Anthropic Awareness

The Human Aspects of Scientific Thinking in NMR Spectroscopy and Mass Spectrometry
 
 
Elsevier (Verlag)
  • 1. Auflage
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  • erschienen am 25. Juni 2015
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  • 464 Seiten
 
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978-0-12-419979-8 (ISBN)
 

Anthropic Awareness: The Human Aspects of Scientific Thinking in NMR Spectroscopy and Mass Spectrometry blends psychology, philosophy, physics, mathematics, and chemistry, describing a human-centered philosophy of the essence of scientific thinking in the natural sciences and in everyday life.

It addresses the reasons why we are prone to make errors in our conclusions and how to avoid such mistakes, also exploring a number of the 'mental traps' that can lead to both individual mistakes and mass misconceptions.

The book advocates that by understanding the nature of these mental traps we can adopt tactics to safely evade them. It includes Illustrative examples of common scientific misunderstandings and mental traps in both the theory and real-life application of NMR spectroscopy and mass spectrometry.


  • Provides strategies on how to deal with molecular challenges and instrument limitations
  • Presents multiple applications of small molecule structure elucidation using NMR, MS, IR, and UV
  • Explores critical topics, including anthropic awareness (AA), NMR Spectroscopy, mass spectrometry, scientific thinking, and more
  • Includes tactics on how to Improve quality control and data interpretation skills while minimizing data analysis time and increasing confidence in results
  • Presents coverage on tactics to optimize experimental NMR parameters and enhance NMR vocabulary


Csaba Szántay, Jr. was born in Budapest, Hungary, but partly attended elementary school in Bufffalo, NY, USA. He obtained an MSc degree in organic chemistry from the Budapest University of Technology and Economics in 1982 with his final thesis involving the methodology and use of NMR spectroscopy. Subsequently, he became a PhD research fellow in Prof. Gábor Tóth's NMR laboratory at the Department of Analytical Chemistry, Budapest University of Technology and Economics, and obtained his PhD in 1986 in NMR. After that, he worked as a postdoctoral fellow in the NMR laboratory of the University of Leeds, UK. Having returned to Hungary in 1989, he became a member of the NMR team of the Spectroscopic Research Division of the Hungarian pharmaceutical company Gedeon Richter Plc. He was promoted as head of the Division in 1994 and has been in this position since then. He has also maintained a teaching position at the Budapest University of Technology and Economics. He received a 'Candidatura" degree in 1991 and a 'Doctor of Sciences" degree in 2000 from the Hungarian Academy of Sciences for his work in NMR spectroscopy. In 2003, he was became a Private Professor at the Budapest University of Technology and Economics. Besides holding several positions in various scientific committees, he is on the Editorial Board of the journal Concepts in Magnetic Resonance and is currently the president of the Hungarian NMR Discussion Group of the Hungarian Academy of Sciences. Along with his managerial duties, his main fields of research interests are the structure elucidation of organic molecules and the theoretical aspects of NMR. He is the author/co-author of more than 100 papers published in international scientific journals.
  • Englisch
  • USA
Elsevier Science
  • 24,25 MB
978-0-12-419979-8 (9780124199798)
0124199798 (0124199798)
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  • Front Cover
  • Anthropic Awareness: The Human Aspects of Scientific Thinking in NMR Spectroscopy and Mass Spectrometry
  • Copyright
  • Contents
  • Contributors
  • Preface
  • Editor's Personal Acknowledgments
  • Part I: ``Anthropic Awareness (AA)´´ (Mind your mind!)
  • Chapter 1: The Philosophy of ``Anthropic Awareness´´ in Scientific Thinking
  • 1.1. Introduction
  • 1.2. The Pillars
  • Pillar 1. AA Is a Tool
  • Pillar 2. The Definition of ``Science´´
  • Pillar 3. The Concepts of ``Science´´ and ``Scientific Truth´´
  • Pillar 4. The AA Model of Scientific Thinking
  • Pillar 5. On the Meaning of ``Description´´ and ``Understanding´´
  • Pillar 6. The Triangle of Understanding
  • Pillar 7. The Relationship Between the AA Model of Thinking and the Triangle of Understanding
  • Pillar 8. Language
  • Pillar 9. The Definition of Definition
  • Pillar 10. Scientific Hypotheses, Models, Theories, Laws, Explanations, Metaphors, and Metaphoric Models
  • Pillar 11. Creativity in Science
  • Pillar 12. Scientific Communication
  • Pillar 13. Sound and Unsound Models
  • Pillar 14. The Role of Refutation in Science
  • Pillar 15. The Practical Versus Theoretical Significance of Exposing Delusors
  • Pillar 16. Paradigm Nests
  • Pillar 17. ``Forward´´ and ``Backward´´ Scientific Research
  • Pillar 18. The Meaning of ``New´´ Scientific Result
  • Pillar 19. The Meaning of ``Significant´´ Scientific Result
  • Pillar 20. Reporting Scientific Results
  • Pillar 21. The ``Spideric´´ Nature of a Scientific Problem
  • Pillar 22. AA in the Context of the Literature and Other Initiatives Addressing Cognitive Errors
  • Pillar 23. ``Everyday Thinking´´ Versus ``Scientific Thinking´´
  • Pillar 24. The Trap-Experience
  • Pillar 25. The Dual Nature of Mental Traps
  • Pillar 26. Mental Traps in Relation to Scientific Knowledge and Intellect (``Educated Error´´)
  • Pillar 27. The Relationship and Synergy of Mental Traps
  • Pillar 28. Identifying the Mental Traps
  • Pillar 29. Trap-Blindness and Avoiding Mental Traps
  • Pillar 30. Trap-Consciousness and the ``Sacredness´´ of Science
  • 1.3. Mental Traps (Mind Your Mind!)
  • Interlude
  • Mental Trap (Master Trap) #1. We Seek Mental Security (the ``Enjoy-Your-Flight´´ Effect)
  • Mental Trap (Master Trap) #2. We Have An Instinctive Urge to Interpret Data
  • Mental Trap (Master Trap) #3. Belief Dominates Over Reason
  • Mental Trap #4. The Initial Belief Syndrome
  • Mental Trap #5. We Accept Anecdotal Evidence
  • Mental Trap #6. We Tend to Trust Authority Without Question (Might is Right)
  • Mental Trap #7. We Go With the Crowd (Herd Instinct)
  • Mental Trap #8. We Accept Knowledge Based on Tradition
  • Mental Trap #9. We Think Inside Our Paradigm Nests
  • Mental Trap #10. We Accept Intuitively Appealing Explanations
  • Mental Trap #11. We Confuse Mathematical Descriptions with a Physical Understanding
  • Mental Trap #12. We Project the Absolute Truths of Mathematics onto Physics
  • Mental Trap #13. ReflectiveVersus Reflexive ``Physicalization´´ of Abstract Mathematical Entities
  • Mental Trap #14. We Confuse Familiarity with Understanding
  • Interlude
  • Mental Trap #15. The Twin Devils of Detail and Entirety
  • Mental Trap #16. Our Mind Loves Metaphors
  • Mental Trap #17. We Are Inclined to Use Superficial Analogies
  • Interlude
  • Mental Trap #18. We Confuse the Model with Reality
  • Mental Trap #19. We Attribute Too Broad a Range of Application to a Model
  • Mental Trap #20. We Confuse a Models Inherent Limitations with Its Flaws
  • Mental Trap #21. The Dont-Look-Any-Further Effect (Confusing Consistency with Correctness)
  • Mental Trap #22. We Rejoice Before Finding the Full Solution
  • Mental Trap #23. Hypothesis Obsession (The Lock-On, Lock-Out Effect)
  • Mental Trap #24. We Seek Novelty-Promising Solutions (The ``Anti-Occam´´ Trap)
  • Mental Trap #25. We Confuse Experimental Evidence with Interpretational Evidence
  • Mental Trap #26. We Confuse Cause and Effect
  • Mental Trap #27. We See Illusory Correlations Between Unrelated Data
  • Mental Trap #28. We Resist Change
  • Mental Trap #29. We Seek to Confirm
  • Interlude
  • Mental Trap #30. Our Mental Perception Is Preferentially Black-and-White
  • Mental Trap #31. We Petrify Assumptions
  • Mental Trap #32. We Objectify Subjective Claims
  • Mental Trap #33. We Disambiguate Our Conclusions
  • Mental Trap #34. We Ignore the Path Leading to a Conclusion
  • Mental Trap #35. We Are Spellbound by Numbers, Graphs, and Mathematical and Chemical Formulas
  • Interlude
  • Mental Trap #36. Affect/Emotycal Heuristic
  • Interlude
  • Mental Trap #37. We Overplay the Meaning of Scientific Truth
  • Mental Trap #38. We Confuse Deductive and Inductive Statements
  • Mental Trap #39. We Love to Generalize (Hasty Induction)
  • Mental Trap #40. We Prefer Quantity Over Quality
  • Mental Trap #41. Semantic Space
  • Mental Trap #42. The Halo Effect
  • Mental Trap #43. Warped Team Dynamics
  • Mental Trap #44. The Prepublication Illusion of Knowledge
  • Mental Trap #45. The Mental Trap of Becoming Obsessed with Mental Traps
  • 1.4. Summary
  • Acknowledgments
  • References
  • Part II: AA in why-science: Examples from NMR theory (if you think you know NMR, think again...)
  • Chapter 2: An ``Anthropically´´ Flavored Look at Some Basic Aspects of NMR Spin Physics Using a Classical Description
  • 2.1. Introduction
  • 2.2. Introductory Thoughts on the Characteristics of NMR Theory
  • 2.3. Classical Portrayal of an Individual Spin
  • 2.4. Classical Portrayal of the Macroscopic Magnetization
  • 2.5. Preliminary Comments on the Quantum-Mechanical Description of Magnetic Resonance
  • 2.6. Summary
  • Acknowledgments
  • References
  • Chapter 3: The Ups and Downs of Classical and Quantum Formulations of Magnetic Resonance
  • 3.1. Introduction
  • 3.2. Quantum Mechanics in General
  • 3.3. Misconceptions in NMR Introductions
  • 3.4. Where Did It Go Wrong?
  • 3.5. A Limited Introduction to Classical and Quantum Mechanics
  • 3.6. Indeterminism vs. Uncertainty and the Role of Measurement
  • 3.7. The Role of Eigenstates in Single-Particle Measurements
  • 3.8. Entanglement
  • 3.9. Superpositions
  • 3.10. The Missing Role of Eigenstates in Ensemble Measurements
  • 3.11. The Role of Eigenstates in Mathematical Descriptions
  • 3.12. Visualization of Spin Distributions
  • 3.13. Thermal Equilibrium
  • 3.14. Classical Eigenstates, Resonance, and Couplings
  • 3.15. The Eigenmode Structure for Nuclear Excitation
  • 3.16. J-coupling
  • 3.17. The Aftermath
  • Acknowledgments
  • References
  • Chapter 4: The RF Pulse and the Uncertainty Principle
  • 4.1. Introduction
  • 4.2. Nomenclature
  • 4.2.1. General notation
  • 4.2.2. Trigonometric and Phasor Frequencies
  • 4.2.3. FT-Contextualized Function Notation in the Time and Frequency Dimensions
  • 4.3. ``Enhanced´´ Fourier transform equations
  • 4.3.1. Eulers identities
  • 4.3.2. Interrelationships in temporal and spectral representations
  • 4.3.3. The Fourier Transform
  • 4.4. Uncertainty Principle(s)
  • 4.4.1. HUP vs. FUP
  • 4.4.2. The Principle of ``Conjugate Physical Equivalence´´
  • 4.4.3. Back to NMR
  • 4.5. Summary
  • Acknowledgment
  • References
  • Chapter 5: On the Nature of the RF Driving Field in NMR (with a Lookout on Optical Rotation)
  • 5.1. Introduction
  • 5.2. Analysis of the ``Decompositional Argument´´ for the NMR RF Field
  • 5.3. Analysis of the ``Decompositional Argument´´ for Optical Rotation
  • 5.4. Summary
  • Acknowledgments
  • References
  • Part III: AA in What-Science: Small-Molecule Structure Elucidation by NMR and MS (Are You Sure You Have Found The Correct ...
  • Chapter 6: An ``Anthropic´´ Modus Operandi of Structure Elucidation by NMR and MS
  • 6.1. Introduction
  • 6.2. An ``Anthropic´´ Look at Structure Elucidation
  • 6.2.1. What (By the Way) Do We Mean By ``Structure´´ and ``Elucidation´´?
  • 6.2.2. The ``Psychology´´ of Structure Elucidation
  • 6.3. ``Anthropic´´ Structure Elucidation in Practice
  • 6.3.1. Centralized Structure Elucidation Service
  • 6.3.2. Full-Time Spectroscopists
  • 6.3.3. Holistic Use of NMR and MS
  • 6.3.4. High-End Spectrometers
  • 6.3.5. Commitment to Scientific Publishing
  • 6.4. Summary
  • Acknowledgments
  • References
  • Chapter 7: NMR Methodological Overview
  • 7.1. Introduction
  • 7.2. One-Dimensional (1D) NMR Measurements
  • 7.2.1. 1D 1H NMR Spectrum
  • 7.2.2. Selective 1D NOESY (ROESY) Spectrum
  • 7.2.3. Selective 1D TOCSY Spectrum
  • 7.2.4. 1D 13C NMR Spectrum
  • 7.3. Two-Dimensional (2D) Methods
  • 7.3.1. COSY
  • 7.3.2. 2D TOCSY
  • 7.3.3. 2D NOESY
  • 7.3.4. 1H,13C-HSQC
  • 7.3.5. HSQC-TOCSY
  • 7.3.6. 1H,13C-HMBC
  • 7.3.7. 1H,15N-HSQC and 1H,15N-HMBC
  • 7.4. An NMR-Based Strategy for the Structure Elucidation of Small Molecules
  • 7.5. Diffusion-Ordered Spectroscopy (DOSY)
  • 7.6. Summary
  • Acknowledgments
  • References
  • Chapter 8: MS Methodological Overview
  • 8.1. Introduction
  • 8.2. MS Basics
  • 8.3. The Evolution of MS Instrumentation in Structure Elucidation
  • 8.3.1. Ionization Methods
  • 8.3.2. Analyzers
  • 8.3.3. Figures of Merit of Mass Spectrometers
  • 8.4. Principles and Pitfalls of Mass Spectrum Interpretation
  • 8.4.1. Interpretation of Mass Spectra
  • 8.4.2. The Role of Databases and Software in Mass Spectrum Interpretation
  • 8.5. MS-Based Structure Investigation Approaches Applied for Small Molecules
  • 8.5.1. Complementary MS-Based de novo Structure Elucidation and Structure Verification
  • 8.5.2. MS-Based Structure Elucidation of Minor Unknown Product-Related Impurities and Metabolites
  • 8.5.3. MS-Based Structure Identification/Elucidation of Minor Unknown Compounds
  • 8.6. Conclusions
  • Acknowledgments
  • References
  • Chapter 9: Computer-Assisted Structure Elucidation in NMR
  • 9.1. Introduction
  • 9.2. Introduction to CASE Systems
  • 9.3. Structure Elucidation Strategy Used by CASE Software
  • 9.4. Motivation for Developing CASE Systems
  • 9.5. Examples
  • 9.5.1. Evaluation of Structure Elucidator
  • 9.5.2. Example 1. Size of the Molecule
  • 9.5.3. Example 2. Structure Elucidation of a Cation
  • 9.5.4. Example 3. Handling Symmetrical Molecules
  • 9.5.5. Example 4. Where Not the ``Best´´ Structural Proposition Is the Chemically Reasonable One
  • 9.5.6. Example 5. The Power of a CASE System
  • 9.5.7. Example 6. Consolidation of a Vague Structural Proposition, Trap #45 in Action
  • 9.5.8. Example 7. Master Trap #3 in Action: A Simple Problem Where a False Assumption Prolongs the Structure Elucidation P ...
  • 9.5.9. Example 8: Structure Elucidation of a Natural Product (Traps #4 and #31)
  • 9.5.10. Example 9: ``Replication´´ of a Degradation Product of Amlodipine (Traps #8 and #32 in Action)
  • 9.5.11. Example 10: Using CASE in Straightforward Cases (Traps #8, #9, and #21)
  • 9.6. Conclusions
  • Acknowledgments
  • References
  • Chapter 10: Structure Elucidation of a Mysterious Trace Component of Ulipristal Acetate
  • 10.1. Introduction
  • 10.2. The Winding Road to Identifying d-ULIPA
  • 10.2.1. About Impurity Profiling in General
  • 10.2.2. Detection and the Chromatographic Behavior of X
  • 10.2.3. High-Resolution HPLC-MS Analysis
  • 10.2.4. Enrichment of X and Spectroscopic Analysis of the Enriched Sample
  • 10.2.5. Flying Out of the Paradigm Nest
  • 10.2.6. Reanalysis of the Analytical Data in Terms of the D-ULIPA Hypothesis
  • 10.2.7. Proof of the D-ULIPA Hypothesis
  • 10.3. Conclusions
  • Acknowledgments
  • References
  • Chapter 11: The Adventurous Discovery of the Structure of a Novel Vincristine Impurity
  • 11.1. Introduction
  • 11.2. Structure Elucidation of a Novel Vincristine Impurity
  • 11.3. Conclusions
  • Acknowledgments
  • References
  • Chapter 12: An Elusive Degradation Product of Ziprasidone
  • 12.1. Introduction
  • 12.2. The Path Toward the Structural Hypotheses
  • 12.3. The Hunt for That Elusive 13C NMR Line
  • 12.4. Acidic Decomposition as an Additional Proof of the Proposed Structure
  • 12.5. Conclusions
  • Acknowledgments
  • References
  • Chapter 13: The Case of an Emotion- and Emotycs-Laden Structure Determination of a Small Synthetic Molecule with an Unexp ...
  • 13.1. Introduction
  • 13.2. Our Surprising Encounter with Compound 13.1
  • Analyst Talking to Chemist
  • Chemist Talking to Technician
  • Chemist Talking to Analyst
  • Analyst 1 Talking to Analyst 2
  • 13.3. Conclusions
  • Acknowledgments
  • Chapter 14: Self-Induced Recognition of Enantiomers (SIRE) in NMR Spectroscopy
  • 14.1. Introduction
  • 14.2. A Puzzling Structural Problem
  • 14.3. Understanding SIRE
  • Condition 1: Pure Enantiomer with No Analyte-Analyte Interaction
  • Condition 2: Racemic Mixture with No Analyte-Analyte Interaction
  • Condition 3: Nonracemic Mixture with No Analyte-Analyte Interaction
  • Condition 4: Pure Enantiomer with Weak Analyte-Analyte Interaction
  • Condition 5: Racemic Mixture with Weak Analyte-Analyte Interaction
  • Condition 6: Nonracemic Mixture with Weak Analyte-Analyte Interaction
  • 14.4. Conclusions
  • Acknowledgments
  • References
  • Chapter 15: Believe It or Not: Carbon Protonation of the Pyrimidine Ring
  • 15.1. Introduction
  • 15.2. The Chemical Background and a False Structural Hypothesis
  • 15.3. Stage 1: A Hunch
  • 15.4. Stage 2: Molecular and Spectral Symmetry
  • 15.5. Stage 3: Believe It or Not: Carbon Protonation
  • 15.6. Stage 4: The ``Geminal´´ Structure
  • 15.7. Stage 5: Assignment of the E and Z Isomer
  • 15.8. Stage 6: Rationalization of the Carbon-Protonated Pyrimidine Structure
  • 15.9. Aftermath
  • 15.10. Conclusions and Summary
  • Acknowledgments
  • References
  • Epilogue
  • Index
Chapter 1

The Philosophy of "Anthropic Awareness" in Scientific Thinking


Csaba Szántay, Jr.    Gedeon Richter Plc, Spectroscopic Research Division, Budapest, Hungary

Abstract


This chapter discusses the philosophical background of the remainder of the book. It outlines a way of thinking called "Anthropic Awareness" that focuses on developing a keen mindfulness of how our human nature influences our thoughts in and about science, and on how this influence can secretly lead us into various "Mental Traps." The chapter comprises of two main parts: Firstly, it discusses 30 "Pillars," each of which addresses a different aspect of science and the Mental Traps from an "anthropic" point of view. The Pillars include such topics as what we mean by scientific truth, the role of emotions in scientific thinking, the assessment of scientific models, metaphors in science, paradigms, and "everyday thinking" versus "scientific thinking." Secondly, it outlines 45 Mental Traps that are the most relevant in understanding scientific descriptions and in conducting scientific research. These Mental Traps are an intrinsic feature of how we think both in science and in our everyday lives, and only by becoming conscious of them can we properly avoid them.

Keywords

Scientific truth

Human factor

Mental traps

Avoiding error

Philosophy

Psychology

Scientific theory

Model

Law

Outline

1.1 Introduction   5

1.2 The Pillars   8

Pillar 1. AA Is a Tool   9

Pillar 2. The Definition of "Science"   9

Pillar 3. The Concepts of "Science" and "Scientific Truth"   9

Pillar 4. The AA Model of Scientific Thinking   16

Pillar 5. On the Meaning of "Description" and "Understanding"   26

Pillar 6. The Triangle of Understanding   27

Pillar 7. The Relationship Between the AA Model of Thinking and the Triangle of Understanding   31

Pillar 8. Language   31

Pillar 9. The Definition of Definition   32

Pillar 10. Scientific Hypotheses, Models, Theories, Laws, Explanations, Metaphors, and Metaphoric Models   32

Pillar 11. Creativity in Science   37

Pillar 12. Scientific Communication   38

Pillar 13. Sound and Unsound Models   38

Pillar 14. The Role of Refutation in Science   41

Pillar 15. The Practical Versus Theoretical Significance of Exposing Delusors   42

Pillar 16. Paradigm Nests   42

Pillar 17. "Forward" and "Backward" Scientific Research   44

Pillar 18. The Meaning of "New" Scientific Result   45

Pillar 19. The Meaning of "Significant" Scientific Result   47

Pillar 20. Reporting Scientific Results   48

Pillar 21. The "Spideric" Nature of a Scientific Problem   48

Pillar 22. AA in the Context of the Literature and Other Initiatives Addressing Cognitive Errors   49

Pillar 23. "Everyday Thinking" Versus "Scientific Thinking"   51

Pillar 24. The Trap-Experience   52

Pillar 25. The Dual Nature of Mental Traps   52

Pillar 26. Mental Traps in Relation to Scientific Knowledge and Intellect ("Educated Error")   52

Pillar 27. The Relationship and Synergy of Mental Traps   53

Pillar 28. Identifying the Mental Traps   54

Pillar 29. Trap-Blindness and Avoiding Mental Traps   54

Pillar 30. Trap-Consciousness and the "Sacredness" of Science   54

1.3 Mental Traps (Mind Your Mind!)   55

Interlude   55

Mental Trap (Master Trap) #1. We Seek Mental Security (the "Enjoy-Your-Flight" Effect)   55

Mental Trap (Master Trap) #2. We Have An Instinctive Urge to Interpret Data   57

Mental Trap (Master Trap) #3. Belief Dominates Over Reason   57

Mental Trap #4. The Initial Belief Syndrome   59

Mental Trap #5. We Accept Anecdotal Evidence   59

Mental Trap #6. We Tend to Trust Authority Without Question (Might is Right)   60

Mental Trap #7. We Go With the Crowd (Herd Instinct)   60

Mental Trap #8. We Accept Knowledge Based on Tradition   61

Mental Trap #9. We Think Inside Our Paradigm Nests   61

Mental Trap #10. We Accept Intuitively Appealing Explanations   62

Mental Trap #11. We Confuse Mathematical Descriptions with a Physical Understanding   62

Mental Trap #12. We Project the Absolute Truths of Mathematics Onto Physics   63

Mental Trap #13. Reflective Versus Reflexive "Physicalization" of Abstract Mathematical Entities   63

Mental Trap #14. We Confuse Familiarity with Understanding   65

Interlude   66

Mental Trap #15. The Twin Devils of Detail and Entirety   67

Mental Trap #16. Our Mind Loves Metaphors   68

Mental Trap #17. We Are Inclined to Use Superficial Analogies   69

Interlude   69

Mental Trap #18. We Confuse the Model with Reality   69

Mental Trap #19. We Attribute Too Broad a Range of Application to a Model   70

Mental Trap #20. We Confuse a Model's Inherent Limitations with Its Flaws   71

Mental Trap #21. The Don't-Look-Any-Further Effect (Confusing Consistency with Correctness)   71

Mental Trap #22. We Rejoice Before Finding the Full Solution   72

Mental Trap #23. Hypothesis Obsession (The Lock-On, Lock-Out Effect)...

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