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skills/hypothesis-generation/assets/FORMATTING_GUIDE.md

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+# Hypothesis Generation Report - Formatting Quick Reference
+
+## Overview
+
+This guide provides quick reference for using the hypothesis generation LaTeX template and style package. For complete documentation, see `SKILL.md`.
+
+## Quick Start
+
+```latex
+% !TEX program = xelatex
+\documentclass[11pt,letterpaper]{article}
+\usepackage{hypothesis_generation}
+\usepackage{natbib}
+
+\title{Your Phenomenon Name}
+\begin{document}
+\maketitle
+% Your content
+\end{document}
+```
+
+**Compilation:** Use XeLaTeX or LuaLaTeX for best results
+```bash
+xelatex your_document.tex
+bibtex your_document
+xelatex your_document.tex
+xelatex your_document.tex
+```
+
+## Color Scheme Reference
+
+### Hypothesis Colors
+- **Hypothesis 1**: Deep Blue (RGB: 0, 102, 153) - Use for first hypothesis
+- **Hypothesis 2**: Forest Green (RGB: 0, 128, 96) - Use for second hypothesis
+- **Hypothesis 3**: Royal Purple (RGB: 102, 51, 153) - Use for third hypothesis
+- **Hypothesis 4**: Teal (RGB: 0, 128, 128) - Use for fourth hypothesis (if needed)
+- **Hypothesis 5**: Burnt Orange (RGB: 204, 85, 0) - Use for fifth hypothesis (if needed)
+
+### Utility Colors
+- **Predictions**: Amber (RGB: 255, 191, 0) - For testable predictions
+- **Evidence**: Light Blue (RGB: 102, 178, 204) - For supporting evidence
+- **Comparisons**: Steel Gray (RGB: 108, 117, 125) - For critical comparisons
+- **Limitations**: Coral Red (RGB: 220, 53, 69) - For limitations/challenges
+
+## Custom Box Environments
+
+### 1. Executive Summary Box
+
+```latex
+\begin{summarybox}[Executive Summary]
+  Content here
+\end{summarybox}
+```
+
+**Use for:** High-level overview at the beginning of the document
+
+---
+
+### 2. Hypothesis Boxes (5 variants)
+
+```latex
+\begin{hypothesisbox1}[Hypothesis 1: Title]
+  \textbf{Mechanistic Explanation:}
+  [2-3 paragraphs explaining HOW and WHY]
+  
+  \textbf{Key Supporting Evidence:}
+  \begin{itemize}
+    \item Evidence point 1 \citep{ref1}
+    \item Evidence point 2 \citep{ref2}
+  \end{itemize}
+  
+  \textbf{Core Assumptions:}
+  \begin{enumerate}
+    \item Assumption 1
+    \item Assumption 2
+  \end{enumerate}
+\end{hypothesisbox1}
+```
+
+**Available boxes:** `hypothesisbox1`, `hypothesisbox2`, `hypothesisbox3`, `hypothesisbox4`, `hypothesisbox5`
+
+**Use for:** Presenting each competing hypothesis with its mechanism, evidence, and assumptions
+
+**Best practices for 4-page main text:**
+- Keep mechanistic explanations to 1-2 brief paragraphs only (6-10 sentences max)
+- Include 2-3 most essential evidence points with citations
+- List 1-2 most critical assumptions
+- Ensure each hypothesis is genuinely distinct
+- All detailed explanations go to Appendix A
+- **Use `\newpage` before each hypothesis box to prevent overflow**
+- Each complete hypothesis box should be ≤0.6 pages
+
+---
+
+### 3. Prediction Box
+
+```latex
+\begin{predictionbox}[Predictions: Hypothesis 1]
+  \textbf{Prediction 1.1:} [Specific prediction]
+  \begin{itemize}
+    \item \textbf{Conditions:} When/where this applies
+    \item \textbf{Expected Outcome:} Specific measurable result
+    \item \textbf{Falsification:} What would disprove it
+  \end{itemize}
+\end{predictionbox}
+```
+
+**Use for:** Testable predictions derived from each hypothesis
+
+**Best practices for 4-page main text:**
+- Make predictions specific and quantitative when possible
+- Clearly state conditions under which prediction should hold
+- Always specify falsification criteria
+- Include only 1-2 most critical predictions per hypothesis in main text
+- Additional predictions go to appendices
+
+---
+
+### 4. Evidence Box
+
+```latex
+\begin{evidencebox}[Supporting Evidence]
+  Content discussing supporting evidence
+\end{evidencebox}
+```
+
+**Use for:** Highlighting key supporting evidence or literature synthesis
+
+**Best practices:**
+- Use sparingly in main text (detailed evidence goes in Appendix A)
+- Include citations for all evidence
+- Focus on most compelling evidence
+
+---
+
+### 5. Comparison Box
+
+```latex
+\begin{comparisonbox}[H1 vs. H2: Key Distinction]
+  \textbf{Fundamental Difference:}
+  [Description of core difference]
+  
+  \textbf{Discriminating Experiment:}
+  [Description of experiment]
+  
+  \textbf{Outcome Interpretation:}
+  \begin{itemize}
+    \item \textbf{If [Result A]:} H1 supported
+    \item \textbf{If [Result B]:} H2 supported
+  \end{itemize}
+\end{comparisonbox}
+```
+
+**Use for:** Explaining how to distinguish between competing hypotheses
+
+**Best practices:**
+- Focus on fundamental mechanistic differences
+- Propose clear, feasible discriminating experiments
+- Specify concrete outcome interpretations
+- Create comparisons for all major hypothesis pairs
+
+---
+
+### 6. Limitation Box
+
+```latex
+\begin{limitationbox}[Limitations \& Challenges]
+  Discussion of limitations
+\end{limitationbox}
+```
+
+**Use for:** Highlighting important limitations or challenges
+
+**Best practices:**
+- Use when limitations are particularly important
+- Be honest about challenges
+- Suggest how limitations might be addressed
+
+---
+
+## Document Structure
+
+### Main Text (Maximum 4 Pages - Highly Concise)
+
+1. **Executive Summary** (0.5-1 page)
+   - Use `summarybox`
+   - Brief phenomenon overview
+   - List all hypotheses in 1 sentence each
+   - Recommended approach
+
+2. **Competing Hypotheses** (2-2.5 pages)
+   - Use `hypothesisbox1`, `hypothesisbox2`, etc.
+   - One box per hypothesis
+   - Brief mechanistic explanation (1-2 paragraphs) + essential evidence (2-3 points) + key assumptions (1-2)
+   - Target: 3-5 hypotheses
+   - Keep highly concise - details go to appendices
+
+3. **Testable Predictions** (0.5-1 page)
+   - Use `predictionbox` for each hypothesis
+   - 1-2 most critical predictions per hypothesis only
+   - Very brief - full predictions in appendices
+
+4. **Critical Comparisons** (0.5-1 page)
+   - Use `comparisonbox` for highest priority comparison only
+   - Show how to distinguish top hypotheses
+   - Additional comparisons in appendices
+
+**Main text total: Maximum 4 pages - be extremely selective about what goes here**
+
+### Appendices (Comprehensive, Detailed)
+
+**Appendix A: Comprehensive Literature Review**
+- Detailed background (extensive citations)
+- Current understanding
+- Evidence for each hypothesis (detailed)
+- Conflicting findings
+- Knowledge gaps
+- **Target: 40-60+ citations**
+
+**Appendix B: Detailed Experimental Designs**
+- Full protocols for each hypothesis
+- Methods, controls, sample sizes
+- Statistical approaches
+- Feasibility assessments
+- Timeline and resource requirements
+
+**Appendix C: Quality Assessment**
+- Detailed evaluation tables
+- Strengths and weaknesses analysis
+- Comparative scoring
+- Recommendations
+
+**Appendix D: Supplementary Evidence**
+- Analogous mechanisms
+- Preliminary data
+- Theoretical frameworks
+- Historical context
+
+**References**
+- **Target: 50+ total references**
+
+## Citation Best Practices
+
+### In Main Text
+- Cite 15-20 key papers
+- Use `\citep{author2023}` for parenthetical citations
+- Use `\citet{author2023}` for textual citations
+- Focus on most important/recent evidence
+
+### In Appendices
+- Cite 40-60+ papers total
+- Comprehensive coverage of relevant literature
+- Include reviews, primary research, theoretical papers
+- Cite every claim and piece of evidence
+
+### Citation Density Guidelines
+- Main hypothesis boxes: 2-3 citations per box (most essential only)
+- Main text total: 10-15 citations maximum (keep concise)
+- Appendix A literature sections: 8-15 citations per subsection
+- Experimental designs: 2-5 citations for methods/precedents
+- Quality assessments: Citations as needed for evaluation criteria
+- Total document: 50+ citations (vast majority in appendices)
+
+## Tables
+
+### Professional Table Formatting
+
+```latex
+\begin{hypotable}{Caption}
+\begin{tabular}{|l|l|l|}
+\hline
+\tableheadercolor
+\textcolor{white}{\textbf{Header 1}} & \textcolor{white}{\textbf{Header 2}} \\
+\hline
+Data row 1 & Data \\
+\hline
+\tablerowcolor  % Alternating gray background
+Data row 2 & Data \\
+\hline
+\end{tabular}
+\caption{Your caption}
+\end{hypotable}
+```
+
+**Best practices:**
+- Use `\tableheadercolor` for header rows
+- Alternate `\tablerowcolor` for tables >3 rows
+- Keep tables readable (not too wide)
+- Use for quality assessments, comparisons
+
+## Common Formatting Patterns
+
+### Hypothesis Section Pattern
+
+```latex
+% Use \newpage before hypothesis box to prevent overflow
+\newpage
+\subsection*{Hypothesis N: [Concise Title]}
+
+\begin{hypothesisboxN}[Hypothesis N: [Title]]
+
+\textbf{Mechanistic Explanation:}
+
+[1-2 brief paragraphs of explanation - 6-10 sentences max]
+
+\vspace{0.3cm}
+
+\textbf{Key Supporting Evidence:}
+\begin{itemize}
+  \item [Evidence 1] \citep{ref1}
+  \item [Evidence 2] \citep{ref2}
+  \item [Evidence 3] \citep{ref3}
+\end{itemize}
+
+\vspace{0.3cm}
+
+\textbf{Core Assumptions:}
+\begin{enumerate}
+  \item [Assumption 1]
+  \item [Assumption 2]
+\end{enumerate}
+
+\end{hypothesisboxN}
+
+\vspace{0.5cm}
+```
+
+**Note:** The `\newpage` before the hypothesis box ensures it starts on a fresh page, preventing overflow. This is especially important when boxes contain substantial content.
+
+### Prediction Section Pattern
+
+```latex
+\subsection*{Predictions from Hypothesis N}
+
+\begin{predictionbox}[Predictions: Hypothesis N]
+
+\textbf{Prediction N.1:} [Statement]
+\begin{itemize}
+  \item \textbf{Conditions:} [Conditions]
+  \item \textbf{Expected Outcome:} [Outcome]
+  \item \textbf{Falsification:} [Falsification]
+\end{itemize}
+
+\vspace{0.2cm}
+
+\textbf{Prediction N.2:} [Statement]
+[... continue ...]
+
+\end{predictionbox}
+```
+
+### Comparison Section Pattern
+
+```latex
+\subsection*{Distinguishing Hypothesis X vs. Hypothesis Y}
+
+\begin{comparisonbox}[HX vs. HY: Key Distinction]
+
+\textbf{Fundamental Difference:}
+
+[Description of core difference]
+
+\vspace{0.3cm}
+
+\textbf{Discriminating Experiment:}
+
+[Experiment description]
+
+\vspace{0.3cm}
+
+\textbf{Outcome Interpretation:}
+\begin{itemize}
+  \item \textbf{If [Result A]:} HX supported
+  \item \textbf{If [Result B]:} HY supported
+  \item \textbf{If [Result C]:} Both/neither supported
+\end{itemize}
+
+\end{comparisonbox}
+```
+
+## Spacing and Layout
+
+### Vertical Spacing
+- `\vspace{0.3cm}` - Between elements within boxes
+- `\vspace{0.5cm}` - Between major sections or boxes
+- `\vspace{1cm}` - After title, before main content
+
+### Page Breaks and Overflow Prevention
+
+**CRITICAL: Prevent Content Overflow**
+
+LaTeX boxes (tcolorbox environments) do not automatically break across pages. Content that exceeds the remaining page space will overflow and cause formatting issues. Follow these guidelines:
+
+1. **Strategic Page Breaks Before Long Boxes:**
+```latex
+\newpage  % Start on fresh page if box will be long
+\begin{hypothesisbox1}[Hypothesis 1: Title]
+  % Substantial content here
+\end{hypothesisbox1}
+```
+
+2. **Monitor Box Content Length:**
+   - Each hypothesis box should be ≤0.7 pages maximum
+   - If mechanistic explanation + evidence + assumptions exceeds ~0.6 pages, content is too long
+   - Solution: Move detailed content to appendices, keep only essentials in main text boxes
+
+3. **When to Use `\newpage`:**
+   - Before any hypothesis box with >3 subsections or >15 lines of content
+   - Before comparison boxes with extensive experimental descriptions
+   - Between major appendix sections
+   - If less than 0.6 pages remain on current page before starting a new box
+
+4. **Content Length Guidelines for Main Text:**
+   - Executive summary box: 0.5-0.8 pages max
+   - Each hypothesis box: 0.4-0.6 pages max
+   - Each prediction box: 0.3-0.5 pages max
+   - Each comparison box: 0.4-0.6 pages max
+
+5. **Breaking Up Long Content:**
+   ```latex
+   % GOOD: Concise main text with page break
+   \newpage
+   \begin{hypothesisbox1}[Hypothesis 1: Brief Title]
+   \textbf{Mechanistic Explanation:}
+   Brief overview in 1-2 paragraphs (6-10 sentences).
+   
+   \textbf{Key Supporting Evidence:}
+   \begin{itemize}
+     \item Evidence 1 \citep{ref1}
+     \item Evidence 2 \citep{ref2}
+   \end{itemize}
+   
+   \textbf{Core Assumptions:}
+   \begin{enumerate}
+     \item Assumption 1
+   \end{enumerate}
+   
+   See Appendix A for detailed mechanism and comprehensive evidence.
+   \end{hypothesisbox1}
+   ```
+
+   ```latex
+   % BAD: Overly long content that will overflow
+   \begin{hypothesisbox1}[Hypothesis 1]
+   \subsection{Very Long Section}
+   Multiple paragraphs...
+   \subsection{Another Long Section}
+   More paragraphs...
+   \subsection{Even More Content}
+   [Content continues beyond page boundary → OVERFLOW!]
+   \end{hypothesisbox1}
+   ```
+
+6. **Page Break Commands:**
+   - `\newpage` - Force new page (recommended before long boxes)
+   - `\clearpage` - Force new page and flush floats (use before appendices)
+
+### Section Spacing
+Already handled by style package, but you can adjust:
+```latex
+\vspace{0.5cm}  % Add extra space if needed
+```
+
+## Troubleshooting
+
+### Common Issues
+
+**Issue: "File hypothesis_generation.sty not found"**
+- Solution: Ensure the .sty file is in the same directory as your .tex file, or in your LaTeX path
+
+**Issue: Boxes don't have colors**
+- Solution: Compile with XeLaTeX or LuaLaTeX, not pdfLaTeX
+- Command: `xelatex yourfile.tex`
+
+**Issue: Citations show as [?]**
+- Solution: Run bibtex after first xelatex compilation
+```bash
+xelatex yourfile.tex
+bibtex yourfile
+xelatex yourfile.tex
+xelatex yourfile.tex
+```
+
+**Issue: Fonts not found**
+- Solution: Comment out font lines in the .sty file if custom fonts aren't installed
+- Lines to comment: `\setmainfont{...}` and `\setsansfont{...}`
+
+**Issue: Box titles overlap with content**
+- Solution: Add more vertical space with `\vspace{0.3cm}` after titles
+
+**Issue: Tables too wide**
+- Solution: Use `\small` or `\footnotesize` before tabular, or use `p{width}` column specs
+
+**Issue: Content overflowing off the page**
+- **Cause:** Boxes (tcolorbox environments) are too long to fit on remaining page space
+- **Solution 1:** Add `\newpage` before the box to start it on a fresh page
+- **Solution 2:** Reduce box content - move detailed information to appendices
+- **Solution 3:** Break content into multiple smaller boxes
+- **Prevention:** Keep each hypothesis box to 0.4-0.6 pages maximum; use `\newpage` liberally before boxes with substantial content
+
+**Issue: Main text exceeds 4 pages**
+- **Cause:** Boxes contain too much detailed information
+- **Solution:** Aggressively move content to appendices - main text boxes should contain only:
+  - Brief mechanistic overview (1-2 paragraphs)
+  - 2-3 key evidence bullets
+  - 1-2 core assumptions
+- All detailed explanations, additional evidence, and comprehensive discussions belong in Appendix A
+
+### Package Requirements
+
+Ensure these packages are installed:
+- `tcolorbox` (with `most` option)
+- `xcolor`
+- `fontspec` (for XeLaTeX/LuaLaTeX)
+- `fancyhdr`
+- `titlesec`
+- `enumitem`
+- `booktabs`
+- `natbib`
+
+Install missing packages:
+```bash
+# For TeX Live
+tlmgr install tcolorbox xcolor fontspec fancyhdr titlesec enumitem booktabs natbib
+
+# For MiKTeX (Windows)
+# Use MiKTeX Package Manager GUI
+```
+
+## Style Consistency Tips
+
+1. **Color Usage**
+   - Always use the same color for each hypothesis throughout the document
+   - H1 = blue, H2 = green, H3 = purple, etc.
+   - Don't mix colors for the same hypothesis
+
+2. **Box Usage**
+   - Main text: Hypothesis boxes, prediction boxes, comparison boxes
+   - Appendix: Can use evidence boxes, limitation boxes as needed
+   - Don't overuse boxes - reserve for key content
+
+3. **Citation Style**
+   - Consistent citation format throughout
+   - Use `\citep{}` for most citations
+   - Group multiple citations: `\citep{ref1, ref2, ref3}`
+
+4. **Hypothesis Numbering**
+   - Number hypotheses consistently (H1, H2, H3, etc.)
+   - Use same numbering in predictions (P1.1, P1.2 for H1)
+   - Use same numbering in comparisons (H1 vs. H2)
+
+5. **Language**
+   - Be precise and specific
+   - Avoid vague language ("may", "could", "possibly")
+   - Use active voice when possible
+   - Make predictions quantitative when feasible
+
+## Quick Checklist
+
+Before finalizing your document:
+
+- [ ] Title page has phenomenon name
+- [ ] **Main text is 4 pages maximum**
+- [ ] Executive summary is concise (0.5-1 page)
+- [ ] Each hypothesis in its own colored box
+- [ ] 3-5 hypotheses presented (not more)
+- [ ] Each hypothesis has brief mechanistic explanation (1-2 paragraphs)
+- [ ] Each hypothesis has 2-3 most essential evidence points with citations
+- [ ] Each hypothesis has 1-2 most critical assumptions
+- [ ] Predictions boxes with 1-2 key predictions per hypothesis
+- [ ] Priority comparison box in main text (others in appendix)
+- [ ] Priority experiments identified
+- [ ] **Page breaks (`\newpage`) used before long boxes to prevent overflow**
+- [ ] **No content overflows off page boundaries (check PDF carefully)**
+- [ ] **Each hypothesis box is ≤0.6 pages (if longer, move details to appendix)**
+- [ ] Appendix A has comprehensive literature review with detailed evidence
+- [ ] Appendix B has detailed experimental protocols
+- [ ] Appendix C has quality assessment tables
+- [ ] Appendix D has supplementary evidence
+- [ ] 10-15 citations in main text (selective)
+- [ ] 50+ total citations in full document
+- [ ] All boxes use correct colors
+- [ ] Document compiles without errors
+- [ ] References formatted correctly
+- [ ] **Compiled PDF checked visually for overflow issues**
+
+## Example Minimal Document
+
+```latex
+% !TEX program = xelatex
+\documentclass[11pt,letterpaper]{article}
+\usepackage{hypothesis_generation}
+\usepackage{natbib}
+
+\title{Role of X in Y}
+
+\begin{document}
+\maketitle
+
+\section*{Executive Summary}
+\begin{summarybox}[Executive Summary]
+Brief overview of phenomenon and hypotheses.
+\end{summarybox}
+
+\section{Competing Hypotheses}
+
+% Use \newpage before each hypothesis box to prevent overflow
+\newpage
+\subsection*{Hypothesis 1: Title}
+\begin{hypothesisbox1}[Hypothesis 1: Title]
+\textbf{Mechanistic Explanation:}
+Brief explanation in 1-2 paragraphs.
+
+\textbf{Key Supporting Evidence:}
+\begin{itemize}
+  \item Evidence point \citep{ref1}
+\end{itemize}
+\end{hypothesisbox1}
+
+\newpage
+\subsection*{Hypothesis 2: Title}
+\begin{hypothesisbox2}[Hypothesis 2: Title]
+\textbf{Mechanistic Explanation:}
+Brief explanation in 1-2 paragraphs.
+
+\textbf{Key Supporting Evidence:}
+\begin{itemize}
+  \item Evidence point \citep{ref2}
+\end{itemize}
+\end{hypothesisbox2}
+
+\section{Testable Predictions}
+
+\subsection*{Predictions from Hypothesis 1}
+\begin{predictionbox}[Predictions: Hypothesis 1]
+Predictions here.
+\end{predictionbox}
+
+\section{Critical Comparisons}
+
+\subsection*{H1 vs. H2}
+\begin{comparisonbox}[H1 vs. H2]
+Comparison here.
+\end{comparisonbox}
+
+% Force new page before appendices
+\appendix
+\newpage
+\appendixsection{Appendix A: Literature Review}
+Detailed literature review here.
+
+\newpage
+\bibliographystyle{plainnat}
+\bibliography{references}
+
+\end{document}
+```
+
+**Key Points:**
+- `\newpage` used before each hypothesis box to ensure they start on fresh pages
+- This prevents content overflow issues
+- Main text boxes kept concise (1-2 paragraphs + bullet points)
+- Detailed content goes to appendices
+
+## Additional Resources
+
+- See `hypothesis_report_template.tex` for complete annotated template
+- See `SKILL.md` for workflow and methodology guidance
+- See `references/hypothesis_quality_criteria.md` for evaluation framework
+- See `references/experimental_design_patterns.md` for design guidance
+- See treatment-plans skill for additional LaTeX styling examples
+

skills/hypothesis-generation/assets/hypothesis_generation.sty

@@ -0,0 +1,307 @@
+% hypothesis_generation.sty
+% Professional Scientific Hypothesis Generation Report Style
+% Provides modern, color-coded styling for hypothesis generation documents
+
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{hypothesis_generation}[2025/11/17 Hypothesis Generation Report Style]
+
+% Required packages
+\RequirePackage[margin=1in, top=1.2in, bottom=1.2in]{geometry}
+\RequirePackage{graphicx}
+\RequirePackage{xcolor}
+\RequirePackage[most]{tcolorbox}
+\RequirePackage{tikz}
+\RequirePackage{fontspec}
+\RequirePackage{fancyhdr}
+\RequirePackage{titlesec}
+\RequirePackage{enumitem}
+\RequirePackage{booktabs}
+\RequirePackage{longtable}
+\RequirePackage{array}
+\RequirePackage{colortbl}
+\RequirePackage{hyperref}
+\RequirePackage{natbib}
+
+% Color scheme - Distinct colors for each hypothesis plus utility colors
+\definecolor{hypothesis1}{RGB}{0, 102, 153}      % Deep Blue
+\definecolor{hypothesis2}{RGB}{0, 128, 96}       % Forest Green
+\definecolor{hypothesis3}{RGB}{102, 51, 153}     % Royal Purple
+\definecolor{hypothesis4}{RGB}{0, 128, 128}      % Teal
+\definecolor{hypothesis5}{RGB}{204, 85, 0}       % Burnt Orange
+\definecolor{predictioncolor}{RGB}{255, 191, 0}  % Amber
+\definecolor{evidencecolor}{RGB}{102, 178, 204}  % Light Blue
+\definecolor{comparisoncolor}{RGB}{108, 117, 125} % Steel Gray
+\definecolor{limitationcolor}{RGB}{220, 53, 69}  % Coral Red
+\definecolor{darkgray}{RGB}{64, 64, 64}          % Dark gray for text
+\definecolor{lightgray}{RGB}{245, 245, 245}      % Light background
+
+% Fonts (if using XeLaTeX/LuaLaTeX)
+% Comment these out if fonts are not available
+% \setmainfont{Lato}
+% \setsansfont{Roboto}
+
+% Hyperlink setup
+\hypersetup{
+    colorlinks=true,
+    linkcolor=hypothesis1,
+    citecolor=hypothesis1,
+    urlcolor=evidencecolor,
+    pdfborder={0 0 0}
+}
+
+% Header and footer styling
+\setlength{\headheight}{22pt}
+\pagestyle{fancy}
+\fancyhf{}
+\fancyhead[L]{\color{hypothesis1}\sffamily\small\textbf{Hypothesis Generation Report}}
+\fancyhead[R]{\color{darkgray}\sffamily\small\thepage}
+\fancyfoot[C]{\color{darkgray}\small Generated: \today}
+\renewcommand{\headrulewidth}{2pt}
+\renewcommand{\headrule}{\hbox to\headwidth{\color{hypothesis1}\leaders\hrule height \headrulewidth\hfill}}
+\renewcommand{\footrulewidth}{0.5pt}
+\renewcommand{\footrule}{\hbox to\headwidth{\color{lightgray}\leaders\hrule height \footrulewidth\hfill}}
+
+% Section styling
+\titleformat{\section}
+  {\color{hypothesis1}\Large\sffamily\bfseries}
+  {\thesection}{1em}{}
+  [\color{hypothesis1}\titlerule]
+
+\titleformat{\subsection}
+  {\color{evidencecolor}\large\sffamily\bfseries}
+  {\thesubsection}{1em}{}
+
+\titleformat{\subsubsection}
+  {\color{darkgray}\normalsize\sffamily\bfseries}
+  {\thesubsubsection}{1em}{}
+
+% Title page styling
+\renewcommand{\maketitle}{
+  \begin{tcolorbox}[
+    enhanced,
+    colback=hypothesis1,
+    colframe=hypothesis1,
+    arc=0mm,
+    boxrule=0pt,
+    left=20pt,
+    right=20pt,
+    top=30pt,
+    bottom=30pt,
+    width=\textwidth
+  ]
+    \color{white}
+    \begin{center}
+      {\Huge\sffamily\bfseries Scientific Hypothesis\\Generation Report}\\[10pt]
+      {\Large\sffamily\@title}\\[15pt]
+      {\large\sffamily Evidence-Based Competing Hypotheses}\\[8pt]
+      {\normalsize\sffamily\color{evidencecolor}\today}
+    \end{center}
+  \end{tcolorbox}
+  \vspace{1cm}
+}
+
+% Custom boxes for hypotheses (5 different colors)
+\newtcolorbox{hypothesisbox1}[1][Hypothesis 1]{
+  enhanced,
+  colback=hypothesis1!5,
+  colframe=hypothesis1,
+  arc=3mm,
+  boxrule=2pt,
+  left=12pt,
+  right=12pt,
+  top=12pt,
+  bottom=12pt,
+  title=#1,
+  fonttitle=\sffamily\bfseries\large,
+  coltitle=white,
+  colbacktitle=hypothesis1,
+  attach boxed title to top left={yshift=-3mm, xshift=5mm},
+  boxed title style={arc=2mm}
+}
+
+\newtcolorbox{hypothesisbox2}[1][Hypothesis 2]{
+  enhanced,
+  colback=hypothesis2!5,
+  colframe=hypothesis2,
+  arc=3mm,
+  boxrule=2pt,
+  left=12pt,
+  right=12pt,
+  top=12pt,
+  bottom=12pt,
+  title=#1,
+  fonttitle=\sffamily\bfseries\large,
+  coltitle=white,
+  colbacktitle=hypothesis2,
+  attach boxed title to top left={yshift=-3mm, xshift=5mm},
+  boxed title style={arc=2mm}
+}
+
+\newtcolorbox{hypothesisbox3}[1][Hypothesis 3]{
+  enhanced,
+  colback=hypothesis3!5,
+  colframe=hypothesis3,
+  arc=3mm,
+  boxrule=2pt,
+  left=12pt,
+  right=12pt,
+  top=12pt,
+  bottom=12pt,
+  title=#1,
+  fonttitle=\sffamily\bfseries\large,
+  coltitle=white,
+  colbacktitle=hypothesis3,
+  attach boxed title to top left={yshift=-3mm, xshift=5mm},
+  boxed title style={arc=2mm}
+}
+
+\newtcolorbox{hypothesisbox4}[1][Hypothesis 4]{
+  enhanced,
+  colback=hypothesis4!5,
+  colframe=hypothesis4,
+  arc=3mm,
+  boxrule=2pt,
+  left=12pt,
+  right=12pt,
+  top=12pt,
+  bottom=12pt,
+  title=#1,
+  fonttitle=\sffamily\bfseries\large,
+  coltitle=white,
+  colbacktitle=hypothesis4,
+  attach boxed title to top left={yshift=-3mm, xshift=5mm},
+  boxed title style={arc=2mm}
+}
+
+\newtcolorbox{hypothesisbox5}[1][Hypothesis 5]{
+  enhanced,
+  colback=hypothesis5!5,
+  colframe=hypothesis5,
+  arc=3mm,
+  boxrule=2pt,
+  left=12pt,
+  right=12pt,
+  top=12pt,
+  bottom=12pt,
+  title=#1,
+  fonttitle=\sffamily\bfseries\large,
+  coltitle=white,
+  colbacktitle=hypothesis5,
+  attach boxed title to top left={yshift=-3mm, xshift=5mm},
+  boxed title style={arc=2mm}
+}
+
+% Prediction box (amber)
+\newtcolorbox{predictionbox}[1][Testable Predictions]{
+  enhanced,
+  colback=predictioncolor!10,
+  colframe=predictioncolor!80!black,
+  arc=3mm,
+  boxrule=1.5pt,
+  left=10pt,
+  right=10pt,
+  top=10pt,
+  bottom=10pt,
+  title=#1,
+  fonttitle=\sffamily\bfseries,
+  coltitle=black,
+  colbacktitle=predictioncolor
+}
+
+% Evidence/Support box (light blue)
+\newtcolorbox{evidencebox}[1][Supporting Evidence]{
+  enhanced,
+  colback=evidencecolor!8,
+  colframe=evidencecolor,
+  arc=3mm,
+  boxrule=1.5pt,
+  left=10pt,
+  right=10pt,
+  top=10pt,
+  bottom=10pt,
+  title=#1,
+  fonttitle=\sffamily\bfseries,
+  coltitle=white,
+  colbacktitle=evidencecolor
+}
+
+% Comparison box (steel gray)
+\newtcolorbox{comparisonbox}[1][Critical Comparison]{
+  enhanced,
+  colback=comparisoncolor!8,
+  colframe=comparisoncolor,
+  arc=3mm,
+  boxrule=1.5pt,
+  left=10pt,
+  right=10pt,
+  top=10pt,
+  bottom=10pt,
+  title=#1,
+  fonttitle=\sffamily\bfseries,
+  coltitle=white,
+  colbacktitle=comparisoncolor
+}
+
+% Limitation box (coral red)
+\newtcolorbox{limitationbox}[1][Limitations \& Challenges]{
+  enhanced,
+  colback=limitationcolor!8,
+  colframe=limitationcolor,
+  arc=3mm,
+  boxrule=1.5pt,
+  left=10pt,
+  right=10pt,
+  top=10pt,
+  bottom=10pt,
+  title=#1,
+  fonttitle=\sffamily\bfseries,
+  coltitle=white,
+  colbacktitle=limitationcolor
+}
+
+% Executive summary box (using evidence color for consistency)
+\newtcolorbox{summarybox}[1][Executive Summary]{
+  enhanced,
+  colback=evidencecolor!15,
+  colframe=hypothesis1,
+  arc=3mm,
+  boxrule=2pt,
+  left=15pt,
+  right=15pt,
+  top=15pt,
+  bottom=15pt,
+  title=#1,
+  fonttitle=\sffamily\bfseries\Large,
+  coltitle=white,
+  colbacktitle=hypothesis1
+}
+
+% Table styling
+\newcommand{\tableheadercolor}{\rowcolor{hypothesis1}}
+\newcommand{\tablerowcolor}{\rowcolor{lightgray}}
+
+% Custom table environment
+\newenvironment{hypotable}[1]{
+  \begin{table}[h]
+  \centering
+  \small\sffamily
+  \renewcommand{\arraystretch}{1.3}
+}{
+  \end{table}
+}
+
+% Custom list styling
+\setlist[itemize,1]{label=\textcolor{hypothesis1}{\textbullet}, leftmargin=*, itemsep=3pt}
+\setlist[enumerate,1]{label=\textcolor{hypothesis1}{\arabic*.}, leftmargin=*, itemsep=3pt}
+
+% Appendix styling
+\newcommand{\appendixsection}[1]{
+  \section*{#1}
+  \addcontentsline{toc}{section}{#1}
+}
+
+% Citation styling helper
+\newcommand{\citehighlight}[1]{\textcolor{evidencecolor}{\citep{#1}}}
+
+\endinput
+

skills/hypothesis-generation/assets/hypothesis_report_template.tex

@@ -0,0 +1,572 @@
+% !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
+% ============================================================================
+% NOTE: Keep main text to 4 pages maximum. All details go to appendices.
+% Executive Summary: 0.5-1 page
+
+\section*{Executive Summary}
+\addcontentsline{toc}{section}{Executive Summary}
+
+\begin{summarybox}[Executive Summary]
+\textbf{Phenomenon:} [One paragraph: What was observed? Why is it important?]
+
+\vspace{0.2cm}
+\textbf{Key Question:} [Single sentence stating the central question]
+
+\vspace{0.2cm}
+\textbf{Competing Hypotheses:}
+\begin{enumerate}
+  \item \textbf{[H1 Title]:} [One sentence mechanistic summary]
+  \item \textbf{[H2 Title]:} [One sentence mechanistic summary]
+  \item \textbf{[H3 Title]:} [One sentence mechanistic summary]
+  \item \textbf{[Add H4 \& H5 if applicable]}
+\end{enumerate}
+
+\vspace{0.2cm}
+\textbf{Recommended Approach:} [One sentence on priority experiments]
+
+\end{summarybox}
+
+\vspace{0.3cm}
+
+% ============================================================================
+% COMPETING HYPOTHESES
+% ============================================================================
+% NOTE: Keep this section to 2-2.5 pages for 3-5 hypotheses
+% Each hypothesis: 1-2 brief paragraphs + 2-3 key evidence points + 1-2 assumptions
+% Detailed explanations and additional evidence go to Appendix A
+
+\section{Competing Hypotheses}
+
+This section presents [3-5] distinct mechanistic hypotheses. Detailed literature review and comprehensive evidence are in Appendix A.
+
+\subsection*{Hypothesis 1: [Concise Descriptive Title]}
+
+\begin{hypothesisbox1}[Hypothesis 1: [Title]]
+
+\textbf{Mechanistic Explanation:}
+
+[Provide a BRIEF mechanistic explanation (1-2 paragraphs) of HOW and WHY. Keep concise - main text is limited to 4 pages total. Include only the essential mechanism. All detailed explanations go to Appendix A.
+
+Example: "This hypothesis proposes that [mechanism X] operates through [pathway Y], resulting in [outcome Z]. The process initiates when [trigger], activating [component A] and ultimately producing the observed [phenomenon] \citep{key-ref}."
+]
+
+\vspace{0.2cm}
+
+\textbf{Key Supporting Evidence:}
+\begin{itemize}
+  \item [Most essential evidence point 1 \citep{author2023}]
+  \item [Most essential evidence point 2 \citep{author2022}]
+  \item [Most essential evidence point 3 \citep{author2021}]
+\end{itemize}
+
+\vspace{0.2cm}
+
+\textbf{Core Assumptions:}
+\begin{enumerate}
+  \item [Most critical assumption 1]
+  \item [Most critical assumption 2]
+\end{enumerate}
+
+\end{hypothesisbox1}
+
+\vspace{0.3cm}
+
+\subsection*{Hypothesis 2: [Concise Descriptive Title]}
+
+\begin{hypothesisbox2}[Hypothesis 2: [Title]]
+
+\textbf{Mechanistic Explanation:}
+
+[BRIEF mechanistic explanation (1-2 paragraphs) distinct from Hypothesis 1. Keep concise.]
+
+\vspace{0.2cm}
+
+\textbf{Key Supporting Evidence:}
+\begin{itemize}
+  \item [Essential evidence point 1 with citation]
+  \item [Essential evidence point 2 with citation]
+  \item [Essential evidence point 3 with citation]
+\end{itemize}
+
+\vspace{0.2cm}
+
+\textbf{Core Assumptions:}
+\begin{enumerate}
+  \item [Critical assumption 1]
+  \item [Critical assumption 2]
+\end{enumerate}
+
+\end{hypothesisbox2}
+
+\vspace{0.3cm}
+
+\subsection*{Hypothesis 3: [Concise Descriptive Title]}
+
+\begin{hypothesisbox3}[Hypothesis 3: [Title]]
+
+\textbf{Mechanistic Explanation:}
+
+[BRIEF mechanistic explanation (1-2 paragraphs) distinct from previous hypotheses.]
+
+\vspace{0.2cm}
+
+\textbf{Key Supporting Evidence:}
+\begin{itemize}
+  \item [Essential evidence point 1 with citation]
+  \item [Essential evidence point 2 with citation]
+  \item [Essential evidence point 3 with citation]
+\end{itemize}
+
+\vspace{0.2cm}
+
+\textbf{Core Assumptions:}
+\begin{enumerate}
+  \item [Critical assumption 1]
+  \item [Critical assumption 2]
+\end{enumerate}
+
+\end{hypothesisbox3}
+
+\vspace{0.3cm}
+
+% 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
+% ============================================================================
+% NOTE: Keep this section to 0.5-1 page
+% Include only 1-2 most critical predictions per hypothesis
+% Additional predictions go to Appendix B with experimental designs
+
+\section{Testable Predictions}
+
+Key predictions from each hypothesis. Full prediction details and additional predictions in Appendix B.
+
+\subsection*{Predictions from Hypothesis 1}
+
+\begin{predictionbox}[Predictions: Hypothesis 1]
+
+\textbf{Prediction 1.1:} [Most critical prediction]
+\begin{itemize}
+  \item \textbf{Expected Outcome:} [Specific result with magnitude if possible]
+  \item \textbf{Falsification:} [What would disprove it]
+\end{itemize}
+
+\vspace{0.15cm}
+
+\textbf{Prediction 1.2:} [Second most critical prediction]
+\begin{itemize}
+  \item \textbf{Expected Outcome:} [Specific result]
+  \item \textbf{Falsification:} [What would disprove it]
+\end{itemize}
+
+\end{predictionbox}
+
+\vspace{0.3cm}
+
+\subsection*{Predictions from Hypothesis 2}
+
+\begin{predictionbox}[Predictions: Hypothesis 2]
+
+\textbf{Prediction 2.1:} [Most critical prediction]
+\begin{itemize}
+  \item \textbf{Expected Outcome:} [Specific result]
+  \item \textbf{Falsification:} [What would disprove it]
+\end{itemize}
+
+\vspace{0.15cm}
+
+\textbf{Prediction 2.2:} [Second most critical prediction]
+\begin{itemize}
+  \item \textbf{Expected Outcome:} [Specific result]
+  \item \textbf{Falsification:} [What would disprove it]
+\end{itemize}
+
+\end{predictionbox}
+
+\vspace{0.3cm}
+
+\subsection*{Predictions from Hypothesis 3}
+
+\begin{predictionbox}[Predictions: Hypothesis 3]
+
+[1-2 most critical predictions only, following same brief structure]
+
+\end{predictionbox}
+
+% Add prediction boxes for Hypotheses 4 and 5 if applicable
+
+% ============================================================================
+% CRITICAL COMPARISONS
+% ============================================================================
+% NOTE: Keep this section to 0.5-1 page
+% Include only the HIGHEST PRIORITY comparison
+% Additional comparisons go to Appendix B
+
+\section{Critical Comparisons}
+
+Highest priority comparison for distinguishing hypotheses. Additional comparisons in Appendix B.
+
+\subsection*{Priority Comparison: Hypothesis 1 vs. Hypothesis 2}
+
+\begin{comparisonbox}[H1 vs. H2: Key Distinction]
+
+\textbf{Fundamental Difference:} [One sentence on core mechanistic difference]
+
+\vspace{0.2cm}
+
+\textbf{Discriminating Experiment:} [Brief description of key experiment to distinguish them]
+
+\vspace{0.2cm}
+
+\textbf{Outcome Interpretation:}
+\begin{itemize}
+  \item \textbf{If [Result A]:} H1 supported
+  \item \textbf{If [Result B]:} H2 supported
+\end{itemize}
+
+\end{comparisonbox}
+
+\vspace{0.3cm}
+
+\textbf{Highest Priority Test:} [Name of single most important experiment]
+
+\textbf{Justification:} [2-3 sentences on why this is highest priority considering informativeness and feasibility. Full experimental details in Appendix B.]
+
+% ============================================================================
+% 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}
+