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Integration and Application of the
Scientic Method, Evidence-Based
Practice, and Clinical Reasoning
Independent Study
Course 31.2.1
Sean P. Riley, PT, DPT, ScD
Sacred Heart University
Faireld, CT

Integration and Application of the
Scientic Method, Evidence-Based
Practice, and Clinical Reasoning
Guy G. Simoneau, PT, PhD, FAPTA—Editor
Gordon Riddle, PT, DPT, ATC, OCS, SCS, CSCS—Associate Editor
Cover Illustration by Joseph Kinstler
Dear Colleagues,
I am pleased to welcome you to Integration and Application of the Scientic Method, Evidence-Based Practice, and Clinical Reasoning by
Sean P. Riley, PT, DPT, ScD. is is the first monograph in the Academy of Orthopaedic Physical erapy Independent Study Course
series 31.2, Current Concepts of Orthopaedic Physical erapy, 5th Edition. In this edition, the material is presented both as a narrated
PowerPoint, consisting of 7 sections, and a matching written outline.
Sean P. Riley is an Assistant Professor in the Physical erapy program at Sacred Heart University in Fairfield, CT, USA. He graduated
from the University of Connecticut Physical erapy Program in 2004 and completed his Doctorate in Physical erapy at Simmons
College in 2006. He obtained his Doctor of Science from Texas Tech University Health Science Center in 2013. Sean became board
certified in Orthopaedics through the American Board of Physical erapy Specialties in 2007. He completed his certification in Orthopaedic and Manual erapy (COMT) in the Extremities in 2012 through the International Academy of Orthopaedic Medicine-US.
He completed his Fellowship in Manual erapy from Regis University in 2018. Sean has 16 published manuscripts in peer-reviewed
journals since 2014 and has presented his research at the national level each of the last 7 years. He has reviewed articles for e Journal of
Manual and Manipulative erapy, Musculoskeletal Science and Practice, and Physiotherapy eory and Practices within the previous year.
Sean is also an Associate Editor for e Journal of Manual and Manipulative erapy. He is part of the team revising the Clinical Practice
Guideline for Adhesive Capsulitis. Sean serves as a research committee member for the American Academy of Orthopedic Manual Physical erapists. He has served as a grant reviewer, poster presentation judge, and abstract mentor for research submissions.
In the monograph, Dr. Riley integrates concepts related to the scientific method, evidence-based-practice, and clinical reasoning to guide
the reader on how to apply this knowledge in clinical practice. e author first discusses the process of clinical reasoning along with common errors in reasoning – a section every clinician will be able to relate to. is section is followed by a discussion of what evidence-based
practice is and what it is not, along with the process to formulate a meaningful question relevant to patient care. is section ends by
providing the reader a list of on-line resources for evidence-based practice, several with “pre-processed” information. Finally, the author
provides a theoretical model of clinical reasoning based on the type of pain perceived by the patient (pain mechanism), a systematic process of symptom modification (the origin of the pain), and an understanding of the mechanical input associated with pain generation.
Considerations for interpretation of the quality of diagnostic, prognostic, and intervention type research is also presented.
Clinical reasoning based on current evidence is key to optimal clinical decision-making and outcomes in clinical practice. e author has
provided an excellent background for readers to gain an increased appreciation for clinical reasoning. I would like to extend my sincere
gratitude to Dr. Riley for sharing his expertise on a topic so challenging to master.
Sincerely,
Sincerely,
Guy Simoneau, PT, PhD, FAPTA
Editor
2920 East Avenue South, Suite 200 | La Crosse, WI 54601 | Office 608-788-3982 | Toll Free 800-444-3982 | Fax 608-788-3965

TABLE OF CONTENTS
ACRONYM LIST ................................................................................................................................................................................................................4
SECTION 1
SECTION 2
SECTION 3
SECTION 4
SECTION 5
SECTION 6
SECTION 7
..........................................................................................................................................................................................................................5
.......................................................................................................................................................................................................................10
.......................................................................................................................................................................................................................15
.......................................................................................................................................................................................................................20
.......................................................................................................................................................................................................................31
.......................................................................................................................................................................................................................43
.......................................................................................................................................................................................................................48
Academy of Orthopaedic Physical erapy, APTA.
For personal use only. No other uses without permission.
© 2021 Academy of Orthopaedic Physical erapy, APTA, Inc. All rights reserved.
3

ACRONYM LIST
ADTO: assessment-diagnosis-treatment-outcome
APTA: American Physical erapy Association
CEBM: Centre for Evidence-Based Medicine
CINAHL: Cumulative Index of Nursing and Allied Health Literature
CPG: clinical practice guideline
EBP: evidence-based practice
FABER: flexion, abduction, external rotation
LBP: low back pain
LR: likelihood ratio
MCID: minimal clinically important difference
MDC: minimal detectable change
MRI: magnetic resonance imaging
NLM: National Library of Medicine
PICO: patient, intervention, comparison, outcome
PMC: PubMed Central
RRC: rehabilitation reference center
SI: sacroiliac
SIJ: sacroiliac joint
SLR: straight leg raise
Opinions expressed by the authors are their own and do not necessarily reflect the view of the
Academy of Orthopaedic Physical erapy. e authors declare no conflict of interest.
e publishers have made every effort to trace the copyright holders for borrowed material.
If we have inadvertently overlooked any, we would be willing to correct the situation at the first opportunity.
© 2021, Academy of Orthopaedic Physical erapy. For personal use only. No other uses without permission.
Course content is not intended for use by participants outside the scope of their license or regulations.
4

Integration and Application of the Scientic Method,
https://t.me/med1917
Evidence-Based Practice, and Clinical Reasoning
Sean P. Riley, PT, DPT, ScD
Sacred Heart University
Fairfield, CT
e outline contained in this written format is from Dr. Riley’s PowerPoint presentation titled, “Integration and Application of Clinical
Reasoning, Evidence-based Practice, and the Scientic Method”.
1.1 Title: Integration and Application of the Scientific Method, Evidence-Based
Practice, and Clinical Reasoning-Sean P. Riley, PT, DPT, ScD
e purpose of this monograph is to discuss evidence-based practice (EBP), clinical
reasoning, the relationship between these concepts, and how to apply these concepts in a clinical context. Having a better understanding of these concepts individually and how they are related may help to improve the integration of evidence and
reasoning into practice and help to facilitate better communication with colleagues
and patients.
Disclaimer
1.2
• e purpose of this monograph is to help clinicians clinically integrate and ap-
ply the concepts of clinical reasoning, evidence-based practice, and the scientific
method
• It is expected that the reader of this monograph has a foundational understand-
ing of the concepts that are discussed
• If the reader is not familiar with or does not have a comprehensive understanding
of any of the information that this monograph seeks to integrate, the reader is
encouraged to explore that topic further
• is monograph is not meant to be a comprehensive resource for all the princi-
ples discussed
—NOTES —
1.3 Conflict of Interest and Acknowledgement
• Conflict of Interest-e author of this monograph certifies that he has NO affiliations with or involvement in any organization or entity with any financial interest (such as honoraria; educational grants; participation in speakers’ bureaus;
membership, employment, consultancies, stock ownership, or other equity interest; and expert testimony or patent-licensing arrangements), or non-financial
interest (such as personal or professional relationships, affiliations, knowledge, or
beliefs) in the subject matter or materials discussed in this manuscript.
• Acknowledgement-I would like to thank Brian Swanson and Josh Cleland for
their assistance with writing “e why, where, and how clinical reasoning model
for the evaluation and treatment of patients with low back pain.” is clinical
reasoning model served as the foundation for the integration and application for
the concepts discussed in this monograph.
Academy of Orthopaedic Physical erapy, APTA.
For personal use only. No other uses without permission.
© 2021 Academy of Orthopaedic Physical erapy, APTA, Inc. All rights reserved.
5

—NOTES—
https://t.me/med1917
1.4 Table of Contents
Section Content
Section 1 Truth, Reasoning, and the Scientific Method
Section 2 Evidence-based Practice, Statistical Tools, and Methodological
Rules
Section 3 Clinical Reasoning and Diagnosis
Section 4 Integration of Clinical Reasoning Concepts and Suggestions for
Improvement
Section 5 Using the Literature in a Reasoned Approach to Evidence-based
Practice
Section 6 Review Questions & Case Scenarios
Section 7 References
• e table of contents for the entire presentation is included here
• Additionally, at the end of this presentation, you will find a list of references
• e references are cited using the preferences of the AMA Manual of Style, 11th
edition and are located either in the PowerPoint slides, the slide notes, or both
Learning Objectives
1.5
• Upon completion of this monograph, the course participant will be able to:
° Identify and describe the different types of clinical reasoning strategies used
during patient management.
° Discuss the process of clinical reasoning.
° Identify common errors in reasoning.
° Identify, compare, and contrast commonly accepted definitions of evi-
dence-based practice (EBP).
° Create a specific, answerable clinically meaningful question.
° Identify the best available evidence.
° Analyze examples of clinical reasoning strategies and apply research evidence to
clinical decision-making.
° Discuss the challenges with the clinical application of EBP and the need for a
reasoned approach.
° Discuss the intent and purpose of the scientific method.
1.6 Truth, Reasoning, and the Scientific Method
• Section 1
1.7 Do you promise to tell the truth, the whole truth, and nothing but the truth?
• is is an oath taken by individuals prior to giving sworn testimony
• e oath attempts to capture all aspect of the truth and prevent individuals from
leaving out important contextual elements of the truth as well as preventing the
sworn testimony from being tainted by mixing the truth with things that are not
true or that are partially true
1.8 What is truth?
1.9 “It depends on what the meaning of the word ‘is’ is.”-Bill Clinton
1.10 Getting to the Truth
• A common meaning of truth is information related to facts, reality, or informa-
1
tion that is consistent with a gold standard
6
© 2021 Academy of Orthopaedic Physical erapy, APTA, Inc. All rights reserved.
Academy of Orthopaedic Physical erapy, APTA.
For personal use only. No other uses without permission.

• e problem is that there are several theories and views regarding what the truth
https://t.me/med1917
2
‘is’ that scholars, philosophers, and theologians have debated
• Without getting into an in-depth discussion regarding truth from these various
perspectives, I am going to discuss truth from the perspective of Neil deGrasse
Tyson
° Objective truths are established by evidence
° Personal truths by faith
° Partisan truths by incessant repetition
• e purpose of science is to identify an objective and measurable truth that may
be independent of personal and partisan truths (aka biases)
• Science also looks to control for the biases that may occur as our brains interpret
incomplete information gathered through our senses
Why is the interpretation of the truth important?
1.11
• Does an empirical truth exist beyond the biases related to personal truth and
partisan truth?
• Do you believe that the scientific method is a valid means of answering clinical
questions?
• If you don’t believe that the scientific method is valid, can the process of EBP be
valid?
• Can EBP be valid without accurate critical appraisal of the literature?
• If a clinician does not understand what reasoning is and what it is not, they can-
not apply a clinically reasoned approach in the clinic
• If a clinician does not believe that an empirical truth exists beyond the biases
related to their personal truth and political truth, they do not believe that the
scientific method is a valid means of answering clinical questions
• If a clinician does not believe that the scientific method is valid, they do not
believe that the process of EBP that is based on the scientific method is valid
• If a clinician does not believe in the validity of EBP or the importance of accu-
rate, critical appraisal in the process of EBP they cannot use clinical reasoning to
apply the best available evidence in a clinical context
• If a clinician does not understand what reasoning is and what it isn’t, they cannot
accurately apply a clinically reasoned approach in the clinic
• is is a linear (deductive) reasoning framework that connects a to b, b to c, and
c to d. If the premises are correct, then a deductive connection has been created
that directly links a to d in a linear framework through deductive reasoning
• More to come moving forward on the details of what reasoning is and is not and
why these concepts are essential in a reasoned approach to clinical practice
—NOTES—
1.12 What does it mean to be rational, and why is it important?
• In order to understand what clinical reasoning is, we must understand what it is
to be rational.
• Rational clinicians formulate opinions and make decisions based on facts and/or
a reasoned approach by eliminating or minimizing logically fallacious thinking
and cognitive biases
• Professional opinions that are not supported by the best available evidence using
an overt reasoned approach are irrational
• It, therefore, becomes vital to recognize what reasoning is and isn’t
1.13 Are you rational, or are you rationalizing?
• Rational thinking involves generating a hypothesis (abductive reasoning), col-
lecting data (deductively, inductively, or probabilistically) and then linking the
data together (deductively, inductively, or probabilistically) to make a conclusion
in the context of the best available evidence
Academy of Orthopaedic Physical erapy, APTA.
For personal use only. No other uses without permission.
© 2021 Academy of Orthopaedic Physical erapy, APTA, Inc. All rights reserved.
7

—NOTES—
https://t.me/med1917
• Rationalization starts with the answer and then uses hypotheses and data that
supports the answer with disregard for the data that do not
° Rationalizing is a logical fallacy that is recognized in the Diagnostic and Statis-
tical Manual of Mental Disorders (DSM) IV
° If you are starting with the answer during your clinical reasoning process, you
are rationalizing
What is reasoning?
1.14
• Reasoning is the process of thinking about something in a logical manner
• Formally, logic is deductive reasoning
• Deductive reasoning attempts to use a reasoned approach to link all the com-
ponents of evidence together in a linear fashion to prove that something is true
beyond a reasonable doubt
° An example of a deductive framework is the ADTO clinical research model.
is model uses a linear deductive process to create a direct link between the
assessment and patient’s outcome by linking the Assessment-Diagnosis, Diag-
3
nosis-Treatment, and Treatment-Outcome
Other Primary Forms of Reasoning
1.15
• Inductive reasoning - reasoning that collects disconnected pieces of evidence that
increases the probability of something being true. It can never create absolute
proof that something is true
• Abductive reasoning - reasoning is used to generate and modify hypotheses
3
Common Reasoning Errors
1.16
• Logical Fallacies and Cognitive Biases
Common Logical Fallacies
1.17
• Two of the most common logical fallacies are post hoc ergo propter hoc and
cum hoc ergo propter hoc. e Latin translations for these two logical fallacies
are “after this therefore because of this” and “with this therefore because of this,”
respectively. An example of this would be that you treat your patients, and they
get better. You then connect the reason they improved to the treatment that you
provided. ere are many different reasons why patients get better. e most
common reason is the natural passage of time. If most of your patients are getting
better in 4 to 6 weeks, it is likely that their improvement is not related to the
interventions that are being provided to them
• An ad hominem occurs when an individual attacks somebody personally instead
of discussing the problems with the evidence that they are using or their reasoning process. An example of this may be when somebody suggests that a clinician’s
point of view is invalid because they are a novice or because they haven't done
any research on a topic of interest. Just because an individual is a novice and/
or doesn’t do any research does not mean that their point of view is invalid. A
proper discussion would discuss why their specific point of view isn’t valid related
to the best available evidence and by discussing errors in their reasoning process
• An appeal to authority is when an individual will state that something is true
because an authoritative source has said that it is true. Just because somebody is
an authority does not mean that their point of view is accurate, followed the EBP
process, or used a reasoned approach
• A straw man argument occurs when somebody counter argues a point that a per-
son has made by creating an argument to refute a point that the individual never
made. For example, if during a professional conversation, a clinician says that
Academy of Orthopaedic Physical erapy, APTA.
8
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For personal use only. No other uses without permission.

there is no high-level evidence to support the use of ultrasound for the treatment
https://t.me/med1917
of patients with musculoskeletal disorders, and the responding clinician says that
this clinician is denying treatment to the patient. e clinician is not denying
treatment to the patient. ey are just suggesting that this may not be the best
treatment for the patient
• An appeal to ignorance is a logical fallacy based on the assumption that a state-
ment must be true if it cannot be proved false. is logical fallacy involves shifting the burden of proof from somebody that is making a claim that holds the
burden of truth to somebody that is saying that there is no high-level evidence
that something is true that does not hold the burden of truth. In a clinical context, the burden of proof is always on the clinician that is purporting the efficacy
of an intervention to provide moderate to high-quality evidence that has a moderate to low risk of bias that it is effective. e burden is never on the individual
that suggests that it is ineffective
• e bandwagon logical fallacy simply suggests that because everybody else is
doing it that it is the best way to do it or the way that it should be done
• A red herring is information that misleads the clinician or distracts the clinician
from what is important. For example, meniscal tears are a common finding in
the older asymptomatic healthy population. e assumption that a meniscal tear
in an older population is the cause of an individual’s symptoms may therefore
not be accurate, and, thus, may create a red herring argument as to the cause of
a patient’s symptoms
—NOTES—
1.18
Common Cognitive Biases
• Some common cognitive biases include confirmation bias, hindsight bias, an-
choring bias, false consensus bias, and recall bias.
• Confirmation bias occurs when a clinician only uses evidence that supports
their point of view and disregards the higher quality of evidence with a low risk
of bias that does not support their point of view. is can also occur clinically if
a clinician prefers using a specific system to evaluate and treat patients. Does the
patient fit the system, or is the clinician just recognizing the parts of the system
that fit and ignoring the parts of the system that don’t fit the patient’s presentation?”
• Hindsight bias occurs when, after events unfold, the clinician treats the outcome
as being predictable or foreseeable. is may occur when a clinician applies their
favorite intervention, the patient responds positively, and the clinician expresses
the outcome as if they knew it was going to happen or predicted that it was going
to happen. It is always easier to predict an outcome after it has already happened.
• Anchoring bias may occur when a clinician is overly influenced by the first evi-
dence they collect and the hypothesis it generates. It happens when clinicians fail
to modify or change their hypothesis when additional evidence does not support
this hypothesis.
• False consensus bias occurs when a clinician overestimates how much his/her
peers agree with their clinical approach.
• Recall bias is the tendency of a clinician to remember their favorable results and
not remember the less than spectacular outcomes.
1.19 What the Scientific Method Is
• Traditionally, the scientific method is a reasoning process that uses observational
inductive reasoning to formulate questions
• For example, a clinician may observe a response to a specific intervention in a
specific patient population repeatedly. e more times that they make this ob-
Academy of Orthopaedic Physical erapy, APTA.
For personal use only. No other uses without permission.
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4
9

—NOTES—
https://t.me/med1917
servation the more refined their question may become and the more likely they
are to believe that what they are seeing is true
• is question however must be refined into a hypothesis through abductive rea-
5
and tested to make sure that these observations are not being driven by
soning
confirmation and hindsight biases
• A key component to consider when generating a hypothesis is that it must be
falsifiable
5
• e hypotheses are then tested through a deductive reasoning process5
• It has been argued that a scientific hypothesis can never be proven to be true
4,6
through one experiment but that it can be proven false by one experiment
• e objective, measurable truth is therefore attained by repeatedly testing hy-
potheses that survive falsification
7
1.20 What the Scientific Method Isn’t
• Generate a question
• Formulate a hypothesis
• Test the hypothesis
• If the hypothesis is found to be false, retest the hypothesis
• If the hypothesis is found to be false, retest the hypothesis
• If the hypothesis is found to be false, retest the hypothesis
• e emphasis here is that once a hypothesis is tested and not verified, it is clearly
not universal or generalizable to the population of interest
2.1 Evidence-based Practice, Statistical Tools, and Methodological Rules
• Section 2
Myth of EBP
2.2
• “I think that we need to abandon the quest for absolute truth and look, in-
stead, at clinical research as way to develop a reasoned philosophy about patient
8
-Richard Di Fabio
care.”
• If a hypothesis is rejected, it strongly suggests that the approach should not be
used
• If the hypothesis is not rejected, it may be a poor assumption that one study or
a small group of studies, that may have low methodological quality with a high
risk of bias represent the only, right, or best answer to a clinical question for an
individual
• Keep in mind that hypotheses need to be consistently verified to be considered
accurate
• A major reasoning challenge for clinical research is that it seeks to collect data on
a sample of individuals that represent a population of interest. From that sample,
conclusions are drawn from statistical analyses that use measures of central tendency (such as the mean for parametric statistics and median for non-parametric
statistics)
• If your patients are not accurately represented by these measures of central ten-
dency, the research findings may not be applicable to them
• Clinicians, therefore, need disciplined reasoning strategies to answer clinically
meaningful questions when using research evidence in the context of the individual patient
2.3 “ere are three kinds of lies: lies, damned lies, and statistics.” -Mark Twain
• “is is a logically fallacious ad hominem attack on math and those that use math
to make decisions. Does math have the ability to lie? Of course not?
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10
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For personal use only. No other uses without permission.
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