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



3. Methods

4. Results

5. Discussion

6. Introduction


Good Science?



3. Methods

4. Results

5. Discussion

6. Introduction


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 trueHypothesis 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.

https://www.youtube.com/watch?v=fXWuB7fmGv0

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)



3. Methods

4. Results

5. Discussion

6. Introduction


MethodsWhat 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: Methods1. 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 (Detecto6800, 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



3. Methods

4. Results

5. Discussion

6. Introduction


ResultsWhat 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• Focus on results relating to your hypothesis /

objectives

Results• Focus on results relating to your hypothesis /

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 fromwikipedia.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 siblingsUnit 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:

425.180

11x15x14x73x32x171x270x24

11 5 4 4 4 4 4 4 4 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2

2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Display numerical continuous data

• Stem-and-leaf plot of HeightUnit 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=500Median=500

Mean=495Median=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

Randomisation- Task 2

Some Random Numbers

18 48 20 16 5 47 45 23 38 1715 22 44 46 13 30 7 25 50 416 29 2 27 19 2 9 11 50 27

45 35 1 13 46 38 32 41 31 266 15 40 19 44 39 49 48 43 84 29 14 37 36 22 16 7 47 5

17 42 21 25 3 34 23 30 28 3318 12 10 24 20 34 19 10 35 2324 18 41 43 28 40 47 4 48 72 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’.



3. Methods

4. Results

5. Discussion

6. Introduction


DiscussionWhat 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

DiscussionWhat 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.”



3. Methods

4. Results

5. Discussion

6. Introduction


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 SectionsSentence Change

BlindnessAtkinsDiet

At any given time, 45% of women and 30% of men in the US are trying to lose weight.

Task: Match Sentences with Sections

Sentence Change Blindness

AtkinsDiet

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


BlindnessAtkinsDiet


All participants completed a comprehensive medical examination and routine blood tests.


BlindnessAtkinsDiet



M


BlindnessAtkinsDiet



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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.


BlindnessAtkinsDiet



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BlindnessAtkinsDiet



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BlindnessAtkinsDiet



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3. Methods

4. Results

5. Discussion

6. Introduction


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.”

Task: Scientific Writing“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

Task: Scientific Writing“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?



• Clarity

• What is mounted in the container?



• Clarity

• What is mounted in the container?

• “Because the receiver presented the radiometer with a high-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 NOTexpect 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

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Teaching and Learning, Massey University, Albany and may not be used, except for personal study, without written permission from the copyright

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introduction to scientific method, basic statistics and scientific writing

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