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The Ultimate Student’s Guide to
Scientific Research
Features:
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Dedication
To all our mentors and mentees – past, present, and future – this is
inspired by you, this is for you, and this is in your honor. This is
especially in the loving memory of Jonathan C. Wright, PhD.
Contents
About the Authors ....................................................................................................ix
Chapter 1 Introduction..........................................................................................1
Samuel J. S. Rubin and Nir Qvit
vii
viii Contents
Index......................................................................................................................137
About the Authors
Samuel J. S. Rubin, PhD, MD
Dr. “Yoni” Samuel J. S. Rubin completed his PhD in immunology at Stanford
University School of Medicine, followed by postdoctoral training, MD, and
postgraduate clinical training at Stanford. His research focuses on better
understanding the molecular and cellular mechanisms underlying chronic immune-
mediated diseases and using this knowledge to develop safer, cheaper, and more
effective tools for detecting and treating illness worldwide. In the field of mucosal
immunology and immune cell trafficking, Dr. Rubin’s findings have inspired the
development of novel blood-based methods for detection of gastroenterological
conditions. His work has also led to the development of precision medicine biologics
for the treatment of chronic auto-inflammatory conditions. Dr. Rubin is especially
appreciative for the circuitous and often unexpected path that continues to define his
career. Especially influential were the many instructors and mentors who inspired his
dedication to teaching the student and shaped his past and ongoing endeavors. He has
published Peptides and Peptidomimetics: From Bench to Bedside, served as a guest
editor for Current Topics in Medicinal Chemistry, and continues to serve as a
reviewer for numerous scientific journals. Amongst other awards and recognitions,
Dr. Rubin received the United States National Science Foundation Graduate Research
Fellowship and the Hugh McDevitt Prize in Immunology.
ix
1 Introduction
GUIDING VALUES
Becoming and excelling as a scientist is a tremendously challenging endeavor,
requiring immense stamina, passion, and curiosity. Much like the experiments
DOI: 10.1201/9781003301400-1 1
2 The Ultimate Student’s Guide to Scientific Research
conducted, scientific training and career advancement can often involve substantial
trial and error, as the profession is largely decentralized and heterogeneous. Having
experienced this first hand, we decided to compile this work as a guide and
reference for potential scientists, aspiring scientists, scientists in training, scientists
seeking advice, and anyone else seeking a window into the scientific world. Equally
and perhaps more important is our philosophy of paying it forward. Though we both
navigated our paths by significant trial and error, we also benefited greatly from the
advice, guidance, and counsel of others who took the time and effort to share their
experiences with us – never in exchange for compensation but solely on the
condition that we continue to pass on what we learn to others.
As you will see throughout this book, paying it forward is one of our most
important guiding values for being a successful scientist and a responsible
individual. This also translates into treating others the way you wish to be treated,
which will get you much farther in the world than alternative approaches. Other
requirements for being a successful scientific investigator are an unquenchable
thirst for continual learning, insatiable curiosity, and a healthy dose of skepticism.
These attributes are key for maintaining inspiration, gaining new knowledge,
making novel discoveries, and avoiding all too common pitfalls of cognitive bias.
Other important practices are seeking different perspectives and learning to teach
yourself anything you may need. Actively pursuing distinct perspectives will broaden
your options and capabilities, teach you things that you did not realize you needed to
learn, allow you to ask better questions, and help avoid different forms of cognitive
bias. Learning to teach yourself anything will empower you to excel, to be agile, and
to avoid dependence on any single entity. Teaching yourself can assume a variety of
forms, ranging from reading a textbook, searching the Internet, seeking out and
consulting with experts, taking a course, or performing an experiment. Building this
dexterity and initiative is invaluable for the ever-evolving pursuit of science.
Learning from failure is immensely helpful in streamlining subsequent efforts
and is central to the process of trial and error. However, learning from the error of
others or by observing something done in a manner incongruent with scientific
standards or your own values is equally or perhaps more critical than growth from
your own trial and error because with this external awareness you may be able to
avoid making crucial mistakes in the first place. Paying attention to others’ failures,
their challenges, how someone accomplishes a task even successfully but in a
manner that may be right for them but wrong for you, or simply identifying that a
particular approach feels wrong to you, are all important for heading off your own
missteps before they occur and choosing an appropriate path forward. Some of the
most valuable lessons we have learned about how we want to conduct experiments,
run a lab, write a paper, etc. have originated from observing the way others
approach these tasks – both successfully and unsuccessfully – and using those
observations and our values to hone our own approaches.
4 DOI: 10.1201/9781003301400-2
The History of Science 5
settlements with wood, brick, and stone structures. These villages later developed
into the first cities.
Sumerians formed the first human civilization in Mesopotamia (Greek: “Land
between the Rivers”) around 5,500 years ago. They are credited with many
advances in technology, such as irrigation systems, the wheel, the plow, and writing
(cuneiform). Sumerians also had an interest in science including astronomy and
created a calendar adjusted to the phases of the moon. In addition, they created a
system of degrees, minutes, and seconds.
Other civilizations also studied science and developed similar technology. For
example, the Egyptians also invented the plow, used copper materials, invented
writing (hieroglyphic), and the first 365-day calendar. The Chinese were skilled
chemists, and they performed sophisticated reactions, such as distilling alcohol and
extracting copper. In addition, they developed gunpowder by blending charcoal,
sulfur, and potassium nitrate.
In many of these civilizations, people studied the moon, sun, and planet
movements to calculate seasons, establishing a ritual calendar. Therefore, it is not
surprising that astronomy is ranked as one of the oldest sciences and the first natural
science developed by early civilizations, as knowledge of the stars proved essential
to running a complex agricultural society. Ancient civilizations also used
mathematics for practical applications in various fields, such as astronomy (e.g.,
measuring the motion of celestial bodies), engineering (e.g., construction of
monumental structures), agriculture (e.g., measuring land and calculating field
area), and timekeeping. Texts from about 1,700 BCE demonstrate remarkable
mathematical elegance, and Babylonian mathematicians understood the
Pythagorean relationship. However, there are fewer examples of these early groups
studying beyond practical calculations applied to their real world needs.
In all these early civilizations, humans developed methods to describe and
harness nature. However, to understand nature was the function of religion and
magic, not reason. The Greeks were the first to explore beyond description
and arrive at reasonable explanations for natural phenomena, which did not involve
the divine will.
CLASSICAL ANTIQUITY
Based on the contributions of ancient civilizations across fields, ancient Greeks
attempted to explain world events by invoking natural causes. They are often called
the first scientists or natural philosophers. Numerous inventions and discoveries are
attributed to ancient Greek scientists in various fields, such as astronomy,
geography, and mathematics. It was a period characterized by a flourishing and
confident Greek culture in many aspects. This included politics, philosophy,
science, architecture, theater, athletic games, and military strength that formed a
legacy with unparalleled influence on Western civilization.
The ancient Greeks used science and logic to begin understanding events
happening in the world around them. They made many advancements in science and
technology. Thales, one of the first Greek mathematicians, focused on geometry and
observed many key relationships (such as Thale’s theorem) concerning shapes,
6 The Ultimate Student’s Guide to Scientific Research
angles, and lines. Pythagoras defined the Pythagorean Theorem, which describes the
sides of a right triangle and is still regularly utilized to this day across numerous
fields. Euclid, regarded as the most significant Greek mathematician, wrote several
books on the subject of geometry. Euclid’s compilation Elements includes 13 books
on geometry, which served as the world’s main text for almost two millennia.
Archimedes is also well known for many discoveries such as the relationship
between the surface and volume of a sphere and its circumscribed cylinder,
formulation of the hydrostatic principle (Archimedes’ principle), and a strategy to
move water (Archimedes’ screw).
Astronomy was critical for navigation, understanding and regulating agriculture,
and creating an accurate calendar. Development of the field by ancient Greek
astronomers is considered a major phase in the history of astronomy. The Greeks
introduced mathematics into astronomy, seeking a geometrical model for celestial
phenomena. The Greek astronomer Aristarchus believed the sun was the center of
the solar system. He also placed the planets in the correct order from the sun.
Eratosthenes was the first to calculate the Earth’s circumference accurately. They
even developed a device called the Antikythera mechanism, which is considered the
world’s first analog computer. This device was used for calculating movements of
the planets. The Greeks also applied their learning to many other practical
inventions, such as the watermill, alarm clock, central heating, and crane, etc.
Ancient Greek society also made its mark in many other fields, such as physics.
Their study was the first to be led by intellectual pursuit in a controlled manner,
which is standard practice today. The Greeks also studied medicine as a scientific
way to cure illnesses and diseases. Hippocrates, the most famous Greek doctor and
sometimes considered to be the forebearer of Western medicine, taught that diseases
had natural causes and could sometimes be cured by natural means. Indeed, Greek
doctors studied sick people and devised treatments based on their symptoms. The
Greeks likewise developed an encyclopedic range of herbal medicines. Many
medical students still take the Hippocratic Oath upon graduation, although there are
several antiquated portions that in many cases are modified and updated.
The ancient Greeks also explored biological processes and living organisms. The
term “biology” is derived from the Greek terms “bios” (“life”) and “logia” (“study
of”). Aristotle studied animals in detail and made what is considered a record of the
first systematic and comprehensive study of animals. He also noted his observations
in a book titled History of Animals. Aristotle’s work laid the foundations of zoology
and botany by classifying animals and plants according to their different
characteristics. Darwin considered Aristotle the most significant early contributor
to biological thought. In an 1882 letter, Darwin wrote that “Linnaeus and Cuvier are
my two gods, though in very different ways, but they were mere schoolboys to old
Aristotle” (Gotthelf, 1999).
through the late 18th century. At that time, a series of events changed scholarly
thought, leading to the birth of modern science. During the scientific revolution,
science became an autonomous discipline, distinct from philosophy and technology.
Some scholars claim that at the end of this period, science replaced Christianity as
the focal point of European civilization. The scientific revolution generated a new
view of science, bringing about the following transformations: an emphasis on
abstract reasoning; focus on quantitative description of nature; understanding of
how nature works; the view of nature as a machine rather than an organism; and the
development of an experimental scientific method.
A few of the key people and discoveries in this area include the astronomer Nicolas
Copernicus, who demonstrated that Earth revolves around the sun and that the Earth is
not the center of the universe, an idea that was embedded in the European conscience,
which challenged societal values of the time. Galileo Galilei was an astronomer and
physicist who was placed under house arrest for much of his life due to views that did
not align with the Church; building on Copernicus’ work, Galilei provided scientific
insights that laid the foundation for many future scientists, sparking the field of
modern astronomy. He was the first to use a refractory telescope to make significant
astronomical discoveries. Galilei observed the moon, Venus phases, moons around
Jupiter, sunspots, and seemingly countless individual stars that make up the Milky
Way Galaxy. Galilei is often credited with the origin of modern physics for his role in
the scientific revolution. His pioneering work on body motions was a precursor to
Isaac Newton’s classical mechanics. Later, Newton published Philosophiæ Naturalis
Principia Mathematica (Mathematical Principles of Natural Philosophy) in 1687,
which provided the foundations for classical mechanics, establishing the laws of
motion and gravitation that revolutionized science.
In the early 1600s, the astronomer and physicist Johannes Kepler published
Kepler’s laws of planetary motion, which concern the elliptical motion of planets
around the sun. Kepler’s laws became part of the scientific revolution’s central
dogma and have been utilized in the development of numerous transformative
technologies such as satellites and rockets.
Andreas Vesalius was an anatomist who published groundbreaking work on
blood circulation in the 1500s. Based on that foundation, William Harvey
demonstrated how blood circulates in the body and explained how the heart
propels blood through the body, a transformational discovery for the time.
Francis Bacon was a politician and philosopher in the late 1500s and early 1600s
who proposed a focus on observation and reasoning in the scientific method. He
developed the scientific methodology, for which he is known as the creator of
empiricism. Therefore, rigorous experimentation was to be used to prove or
disprove hypotheses in the quest for understanding the universe.
SUMMARY
Methodical study of the physical, natural, and social worlds’ behavior through
experimentation and observation is understood to define modern science. Science
tests theories against evidence. The study of science is one of the oldest and most
significant academic disciplines, as it allows us to understand the world around us.
8 The Ultimate Student’s Guide to Scientific Research
Moreover, science influences the countless decisions we make each day. Science is
dynamic and built upon ideas and discoveries from previous generations. Therefore,
the ability to recount the past and pass it on to future generations is critical. The
history of science covers its development from ancient times to the present. Despite
the limited examples presented in this chapter, it is particularly worthwhile to
remember that science has no single origin. Rather, systematic methods emerged
gradually and in parallel over thousands of years from a diversity of cultural
traditions. What remains unchanged is the curiosity, imagination, and intelligence
across generations and cultures.
REFERENCES
Casadevall, Arturo, and Ferric C. Fang. “(a) Historical Science.” 4460-4464: American
Society for Microbiology, 2015.
Daston, Lorraine. “History of Science.” In International Encyclopedia of the Social &
Behavioral Sciences, edited by Neil J. Smelser and Paul B. Baltes, 6842–6848. Oxford:
Pergamon, 2001.
Gotthelf, Allan. “Darwin on Aristotle.” Journal of the History of Biology 32, no.
1(1999): 3–30.
Hooykaas, R. “The Rise of Modern Science: When and Why?” The British Journal for the
History of Science 20, no. 4 (1987): 453–473.
Kuhn, Thomas. “The History of Science.” In Philosophy, Science, and History, 106–121.
Routledge, 2014. Pages16, Taylor and Francis group. eBook ISBN9780203802458.
Lloyd, Geoffrey. “Science in Ancient Civilizations?” In Ancient Worlds, Modern Reflections:
Philosophical Perspectives on Greek and Chinese Science and Culture, edited by
Geoffrey Lloyd. Oxford University Press, 2004. 10.1093/0199270163.003.0002
3 Scientific Impacts
EDUCATION
Science is an essential part of our education as it helps us comprehend the natural
world around us. In learning about the world through scientific studies, we can
understand fundamental principles that govern the universe, from the behavior of
living organisms to the laws of physics. Moreover, science enables us to understand
and address global challenges (e.g., reducing greenhouse gas emissions, as well as
pollution and poverty), and many of these challenges require deep scientific
understanding. Scientific research also advances cutting-edge technologies, which
improve quality and quantity of life (e.g., life-saving medical treatments) and assist
us in solving societal problems (e.g., more efficient forms of energy).
First and foremost, science is based on evidence, and scientific methodology
includes observation, experimentation, and analysis. Learning this method helps
students develop critical thinking skills (e.g., asking questions, seeking answers, and
exploring the world around them), which they can apply to all aspects of their lives. In
addition, by studying science, students learn to think creatively and develop creative
ideas, since science education teaches us to think logically, analyze data, and make
logical decisions based on evidence. In summary, science education is vital for our
personal and societal well-being. Learning science helps us understand and solve
problems, advances technology, and improves our quality of life.
MEDICINE
Science has allowed society to study and advance knowledge of the human body
and the pathogenesis of diseases. This knowledge advances the development of
more effective treatments and cures (e.g., vaccines and antibiotics), saving millions
of lives worldwide and significantly improving public health. Diseases such as
smallpox and polio have been all but eradicated thanks to vaccinations. In addition,
science has a vital role in the regulation of infectious diseases (e.g., identifying and
tracking COVID-19), as well as developing strategies to prevent and control
outbreaks.
Without a doubt, science is one of the most significant pillars of medicine.
Scientific research has led to fewer infections and lethal diseases, allowing
physicians to cure or control them based on interdisciplinary inventions. Medical
science has led to countless innovations, from new technologies and materials to
effective treatments and therapies (e.g., antibiotics, chemotherapy, immunotherapy,
DOI: 10.1201/9781003301400-3 9
10 The Ultimate Student’s Guide to Scientific Research
COMMUNICATION
Science plays a crucial role in communication, and communication is also an
essential aspect of science. Telegrams, telephones, networking, fax, the Internet,
laptops, and mobile phones are only some of the most significant contributions of
science to communication, which have all transformed human life. As science is
also of importance to the public, communicating it to the public can increase
understanding of scientific concepts that can lead to better-informed decisions in
numerous areas.
Effective communication is essential to ensure that scientific knowledge is
disseminated accurately, efficiently, and ethically to a wider audience (e.g., other
scientists, funders, policymakers, consumers, and the public at large). Since in many
cases science is a collaborative effort, effective communication is necessary to share
ideas, methods, and data with colleagues to advance science. Efficient communica-
tion can help advance knowledge and understanding in a particular field and lead to
new discoveries. Overall, communication is an essential component of the scientific
process and improves our understanding of the world around us. Effective
communication facilitates collaboration, promotes scientific research, and informs
policy decisions, hopefully resulting in better-informed decisions.
AGRICULTURE
Agriculture is the second oldest and most fundamental occupation of humans
since the stone age. Moreover, agriculture has undergone significant changes
throughout history. Science shaped the development of modern agriculture, from
traditional subsistence farming to modern agribusiness. Science has made farming
easier and faster in many ways (e.g., sowing seeds, harvesting, spraying
fertilizers, irrigation, etc.) through improved technologies and machines.
Agricultural science is an interdisciplinary field of food and fiber manufacture
that includes many steps (e.g., production, processing, and distribution) and deals
with various disciplines (e.g., plant breeding, genetics, soil science, entomology,
plant pathology, and food science). Scientists have used plant selection and
breeding techniques to improve crop production, yield, and quality, as well as
enhance the nutritional content of crops. This helps meet the growing demand for
food as the global population increases.
By adopting modern techniques (e.g., precision farming, integrated pest
management, improving water management practices, and soil conservation), it is
Scientific Impacts 11
possible to practice sustainable agriculture and allow farmers to cope with climate
change. Science has revolutionized the way we farm and has led to significant
improvements in food and nutrition security (more individuals have reliable access
to nutritious food), as well as economic development (creating new jobs and
increasing productivity).
ELECTRICITY
Electricity is one of the most important discoveries in the history of science, and it
has transformed all aspects of life (e.g., power to our houses, public places,
transportation systems, and medical equipment to mention a few). Electricity is a
form of energy that is generated from various sources (e.g., fossil fuels, wind, solar,
hydropower, and nuclear power), and currently power generation is being
transitioned from antiquated methods (e.g., burning coal and fossil fuels) to
renewable sources. Electrical power is an area of major scientific research, which
has led to many new technologies (e.g., drawing water from oceans and rivers to
supply to homes and other sources of renewable energy). Electricity is a
fundamental aspect of modern life, which has tremendously shaped and been
shaped by science.
TRANSPORTATION
Transport is necessary for the movement of people and goods from one corner
of the globe to another. Science has led to significant progress in transportation
technology in various aspects, such as efficiency, safety, environmental impact,
and sustainability of transportation. For example, science helps to develop more
efficient modes of transportation (e.g., hybrid and electric vehicles), which
reduce carbon emissions and transportation costs. Science also helps us
understand the physical principles involved in transportation (e.g., the laws of
motion), leading to the production of vehicles with better safety features (e.g.,
airbags and seat belts), resulting in systems that minimize accidents and
injuries.
Finally, science also drives innovation in various advanced aspects of transpor-
tation, including (1) development of lightweight materials (e.g., carbon fiber) that
significantly reduce vehicle weight making them more fuel efficient; (2) design of
modern transportation infrastructure (e.g., roads, bridges, airports, and tunnels) and
optimized construction material properties; (3) innovation of advanced modes of
transportation (e.g., airplanes, electric vehicles, high-speed trains, autonomous
vehicles, and the hyperloop) to make transportation faster, safer, and more efficient.
Overall, science is essential for transportation, and advances in science will
continue to play a critical role in shaping the future of transportation.
SUMMARY
Although career scientists play an active role in the advancement of scientific
knowledge, we all have a part to play in some way. As part of our daily lives, we
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