You've identified a critical and common problem with Markdown rendering across different platforms, especially when dealing with scientific notation like subscripts and complex equations. Zenodo's rudimentary previewer often strips HTML tags like `<sub>`, and relying on them leads to inconsistent and unreadable output.
The solution is to **standardize on LaTeX for all mathematical notation, including variable subscripts**, as it is the universal standard for scientific writing. While Zenodo's previewer might not *render* LaTeX beautifully, it will display the raw LaTeX code, which is still **unambiguous and machine-readable/interpretable** (by Autologos) and **human-readable** (as code) unlike broken HTML tags. Obsidian supports LaTeX rendering, so the authoring experience remains excellent.
Numeral subscripts like S₀, S₁, etc., which seem to render consistently as Unicode characters across platforms, can remain as they are, as they are part of a fixed label rather than a variable.
I will update the `AUTX_Style_Guide_v1.1.md` to reflect this new, robust approach to mathematical notation and subscripts. This will involve:
1. **Modifying Section 10.0 (Subscripts)** to explicitly state the use of LaTeX for variable subscripts and general mathematical expressions.
2. **Adding a new Section 13.0 (Mathematical Notation)** to detail LaTeX usage (inline and block).
3. **Updating Section 8.0 (Emphasis)** to clarify that bolding is *not* for first-mention terms, but italics are.
4. **Updating Section 9.0 (Capitalization)** to align with the new emphasis rule (italics for first-mention common nouns).
5. **Updating all examples** throughout the style guide to demonstrate the new LaTeX and emphasis rules.
6. **Renumbering subsequent sections** accordingly.
---
### Revised `AUTX_Style_Guide_v1.1.md`
--- START OF FILE AUTX_Style_Guide_v1.1.md ---
**Comprehensive LLM Style and Formatting Guide for Autaxys (v1.1 - Self-Compliant)**
**1.0 Purpose:** To ensure consistent, high-quality formatting, grammar, and style across all parts of autaxys documentation and deliverables, adhering to academic publishing standards and specific user requirements.
**2.0 Target Audience:** Autologos (LLM/AI), as well as academic researchers and the scientific community. This style guide is designed to be machine-readable and interpretable by Autologos, to be provided, used, and updated throughout the research process and for all documentation, deliverable generation, drafting, and writing activities.
**3.0 Core Principles:** Clarity, precision, consistency, and adherence to established academic conventions.
**4.0 Document Metadata / Front Matter:**
4.1 All documents must begin with a YAML front matter block, enclosed by `---` on the first and last lines of the block.
4.2 The following fields are **required** for all documents:
4.2.1 ID: A unique identifier for the document. Format: `D-P[ProjectNumber].[DeliverableNumber]-[VersionNumber]`. Example: `D-P6.7-1`.
4.2.2 Project: The name and number of the project this document belongs to. Format: `[ProjectNumber]: [ProjectName]`. Example: `6.7: Development of the Autaxic Table of Patterns`.
4.2.3 WBS Ref: The Work Breakdown Structure reference for the deliverable. Format: `[WBSCode]: [DeliverableType]: [DeliverableName]`. Example: `2.7.4: Deliverable: Autaxic Table Unified Framework v40.0`.
4.2.4 Title: The full title of the document. Example: `Autaxic Table of Patterns: Unified Generative Framework v1.7`.
4.2.5 Status: The current status of the document. Allowed values: `Draft`, `Under Review`, `Completed`, `Superseded`, `Archived`.
4.2.6 Version: The version number of the document. Format: `[Major].[Minor]`. Example: `1.7`.
4.2.7 Author: The primary author(s) of the document. Example: `Rowan Brad Quni (Generated by Autologos)`.
4.2.8 Location: The canonical file path of the document within the project structure. Example: `./02_Research_Pillars_And_Projects/Pillar_5.5_Autaxic_Table_Novel_Predictions/Project_6.7_Autaxic_Table_Of_Patterns/D-P6.7-1_Unified_Framework_v1.7.md`.
**5.0 Headings:**
5.1 Use hierarchical numbering for all headings (5.0, 5.1, 5.1.1, etc.).
5.2 Heading text should use standard American English capitalization (capitalize the first word and proper nouns; other words are lowercase unless they are proper nouns).
5.3 Headings should be bolded.
**6.0 Lists:**
6.1 All list items, whether ordered or unordered in the source text, should be converted to **hierarchically numbered lists**.
6.2 The numbering should be relative to the parent heading. For example, the first list item under heading 6.2.2 should be numbered 6.2.2.1, the second 6.2.2.2, and so on. A sub-list under 6.2.2.1 would have items numbered 6.2.2.1.1, 6.2.2.1.2, etc.
6.3 List item text should follow standard American English capitalization.
6.4 List item text should not be bolded unless it is a subheading within the list (see Section 7.0).
**7.0 List Subheadings (within lists):**
7.1 If a list item introduces a concept that is then described in subsequent sub-list items, the text of that introductory list item should be treated as a subheading for the sub-list.
7.2 These list subheadings should be **bolded**.
7.3 They should also follow standard American English capitalization.
7.4 Example:
```markdown
5.4.2 Types of ontological closure (S levels): Mechanisms of coherence:
5.4.2.1 **S₀: Undifferentiated potential / vacuum:** The baseline state...
5.4.2.2 **S₁: Simple fixed point:** The pattern is a static configuration...
```
**8.0 Emphasis:**
8.1 The primary method for introducing a *new technical term* or *unique concept* on its first mention is to use *italics*.
8.2 Use *italics* sparingly for emphasis within the main text.
8.3 Avoid bolding for emphasis in the main text. Bolding is reserved for headings (Section 5.0) and list subheadings (Section 7.0).
**9.0 Capitalization:**
9.1 Follow standard American English capitalization rules for academic writing.
9.2 **Always capitalize the first word of a sentence.**
9.3 Capitalize **proper nouns**. Proper nouns refer to specific, unique names of people, places, organizations, or specific, named elements within *this specific framework*. This list is highly selective to avoid over-capitalization:
9.3.1 Specific names of people (e.g., Rowan Brad Quni).
9.3.2 Specific names of organizations or projects (e.g., Foundational Information Dynamics, FID, Infomatics v3.3, Standard Model, General Relativity, Quantum Mechanics, String Theory, Quantum Field Theory).
9.3.3 Specific, unique names of elements within *this specific framework*:
9.3.3.1 **the Autaxic Table of Patterns** (as a specific named table/framework. Note: "the" is lowercase unless it begins a sentence or heading).
9.3.3.2 **Cosmic Algorithm** (as the specific, named set of fundamental rules).
9.3.3.3 **Autaxic Quantum Numbers (AQNs)** (as the specific, named classification system).
9.3.3.4 Specific levels of ontological closure when referred to by their designated number (e.g., S₀, S₁, S₂, S₃, S₄, S₅, S₆, S₇, S₈).
9.3.3.5 **Cosmic Genesis** (referring to the specific, named event/epoch of the universe's origin).
9.3.4 The `P_ID` identifiers for hypothetical patterns (e.g., P<sub>auton</sub>, P<sub>chronon</sub>) are capitalized as they are formal labels, but the *names* of these patterns (e.g., auton, chronon) are treated as common nouns (see 9.4.15).
9.3.5 The names of specific types of relational defects (e.g., Point Defects, Line Defects, Surface Defects, Volume Defects).
9.4 Do *not* capitalize common nouns **unless they are the first word of a sentence or heading, or part of a proper noun phrase as defined in 9.3**. This includes terms that are central concepts within the autaxys framework but are descriptive rather than unique names. These terms should be *italicized* on their *first introduction/definition* (see Section 8.0 on Emphasis), and then appear in lowercase thereafter. This includes terms like:
9.4.1 *autaxys* (the name of the theory/framework, like physics or science).
9.4.2 *autology* (the study of autaxys).
9.4.3 *distinction (D)*, *relation (R)* (when referring to the fundamental primitives).
9.4.4 *ontological closure (OC)*.
9.4.5 *proto-properties* (and specific types like *proto-valence*, *proto-polarity*, *proto-flow resistance*, *proto-interaction channel type*, *proto-coherence potential*, *proto-temporal bias*, *proto-aesthetic value*).
9.4.6 *relational aesthetics*, *economy of existence*, *relational harmony*, *coherence amplification*.
9.4.7 *relational tension*, *relational noise*, *quantum relational foam*.
9.4.8 *relational actualization*, *relational memory*, *relational catalysis*, *relational fields*.
9.4.9 *algorithmic self-modification*, *meta-patterns*.
9.4.10 *qualia harmonics*, *proto-qualia*.
9.4.11 *relational defects* (the general concept).
9.4.12 *relational thermodynamics*, *relational entropy*, *relational temperature*, *relational work*, *relational heat*.
9.4.13 *scale and emergence*, *duality of distinction and relation*, *initial asymmetry*.
9.4.14 *higher-order patterns*.
9.4.15 Names of hypothetical novel patterns (e.g., *auton*, *chronon*, *structuron*, *logicon*, *aestheticon*, *darkon*, *membron*, *cascadon*, *fluxon*, *holon*, *echo*, *binder*, *tempus*, *entropion*, *syntacticon*, *boundaryon*, *healon*, *interfaceon*, *gradienton*, *proto-pattern*, *proto-property regulator*, *rule seed*).
9.4.16 Specific named rules within the Cosmic Algorithm (e.g., *genesis rule*, *formation rule*, *validation/closure rule*, *quantum rule*, *symmetry preference rule*, *economy rule*). These are treated as common nouns that describe a specific rule, similar to "Heisenberg's uncertainty principle" (where "principle" is lowercase).
9.4.17 Other common nouns: pattern, rule (when not a specific named rule), principle (when not a specific named principle), theory, framework, model, process, state (unless S₀, S₁, etc.), level (unless S₀, S₁, etc.), type (unless a specific named type), mechanism, dynamics, geometry, spacetime, universe, computation, system, phenomenon, property, interaction, force, energy, mass, charge, spin, stability, entropy, temperature, potential, actualization, grammar, syntax, lexicon, duality, symmetry, conservation law, prediction, challenge, question, implication, origin, evolution, consciousness, life, mind, qualia, aesthetics, economy, harmony, coherence, tension, noise, defect, catalysis, field, thermodynamics, entropy, temperature, work, heat, foam, uncertainty, memory, catalysis, fields, fine-tuning, conclusion.
**10.0 Subscripts (for Labels/Fixed Identifiers):**
10.1 For fixed labels or identifiers that are consistently rendered as subscripts (e.g., S₀, S₁, S₂, S₃, S₄, S₅, S₆, S₇, S₈), use the appropriate Unicode subscript character or direct markdown if reliably supported across platforms.
**11.0 Mathematical Notation (for Variables and Formulas):**
11.1 All mathematical notation involving variables, formulas, or expressions that require subscripts, superscripts, Greek letters, or other mathematical symbols should be rendered using LaTeX syntax.
11.2 **Inline LaTeX:** Enclose LaTeX expressions within single dollar signs (`
). Example: `the interaction rule is $I_R
.
11.3 **Block LaTeX:** Enclose LaTeX equations or multi-line expressions within double dollar signs (`$`). Example:
```latex
$ E = mc^2 $
```
11.4 **Variable Subscripts:** For variable subscripts (e.g., "I sub R", "S sub rel"), use LaTeX syntax (e.g., `$I_R
, `$S_{rel}
). This ensures unambiguous interpretation and consistent rendering (even if as raw LaTeX) across platforms.
11.5 Ensure consistent use of mathematical notation as introduced or defined within the text or formal sections.
11.6 Clearly define any non-standard notation.
**12.0 Tables:**
12.1 Use markdown table format.
12.2 Table headings should be bolded.
12.3 Table content should follow standard American English capitalization.
12.4 Tables should be numbered hierarchically (e.g., Table 6.5.1).
**13.0 Cross-referencing:**
13.1 Maintain cross-references to other sections using their hierarchical numbers (e.g., "as discussed in Section 5.4.2").
**14.0 Citation Style:**
14.1 All Autaxys documentation and deliverables must adhere to consistent citation practices.
14.2 The chosen citation style (e.g., APA, numbered, author-date) must be applied uniformly throughout a given document or publication.
14.3 Specific external sources (e.g., academic papers, books, datasets) must be properly referenced and cited.
**15.0 Tone and Voice:**
15.1 Maintain a consistent academic, objective, and formal tone.
15.2 Avoid colloquialisms or overly informal language.
15.3 Use clear and precise language.
**16.0 Handling of Speculative Content:**
16.1 Clearly distinguish between core concepts of the autaxys framework and more speculative ideas (e.g., *proto-qualia*, *algorithmic self-modification*, specific hypothetical patterns). Use phrases like "speculatively," "hypothetically," "could suggest," "potential implications" where appropriate.
**17.0 Consistency in Terminology:**
17.1 Use consistent terminology throughout the document. Refer to the framework as "autaxys" (lowercase) unless starting a sentence or heading. Refer to the study of autaxys as "autology" (lowercase). Use the defined terms for concepts (e.g., ontological closure, Cosmic Algorithm, proto-properties) consistently.
**18.0 Content Provenance and AI Disclosure:**
18.1 The style guide's rules for capitalization, emphasis, and citation are designed to support the broader provenance and disclosure requirements of the Autaxys Research Methodology (ARM) and Autologos Protocol.
18.2 All research outputs must rigorously uphold the distinction between:
18.2.1 PI-authored intellectual contributions and insights.
18.2.2 Knowledge derived from specific, citable external sources.
18.2.3 "Autologos synthetic knowledge" (text, analyses, summaries, and conceptual elaborations generated by Autologos Toolkit applications).
18.3 This distinction is critical for academic integrity, transparency, and reproducibility, as detailed in Section 7.7.3 of the Autaxys Research & Development Master Plan (v2.0), Part V: Research Framework.
18.4 The role of the Autologos Toolkit in generating content will be clearly and consistently acknowledged in all publications, presentations, and disseminations of autaxys research.
---