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11.1 Pathological Science: Difference between revisions

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== Useful Links ==
== The Lesson in Context ==


* [[:File:Pathological Science Case Studies.pdf|Pathological Science Case Studies Handout]]
<!-- Always begin section with a description of this lesson in relation to the course as a whole. -->
** [[:File:Arsenic Bacterium.pdf|Article A (Arsenic Bacterium)]]
[Introduction to the lesson.]
** [[:File:Water Memory.pdf|Article B (Water Memory)]]
** [[:File:Superluminal Neutrinos.pdf|Article C (Superluminal Neutrinos)]]
* [https://docs.google.com/document/d/1Ajs_NJ0Y4Uunsz9eVNTqyyFo13jJLjLXKauzbBixYuU/edit?usp=sharing Three Column Overview of the Week]
* [https://docs.google.com/presentation/d/1CgRwwPNdaDf7wYtcMSQ6OhD9O56eHrE5Q0buh76DSGw/edit?usp=drivesdk Lesson Slides (2023 Master)]
* [https://sensesensibilityscience.berkeley.edu/topic/18 Website Page]


=== Readings and Assignments ===
<!-- Expandable section relating this lesson to earlier lessons. -->
{{Expand|Relation to Earlier Lessons|
{{ContextLesson|[Lesson Name]}}
{{ContextRelation|[Relation to current lesson.]}}
{{ContextLesson|[Lesson Name]}}
{{ContextRelation|[Relation to current lesson.]}}
}}
<!-- Expandable section relating this lesson to later lessons. -->
{{Expand|Relation to Later Lessons|
{{ContextLesson|[Lesson Name]}}
{{ContextRelation|[Relation to current lesson.]}}
{{ContextLesson|[Lesson Name]}}
{{ContextRelation|[Relation to current lesson.]}}
}}


* [[:File:Pathological Science - Langmuir.pdf|Pathological Science]]
== Takeaways ==
* [[:File:Cargo Cult Science - Feynman.pdf|Cargo Cult Science]]


==== Lecture Video ====
<tabber>


<youtube>https://youtu.be/oaxHKHpwlxw</youtube>
|-|Learning Goals=
 
== Learning Goals ==


After this lesson, students should
After this lesson, students should
<!-- Learning goals are written as a numbered list. -->
# Be able to distinguish roughly among the following:
# Be able to distinguish roughly among the following:
## Good science that gets the wrong answer.
## Good science that gets the wrong answer.
Line 36: Line 42:
# Be able to identify what is wrong in cases of fraudulent, pathological, poorly-done, and pseudo-science.
# Be able to identify what is wrong in cases of fraudulent, pathological, poorly-done, and pseudo-science.


=== Definitions ===
|-|Definitions=


* Spectrum of poor research:
<!-- Definitions must be written with the Definition and Subdefinition templates. The first Definition should have the "first=yes" flag at the end. -->
** '''Good science (that gets the wrong answer)'''
{{Definition|Spectrum of Poor Research|There are many gradations to poor research and poor results. Several approximate categories are listed below.|first=yes}}
**: Even with a confidence level of 95%, 5% of the time the results will be wrong. This is normal.
{{Subdefinition|Good Science|This includes good well-done science that gets the wrong result. Even with a confidence interval of 95%, 5% of the time the results will be wrong. This is normal.}}
** '''Poorly-done Science'''
{{Subdefinition|Poorly-done Science|Science done honestly, but not done well.}}
**: Science done honestly, but not done well.
{{Subdefinition|Pathological Science|This is what happens when a researcher falls a little too "in love" with their ideas. It is indicated by Langmuir's criteria.}}
** '''Pathological Science'''
{{Subdefinition|Pseudo-science|Pseudo-science is characterized by using scientific vocabulary without aligning with the corresponding concepts or engaging in real scientific practices (i.e.,  science being "skin deep," not scientific below the surface).}}
**: Indicated by Langmuir's criteria.
{{Subdefinition|Fraudulent Science|Research that involves intentional deception, such as deliberately fabricating data or deliberately deceiving the reader about the strength of evidence.}}
** '''Pseudo-science'''
{{Definition|Langmuir's Pathological Science Indicators|A set of seven indicators that can be used to flag when something might be pathological science.
**: Pseudo-science is characterized by using scientific vocabulary without aligning with the corresponding concepts or engaging in real scientific practices (i.e.,  science being "skin deep," not scientific below the surface).
:# The effect is produced by a barely detectable cause, and the magnitude of the effect is substantially independent of the intensity of the cause.  
** '''Fraudulent Science'''
:# The effect is barely detectable, or has very low statistical significance. Claims of great accuracy.
**: Research that involves intentional deception, such as deliberately fabricating data or deliberately deceiving the reader about the strength of evidence.
:# Claims of great accuracy.
* '''Langmuir's Pathological Science Indicators'''
:# Involving fantastic theories contrary to experience.  
*# The effect is produced by a barely detectable cause, and the magnitude of the effect is substantially independent of the intensity of the cause.  
:# Criticisms are met with ad hoc excuses.  
*# The effect is barely detectable, or has very low statistical significance. Claims of great accuracy.
:# Ratio of supporters to critics rises to near 50%, then drops back to near zero.   
*# Claims of great accuracy.
:# Conclusion-motivated design & analysis.}}
*# Involving fantastic theories contrary to experience.  
{{BoxCaution|There is no set number of Langmuir's criteria that determines whether something is pathological science or not. The criteria serve as a useful guide, but detecting pathological science is ultimately something of an art.}}
*# Criticisms are met with ad hoc excuses.  
{{Subdefinition|[Term]|[Explanation]}}
*# Ratio of supporters to critics rises to near 50%, then drops back to near zero.   
<br />
*# Conclusion-motivated design & analysis.


=== Examples ===
|-|Examples=


{{Todo|Fill in some examples.}}
<!-- Example formatting is still experimental. -->
* [item 1]
'''[Example Name]'''
: [Example Description]
{{Line}}
'''[Example Name]'''
: [Example Description]


=== Common Misconceptions ===
|-|Common Misconceptions=


* ''This paper's result could not be replicated by others in the field, therefore the authors have committed pathological science.''
<!-- Misconceptions must be written with the Misconception template. The first Misconception should have the "first=yes" flag at the end. -->
*: There may be a genuine difference in the way the study is conducted between these papers, contributing to a difference in result. The original study may have reached the wrong conclusion from correct analysis simply due to the random noise in the data. The original study may have made an error in their analysis that has not been discovered (e. g. superluminal neutrinos).
{{Misconception|[Description of misconception.]|[Resolution.]|first=yes}}
{{Misconception|[Description of misconception.]|[Resolution.]}}


== Context ==
</tabber>


This lesson teaches students to be cautious of bad science of all kinds and aware of the signs thereof. We ask students to study a few established examples of pathological science in history dressed as science merely in ''form''. The emphasis is on well-intentioned researchers "falling in love" with their own ideas, finding excuses to justify them even when reality has turned out to be contrary to them.
== Useful Resources ==
{{Caution|Although blatant pseudoscience such as flat earth, astrology, creationism, and alternative medicine are also included, what deserves particular caution is seemingly genuine science done by seemingly genuine people that is nevertheless incorrect, possibly due to the researchers' own hubris.}}


=== Before ===
<tabber>


: '''[[1.2 Shared Reality and Modeling]]'''
|-|Lecture Video=
:: Everyone in principle has access to the same shared reality. If a certain (amazing) result by one research group cannot seem to be replicated by many other groups, it is a good sign that it does not accurately describe the shared reality.
: '''[[3.2 Calibration of Credence Levels]]'''
:: Overstating the confidence level of a scientific result is a sign of bad science.
: '''[[4.2 Finding Patterns in Random Noise]]'''
:: It is expected that patterns arise from random noise. Good science can also turn out to be wrong just by chance, but stubbornly sticking with the original result would turn it into bad science.
: '''[[5.2 Scientific Optimism]]'''
:: In the spirit of personal persistence and iterative progress, setbacks such as a wrong or disappointing result should be accepted as an inevitable part of this progress.
: '''[[10.2 Blinding]]'''
:: Though not yet widely employed in all fields of science, various blind analysis techniques can help reduce the possibility that a scientific result may be contaminated by subtle analysis choices made by the researchers that are (often subconsciously) motivated by the desire for a certain anticipated result.


=== After ===
<br /><center><youtube>oaxHKHpwlxw</youtube></center><br />


: '''[[11.2 When Is Science Suspect]]'''
|-|Discussion Slides=
:: Bad science is particularly problematic when it concerns the study of human subgroups, as it may be motivated by or may perpetuate preexisting inequitable power structures in society.


== Recommended Outline ==
{{LinkCard
|url=[address]
|title=Discussion Slides Template
|description=The discussion slides for this lesson.
}}
<br />


=== Before Class ===
|-|Handouts and Activities=


* Each student will have read one of the three articles that we discuss in this section, as well as an article by Langmuir. ([[:File:Arsenic Bacterium.pdf|Article A]], [[:File:Water Memory.pdf|Article B]], [[:File:Superluminal Neutrinos.pdf|Article C]], [[:File:Langmuir.pdf|Langmuir's reading]]) Assign each group to one of the three articles one week ahead of time, and then send another reminder to read them one or two days before the lesson.
{{LinkCard
* Print the handout (linked below).
|url=[address]
* Prepare a seating chart.
|title=[Title]
* Review PlayPosit and discussion questions and ask faculty, Gabriel, or Emlen any questions you have.
|description=[Description.]}}
* (Optional) Prepare a presentation.
{{LinkCard
|url=[address]
|title=[Title]
|description=[Description.]}}
<br />


=== During Class ===
|-|Readings and Assignments=


* (5 min) Come up with some fun way to assign the roles of spokesperson and notetaker (e.g. earliest birthday in the year, lives furthest from campus). Remind them of the responsibilities of these roles.
{{LinkCard
* (15 min) Review definitions.
|url=[address]
*(15 min) Students review assigned articles in small groups
|title=[Title]
*(20 min) Jigsaw groups so each group has two students who read each article present to the others
|description=[Description.]}}
*(20 min) Whole class discussion
{{LinkCard
|url=[address]
|title=[Title]
|description=[Description.]}}
<br />


=== After Class ===
</tabber>


* Collect answers from notetakers for the forum / plenary.
== Recommended Outline ==


== Lesson Content ==
=== Before Class ===


=== Concept Review ===
[Any steps that need to be taken before class.]


(10-15 min) Review the [[#Definitions|definitions]] and differences between different kinds of problematic science practices. Briefly answer clarifying questions from students.
=== During Class ===


=== Article Review ===
{| class="wikitable" style="margin-left: 0px; margin-right: auto;"
|[n] Minutes
|[Activity.]
|-
|[n] Minutes
|[Activity.]
|}


Students are assigned one of three scientific articles to skim through before class and asked to assess the validity of its methodology, with reference to Langmuir's indicators for pathological science. They may follow the [[:File:Pathological Science Case Studies.pdf|given handout]].
== Lesson Content ==


* [[:File:Arsenic Bacterium.pdf|Article A (Arsenic Bacterium)]]
=== Activity 1 ===
* [[:File:Water Memory.pdf|Article B (Water Memory)]]
 
* [[:File:Superluminal Neutrinos.pdf|Article C (Superluminal Neutrinos)]]
[Brief description of and motivation for the activity]
* [[:File:Langmuir.pdf|Langmuir's reading]]
{{BoxCaution|[Common misconception or thing to look out for.]}}
{{BoxWarning|[Thing you really need to look out for!]}}
{{BoxTip|title=[Title]|[Useful tip, guideline, or other background.]}}


==== Instructions ====
==== Instructions ====


# (10-12 min) Review the article in small groups and answer the questions in the handout. The notetaker should be responsible for writing down ideas from the group.
{| class="wikitable" style="margin-left: 0px; margin-right: auto;"
# (20-25 min) Since each group has been assigned one of three articles, we now bring three groups with different articles together. Each group's spokesperson will spend 3-5 min presenting their group's article to the other groups using the questions on the handout as a guide. {{Caution|small=right|If the number of groups is not divisible by 3, the odd ones out may be merged into the other large groups.}}
|[n] Minutes
# The instructor should go from group to group to make sure they are on task, offer assistance, and keep time. Feel free to end this part sooner if students complete their discussion early.
|[Activity.]
# (20-25 min) Discuss as a whole class. For each of the three articles, poll the students on the following questions.
|-
|[n] Minutes
|[Activity.]
|}


==== Discussion Questions ====
==== Discussion Questions ====


# Where would this article fall in the following continuum, and why would you argue this?
[Question 1]
## Good scientific practice, right results
{{BoxCaution|[Possible misconception that may need to be corrected and clarified.]|small=right}}
## Good scientific practice, wrong results
{{BoxAnswer|[Intended answer to the above question.]}}
## Poor scientific practice, right results
{{Line}}
## Poor scientific practice, wrong results
[Question 2]
## Pathological science
{{BoxCaution|[Possible misconception that may need to be corrected and clarified.]|small=right}}
## Pseudo-science
{{BoxAnswer|[Intended answer to the above question.]}}{{NavCard|prev=[Previous Lesson]|next=[Next Lesson]}}
## Fraudulent science
<includeonly>[[Category:Lesson plans]]</includeonly>
# Discuss which of Langmuir's criteria (if any) apply to this article, citing quotes and/or evidence from the article to explain your reasoning:
## The effect is produced by a barely detectable cause, and the magnitude of the effect is substantially independent of the intensity of the cause.
## The effect is barely detectable, or has very low statistical significance.
## Claims of great accuracy.
## Involving fantastic theories contrary to experience.
## Criticisms are met with ad hoc excuses.
## Ratio of supporters to critics rises to near 1:1, then drops back to near zero.
# Where, if relevant, did this study go wrong?
 
==== Suggested Answers ====
 
===== Study A: Arsenic Bacteria =====
 
: '''Summary:''' This paper discussed a novel substitution of arsenic for phosphorus in bacterial DNA, which would have profound implications on requirements for life in any form. They reported the discovery of an unusual microbe that could vary elemental composition of its basic biomolecules by substituting arsenic for phosphorus. Mechanisms for such substitution were unknown. Many criticisms were published as technical comments in ''Science'' and online, such as accusing the original team of failing to "meticulously clean up the DNA first". An Israeli team worked out the mechanism by which the bacterium in question discriminated between nearly identical molecules of phosphate and arsenate. ''Science'' also published an official statement saying some of the findings in the original paper were incorrect in 2012.
 
{{Answer|
: Question 1: d.
: Question 2: a, d, e.
: Question 3: The experiment was not done carefully enough.}}
 
===== Study B: Water Memory =====
 
: '''Summary:'''  This paper provided evidence for the theory that water retains memory of previously dissolved substances, which has been claimed to be a mechanism by which homeopathic remedies work, but runs contradictory to our current understanding of chemistry and physics. However, since the paper had no apparent methodological problems, it was published in ''Nature'' accompanied with an editorial that noted "There are good and particular reasons why prudent people should, for the time being, suspend judgment" and described some of the fundamental laws of chemistry and physics which it would violate, if shown to be true. Additionally, the editor of ''Nature'' demanded that the experiments be re-run under supervision. In the supervised double-blind experiments, no memory effect was observed. ''Nature'' published a follow-up report of these findings, and their editor said: "We believe the laboratory has fostered and then cherished a delusion about the interpretation of its data." and pointed out that two of the researchers were being paid for by a homeopathic company. The PI also published a follow-up letter where he compared his treatment by the ''Nature'' team to "Salem witchhunts or McCarthy-like prosecutions". More drama ensued, and the results of the paper are still used to claim that the experiments "prove" that homeopathy works.
 
{{Answer|
: Question 1: e.
: Question 2: b, d, e, f.
: Question 3: The researchers were very attached to their scientific findings and criticized the supervised experiments.}}
 
===== Study C: Superluminal Neutrinos =====
 
: '''Summary:''' Neutrinos are subatomic particles with extremely small masses, which means that they should move at very nearly (but slightly slower than) the speed of light. In this paper, neutrinos created at CERN were detected at another site in Italy to measure the precise arrival time and distance, and therefore the speed at which neutrinos travel. They found that neutrinos traveled slightly faster than the speed of light with high significance (over 15,000 separate neutrino events). If this is correct, it would overturn a cornerstone of modern physics. The team published their preliminary data to the public to enlist the help of other scientists for searching for an explanation, and doubled down on their efforts to find an explanation for this result. The team's in-depth investigation of their experiment turned up a few errors, which when corrected found that the speed was consistent with the speed of light. Other independent experiments also found that neutrinos traveled at the speed of light, but showed no evidence for faster than the speed of light.
 
{{Answer|
: Question 1: b.
: Question 2: b, d.
: Question 3: Even very carefully done science may inevitably contain errors. The team recognised the implications of the results and openly invited other scientists to critique their procedure, leading to the discovery and correction of the relevant errors.}}
 
{{NavCard|prev=10.2 Blinding|next=11.2 When Is Science Suspect}}
[[Category:Lesson plans]]

Revision as of 09:53, 14 August 2023

How to catch bad science.



The Lesson in Context

[Introduction to the lesson.]

[[[Lesson Name]]][[Image:Topic Icon - [Lesson Name].png|32px|frameless|link=[Lesson Name]]]
  • [Relation to current lesson.]
[[[Lesson Name]]][[Image:Topic Icon - [Lesson Name].png|32px|frameless|link=[Lesson Name]]]
  • [Relation to current lesson.]
[[[Lesson Name]]][[Image:Topic Icon - [Lesson Name].png|32px|frameless|link=[Lesson Name]]]
  • [Relation to current lesson.]
[[[Lesson Name]]][[Image:Topic Icon - [Lesson Name].png|32px|frameless|link=[Lesson Name]]]
  • [Relation to current lesson.]


Takeaways

After this lesson, students should

  1. Be able to distinguish roughly among the following:
    1. Good science that gets the wrong answer.
    2. Fraudulent science.
    3. Pathological science.
    4. Poorly-done science.
    5. Pseudo-science.
  2. Feel comfortable using Langmuir's Pathological Science Indicators to assess scientific articles.
  3. Be able to identify what is wrong in cases of fraudulent, pathological, poorly-done, and pseudo-science.

Spectrum of Poor Research

There are many gradations to poor research and poor results. Several approximate categories are listed below.
  • Good Science
This includes good well-done science that gets the wrong result. Even with a confidence interval of 95%, 5% of the time the results will be wrong. This is normal.
  • Poorly-done Science
Science done honestly, but not done well.
  • Pathological Science
This is what happens when a researcher falls a little too "in love" with their ideas. It is indicated by Langmuir's criteria.
  • Pseudo-science
Pseudo-science is characterized by using scientific vocabulary without aligning with the corresponding concepts or engaging in real scientific practices (i.e., science being "skin deep," not scientific below the surface).
  • Fraudulent Science
Research that involves intentional deception, such as deliberately fabricating data or deliberately deceiving the reader about the strength of evidence.

Langmuir's Pathological Science Indicators

A set of seven indicators that can be used to flag when something might be pathological science.
  1. The effect is produced by a barely detectable cause, and the magnitude of the effect is substantially independent of the intensity of the cause.
  2. The effect is barely detectable, or has very low statistical significance. Claims of great accuracy.
  3. Claims of great accuracy.
  4. Involving fantastic theories contrary to experience.
  5. Criticisms are met with ad hoc excuses.
  6. Ratio of supporters to critics rises to near 50%, then drops back to near zero.
  7. Conclusion-motivated design & analysis.

There is no set number of Langmuir's criteria that determines whether something is pathological science or not. The criteria serve as a useful guide, but detecting pathological science is ultimately something of an art.

  • [Term]
[Explanation]


[Example Name]

[Example Description]

[Example Name]

[Example Description]

[Description of misconception.]

[Resolution.]

[Description of misconception.]

[Resolution.]

Useful Resources



[[address] Discussion Slides Template]

[[address] The discussion slides for this lesson.]


[[address] [Title]]

[[address] [Description.]]

[[address] [Title]]

[[address] [Description.]]


[[address] [Title]]

[[address] [Description.]]

[[address] [Title]]

[[address] [Description.]]


Recommended Outline

Before Class

[Any steps that need to be taken before class.]

During Class

[n] Minutes [Activity.]
[n] Minutes [Activity.]

Lesson Content

Activity 1

[Brief description of and motivation for the activity]

[Common misconception or thing to look out for.]

[Thing you really need to look out for!]

[Title]

[Useful tip, guideline, or other background.]


Instructions

[n] Minutes [Activity.]
[n] Minutes [Activity.]

Discussion Questions

[Question 1]

[Possible misconception that may need to be corrected and clarified.]

[Intended answer to the above question.]

[Question 2]

[Possible misconception that may need to be corrected and clarified.]

[Intended answer to the above question.]

[[[Previous Lesson]|⟨]]

[[[Previous Lesson]|Previous]]

[[[Previous Lesson]]]

[[[Next Lesson]|⟩]]

[[[Next Lesson]|Next]]

[[[Next Lesson]]]


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