Clear Thought Server

Instructions

Implementation Reference

• src/tools/scientificMethodServer.ts:171-207 (handler)

  Core handler function that validates input, processes hypothesis and experiment data, formats detailed output for logging, and returns structured JSON response with status.
  public processScientificMethod(input: unknown): { content: Array<{ type: string; text: string }>; isError?: boolean } { try { const validatedData = this.validateInputData(input); const processedData: ScientificInquiryData = { ...validatedData, hypothesis: this.processHypothesis(validatedData.hypothesis), experiment: this.processExperiment(validatedData.experiment) }; const formattedOutput = this.formatOutput(processedData); console.error(formattedOutput); return { content: [{ type: "text", text: JSON.stringify({ stage: processedData.stage, inquiryId: processedData.inquiryId, iteration: processedData.iteration, nextStageNeeded: processedData.nextStageNeeded, status: 'success' }, null, 2) }] }; } catch (error) { return { content: [{ type: "text", text: JSON.stringify({ error: error instanceof Error ? error.message : String(error), status: 'failed' }, null, 2) }], isError: true }; } }
• src/index.ts:689-823 (schema)

  Tool definition object including name, description, and comprehensive inputSchema defining validation for all stages of scientific inquiry (observation, hypothesis with variables/assumptions, experiment with predictions/controls, etc.).
  const SCIENTIFIC_METHOD_TOOL: Tool = { name: "scientificmethod", description: `A detailed tool for applying formal scientific reasoning to questions and problems. This tool guides models through the scientific method with structured hypothesis testing. It enforces explicit variable identification, prediction making, and evidence evaluation.`, inputSchema: { type: "object", properties: { stage: { type: "string", enum: [ "observation", "question", "hypothesis", "experiment", "analysis", "conclusion", "iteration", ], }, observation: { type: "string" }, question: { type: "string" }, hypothesis: { type: "object", properties: { statement: { type: "string" }, variables: { type: "array", items: { type: "object", properties: { name: { type: "string" }, type: { type: "string", enum: [ "independent", "dependent", "controlled", "confounding", ], }, operationalization: { type: "string" }, }, required: ["name", "type"], }, }, assumptions: { type: "array", items: { type: "string" } }, hypothesisId: { type: "string" }, confidence: { type: "number", minimum: 0, maximum: 1 }, domain: { type: "string" }, iteration: { type: "number", minimum: 0 }, alternativeTo: { type: "array", items: { type: "string" } }, refinementOf: { type: "string" }, status: { type: "string", enum: [ "proposed", "testing", "supported", "refuted", "refined", ], }, }, required: [ "statement", "variables", "assumptions", "hypothesisId", "confidence", "domain", "iteration", "status", ], }, experiment: { type: "object", properties: { design: { type: "string" }, methodology: { type: "string" }, predictions: { type: "array", items: { type: "object", properties: { if: { type: "string" }, then: { type: "string" }, else: { type: "string" }, }, required: ["if", "then"], }, }, experimentId: { type: "string" }, hypothesisId: { type: "string" }, controlMeasures: { type: "array", items: { type: "string" }, }, results: { type: "string" }, outcomeMatched: { type: "boolean" }, unexpectedObservations: { type: "array", items: { type: "string" }, }, limitations: { type: "array", items: { type: "string" } }, nextSteps: { type: "array", items: { type: "string" } }, }, required: [ "design", "methodology", "predictions", "experimentId", "hypothesisId", "controlMeasures", ], }, analysis: { type: "string" }, conclusion: { type: "string" }, inquiryId: { type: "string", description: "Unique identifier for this scientific inquiry", }, iteration: { type: "number", minimum: 0, description: "Current iteration of the scientific process", }, nextStageNeeded: { type: "boolean", description: "Whether another stage is needed in the process", }, }, required: ["stage", "inquiryId", "iteration", "nextStageNeeded"], }, };
• src/index.ts:996-1012 (registration)

  Registration of the 'scientificmethod' tool in the MCP server's capabilities, making it available via listTools and callTool.
  capabilities: { tools: { sequentialthinking: SEQUENTIAL_THINKING_TOOL, mentalmodel: MENTAL_MODEL_TOOL, designpattern: DESIGN_PATTERN_TOOL, programmingparadigm: PROGRAMMING_PARADIGM_TOOL, debuggingapproach: DEBUGGING_APPROACH_TOOL, collaborativereasoning: COLLABORATIVE_REASONING_TOOL, decisionframework: DECISION_FRAMEWORK_TOOL, metacognitivemonitoring: METACOGNITIVE_MONITORING_TOOL, scientificmethod: SCIENTIFIC_METHOD_TOOL, structuredargumentation: STRUCTURED_ARGUMENTATION_TOOL, visualreasoning: VISUAL_REASONING_TOOL, }, }, } );
• src/index.ts:1137-1149 (registration)

  Dispatcher switch case that handles CallToolRequest for 'scientificmethod' by invoking the ScientificMethodServer's process method and formatting response.
  case "scientificmethod": { const result = scientificMethodServer.processScientificMethod( request.params.arguments ); return { content: [ { type: "text", text: JSON.stringify(result, null, 2), }, ], }; }
• src/models/interfaces.ts:233-290 (schema)

  TypeScript interfaces defining the structure for scientific inquiry data, hypothesis (with variables, assumptions), experiment (with predictions, controls), used for type safety and matching inputSchema.
  export interface Variable { name: string; type: "independent" | "dependent" | "controlled" | "confounding"; operationalization?: string; } export interface HypothesisData { statement: string; variables: Variable[]; assumptions: string[]; hypothesisId: string; confidence: number; domain: string; iteration: number; alternativeTo?: string[]; refinementOf?: string; status: "proposed" | "testing" | "supported" | "refuted" | "refined"; } export interface Prediction { if: string; then: string; else?: string; } export interface ExperimentData { design: string; methodology: string; predictions: Prediction[]; experimentId: string; hypothesisId: string; controlMeasures: string[]; results?: string; outcomeMatched?: boolean; unexpectedObservations?: string[]; limitations?: string[]; nextSteps?: string[]; } export interface ScientificInquiryData { stage: | "observation" | "question" | "hypothesis" | "experiment" | "analysis" | "conclusion" | "iteration"; observation?: string; question?: string; hypothesis?: HypothesisData; experiment?: ExperimentData; analysis?: string; conclusion?: string; inquiryId: string; iteration: number; nextStageNeeded: boolean; }