Lecture 1: Research & Papers

Announcements

‣ Please register to Piazza at

[Link]/cmu/fall2024/04701a

‣ It is recommended to use Piazza for questions that may be

relevant to the entire class and to use the Canvas mailbox
(or regular email) for other questions.

‣ A poll for weekly recitation times has been posted on Canvas.

Please make sure that you answer by midnight 9/30.

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 Research

‣ This course is about research methods. Let us rst de ne this

important term.

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 Research

‣ This course is about research methods. Let us rst de ne this

important term.

De nition | Research

Research is a detailed study of subject to create new generalizable

knowledge. Research can be applied to learn new information, create
new products or develop new solutions to a given problem.

‣ Example. Consider the case

of a broken window…

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 Research

‣ This course is about research methods. Let us rst de ne this

important term.

De nition | Research

Research is a detailed study of subject to create new generalizable

knowledge. Research can be applied to learn new information, create
new products or develop new solutions to a given problem.

‣ Example. Consider the case

of a broken window…

If we perform a detailed
study to determine who broke
the window, we are not
conducting research (but rather a detective investigation).
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 Research

‣ This course is about research methods. Let us rst de ne this

important term.

De nition | Research

Research is a detailed study of subject to create new generalizable

knowledge. Research can be applied to learn new information, create
new products or develop new solutions to a given problem.

‣ Example. Consider the case

of a broken window…

In contrast, if we develop a new

computational model to analyze
microscopic images of the crack for determining the time
when it rst appeared, we are conducting a research study.
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 Scienti c research

‣ Let us now discuss the distinction between scienti c research

and other forms of research.

‣ Below is the owchart of a scienti c research study

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 Scienti c research

‣ Let us now discuss the distinction between scienti c research

and other forms of research.

‣ Below is the owchart of a scienti c research study

Collect Formulate
observations hypothesis

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 Scienti c research

‣ Let us now discuss the distinction between scienti c research

and other forms of research.

‣ Below is the owchart of a scienti c research study

Collect Formulate Make

observations hypothesis predictions

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 Scienti c research

‣ Let us now discuss the distinction between scienti c research

and other forms of research.

‣ Below is the owchart of a scienti c research study

Collect Formulate Make Test

observations hypothesis predictions predictions

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 Scienti c research

‣ Let us now discuss the distinction between scienti c research

and other forms of research.

‣ Below is the owchart of a scienti c research study

Revise
hypothesis

No

Collect Formulate Make Test Yes Report

observations hypothesis predictions predictions conclusions
Valid?

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 Scienti c research

‣ Let us now discuss the distinction between scienti c research

and other forms of research.

‣ Below is the owchart of a scienti c research study

Revise
hypothesis

Induction Deduction No

Collect Formulate Make Test Yes Report

observations hypothesis predictions predictions conclusions
Valid?

In the inductive–deductive approach, induction is rst used to infer explanations

(the hypotheses) from observations. Then, deduction is applied to propose
predictions from these explanations. Finally, critical tests are conducted to check
predictions. The process is repeated until reaching new generalizable conclusions.
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 Scienti c research

‣ The previous owchart is the basis of the method of scienti c

research

De nition | Scienti c method

The scienti c (inductive–deductive) method consists of three steps:

- making hypotheses based on observations (induction);
- deriving predictions from these hypotheses (deduction);
- validating the predictions (critical testing).
This process is iterated until reaching generalizable knowledge.

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 Scienti c research

‣ The previous owchart is the basis of the method of scienti c

research

De nition | Scienti c method

The scienti c (inductive–deductive) method consists of three steps:

- making hypotheses based on observations (induction);
- deriving predictions from these hypotheses (deduction);
- validating the predictions (critical testing).
This process is iterated until reaching generalizable knowledge.

‣ Note. The critical test may be an observation

(the passive study of the evolution of a
system) and an experiment (the active study
of the response of a system)…

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 Scienti c research

‣ The previous owchart is the basis of the method of scienti c

research

De nition | Scienti c method

The scienti c (inductive–deductive) method consists of three steps:

- making hypotheses based on observations (induction);
- deriving predictions from these hypotheses (deduction);
- validating the predictions (critical testing).
This process is iterated until reaching generalizable knowledge.

‣ Note (cont’d). The critical test may also be

interview (the interactive questioning of a
subject) or it may be a survey (a non-
interactive questioning of a subject).

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 Scienti c hypothesis

‣ Important. Not all proposed explanations qualify as

acceptable scienti c hypotheses.

De nition | Scienti c hypothesis

A hypothesis is a proposed explanation (an educated guess) for a

observation. For this explanation to be a scienti c hypothesis, it must
be falsi able, meaning that one should be able to nd evidence
that would disprove it.

‣ Example. Consider the following two hypotheses to explain

the inef ciency of a given data processing task:

Data loading accounts for more than half of the time for
processing the data

There is an undetectable bottleneck in processing the data

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 Scienti c hypothesis

‣ Important. Not all proposed explanations qualify as

acceptable scienti c hypotheses.

De nition | Scienti c hypothesis

A hypothesis is a proposed explanation (an educated guess) for a

observation. For this explanation to be a scienti c hypothesis, it must
be falsi able, meaning that one should be able to nd evidence
that would disprove it.

‣ Example. Consider the following two hypotheses to explain

the inef ciency of a given data processing task:

Data loading accounts for more than half of the time for
processing the data

There is an undetectable bottleneck in processing the data

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 Scienti c hypothesis

‣ Important. Not all proposed explanations qualify as

acceptable scienti c hypotheses.

De nition | Scienti c hypothesis

A hypothesis is a proposed explanation (an educated guess) for a

observation. For this explanation to be a scienti c hypothesis, it must
be falsi able, meaning that one should be able to nd evidence
that would disprove it.

‣ Question. Consider a research

topic of interest to you and an Collect Formulate
interesting observation you observations hypothesis

made. Can you formulate a

scienti c falsi able hypothesis Make Test
for this observation? Then, try to predictions predictions

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formulate a non-falsi able one.
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 Basic and applied research

‣ Let us now discuss the relation and distinction between

basic research and applied research
Quest for fundamental understanding

High

Niels Bohr Thomas Edison

Low

Louis Pasteur Dilettante/tinkerer

Low High
Question. Can you place these four
Consideration of practical use individuals in their respective box?
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 Basic and applied research

‣ Let us now discuss the relation and distinction between

basic research and applied research
Answer. Niels Bohr contributed to
Quest for fundamental understanding

understanding the structure of

atoms, leading to fundamental
High

physics discovery. Thomas Edison

developed the rst light bulb by
Niels Bohr Louis Pasteur trial-and-error search (now called the
Edisonian approach). Louis Pasteur
discovered the fundamental
Low

principles of immunization and

developed anti-rabies vaccination. A
Dilettante/tinkerer Thomas Edison dilettante or tinkerer does not seek
generalizable knowledge.
Low High
_____
Consideration of practical use Tinkerer: one who likes modifying objects without understanding
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 Basic and applied research

‣ Question. Here are examples of research topics from the

web. Which ones belong to Bohr’s or Edison’s quadrant?

A study searching for the causes of cancer

A study of the molecular components that make up human DNA
A development of a statistical model to predict battery lifetime
A study on how to treat patients with insomnia
A data-driven investigation to improve agricultural crop production
An examination into whether a vegetarian diet is healthier than regular diet
A study on how to treat patients with insomnia
An investigation into how the universe began
A study to learn which areas in the world get the most precipitation

‣ Question. How would you complement these topics so that

they t into Pasteur’s quadrant?
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 Scienti c papers

‣ One of the primary outputs of scienti c research are scienti c

papers to report a new piece of information, a new product.,
or a new solution.

De nition | Scienti c paper

A scienti c paper is a document that describes a research study and

reports its generalizable conclusion. Typical scienti c papers are a
discussion of an unknown phenomenon, a presentation of a discovery,
an addition to a previous research study, or a comparative study
between different approaches.

‣ Question 1. What is the difference between a paper, a

manuscript, and an article?

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 Scienti c papers

‣ One of the primary outputs of scienti c research are scienti c

papers to report a new piece of information, a new product.,
or a new solution.

De nition | Scienti c paper

A scienti c paper is a document that describes a research study and

reports its generalizable conclusion. Typical scienti c papers are a
discussion of an unknown phenomenon, a presentation of a discovery,
an addition to a previous research study, or a comparative study
between different approaches.

‣ Question 1. What is the difference between a paper, a

manuscript, and an article?

‣ Answer. An article is a published paper while a manuscript

is a paper that has not yet been published.
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 Scienti c papers
THE PAPER
Height
6,000 m

MOUNTAIN
100–999 CITATIONS
(1,066,046 papers)

TOP-100
5,500 m

‣ Here is a visual illustration

If you were to print out just the first page
PAPERS of every item indexed in Web of Science,

10–99 CITATIONS (13,104,875 items)

the stack of paper would reach almost to
the top of Mt Kilimanjaro. Only the top
metre and a half of that stack would have

of the amount of scienti c

received 1,000 citations or more, and just
5,000 m a centimetre and a half would have been
cited more than 10,000 times. All of the

1,000–9,999 CITATIONS (14,351 items)

top 100 are cited more than 12,000 times,
besting some of the most recognizable
Watson and Crick
scientific discoveries in history.
on structure of

articles in the history of

DNA (1953)
5,207 citations
4,500 m

10,000+
CITATIONS
(148 papers)

humanity. 4,000 m

Farman, Gardiner &

TOP-10 PAPERS
Shanklin discover the
ozone hole (1985)
1,871 citations
Just 3 papers have received more than 100,000
citations, putting them well ahead of the rest. These
3,500 m runaway hits all cover biological lab techniques, which
in general dominate the list of most-cited literature,

1–9 CITATIONS (18,280,005 items)

‣ Questions. What does this
including 7 of the top 10.
305,148 citations

Hirsch proposes
1
Protein measurement with the folin phenol reagent (1951)
the h index to
measure scientific
3,000 m
2

paper mountain represent?

Light 213,005
productivity (2005)
aircraft Cleavage of structural proteins during the assembly of head of
1,797 citations
cruising the bacteriophage T4 (1970)
altitude
3,000 m 3 155,530
A rapid and sensitive method for the quantitation of microgram
quantities of protein utilizing the principle of protein-dye binding (1976)

2,500 m
4 65,335
DNA sequencing with chain-terminating inhibitors (1977)

5 60,397
Single-step method of RNA isolation by acid guanidinium
thiocyanate-phenol-chloroform extraction (1987)

How are the papers

6 53,349
Electrophoretic transfer of proteins from polyacrylamide gels
2,000 m
to nitrocellulose sheets: procedure and some applications (1979)
7 46,702
Development of the Colle–Salvetti correlation-energy formula
into a functional of the electron density (1988)

ranked? Why are they

8 46,145
Density-functional thermochemistry. III. The role of exact
exchange (1993)
1,500 m
9 45,131
A simple method for the isolation and purification of total
lipides from animal tissues (1957)

ranked that way?

10 40,289
CLUSTAL W: improving the sensitivity of progressive multiple
sequence alignment through sequence weighting, position-
specific gap penalties and weight matrix choice (1994)
1,000 m
Burj
Khalifa
828 m
[Link]

0 CITATIONS (25,332,701 items)

To explore the full list, and
to see each paper’s citation
history over time, visit
[Link]/top100
500 m

Do you agree with the

Eiffel
Tower
301 m

ranking? How should it be

Data provided by Thomson Reuters/Web of Science. Individual paper citation figures
0m extracted 7 October 2014. Distribution of citations in database: 19 September 2014

3 0 O C T O B E R 2 0 1 4 | VO L 5 1 4 | NAT U R E | 5 5 1
© 2014 Macmillan Publishers Limited. All rights reserved

modi ed?
Van Noorden et al., Nature 514, 550 (2014)

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 Summary

‣ Research targets generalizable knowledge.

‣ Scienti c research typically consists of the three steps, which

are induction, deduction, and critical testing.

‣ A scienti c hypothesis must be falsi able.

‣ Pasteur’s quadrant refers to

the intersection between basic
research and applied research.

‣ A manuscript is an unpublished
paper while an article is a paper
that has already been published
in a journal.

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 Addendum/erratum

‣ P. 11: De nitions for dilettante and tinkerer have been added

‣ P. 15: Summary slide has been added.

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