Introduction to scientific method, basic statistics and scientific writing

Introduction to
the Scientific Method,
basic statistics
& Scientific Writing

1. Introduction & Quiz
2. The Scientific Method
3. Methods
4. Results
5. Discussion
6. Introduction
7. Scientific Writing
Overview

1. Introduction & Quiz
2. The Scientific Method
3. Methods
4. Results
5. Discussion
6. Introduction
7. Scientific Writing

The Scientific Method
• A systematic process that involves:
• Recognising and formulating a problem
• Collecting data through observation and
experiment
• Formulating and testing a hypothesis
• Requires:
• Objectivity
• Repeatability
• Full disclosure of methods, data and results

What is a Hypothesis?
• A tentative statement that proposes a
possible explanation for a phenomenon or
event.
• Two types:
• Alternative hypothesis (H1)
• Null hypothesis (H0)

What is a Hypothesis?
• H1: Exposure to pure oxygen kills cancer cells.
• H0: Exposure to pure oxygen does not kill
cancer cells.
• H1 can never be proven.
• Experiments are based around
accepting or rejecting H0.
• Aim of scientific research is to
reject H0.

Task: Steps of the Scientific Method
Ask question
Do background
research
Construct
hypothesis
Test with
experiment
Analyse results
Draw conclusion
Hypothesis is true
Hypothesis is false
or partly false
Report results
Think! Try again

Peer-Reviewed Scientific Journals
• Articles are rigorously reviewed by experts in
the same field
• Critical in establishing a reliable body of
knowledge
• Should be objective, repeatable and provide full
disclosure
“A one-year, multicenter,
randomized, controlled trial to
evaluate the effect of the low-
carbohydrate, high-protein, high-fat
Atkins diet on weight loss and risk
factors for coronary heart disease in
obese persons.”

Introduction
Method
Results
Discussion & conclusion
Scientific Report

Introduction
Method
Results
Discussion & conclusion
Question
Background
Hypothesis
Perform experiment
Collect data
Analyse data
Interpret data
Draw conclusions
Scientific Report Scientific Method

Task: Change Blindness Clip
Watch the clip at:
https://www.youtube.com/watch?v=fXWuB7fmGv0
And put the sentences on the next slide, from a Method
section describing this experiment, into the correct
order.

Task: Reorder these sentences
a) The participants were asked to enter an adjacent hallway.
b) A sign saying ‘Experiment’ was placed above a counter in a
reception area.
c) Participants were recruited through advertisements placed
around the university.
d) The participants were asked to describe what they had just
experienced.
e) A different experimenter stood up from behind the counter and
handed the participant an information pack.
f) The researcher crouched down behind the counter, obscured
from view, to file the consent form.
g) Participants approached one of the researchers, who was
standing behind the counter, and were asked to fill in a consent
form.

Task: Original order
1. Participants were recruited through advertisements placed
around the university.
2. A sign saying ‘Experiment’ was placed above a counter in a
reception area.
3. Participants approached one of the researchers, who was
standing behind the counter, and were asked to fill in a consent
form.
4. The researcher crouched down behind the counter, obscured
from view, to file the consent form.
5. A different experimenter stood up from behind the counter and
handed the participant an information pack.
6. The participants were asked to enter an adjacent hallway.
7. The participants were asked to describe what they had just
experienced.

The Writing Process
Write in this order:
1. Methods
2. Results
3. Discussion
4. Introduction
5. (Abstract)

Methods
What did you do and how?
• Logically ordered sections describing:
• Focus of the study (e.g. participants, bacteria...)
• Experimental design
• Procedures
• Materials
• Statistical methods
• Requires accuracy and precision
• Demonstrates the validity of a study
• Needs to be reproducible

Methods
• Subsections in Atkins article
• Subjects (participants)
• Study design
• Study procedures
• Analyses of samples
• Statistical analysis

Methods
• Sub-sections in Atkins article
• Subjects (participants)
• Study design
• Study procedures
• Analyses of samples
• Statistical analysis

Task: Which part of the Methods section did
these 8 sentences come from?
1. Subjects were instructed to read the manual and follow the
program as described.
2. Potential subjects were excluded if they had clinically significant
illnesses, were taking lipid-lowering medications, were pregnant
or lactating, or were taking medications that affect body weight.
3. Serum total cholesterol, high-density (HDL) cholesterol and
triglyceride concentrations were assayed according to procedures
recommended by the Centers for Disease Control and Prevention.
4. The subjects were randomly assigned at each site, with use of a
random-number generator, to follow either the low carbohydrate
diet or the conventional diet.

5. For the first two weeks, carbohydrate is limited to 20g per day
and is then gradually increased until a stable and desired weight
is achieved.
6. Triglyceride values were not normally distributed, so the log-
transformed values were analyzed.
7. Body weight was measured with the use of calibrated scales
(Detecto 6800, Cardinal) while the subjects were wearing light
clothing and no shoes at baseline and at weeks 2, 12 and 52.
8. All subjects provided written informed consent.

Task: Methods
1. Subjects were instructed to read the manual and follow the
program as described.
Study procedures
2. Potential subjects were excluded if they had clinically significant
illnesses, were taking lipid-lowering medications, were pregnant
or lactating, or were taking medications that affect body weight.
Subjects
3. Serum total cholesterol, high-density (HDL) cholesterol and
triglyceride concentrations were assayed according to procedures
recommended by the Centers for Disease Control and Prevention.
Analyses of samples
4. The subjects were randomly assigned at each site, with use of a
random-number generator, to follow either the low carbohydrate
diet or the conventional diet.
Study design

Task: Methods
5. For the first two weeks, carbohydrate was limited to 20g per day and
was then gradually increased until a stable and desired weight was
achieved.
Study procedures
6. Triglyceride values were not normally distributed, so the log-
transformed values were analyzed.
Statistical analysis
7. Body weight was measured with the use of calibrated scales (Detecto
6800, Cardinal) while the subjects were wearing light clothing and no
shoes at baseline and at weeks 2, 12 and 52.
Study procedures
8. All subjects provided written informed consent.
Subjects

Results
What did you find or see?
• Focus on results relating to your hypothesis /
objectives
• Group into subsections and order logically
• May be illustrated using tables or figures
• Should document or clarify, but not duplicate, data in
text or other graphics.

Results
objectives

Results
objectives
• Objective: “A one-year, multicenter, randomized, controlled trial to
evaluate the effect of the low-carbohydrate, high-protein, high-fat
Atkins diet on weight loss and risk factors for coronary heart
disease in obese persons.”

Results

Results
• Subsections
• Weight
• Attrition (drop outs)
• Urinary ketones
• Blood pressure
• Oral glucose tolerance test
• Serum lipoproteins

Results
• Subsections
• Weight Main focus of study
• Attrition (drop outs) Related to weight results
• Urinary ketones Related to weight results
• Blood pressure
• Oral glucose tolerance test
• Serum lipoproteins

Results
• Subsections
• Weight Main focus of study
• Attrition (drop outs) Related to weight results
• Urinary ketones Related to weight results
• Blood pressure Secondary focus of study
• Oral glucose tolerance test Secondary focus of study
• Serum lipoproteins Secondary focus of study

Results
• May be illustrated using tables or figures
• Should document or clarify, but not duplicate,
data in text or other graphics.

Descriptive statistics
• Variables- characteristics of interest
Eye colour StatsAbility Siblings Height
• Observations - observed values of variables
green Good 0 174
hazel Very good 1 155
blue Good 3 167
green Poor 0 165
brown Poor 2 148
brown Moderate 5 160
…

• Categorical
Nominal e.g. eye colour (brown,blue,green,…)
Ordinal e.g level of statistics experience prior
to this course (poor,moderate,…)
• Numerical
Discrete e.g Number of siblings (0,1,2,…)
Continuous e.g. Height (140-210cm)
Types of Data

Display categorical nominal data
Mode

Display categorical nominal data

But generally piecharts are better avoided
Example taken from
wikipedia.org/wiki/Pie_chart

Display categorical ordinal data
Mode

Display numerical discrete data
Mode

Display numerical discrete data
• Stem-and-leaf plot of number of siblings
Unit of stem: 1
0 | 000000000000000000000000
1 | 000000000000000000000000000
2 | 00000000000000000
3 | 000
4 | 0000000
5 | 0
6 |
7 |
8 |
9 |
10 |
11 | 0

…but wait, there’s more!
• Mean – add answers up, then divide by
number of replies:
• Median – middle value of sorted answers:
425.1
80
11x15x14x73x32x171x270x24


11544444443332222222222222
222211111111111111111111111111
1000000000000000000000000

Display numerical continuous data
• Stem-and-leaf plot of Height
Unit of stem: 100cm
14 | 111478889
15 | 012223355677788889
16 | 000022333344555556777778888999
17 | 00111244555566789
18 | 012335

Display numerical continuous data
Mode Mean
171.5
Median
171.7

Same centre – but…
Mean=500
Median=500
Mean=495
Median=497

Measure of spread
• Variance – amount of variability around
the mean
• Standard deviation –
• IQR – Interquartile range

And beware of outliers
outlier

Shape
• Skewness – measure of extent to which
shape is lopsided rather than
symmetrical(i.e. when mean=median).
• Positive skew – more data to the right of
the mode than left (i.e. mean > median)
• Negative skew – more data to the left of
the mode than right (i.e. mean < median)

Histogram versus Frequency curve

Normal distribution
• Most common
• Symmetrical –
mean=median
• ‘bell-shaped’
• ‘normal’ – it was
once thought that
all things in
natural world
corresponded to
this shape

The z- transformation
• Values of data come in many forms, e.g.
1. x=50 marks out of 100
2. x=178cm
3. x=55s
• Transform into z-scores via formula:
std
meanx 

The z- transformation
• Comparing marks
My mark was 80 out of 100, where the average
mark was 60, and the std deviation was 10.
My friend’s mark was 26 out of 30, where the
average mark was 20, and the std deviation
was 2.
Who did better, taking into account that the
marks are scaled?

Task 1 – Summarising
• Age of cars: 1,1,1,2,2,4,5,7
• Age of cars with outlier: 1,1,1,2,2,4,5,70
 Calculate the mean and the median
• Questions:
 When should you use the median instead of the
mean?
 How would you describe the shape of the data sets?

Randomisation
Let’s look at this video on random sequences….
Random Sequences: Human vs Coin
(http://www.youtube.com/watch?v=H2lJLXS3AYM)

Take-home message
Humans are terrible at intuitively
understanding the concept of random

Drawing a random sample
1.identify all of the members in your population,
you must be able to list them in what is called a
sampling frame.
2.use a Table of Random Numbers, or use a
Random Number generator to get a set of
random numbers
3.draw the corresponding elements from the
sampling frame

Some Random Numbers
18 48 20 16 5 47 45 23 38 17
15 22 44 46 13 30 7 25 50 41
6 29 2 27 19 2 9 11 50 27
45 35 1 13 46 38 32 41 31 26
6 15 40 19 44 39 49 48 43 8
4 29 14 37 36 22 16 7 47 5
17 42 21 25 3 34 23 30 28 33
18 12 10 24 20 34 19 10 35 23
24 18 41 43 28 40 47 4 48 7
2 32 15 27 1 30 44 6 16 36
49 31 46 8 21 38 37 25 17 22

Moral of the story
Humans are not very
good at picking at
random –
Bias is almost
guaranteed to be
introduced
Use random numbers when drawing a sample!

Inferential statistics
Use of information from a sample to draw
conclusions about a population

Inferential statistics
population parameter sample statistic
µ
Population Sample

4. P-value
• Probability of getting a test statistic equal
or more extreme than the one sampled,
given that the null hypothesis is correct
• ‘evidence for the null’
• Use computer program to calculate, here
the p-value would essentially be equal to
0.

5. Conclusion
• Compare p-value to significance level and
either accept or reject the null hypothesis
based on the evidence
‘if the p-value is low, the null must go!’
• p-value=0 < α=0.05, so reject the null
• In conclusion: ‘We have strong evidence
that marine reserves do lead to bigger fish
within their boundaries’

Results: Tables
• Good for showing specific data or
statistics in a small space.
• More concise than text
• More accurate than figures

Results: Tables
• Good for showing specific data or
statistics in a small space.
• More concise than text
• More accurate than figures
• Table number and title always go at the top
• Most important elements read down, not
across
• Each row and column title starts with a capital
letter
• There is ‘white space’ in the table
• The table ‘stands alone’
• The reader doesn’t need to refer to the text to
understand the data

Results: Figures
• Present numeric data in visual form
• Graph
• Photograph
• Flow-chart
• Map
• Diagram
• Good for general comparisons,
trends, distributions and cycles
• Figure number and title always go below
• Label axes clearly and include units
• Distinguish data sets from each other and
include a key
• Figure should ‘stand alone’.

Discussion
What do your results mean?
Elements to include:
• State the study’s major findings
• Explain the meaning and importance of the
findings
• Relate the findings to those of similar studies
• Consider alternative explanations for the findings
• State the clinical relevance of the findings
• Acknowledge the study’s limitations
• Make suggestions for future research

Discussion
What do your results mean?
Things to avoid:
• Overpresentation of results
• Overinterpretation of results
• Unwarranted speculation
• Inflation of the importance of the findings
• Tangential issues
• Criticism of other studies
• Conclusions that are not supported by the data

Discussion
• State the major findings of the study
• Should be the first paragraph
• Should not include data or refer to the study design
“The results...demonstrate that the low-carbohydrate, high-protein,
high-fat Atkins diet produces greater weight loss...than a
conventional high-carbohydrate, low-fat diet for up to six months,
but that the differences do not persist at one year.”

Discussion
• Explain the meaning of the findings and why they
are important
“The difference in weight loss between the two groups in the first six
months demonstrates an overall greater energy deficit in the low-
carbohydrate group, despite unrestricted protein and fat intake in
this group and instructions to restrict energy intake in the
conventional diet group.”
The lack of significant difference between the groups at one year
is most likely due to greater weight regain in the low-carbohydrate
group and the small sample size.
These data suggest that long-term adherence to the Atkins diet
may be difficult.”

Discussion
• Relate the results to those of similar studies
• Point out similarities
“Our data suggest that ketosis was unlikely to be responsible for the
increased weight loss with the low-carbohydrate diet, since we did not
find any relation between the presence of urinary ketones and weight
loss. This suggestion is supported by Smith et al (2005) and Jones et
al (2006), who also found a lack of relationship between ketosis and
weight loss.”

Discussion
• Relate the results to those of similar studies
• Point out similarities
“Our data suggest that ketosis was unlikely to be responsible for the
increased weight loss with the low-carbohydrate diet, since we did not
find any relation between the presence of urinary ketones and weight
loss. This suggestion is supported by Smith et al (2005) and Jones et
al (2006), who also found a lack of relationship between ketosis and
weight loss.”
• Explain differences
“Concerns that diets high in meat might have negative effects on
cardiovascular risk factors were not substantiated by this study.
Unlike Skov et al (2001), LDL cholesterol remained unchanged from
baseline in the low-carbohydrate group. This may be because
absolute meat intakes were considerably lower in our study.”

Introduction
Nature and scope of the problem
Brief review of literature
Justification of investigation
(incl. hypothesis)
Objectives
Create
A
Research
Space

Task: Introduction
1. At any given time, approximately 45% of women...a major public health problem.
2. The conventional dietary approach to weight.... have promoted this approach.
3. The Atkins diet, originally published...be the most popular of these diets.
4. More than 10 million copies of Atkins’s...have read any other book.
5. Despite its longevity and popularity...percent after 24 weeks.
6. We conducted a one-year...disease in obese persons.
7. The subjects were randomly...by most dieters.

Task: Match Sentences with Sections
Sentence Change
Blindness
Atkins
Diet
At any given time, 45% of women and 30% of men in the US are trying to lose weight.

Sentence Change
Blindness
Atkins
Diet
At any given time, 45% of women and 30% of men in the US are trying to lose weight. I

Sentence Change
Blindness
Atkins
Diet
All participants completed a comprehensive medical examination and routine blood
tests.

Sentence Change
Blindness
Atkins
Diet
tests.
M

Sentence Change
Blindness
Atkins
Diet
tests.
M
In contrast to similar studies, it was primarily younger participants who failed to
notice a change.
Despite our impression that we retain the visual details of our surroundings from one
moment to the next, we are surprisingly unable to detect changes to such details.
Overall, 59 percent of subjects completed the study, and 88 percent of those who
completed the six-month assessment completed the full study.
Only nine of the 35 participants reported noticing the switch when asked if they had
seen anything unusual.
The self-help nature of treatment probably contributed to the drop-out rate of 41
percent.
Participants were directed into a nearby hallway and were interviewed by two
researchers.

Sentence Change
Blindness
Atkins
Diet
tests.
M
notice a change.
D
percent.
researchers.

Sentence Change
Blindness
Atkins
Diet
tests.
M
notice a change.
D
I
percent.
researchers.

Sentence Change
Blindness
Atkins
Diet
tests.
M
notice a change.
D
I
R
percent.
researchers.

Sentence Change
Blindness
Atkins
Diet
tests.
M
notice a change.
D
I
R
R
percent.
researchers.

Sentence Change
Blindness
Atkins
Diet
tests.
M
notice a change.
D
I
R
R
percent.
D
researchers.

Sentence Change
Blindness
Atkins
Diet
tests.
M
notice a change.
D
I
R
R
percent.
D
researchers.
M

Principles of Scientific Writing
• Precision – say what you mean
• Clarity – avoid what you don’t mean
• Conciseness – make every word count
• Objectivity – state things as they are
• Logic – move smoothly from one point to
the next
These principles should be applied
throughout a scientific report.

Task: Scientific Writing
• “This new process reduces emissions from diesel engines
and industrial furnaces.”
• Precision
• Reduces – by how much?

• Precision
• Emissions – of what?

• Precision
• Emissions – of what?
• “This new process eliminates 99 percent of nitrogen oxide
emissions from diesel engines and industrial furnaces.”

“In that the ‘Big Bang’, currently the most credible theory about how
the universe was created, explains only the creation of hydrogen
and helium, we are left to theorise as to how all the other
elements came into being. Having studied the nuclear reactions
that constitute the life and death cycles of stars, many scientists
believe therein lies the key.”
• Clarity
• Over-the-top formality -> bewildered readers

“In that the ‘Big Bang’, currently the most credible theory about how
the universe was created, explains only the creation of hydrogen
and helium, we are left to theorise as to how all the other
elements came into being. Having studied the nuclear reactions
that constitute the life and death cycles of stars, many scientists
believe therein lies the key.”
• Clarity
• Over-the-top formality -> bewildered readers
“The ‘Big Bang’ is the most credible theory for the creation of the
universe. Nevertheless, the ‘Big Bang’ explains the creation of
only helium and oxygen. What about the other elements? Many
scientists believe that they arose from nuclear reactions that occur
in the life and death cycles of stars.”

• “Because the receiver presented the radiometer with a high-
flux environment, it was mounted in a silver-plated stainless
steel container.”
• Clarity
• What is mounted in the container?

flux environment, it was mounted in a silver-plated stainless
steel container.”
• Clarity
• What is mounted in the container?
flux environment, the radiometer was mounted in a silver-
plated stainless steel container.”

• “The achievement of success in these advanced
technologies depends very heavily on a rather detailed
understanding of the complex processes that govern the
velocities of the unburned gases prior to combustion.”
• Conciseness

• “The achievement of success in these advanced
technologies depends very heavily on a rather detailed
understanding of the complex processes that govern the
velocities of the unburned gases prior to combustion.”
• Conciseness
• “The success of these advanced technologies depends on
understanding the velocities in the unburned gases prior to
combustion.”

• “Once sample A had been added to sample B, the contents
of the test tube turned a beautiful blue colour.”
• Objectivity
• ‘Beautiful’ cannot be measured or accurately explained to the
reader.
• How could you re-write this sentence?
• “Once sample A had been added to sample B, the contents
of the test tube turned a bright blue colour.”

• “The Cascade Range, with its prominent chain of towering
cones, is a volcanic region in the western United States.
There are numerous areas across the globe currently
experiencing volcanic activity.”
• Logic
• Broad -> narrow

• “The Cascade Range, with its prominent chain of towering
cones, is a volcanic region in the western United States.
There are numerous areas across the globe currently
experiencing volcanic activity.”
• Logic
• Broad -> narrow
• “There are numerous areas across the globe currently
experiencing volcanic activity. One of these areas is the
Cascade Range, a prominent chain of towering cones in the
western United States.”

Swierk et al. (2011) also used erythrocytes and 3 d weighed
food record as reference methods for validation of the Australian
Dietary Questionnaire (ADQ). Their validity coefficient for
omega-3/b was comparable to that of the NZ Dietary
Questionnaire (NZDQ) (=0.69 [95% CI (0.39, 0.95)]), while
they found slightly higher validity coefficients for omega-3/a
(=0.92 [95% CI (0.63, 0.99)]) and omega-3/c (=0.78 [95%
CI (0.42, 0.98)]). These stronger validity coefficients may be a
result of the different timeframes covered by the questionnaires;
the ADQ assessed dietary intakes over the past three months,
whereas the NZDQ assessed intakes over the past year.
Scientific Writing: Original

As erythrocyte levels have a life cycle of approximately 120
days, it is possible this biomarker correlates more strongly
with the timeframe of the ADQ. In contrast, the NZDQ had
stronger validity coefficients for omega-3/a, omega-3/b and
omega-3/c than were found in two other validation studies for
omega-3 dietary questionnaires. These other questionnaires
covered the whole diet and therefore had reduced specificity
for omega-3, and this may explain their lower validity
coefficients. Further, McNaughton et al. (2010) used plasma
phospholipids as a reference method for a questionnaire that
assessed omega-3 intakes over the past six months, and this
biomarker may only reflect intake over a shorter period.
Scientific Writing: Original

Quiz
1. The Scientific Method is:
a) A process that guarantees the success of
scientific experiments
b) A logical set of steps that allows the
formulation and testing of a hypothesis
c) A comprehensive guide to Laboratory
procedure

Quiz
2. Which of the following is NOT considered
a key principle of scientific writing?
a) Objectivity
b) Rhetoric
c) Conciseness

3. At which stage of their research do
scientists usually construct a hypothesis?
a) When the results of an experiment have been
inconclusive
b) When they find that empirical methods are
inappropriate for their research question
c) When they have gathered sufficient data to
make an ‘educated guess’ about the outcome
of an experiment
Quiz

Quiz
4. Which sources do scientists use for
reliable reports about new discoveries in
their field?
a) Peer-reviewed journals
b) The latest scientific updates to Wikipedia
c) Textbooks written by Nobel-Prize winning
scientists

Quiz
5. Which of these sections would you NOT
expect to find in a standard scientific
report/article?
a) Abstract
b) Discussion
c) Delivery

Quiz
6. Which verb forms are most common in
the Methods section of Scientific Reports?
a) Past tense (was / were / measured ....)
b) Conditionals (would / might / could ...)
c) Future tense (will do ... / going to do ...)

Quiz
7. What is the standard, logical sequence of
statements in Scientific writing?
a) Parallel
b) Recursive
c) From broad to narrow

Quiz
8. Many scientists use the C.A.R.S
framework when writing an introduction
to a report. What does it stand for?
a) Create a Research Space
b) Consider All Reasonable Speculation
c) Conduct a Responsible Study

Quiz
9. Which of these statements might you
expect to read in a Scientific Report?
a) The alternative hypothesis has been
proven
b) The null hypothesis has been rejected
c) The null and alternative hypotheses
have been rejected

Quiz
10. Which of these would be considered a
weakness in a Scientific Report?
a) The experiment it reports on
reproduces an earlier one
b) Limitations are explicitly acknowledged
by the authors
c) Everyday English words are avoided in
favour of Latin and Greek vocabulary

Quiz
11. Which of these factors is especially
relevant in longitudinal studies with
groups of participants?
a) Attrition
b) Synthesis
c) Synchronicity

Quiz
12. What might the term ‘Figure 1’ in a
scientific report refer to?
a) The leader of a research team
b) A chart or graph
c) A table of results

© 2012
This PowerPoint Presentation and the accompanying
handouts are copyrighted by the Centre for
Teaching and Learning, Massey University, Albany
and may not be used, except for personal study,
without written permission from the copyright
owner.

Introduction to scientific method, basic statistics and scientific writing

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