Scientific problem selection

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.

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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:

1. What exactly you want to do
2. How you currently plan to do it
3. If it works, why will it be a big deal
4. 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.

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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:

1. The overall goal of your project (if we have not talked about it before)
2. What exactly went wrong
3. 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.

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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:

1. The setting (i.e., is this about a current or future project)
2. 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.

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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

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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

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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)

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Key Design Principles

1. Conversational Entry - Meet users where they are with three clear starting points
2. Thoughtful Interaction - Ask clarifying questions; low confidence prompts additional input
3. Literature Integration - Use PubMed searches at strategic points for validation
4. Concrete Outputs - Every skill produces tangible 1-2 page documents
5. Building Specificity - Progressive detail emerges through targeted questions
6. Flexibility - Skills work independently, sequentially, or iteratively
7. Scientific Rigor - Claims about generality and feasibility should be evidence-based

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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

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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

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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)

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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.