This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific…
Scientific Problem Selection Skills
A conversational framework for systematic scientific problem selection based on Fischbach & Walsh's "Problem choice and decision trees in science and engineering" (Cell, 2024).
Getting Started
Present users with three entry points:
1) Pitch an idea for a new project — to work it up together
2) Share a problem in a current project — to troubleshoot together
3) Ask a strategic question — to navigate the decision tree together
This conversational entry meets scientists where they are and establishes a collaborative tone.
Option 1: Pitch an Idea
Initial Prompt
Ask: "Tell me the short version of your idea (1-2 sentences)."
Response Approach
After the user shares their idea, return a quick summary (no more than one paragraph) demonstrating understanding. Note the general area of research and rephrase the idea in a way that highlights its kernel—showing alignment and readiness to dive into details.
Follow-up Prompt
Then ask for more detail: "Now give me a bit more detail. You might include, however briefly or even say where you are unsure:
What exactly you want to do
How you currently plan to do it
If it works, why will it be a big deal
What you think are the major risks"
Workflow
From there, guide the user through the early stages of problem selection and evaluation:
Skill 1: Intuition Pumps - Refine and strengthen the idea
Skill 2: Risk Assessment - Identify and manage project risks
Skill 3: Optimization Function - Define success metrics
Skill 4: Parameter Strategy - Determine what to fix vs. keep flexible
See references/01-intuition-pumps.md, references/02-risk-assessment.md, references/03-optimization-function.md, and references/04-parameter-strategy.md for detailed guidance.
Option 2: Troubleshoot a Problem
Initial Prompt
Ask: "Tell me a short version of your problem (1-2 sentences or whatever is easy)."
Response Approach
After the user shares their problem, return a quick summary (no more than one paragraph) demonstrating understanding. Note the context of the project where the problem occurred and rephrase the problem—highlighting its core essence—so the user knows the situation is understood. Also raise additional questions that seem important to discuss.
Follow-up Prompt
Then ask: "Now give me a bit more detail. You might include, however briefly:
The overall goal of your project (if we have not talked about it before)
What exactly went wrong
Your current ideas for fixing it"
Workflow
From there, guide the user through troubleshooting and decision tree navigation:
Skill 5: Decision Tree Navigation - Plan decision points and navigate between execution and strategic thinking
Skill 4: Parameter Strategy - Fix one parameter at a time, let others float
Skill 6: Adversity Response - Frame problems as opportunities for growth
Skill 7: Problem Inversion - Strategies for navigating around obstacles
Always include workarounds that might be useful whether or not the problem can be fixed easily.
See references/05-decision-tree.md, references/06-adversity-planning.md, references/07-problem-inversion.md, and references/04-parameter-strategy.md for detailed guidance.
Option 3: Ask a Strategic Question
Initial Prompt
Ask: "Tell me the short version of your question (1-2 sentences)."
Response Approach
After the user shares their question, return a quick summary (no more than one paragraph) demonstrating understanding. Note the broader context and rephrase the question—highlighting its crux—to confirm alignment with their thinking.
Follow-up Prompt
Then ask: "Now give me a bit more detail. You might include, however briefly:
The setting (i.e., is this about a current or future project)
A bit more detail about what you're thinking"
Workflow
From there, draw on the specific modules from the problem choice framework most appropriate to the question:
Skills 1-4 for future project planning (ideation, risk, optimization, parameters)
Skills 5-7 for current project navigation (decision trees, adversity, inversion)
Skill 8 for communication and synthesis
Skill 9 for comprehensive workflow orchestration
See the complete reference materials in the references/ folder.
Core Framework Concepts
The Central Insight
Problem Choice >> Execution Quality
Even brilliant execution of a mediocre problem yields incremental impact. Good execution of an important problem yields substantial impact.
The Time Paradox
Scientists typically spend:
Days choosing a problem
Years solving it
This imbalance limits impact. These skills help invest more time choosing wisely.
Evaluation Axes
For Evaluating Ideas:
X-axis: Likelihood of success
Y-axis: Impact if successful
Skills help move ideas rightward (more feasible) and upward (more impactful).
The Risk Paradox
Don't avoid risk—befriend it
No risk = incremental work
But: Multiple miracles = avoid or refine
Balance: Understood, quantified, manageable risk
The Parameter Paradox
Too many fixed = brittleness
Too few fixed = paralysis
Sweet spot: Fix ONE meaningful constraint
The Adversity Principle
Crises are inevitable (don't be surprised)
Crises are opportune (don't waste them)
Strategy: Fix problem AND upgrade project simultaneously
The 9 Skills Overview
Skill
Purpose
Output
Time
1. Intuition Pumps
Generate high-quality research ideas
Problem Ideation Document
~1 week
2. Risk Assessment
Identify and manage project risks
Risk Assessment Matrix
3-5 days
3. Optimization Function
Define success metrics
Impact Assessment Document
2-3 days
4. Parameter Strategy
Decide what to fix vs. keep flexible
Parameter Strategy Document
2-3 days
5. Decision Tree Navigation
Plan decision points and altitude dance
Decision Tree Map
2 days
6. Adversity Response
Prepare for crises as opportunities
Adversity Playbook
2 days
7. Problem Inversion
Navigate around obstacles
Problem Inversion Analysis
1 day
8. Integration & Synthesis
Synthesize into coherent plan
Project Communication Package
3-5 days
9. Meta-Framework
Orchestrate complete workflow
Complete Project Package
1-6 weeks
Skill Workflow
SKILL 1: Intuition Pumps
| (generates idea)
v
SKILL 2: Risk Assessment
| (evaluates feasibility)
v
SKILL 3: Optimization Function
| (defines success metrics)
v
SKILL 4: Parameter Strategy
| (determines flexibility)
v
SKILL 5: Decision Tree
| (plans execution and evaluation)
v
SKILL 6: Adversity Planning
| (prepares for failure modes)
v
SKILL 7: Problem Inversion
| (provides pivot strategies)
v
SKILL 8: Integration & Communication
| (synthesizes into coherent plan)
v
SKILL 9: Meta-Skill
(orchestrates complete workflow)
Key Design Principles
Conversational Entry - Meet users where they are with three clear starting points
Thoughtful Interaction - Ask clarifying questions; low confidence prompts additional input
Literature Integration - Use PubMed searches at strategic points for validation
Concrete Outputs - Every skill produces tangible 1-2 page documents
Building Specificity - Progressive detail emerges through targeted questions
Flexibility - Skills work independently, sequentially, or iteratively
Scientific Rigor - Claims about generality and feasibility should be evidence-based
Who Should Use These Skills
Graduate Students (Primary Audience)
When: Choosing thesis projects, qualifying exams, committee meetings
Focus: Skills 1-3 (ideation, risk, impact) + Skill 9 (complete workflow)
Timeline: 2-4 weeks for comprehensive planning
Postdocs
When: Starting new position, planning independent projects, fellowship applications
Focus: All skills, emphasizing independence and risk management
Timeline: 1-2 weeks intensive planning
Principal Investigators
When: New lab, new direction, mentoring trainees, grant cycles
Focus: Skills 1, 3, 4, 6 (ideation, impact, parameters, adversity)
Timeline: Ongoing, integrate into lab culture
Startup Founders
When: Company inception, pivot decisions, investor pitches
Focus: Skills 1-4 (ideation through parameters) + Skill 8 (communication)
Timeline: 1-2 weeks for initial planning, revisit quarterly
Reference Materials
Detailed skill documentation is available in the references/ folder:
File
Content
Search Patterns
01-intuition-pumps.md
Generate research ideas
Intuition Pump #, Trap #, Phase [0-9]
02-risk-assessment.md
Risk identification
Risk.*1-5, go/no-go, assumption
03-optimization-function.md
Success metrics
Generality.*Learning, optimization, impact
04-parameter-strategy.md
Parameter fixation
fixed.*float, constraint, parameter
05-decision-tree.md
Decision tree navigation
altitude, Level [0-9], decision
06-adversity-planning.md
Adversity response
adversity, crisis, ensemble
07-problem-inversion.md
Problem inversion strategies
Strategy [0-9], inversion, goal
08-integration-synthesis.md
Integration and synthesis
narrative, communication, story
09-meta-framework.md
Complete workflow
Phase, workflow, orchestrat
Expected Outcomes
Immediate (After Completing Workflow)
Clear project vision
Honest risk assessment
Contingency plans
Communication materials ready
Confidence in problem choice
6-Month
Faster decisions (have framework)
Productive adversity handling
No existential crises (risks mitigated)
2-Year
Published results or strong progress
Avoided dead-end projects
Career aligned with goals
Time well-spent (ultimate measure)
Foundational Reference
Fischbach, M.A., & Walsh, C.T. (2024). "Problem choice and decision trees in science and engineering." Cell, 187, 1828-1833.
Based on course BIOE 395 taught at Stanford University.don't have the plugin yet? install it then click "run inline in claude" again.