assumptions:}
\begin{enumerate}
  \item [Assumption 1]
  \item [Assumption 2]
  \item [Assumption 3]
\end{enumerate}

\end{hypothesisbox3}

\vspace{0.5cm}

% Optional: Include Hypothesis 4 and 5 if needed
% \subsection*{Hypothesis 4: [Title]}
% \begin{hypothesisbox4}[Hypothesis 4: [Title]]
% [Content following same structure]
% \end{hypothesisbox4}

% \subsection*{Hypothesis 5: [Title]}
% \begin{hypothesisbox5}[Hypothesis 5: [Title]]
% [Content following same structure]
% \end{hypothesisbox5}

% ============================================================================
% TESTABLE PREDICTIONS
% ============================================================================
\section{Testable Predictions}

This section outlines specific, measurable predictions derived from each hypothesis. These predictions are designed to be empirically testable and distinguishable between competing hypotheses.

\subsection*{Predictions from Hypothesis 1}

\begin{predictionbox}[Predictions: Hypothesis 1]

\textbf{Prediction 1.1:} [Specific, measurable prediction]
\begin{itemize}
  \item \textbf{Conditions:} Under what conditions should this be observed?
  \item \textbf{Expected Outcome:} What specific result is predicted? Include magnitude/direction if quantifiable (e.g., "50\% increase", "positive correlation with r > 0.6")
  \item \textbf{Falsification:} What observation would disprove this prediction?
\end{itemize}

\vspace{0.2cm}

\textbf{Prediction 1.2:} [Specific, measurable prediction]
\begin{itemize}
  \item \textbf{Conditions:} [Conditions]
  \item \textbf{Expected Outcome:} [Specific result]
  \item \textbf{Falsification:} [Falsifying observation]
\end{itemize}

\vspace{0.2cm}

\textbf{Prediction 1.3:} [Additional prediction]
\begin{itemize}
  \item \textbf{Conditions:} [Conditions]
  \item \textbf{Expected Outcome:} [Specific result]
  \item \textbf{Falsification:} [Falsifying observation]
\end{itemize}

\end{predictionbox}

\vspace{0.4cm}

\subsection*{Predictions from Hypothesis 2}

\begin{predictionbox}[Predictions: Hypothesis 2]

\textbf{Prediction 2.1:} [Specific, measurable prediction]
\begin{itemize}
  \item \textbf{Conditions:} [Conditions]
  \item \textbf{Expected Outcome:} [Specific result]
  \item \textbf{Falsification:} [Falsifying observation]
\end{itemize}

\vspace{0.2cm}

\textbf{Prediction 2.2:} [Additional prediction]
\begin{itemize}
  \item \textbf{Conditions:} [Conditions]
  \item \textbf{Expected Outcome:} [Specific result]
  \item \textbf{Falsification:} [Falsifying observation]
\end{itemize}

\vspace{0.2cm}

\textbf{Prediction 2.3:} [Additional prediction]
\begin{itemize}
  \item \textbf{Conditions:} [Conditions]
  \item \textbf{Expected Outcome:} [Specific result]
  \item \textbf{Falsification:} [Falsifying observation]
\end{itemize}

\end{predictionbox}

\vspace{0.4cm}

\subsection*{Predictions from Hypothesis 3}

\begin{predictionbox}[Predictions: Hypothesis 3]

[Follow same structure as above for Hypothesis 3 predictions]

\end{predictionbox}

% Add prediction boxes for Hypotheses 4 and 5 if applicable

% ============================================================================
% CRITICAL COMPARISONS
% ============================================================================
\section{Critical Comparisons}

This section identifies key experiments and observations that can distinguish between competing hypotheses, helping prioritize research efforts.

\subsection*{Distinguishing Hypothesis 1 vs. Hypothesis 2}

\begin{comparisonbox}[H1 vs. H2: Key Distinction]

\textbf{Fundamental Difference:}

[What is the core mechanistic or predictive difference between these hypotheses? Be specific about where they diverge.]

\vspace{0.3cm}

\textbf{Discriminating Experiment:}

[Describe an experiment or observation that would clearly favor one hypothesis over the other. Include:
\begin{itemize}
  \item What would be measured or manipulated
  \item What comparisons or controls are needed
  \item What methods would be employed
\end{itemize}]

\vspace{0.3cm}

\textbf{Outcome Interpretation:}
\begin{itemize}
  \item \textbf{If [Result A]:} Hypothesis 1 is strongly supported, Hypothesis 2 is weakened
  \item \textbf{If [Result B]:} Hypothesis 2 is strongly supported, Hypothesis 1 is weakened
  \item \textbf{If [Result C]:} Both hypotheses require revision / Neither is clearly supported
\end{itemize}

\end{comparisonbox}

\vspace{0.4cm}

\subsection*{Distinguishing Hypothesis 1 vs. Hypothesis 3}

\begin{comparisonbox}[H1 vs. H3: Key Distinction]

[Follow same structure as above]

\end{comparisonbox}

\vspace{0.4cm}

\subsection*{Distinguishing Hypothesis 2 vs. Hypothesis 3}

\begin{comparisonbox}[H2 vs. H3: Key Distinction]

[Follow same structure as above]

\end{comparisonbox}

% Add additional comparison boxes as needed for Hypotheses 4 and 5

\vspace{0.5cm}

\subsection*{Priority Experiments}

\textbf{Highest Priority Test:} [Which single experiment would most efficiently distinguish between hypotheses or most definitively test a hypothesis? Provide experiment name/title.]

\textbf{Justification:} [Why is this the highest priority? Consider:
\begin{itemize}
  \item \textbf{Informativeness:} How much would results narrow the field of viable hypotheses?
  \item \textbf{Feasibility:} Can it be done with current methods and reasonable resources?
  \item \textbf{Cost-effectiveness:} What is the information gained relative to effort required?
  \item \textbf{Timeline:} How quickly could results be obtained?
\end{itemize}]

\vspace{0.3cm}

\textbf{Secondary Priority Tests:}
\begin{enumerate}
  \item [Second most important experiment with brief justification]
  \item [Third most important experiment with brief justification]
\end{enumerate}

% ============================================================================
% APPENDICES
% ============================================================================
\newpage
\appendix

% ============================================================================
% APPENDIX A: COMPREHENSIVE LITERATURE REVIEW
% ============================================================================
\appendixsection{Appendix A: Comprehensive Literature Review}

This appendix provides detailed synthesis of existing literature, extensive background context, and comprehensive citations supporting the hypotheses presented in this report.

\subsection*{A.1 Phenomenon Background and Context}

[Provide extensive background on the phenomenon. This section should be comprehensive, including:
\begin{itemize}
  \item Historical context and when the phenomenon was first observed
  \item Detailed description of what is known about the phenomenon
  \item Why this phenomenon is scientifically important
  \item Practical or clinical implications if applicable
  \item Current debates or controversies in the field
\end{itemize}

Include extensive citations throughout. Aim for 10-15 citations in this subsection alone.]

\subsection*{A.2 Current Understanding and Established Mechanisms}

[Synthesize what is currently understood about this phenomenon:
\begin{itemize}
  \item Established theories or frameworks that may apply
  \item Known mechanisms from related systems or analogous phenomena
  \item Molecular, cellular, or systemic processes that are well-characterized
  \item Population-level patterns that have been documented
  \item Computational or theoretical models that have been proposed
\end{itemize}

Include 15-20 citations covering recent reviews, primary research papers, and foundational studies.]

\subsection*{A.3 Evidence Supporting Hypothesis 1}

[Provide detailed discussion of all evidence supporting Hypothesis 1. This goes beyond the brief bullet points in the main text:
\begin{itemize}
  \item Detailed findings from key papers
  \item Mechanistic studies showing relevant pathways
  \item Data from analogous systems
  \item Theoretical support
  \item Any preliminary or indirect evidence
\end{itemize}

Include 8-12 citations specific to this hypothesis.]

\subsection*{A.4 Evidence Supporting Hypothesis 2}

[Same structure as A.3, focused on Hypothesis 2. Include 8-12 citations.]

\subsection*{A.5 Evidence Supporting Hypothesis 3}

[Same structure as A.3, focused on Hypothesis 3. Include 8-12 citations.]

% Add A.6, A.7 for Hypotheses 4 and 5 if applicable

\subsection*{A.6 Conflicting Findings and Unresolved Debates}

[Discuss contradictions in the literature:
\begin{itemize}
  \item Studies with conflicting results
  \item Ongoing debates about mechanisms
  \item Alternative interpretations of existing data
  \item Methodological issues that complicate interpretation
  \item Areas where consensus has not been reached
\end{itemize}

Include 5-10 citations highlighting key controversies.]

\subsection*{A.7 Knowledge Gaps and Limitations}

[Identify what is still unknown:
\begin{itemize}
  \item Aspects of the phenomenon that lack clear explanation
  \item Missing data or unstudied conditions
  \item Limitations of current methods or approaches
  \item Questions that remain unanswered
  \item Assumptions that have not been tested
\end{itemize}

Include 3-5 citations discussing limitations or identifying gaps.]

% ============================================================================
% APPENDIX B: DETAILED EXPERIMENTAL DESIGNS
% ============================================================================
\newpage
\appendixsection{Appendix B: Detailed Experimental Designs}

This appendix provides comprehensive experimental protocols for testing each hypothesis, including methods, controls, sample sizes, statistical approaches, and feasibility assessments.

\subsection*{B.1 Experiments for Testing Hypothesis 1}

\subsubsection*{Experiment 1A: [Descriptive Title]}

\textbf{Design Type:} [e.g., In vitro dose-response / In vivo knockout / Clinical RCT / Observational cohort / Computational model]

\textbf{Objective:} [What specific aspect of Hypothesis 1 does this experiment test? What question does it answer?]

\textbf{Detailed Methods:}
\begin{itemize}
  \item \textbf{System/Model:} [What system, organism, cell type, or population will be studied? Include species, strains, patient populations, etc.]
  \item \textbf{Intervention/Manipulation:} [What will be varied or manipulated? Include specific treatments, genetic modifications, interventions, etc.]
  \item \textbf{Measurements:} [What outcomes will be measured? Include primary and secondary endpoints, measurement techniques, timing of measurements]
  \item \textbf{Controls:} [What control conditions will be included? Negative controls, positive controls, vehicle controls, sham procedures, etc.]
  \item \textbf{Sample Size:} [Estimated n per group with power analysis justification if possible. Include assumptions about effect size and variability.]
  \item \textbf{Randomization \& Blinding:} [How will subjects be randomized? Who will be blinded?]
  \item \textbf{Statistical Analysis:} [Specific statistical tests planned, correction for multiple comparisons, significance thresholds]
\end{itemize}

\textbf{Expected Timeline:} [Rough estimate of duration from start to completion]

\textbf{Resource Requirements:}
\begin{itemize}
  \item \textbf{Equipment:} [Specialized equipment needed]
  \item \textbf{Materials:} [Key reagents, animals, human subjects]
  \item \textbf{Expertise:} [Specialized skills or training required]
  \item \textbf{Estimated Cost:} [Rough cost estimate if applicable]
\end{itemize}

\textbf{Feasibility Assessment:} [High/Medium/Low with justification. Consider technical challenges, resource availability, ethical considerations]

\textbf{Potential Confounds and Mitigation:}
\begin{itemize}
  \item [Confound 1 and how to address it]
  \item [Confound 2 and how to address it]
  \item [Confound 3 and how to address it]
\end{itemize}

\vspace{0.5cm}

\subsubsection*{Experiment 1B: [Alternative or Complementary Approach]}

[Follow same detailed structure as Experiment 1A. This should be an alternative method to test the same aspect of Hypothesis 1, or a complementary experiment that tests a different aspect.]

\vspace{0.5cm}

\subsection*{B.2 Experiments for Testing Hypothesis 2}

\subsubsection*{Experiment 2A: [Descriptive Title]}

[Follow same detailed structure as above]

\subsubsection*{Experiment 2B: [Alternative or Complementary Approach]}

[Follow same detailed structure as above]

\vspace{0.5cm}

\subsection*{B.3 Experiments for Testing Hypothesis 3}

[Continue with same structure for all hypotheses]

\vspace{0.5cm}

\subsection*{B.4 Discriminating Experiments}

[Provide detailed protocols for the priority experiments identified in Section 4 that distinguish between hypotheses]

% ============================================================================
% APPENDIX C: QUALITY ASSESSMENT
% ============================================================================
\newpage
\appendixsection{Appendix C: Quality Assessment}

This appendix provides detailed evaluation of each hypothesis against established quality criteria.

\subsection*{C.1 Comparative Quality Assessment}

\begin{hypotable}{Hypothesis Quality Criteria Evaluation}
\begin{tabular}{|p{2.5cm}|p{3cm}|p{3cm}|p{3cm}|}
\hline
\tableheadercolor
\textcolor{white}{\textbf{Criterion}} & \textcolor{white}{\textbf{Hypothesis 1}} & \textcolor{white}{\textbf{Hypothesis 2}} & \textcolor{white}{\textbf{Hypothesis 3}} \\
\hline
\textbf{Testability} & [Strong/Moderate/Weak] [Brief note: why?] & [Rating \& note] & [Rating \& note] \\
\hline
\tablerowcolor
\textbf{Falsifiability} & [Rating \& note] & [Rating \& note] & [Rating \& note] \\
\hline
\textbf{Parsimony} & [Rating \& note] & [Rating \& note] & [Rating \& note] \\
\hline
\tablerowcolor
\textbf{Explanatory Power} & [Rating \& note] & [Rating \& note] & [Rating \& note] \\
\hline
\textbf{Scope} & [Rating \& note] & [Rating \& note] & [Rating \& note] \\
\hline
\tablerowcolor
\textbf{Consistency} & [Rating \& note] & [Rating \& note] & [Rating \& note] \\
\hline
\textbf{Novelty} & [Rating \& note] & [Rating \& note] & [Rating \& note] \\
\hline
\end{tabular}
\caption{Comparative assessment of hypotheses across quality criteria. Strong = meets criterion very well; Moderate = partially meets criterion; Weak = does not meet criterion well.}
\end{hypotable}

\subsection*{C.2 Detailed Evaluation: Hypothesis 1}

\textbf{Strengths:}
\begin{enumerate}
  \item [Specific strength 1 with explanation of why this is advantageous]
  \item [Specific strength 2]
  \item [Specific strength 3]
  \item [Additional strengths as applicable]
\end{enumerate}

\textbf{Weaknesses:}
\begin{enumerate}
  \item [Specific weakness 1 with explanation of the limitation]
  \item [Specific weakness 2]
  \item [Specific weakness 3]
  \item [Additional weaknesses as applicable]
\end{enumerate}

\textbf{Overall Assessment:}

[Provide a comprehensive 1-2 paragraph assessment of Hypothesis 1's quality and viability. Consider:
\begin{itemize}
  \item How well does it balance the various quality criteria?
  \item What are the key trade-offs?
  \item Under what conditions would this be the most promising hypothesis?
  \item What are the major challenges to testing or validating it?
  \item How does it compare overall to competing hypotheses?
\end{itemize}]

\subsection*{C.3 Detailed Evaluation: Hypothesis 2}

[Follow same structure as C.2]

\subsection*{C.4 Detailed Evaluation: Hypothesis 3}

[Follow same structure as C.2]

% Add C.5, C.6 for Hypotheses 4 and 5 if applicable

\subsection*{C.5 Recommendations Based on Quality Assessment}

[Synthesize the quality assessments to provide recommendations:
\begin{itemize}
  \item Which hypothesis appears most promising overall?
  \item Which hypothesis should be tested first? Why?
  \item Are there scenarios where different hypotheses would be preferred?
  \item Could multiple hypotheses be partially correct?
  \item What would need to be true for each hypothesis to be viable?
\end{itemize}]

% ============================================================================
% APPENDIX D: SUPPLEMENTARY EVIDENCE
% ============================================================================
\newpage
\appendixsection{Appendix D: Supplementary Evidence}

This appendix provides additional supporting information, including analogous mechanisms, relevant data, and context that further informs the hypotheses.

\subsection*{D.1 Analogous Mechanisms in Related Systems}

[Discuss similar mechanisms or phenomena in related systems that provide insight:
\begin{itemize}
  \item How do analogous systems behave?
  \item What mechanisms operate in those systems?
  \item How might lessons from related systems apply here?
  \item What similarities and differences exist?
\end{itemize}

Include citations to relevant comparative studies.]

\subsection*{D.2 Preliminary Data or Observations}

[If applicable, discuss any preliminary data, pilot studies, or anecdotal observations that informed hypothesis generation but weren't formally published or well-documented.]

\subsection*{D.3 Theoretical Frameworks}

[Discuss broader theoretical frameworks that relate to the hypotheses:
\begin{itemize}
  \item What general principles or theories apply?
  \item How do the hypotheses fit within established frameworks?
  \item Are there mathematical or computational models that support any hypothesis?
\end{itemize}]

\subsection*{D.4 Historical Context and Evolution of Ideas}

[Provide historical perspective on how thinking about this phenomenon has evolved, what previous hypotheses have been proposed and tested, and what lessons have been learned from past attempts to explain the phenomenon.]

% ============================================================================
% REFERENCES
% ============================================================================
\newpage
\bibliographystyle{plainnat}
\bibliography{references}

% Alternatively, manually format references if not using BibTeX:
% \begin{thebibliography}{99}
% 
% \bibitem{author2023}
% Author1, A.B., \& Author2, C.D. (2023). 
% Title of paper. 
% \textit{Journal Name}, \textit{Volume}(Issue), pages. 
% DOI or URL
% 
% \bibitem{author2022}
% [Continue with all references...]
%
% [Target: 50+ references covering all citations in main text and appendices]
%
% \end{thebibliography}

\end{document}

