@pikaa-ai/pikaa 0.3.1 → 0.3.4

package/skills/scientific-critical-thinking/references/logical_fallacies.md

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-# Logical Fallacies in Scientific Discourse
-
-## Fallacies of Causation
-
-### 1. Post Hoc Ergo Propter Hoc (After This, Therefore Because of This)
-**Description:** Assuming that because B happened after A, A caused B.
-
-**Examples:**
-- "I took this supplement and my cold went away, so the supplement cured my cold."
-- "Autism diagnoses increased after vaccine schedules changed, so vaccines cause autism."
-- "I wore my lucky socks and won the game, so the socks caused the win."
-
-**Why fallacious:** Temporal sequence is necessary but not sufficient for causation. Correlation ≠ causation.
-
-**Related:** *Cum hoc ergo propter hoc* (with this, therefore because of this) - correlation mistaken for causation even without temporal order.
-
-### 2. Confusing Correlation with Causation
-**Description:** Assuming correlation implies direct causal relationship.
-
-**Examples:**
-- "Countries that eat more chocolate have more Nobel Prize winners, so chocolate makes you smarter."
-- "Ice cream sales correlate with drowning deaths, so ice cream causes drowning."
-
-**Reality:** Often due to confounding variables (hot weather causes both ice cream sales and swimming).
-
-### 3. Reverse Causation
-**Description:** Confusing cause and effect direction.
-
-**Examples:**
-- "Depression is associated with inflammation, so inflammation causes depression." (Could be: depression causes inflammation)
-- "Wealthy people are healthier, so wealth causes health." (Could be: health enables wealth accumulation)
-
-**Solution:** Longitudinal studies and experimental designs to establish temporal order.
-
-### 4. Single Cause Fallacy
-**Description:** Attributing complex phenomena to one cause when multiple factors contribute.
-
-**Examples:**
-- "Crime is caused by poverty." (Ignores many other contributing factors)
-- "Heart disease is caused by fat intake." (Oversimplifies multifactorial disease)
-
-**Reality:** Most outcomes have multiple contributing causes.
-
-## Fallacies of Generalization
-
-### 5. Hasty Generalization
-**Description:** Drawing broad conclusions from insufficient evidence.
-
-**Examples:**
-- "My uncle smoked and lived to 90, so smoking isn't dangerous."
-- "This drug worked in 5 patients, so it's effective for everyone."
-- "I saw three black swans, so all swans are black."
-
-**Why fallacious:** Small, unrepresentative samples don't support universal claims.
-
-### 6. Anecdotal Fallacy
-**Description:** Using personal experience or isolated examples as proof.
-
-**Examples:**
-- "I know someone who survived cancer using alternative medicine, so it works."
-- "My grandmother never exercised and lived to 100, so exercise is unnecessary."
-
-**Why fallacious:** Anecdotes are unreliable due to selection bias, memory bias, and confounding. Plural of anecdote ≠ data.
-
-### 7. Cherry Picking (Suppressing Evidence)
-**Description:** Selecting only evidence that supports your position while ignoring contradictory evidence.
-
-**Examples:**
-- Citing only studies showing supplement benefits while ignoring null findings
-- Highlighting successful predictions while ignoring failed ones
-- Showing graphs that start at convenient points
-
-**Detection:** Look for systematic reviews, not individual studies.
-
-### 8. Ecological Fallacy
-**Description:** Inferring individual characteristics from group statistics.
-
-**Example:**
-- "Average income in this neighborhood is high, so this person must be wealthy."
-- "This country has low disease rates, so any individual from there is unlikely to have disease."
-
-**Why fallacious:** Group-level patterns don't necessarily apply to individuals.
-
-## Fallacies of Authority and Tradition
-
-### 9. Appeal to Authority (Argumentum ad Verecundiam)
-**Description:** Accepting claims because an authority figure said them, without evidence.
-
-**Examples:**
-- "Dr. X says this treatment works, so it must." (If Dr. X provides no data)
-- "Einstein believed in God, so God exists." (Einstein's physics expertise doesn't transfer)
-- "99% of doctors recommend..." (Appeal to majority + authority without evidence)
-
-**Valid use of authority:** Experts providing evidence-based consensus in their domain.
-
-**Invalid:** Authority opinions without evidence, or outside their expertise.
-
-### 10. Appeal to Antiquity/Tradition
-**Description:** Assuming something is true or good because it's old or traditional.
-
-**Examples:**
-- "Traditional medicine has been used for thousands of years, so it must work."
-- "This theory has been accepted for decades, so it must be correct."
-
-**Why fallacious:** Age doesn't determine validity. Many old beliefs have been disproven.
-
-### 11. Appeal to Novelty
-**Description:** Assuming something is better because it's new.
-
-**Examples:**
-- "This is the latest treatment, so it must be superior."
-- "New research overturns everything we knew." (Often overstated)
-
-**Why fallacious:** New ≠ better. Established treatments often outperform novel ones.
-
-## Fallacies of Relevance
-
-### 12. Ad Hominem (Attack the Person)
-**Description:** Attacking the person making the argument rather than the argument itself.
-
-**Types:**
-- **Abusive:** "He's an idiot, so his theory is wrong."
-- **Circumstantial:** "She's funded by industry, so her findings are false."
-- **Tu Quoque:** "You smoke, so your anti-smoking argument is invalid."
-
-**Why fallacious:** Personal characteristics don't determine argument validity.
-
-**Note:** Conflicts of interest are worth noting but don't invalidate evidence.
-
-### 13. Genetic Fallacy
-**Description:** Judging something based on its origin rather than its merits.
-
-**Examples:**
-- "This idea came from a drug company, so it's wrong."
-- "Ancient Greeks believed this, so it's outdated."
-
-**Better approach:** Evaluate evidence regardless of source.
-
-### 14. Appeal to Emotion
-**Description:** Manipulating emotions instead of presenting evidence.
-
-**Types:**
-- **Appeal to fear:** "If you don't vaccinate, your child will die."
-- **Appeal to pity:** "Think of the suffering patients who need this unproven treatment."
-- **Appeal to flattery:** "Smart people like you know that..."
-
-**Why fallacious:** Emotional reactions don't determine truth.
-
-### 15. Appeal to Consequences (Argumentum ad Consequentiam)
-**Description:** Arguing something is true/false based on whether consequences are desirable.
-
-**Examples:**
-- "Climate change can't be real because the solutions would hurt the economy."
-- "Free will must exist because without it, morality is impossible."
-
-**Why fallacious:** Reality is independent of what we wish were true.
-
-### 16. Appeal to Nature (Naturalistic Fallacy)
-**Description:** Assuming "natural" means good, safe, or effective.
-
-**Examples:**
-- "This treatment is natural, so it's safe."
-- "Organic food is natural, so it's healthier."
-- "Vaccines are unnatural, so they're harmful."
-
-**Why fallacious:**
-- Many natural things are deadly (arsenic, snake venom, hurricanes)
-- Many synthetic things are beneficial (antibiotics, vaccines)
-- "Natural" is often poorly defined
-
-### 17. Moralistic Fallacy
-**Description:** Assuming what ought to be true is true.
-
-**Examples:**
-- "There shouldn't be sex differences in ability, so they don't exist."
-- "People should be rational, so they are."
-
-**Why fallacious:** Desires about reality don't change reality.
-
-## Fallacies of Structure
-
-### 18. False Dichotomy (False Dilemma)
-**Description:** Presenting only two options when more exist.
-
-**Examples:**
-- "Either you're with us or against us."
-- "It's either genetic or environmental." (Usually both)
-- "Either the treatment works or it doesn't." (Ignores partial effects)
-
-**Reality:** Most issues have multiple options and shades of gray.
-
-### 19. Begging the Question (Circular Reasoning)
-**Description:** Assuming what you're trying to prove.
-
-**Examples:**
-- "This medicine works because it has healing properties." (What are healing properties? That it works!)
-- "God exists because the Bible says so, and the Bible is true because it's God's word."
-
-**Detection:** Check if the conclusion is hidden in the premises.
-
-### 20. Moving the Goalposts
-**Description:** Changing standards of evidence after initial standards are met.
-
-**Example:**
-- Skeptic: "Show me one study."
-- [Shows study]
-- Skeptic: "That's just one study; show me a meta-analysis."
-- [Shows meta-analysis]
-- Skeptic: "But meta-analyses have limitations..."
-
-**Why problematic:** No amount of evidence will ever be sufficient.
-
-### 21. Slippery Slope
-**Description:** Arguing that one step will inevitably lead to extreme outcomes without justification.
-
-**Example:**
-- "If we allow gene editing for disease, we'll end up with designer babies and eugenics."
-
-**When valid:** If intermediate steps are actually likely.
-
-**When fallacious:** If chain of events is speculative without evidence.
-
-### 22. Straw Man
-**Description:** Misrepresenting an argument to make it easier to attack.
-
-**Example:**
-- Position: "We should teach evolution in schools."
-- Straw man: "So you think we should tell kids they're just monkeys?"
-
-**Detection:** Ask: Is this really what they're claiming?
-
-## Fallacies of Statistical and Scientific Reasoning
-
-### 23. Texas Sharpshooter Fallacy
-**Description:** Cherry-picking data clusters to fit a pattern, like shooting arrows then drawing targets around them.
-
-**Examples:**
-- Finding cancer clusters and claiming environmental causes (without accounting for random clustering)
-- Data mining until finding significant correlations
-
-**Why fallacious:** Patterns in random data are inevitable; finding them doesn't prove causation.
-
-### 24. Base Rate Fallacy
-**Description:** Ignoring prior probability when evaluating evidence.
-
-**Example:**
-- Disease affects 0.1% of population; test is 99% accurate
-- Positive test ≠ 99% probability of disease
-- Actually ~9% probability (due to false positives exceeding true positives)
-
-**Solution:** Use Bayesian reasoning; consider base rates.
-
-### 25. Prosecutor's Fallacy
-**Description:** Confusing P(Evidence|Innocent) with P(Innocent|Evidence).
-
-**Example:**
-- "The probability of this DNA match occurring by chance is 1 in 1 million, so there's only a 1 in 1 million chance the defendant is innocent."
-
-**Why fallacious:** Ignores base rates and prior probability.
-
-### 26. McNamara Fallacy (Quantitative Fallacy)
-**Description:** Focusing only on what can be easily measured while ignoring important unmeasured factors.
-
-**Example:**
-- Judging school quality only by test scores (ignoring creativity, social skills, ethics)
-- Measuring healthcare only by quantifiable outcomes (ignoring quality of life)
-
-**Quote:** "Not everything that counts can be counted, and not everything that can be counted counts."
-
-### 27. Multiple Comparisons Fallacy
-**Description:** Not accounting for increased false positive rate when testing many hypotheses.
-
-**Example:**
-- Testing 20 hypotheses at p < .05 gives ~65% chance of at least one false positive
-- Claiming jellybean color X causes acne after testing 20 colors
-
-**Solution:** Correct for multiple comparisons (Bonferroni, FDR).
-
-### 28. Reification (Hypostatization)
-**Description:** Treating abstract concepts as if they were concrete things.
-
-**Examples:**
-- "Evolution wants organisms to survive." (Evolution doesn't "want")
-- "The gene for intelligence" (Intelligence isn't one gene)
-- "Nature selects..." (Nature doesn't consciously select)
-
-**Why problematic:** Can lead to confused thinking about mechanisms.
-
-## Fallacies of Scope and Definition
-
-### 29. No True Scotsman
-**Description:** Retroactively excluding counterexamples by redefining criteria.
-
-**Example:**
-- "No natural remedy has side effects."
-- "But poison ivy is natural and causes reactions."
-- "Well, no *true* natural remedy has side effects."
-
-**Why fallacious:** Moves goalposts to protect claim from falsification.
-
-### 30. Equivocation
-**Description:** Using a word with multiple meanings inconsistently.
-
-**Example:**
-- "Evolution is just a theory. Theories are guesses. So evolution is just a guess."
-- (Conflates colloquial "theory" with scientific "theory")
-
-**Detection:** Check if key terms are used consistently.
-
-### 31. Ambiguity
-**Description:** Using vague language that can be interpreted multiple ways.
-
-**Example:**
-- "Quantum healing" (What does "quantum" mean here?)
-- "Natural" (Animals? Not synthetic? Organic? Common?)
-
-**Why problematic:** Claims become unfalsifiable when terms are undefined.
-
-### 32. Mind Projection Fallacy
-**Description:** Projecting mental constructs onto reality.
-
-**Example:**
-- Assuming categories that exist in language exist in nature
-- "Which chromosome is the gene for X on?" when X is polygenic and partially environmental
-
-**Better:** Recognize human categories may not carve nature at the joints.
-
-## Fallacies Specific to Science
-
-### 33. Galileo Gambit
-**Description:** "They laughed at Galileo, and he was right, so if they're laughing at me, I must be right too."
-
-**Why fallacious:**
-- They laughed at Galileo, and he was right
-- They also laughed at countless crackpots who were wrong
-- Being an outsider doesn't make you right
-
-**Reality:** Revolutionary ideas are usually well-supported by evidence.
-
-### 34. Argument from Ignorance (Ad Ignorantiam)
-**Description:** Assuming something is true because it hasn't been proven false (or vice versa).
-
-**Examples:**
-- "No one has proven homeopathy doesn't work, so it works."
-- "We haven't found evidence of harm, so it must be safe."
-
-**Why fallacious:** Absence of evidence ≠ evidence of absence (though it can be, depending on how hard we've looked).
-
-**Burden of proof:** Falls on the claimant, not the skeptic.
-
-### 35. God of the Gaps
-**Description:** Explaining gaps in knowledge by invoking supernatural or unfalsifiable causes.
-
-**Examples:**
-- "We don't fully understand consciousness, so it must be spiritual."
-- "This complexity couldn't arise naturally, so it must be designed."
-
-**Why problematic:**
-- Fills gaps with non-explanations
-- Discourages genuine investigation
-- History shows gaps get filled by natural explanations
-
-### 36. Nirvana Fallacy (Perfect Solution Fallacy)
-**Description:** Rejecting solutions because they're imperfect.
-
-**Examples:**
-- "Vaccines aren't 100% effective, so they're worthless."
-- "This diet doesn't work for everyone, so it doesn't work."
-
-**Reality:** Most interventions are partial; perfection is rare.
-
-**Better:** Compare to alternatives, not to perfection.
-
-### 37. Special Pleading
-**Description:** Applying standards to others but not to oneself.
-
-**Examples:**
-- "My anecdotes count as evidence, but yours don't."
-- "Mainstream medicine needs RCTs, but my alternative doesn't."
-- "Correlation doesn't imply causation—except when it supports my view."
-
-**Why fallacious:** Evidence standards should apply consistently.
-
-### 38. Unfalsifiability
-**Description:** Formulating claims in ways that cannot be tested or disproven.
-
-**Examples:**
-- "This energy can't be detected by any instrument."
-- "It works, but only if you truly believe."
-- "Failures prove the conspiracy is even deeper."
-
-**Why problematic:** Unfalsifiable claims aren't scientific; they can't be tested.
-
-**Good science:** Makes specific, testable predictions.
-
-### 39. Affirming the Consequent
-**Description:** If A, then B. B is true. Therefore, A is true.
-
-**Example:**
-- "If the drug works, symptoms improve. Symptoms improved. Therefore, the drug worked."
-- (Could be placebo, natural history, regression to mean)
-
-**Why fallacious:** Other causes could produce the same outcome.
-
-**Valid form:** Modus ponens: If A, then B. A is true. Therefore, B is true.
-
-### 40. Denying the Antecedent
-**Description:** If A, then B. A is false. Therefore, B is false.
-
-**Example:**
-- "If you have fever, you have infection. You don't have fever. Therefore, you don't have infection."
-
-**Why fallacious:** B can be true even when A is false.
-
-## Avoiding Logical Fallacies
-
-### Practical Steps
-
-1. **Identify the claim** - What exactly is being argued?
-
-2. **Identify the evidence** - What supports the claim?
-
-3. **Check the logic** - Does the evidence actually support the claim?
-
-4. **Look for hidden assumptions** - What unstated beliefs does the argument rely on?
-
-5. **Consider alternatives** - What other explanations fit the evidence?
-
-6. **Check for emotional manipulation** - Is the argument relying on feelings rather than facts?
-
-7. **Evaluate the source** - Are there conflicts of interest? Is this within their expertise?
-
-8. **Look for balance** - Are counterarguments addressed fairly?
-
-9. **Assess the evidence** - Is it anecdotal, observational, or experimental? How strong?
-
-10. **Be charitable** - Interpret arguments in their strongest form (steel man, not straw man).
-
-### Questions to Ask
-
-- Is the conclusion supported by the premises?
-- Are there unstated assumptions?
-- Is the evidence relevant to the conclusion?
-- Are counterarguments acknowledged?
-- Could alternative explanations account for the evidence?
-- Is the reasoning consistent?
-- Are terms defined clearly?
-- Is evidence being cherry-picked?
-- Are emotions being manipulated?
-- Would this reasoning apply consistently to other cases?
-
-### Common Patterns
-
-**Good Arguments:**
-- Clearly defined terms
-- Relevant, sufficient evidence
-- Valid logical structure
-- Acknowledges limitations and alternatives
-- Proportional conclusions
-- Transparent about uncertainty
-- Applies consistent standards
-
-**Poor Arguments:**
-- Vague or shifting definitions
-- Irrelevant or insufficient evidence
-- Logical leaps
-- Ignores counterevidence
-- Overclaimed conclusions
-- False certainty
-- Double standards
-
-## Remember
-
-- **Fallacious reasoning doesn't mean the conclusion is false** - just that this argument doesn't support it.
-- **Identifying fallacies isn't about winning** - it's about better understanding reality.
-- **We all commit fallacies** - recognizing them in ourselves is as important as in others.
-- **Charity principle** - Interpret arguments generously; don't assume bad faith.
-- **Focus on claims, not people** - Ad hominem goes both ways.

package/skills/scientific-critical-thinking/references/scientific_method.md

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-# Scientific Method Core Principles
-
-## Fundamental Principles
-
-### 1. Empiricism
-- Knowledge derives from observable, measurable evidence
-- Claims must be testable through observation or experiment
-- Subjective experience alone is insufficient for scientific conclusions
-
-### 2. Falsifiability (Popper's Criterion)
-- A hypothesis must be capable of being proven false
-- Unfalsifiable claims are not scientific (e.g., "invisible, undetectable forces")
-- Good hypotheses make specific, testable predictions
-
-### 3. Reproducibility
-- Results must be replicable by independent researchers
-- Methods must be described with sufficient detail for replication
-- Single studies are rarely definitive; replication strengthens confidence
-
-### 4. Parsimony (Occam's Razor)
-- Prefer simpler explanations over complex ones when both fit the data
-- Don't multiply entities unnecessarily
-- Extraordinary claims require extraordinary evidence
-
-### 5. Systematic Observation
-- Use standardized, rigorous methods
-- Control for confounding variables
-- Minimize observer bias through blinding and protocols
-
-## The Scientific Process
-
-### 1. Question Formation
-- Identify a specific, answerable question
-- Ensure the question is within the scope of scientific inquiry
-- Consider whether current methods can address the question
-
-### 2. Literature Review
-- Survey existing knowledge
-- Identify gaps and contradictions
-- Build on previous work rather than reinventing
-
-### 3. Hypothesis Development
-- State a clear, testable prediction
-- Define variables operationally
-- Specify the expected relationship between variables
-
-### 4. Experimental Design
-- Choose appropriate methodology
-- Identify independent and dependent variables
-- Control confounding variables
-- Select appropriate sample size and population
-- Plan statistical analyses in advance
-
-### 5. Data Collection
-- Follow protocols consistently
-- Record all observations, including unexpected results
-- Maintain detailed lab notebooks or data logs
-- Use validated measurement instruments
-
-### 6. Analysis
-- Apply appropriate statistical methods
-- Test assumptions of statistical tests
-- Consider effect size, not just significance
-- Look for alternative explanations
-
-### 7. Interpretation
-- Distinguish between correlation and causation
-- Acknowledge limitations
-- Consider alternative interpretations
-- Avoid overgeneralizing beyond the data
-
-### 8. Communication
-- Report methods transparently
-- Include negative results
-- Acknowledge conflicts of interest
-- Make data and code available when possible
-
-## Critical Evaluation Criteria
-
-### When Reviewing Scientific Work, Ask:
-
-**Validity Questions:**
-- Does the study measure what it claims to measure?
-- Are the methods appropriate for the research question?
-- Were controls adequate?
-- Could confounding variables explain the results?
-
-**Reliability Questions:**
-- Are measurements consistent?
-- Would the study produce similar results if repeated?
-- Are inter-rater reliability and measurement precision reported?
-
-**Generalizability Questions:**
-- Is the sample representative of the target population?
-- Are the conditions realistic or artificial?
-- Do the results apply beyond the specific context?
-
-**Statistical Questions:**
-- Is the sample size adequate for the analysis?
-- Are the statistical tests appropriate?
-- Are effect sizes reported alongside p-values?
-- Were multiple comparisons corrected?
-
-**Logical Questions:**
-- Do the conclusions follow from the data?
-- Are alternative explanations considered?
-- Are causal claims supported by the study design?
-- Are limitations acknowledged?
-
-## Red Flags in Scientific Claims
-
-1. **Cherry-picking data** - Highlighting only supporting evidence
-2. **Moving goalposts** - Changing predictions after seeing results
-3. **Ad hoc hypotheses** - Adding explanations to rescue a failed prediction
-4. **Appeal to authority** - "Expert X says" without evidence
-5. **Anecdotal evidence** - Relying on personal stories over systematic data
-6. **Correlation implies causation** - Confusing association with causality
-7. **Post hoc rationalization** - Explaining results after the fact without prediction
-8. **Ignoring base rates** - Not considering prior probability
-9. **Confirmation bias** - Seeking only evidence that supports beliefs
-10. **Publication bias** - Only positive results get published
-
-## Standards for Causal Inference
-
-### Bradford Hill Criteria (adapted)
-1. **Strength** - Strong associations are more likely causal
-2. **Consistency** - Repeated observations by different researchers
-3. **Specificity** - Specific outcomes from specific causes
-4. **Temporality** - Cause precedes effect (essential)
-5. **Biological gradient** - Dose-response relationship
-6. **Plausibility** - Coherent with existing knowledge
-7. **Coherence** - Consistent with other evidence
-8. **Experiment** - Experimental evidence supports causation
-9. **Analogy** - Similar cause-effect relationships exist
-
-### Establishing Causation Requires:
-- Temporal precedence (cause before effect)
-- Covariation (cause and effect correlate)
-- Elimination of alternative explanations
-- Ideally: experimental manipulation showing cause produces effect
-
-## Peer Review and Scientific Consensus
-
-### Understanding Peer Review
-- Filters obvious errors but isn't perfect
-- Reviewers can miss problems or have biases
-- Published ≠ proven; it means "passed initial scrutiny"
-- Retraction mechanisms exist for flawed papers
-
-### Scientific Consensus
-- Emerges from convergence of multiple independent lines of evidence
-- Consensus can change with new evidence
-- Individual studies rarely overturn consensus
-- Consider the weight of evidence, not individual papers
-
-## Open Science Principles
-
-### Transparency Practices
-- Preregistration of hypotheses and methods
-- Open data sharing
-- Open-source code
-- Preprints for rapid dissemination
-- Registered reports (peer review before data collection)
-
-### Why Transparency Matters
-- Reduces publication bias
-- Enables verification
-- Prevents p-hacking and HARKing (Hypothesizing After Results are Known)
-- Accelerates scientific progress