Class 1: Why? How? Who? What?

Methodology of Scientific Research

Andrés Aravena, PhD

February 20, 2024

Welcome to

Methodology of Scientific Research

Methodology of Scientific Research

also known as MSR

also known as MıSıR

also known as 🌽

Today’s questions



I am Andres Aravena

  • Assistant Professor at the Molecular Biology and Genomics Department, Istanbul University
  • Mathematical Engineer, U. of Chile
  • PhD Informatics, U Rennes 1, France
  • PhD Mathematical Modeling, U. of Chile
  • not a Biologist
  • Applied Mathematician who can speak “biologist language”

What about you?


Why are you here?

Answer now with your voice


Specific Goal

In this course we will speak about

Good practices doing science

We will learn to observe, communicate and collaborate better

Generic goals

We want to help you to become

  • Better molecular biologists
  • Better scientists
  • Better professionals
  • Better citizens

Better molecular biologists

  • Lower failure rate in your experiments

  • Do better experiments

  • Ask better questions

  • Achieve larger impact

Better scientists

  • Ask better questions

  • Propose better answers

  • Create Knowledge, not only Data

Better professionals

  • Perhaps you will change your career later in life

  • Whatever you do, do your best work

  • Always follow good practices

Better citizens

Perhaps you will win the lottery
(or inherit many million dollars from a distant uncle)

and you do not work anymore

Still, you need to understand the world

Enough so big companies cannot fool you

We need to see the Big Picture,
How did we get to here and now?


Course plan (first part)

  • Asking good questions
  • Observing nature
    • Estimating
    • Measuring
    • Evaluating uncertainty
  • Finding reasonable theories
  • Testing theories with experiments

Key words

  • Estimation and Guesstimation
  • Order of magnitude
  • Confidence Intervals
  • Error propagation
  • Uncertainty budget
  • Dimensional Analysis

Tools & Good Practices

(second part of the course)

Lab Notebook

One of the essential good-practices of laboratory work is the Lab Notebook

They are essential if you want to get a patent for something you create

They are essential to carry long term experiments

We encourage you to use a good quality notebook every day

Do not trust your memory

Course’s Homepage

Our homepage is at

It is part of my blog

Homework and class slides are published there

I also have a YouTube channel

An operational definition of Science

Scientist work is to understand Nature

We start by Observing Nature, usually measuring values

These are exploratory experiments

This is the first part of our course

The thing we study must be reproducible, and we need to see that repetition

We can find them using plots, linear models, clustering, etc.

This is the most important part

Good answers to bad questions are useless

Good questions are good, even if we don’t have answers

We answer these questions using models and explanations

Valid models should make predictions that we can test in the lab…

These are validation experiments.

If the results do not match the prediction, we know that the explanation is wrong. Two steps back.

Now we publish our data and model, so other scientists validate or reject it.

The final validation is to be published.

If the paper is accepted and published, our work becomes part of our shared human knowledge.

The goal of Science is to produce new Knowledge.

When we observe Nature we use our previous Knowledge

We look for new Patterns that raise new Questions.

“Noise becomes Signal”

“Math is hard…”

(some people say)

Well… it depends

3 × 4

3 × 4 + 5

34 × 45

345 × 456

We have two brains

Two systems of thinking

Daniel Kahneman, 2002 Nobel Memorial Prize in Economic Sciences

Two systems of thinking

System 1


  • instinctive
  • emotional
  • automatic
  • cheap

System 2


  • deliberate
  • rational
  • intentional
  • expensive

The priority of our organism is

  1. Survival
  2. Save energy

So System 1 is the default mode

Most of the time we use the cheap intuitive system

Rational thinking (i.e. math) is not spontaneous

Another book recommendation

Even on TV

Intuition vs Rationality

One option is to be like Spock, and suppress all intuition

The other option is to train our intuition

Guesstimation trains our gut

This is why we have been practicing estimating magnitudes

  • Not let our intuition fool us

  • Get a gut feeling about numbers

This last part is important, because we make decisions based on our feelings, and often we do not know what to feel about a number

Estimating quantities

Powers of 10

At first, we estimate by powers of 10
(after choosing the appropriate units)

We even have names for some of them them:

  • deci, centi, milli, micro, nano, pico

  • deca, hecto, kilo, mega, giga, tera, peta, exa


In powers of ten, how many people live in Turkey?

Be brave, take a guess

(no books, no Google, no ChatGPT, no Internet, only guess)

Upper and lower bounds

When estimating a value, we usually can guess that the real value is somewhere between two values

In other words, we guess lower and upper bounds \(L\) and \(U\)

Choose the smallest value that seems right,
then the largest one

How many people live in Istanbul?

Remember: we are looking for two numbers

Order of magnitude

The order of magnitude of a value is its power of 10

More precisely, is the integer part of the logarithm base 10

We say that two quantities are in the same order of magnitude if their ratio is between 0.1 and 10

i.e. if each one is less than ten times the other

Compare populations

Which of these populations are of the same order of magnitude?

  • Istanbul
  • Ankara
  • Tokio
  • USA
  • UK
  • China
  • India

Half order of magnitude

Instead of going \[10^{-1}, 10^{0}, 10^{1}, 10^{2}, 10^{3}\] we can increment the exponent by 0.5 \[10^{-1}, 10^{-0.5}, 10^{0}, 10^{0.5}, 10^{1}\]

Since \(10^{0.5} = \sqrt{10}≈ 3.16≈3\) we can say \[0.1, 0.3, 1, 3, 10, 30, 100,…\]

How many trees?

Our campus has a park, near Astronomy department

How many trees are there?

What is the age of this turtle?

What is the length of the genome of this turtle?

How many hairs do you have in your head?

What is the weight of this boat?

and the weight of this boat?

How many apartments are in the photo?

What is the height of this building?

Writing large numbers

The speed of light is about 300000000 m/s

It is easy to miscount the number of “0”

Instead, we write 3×108 m/s$

Better, in computers we write 3E8

(This is called exponential notation)

Here 3 is called mantissa and 8 is the exponent

The “billion dollars problem”

In USA, a billion is a thousand millions

In the rest of the world, a billion is a million millions
(often called “a milliard”)

There are two conventions: short scale and long scale

To avoid confusion, better use giga or tera

or use scientific notation: 109, 1012

How many cells are there in the human body?

How many stars can we see without a telescope?


Please read The Library of Babel by J.L.Borges