scientific-problem-selection

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npx skills add https://github.com/anthropics/knowledge-work-plugins --skill 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.

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`