1 Nature of Science

Andrea Bierema

Learning Objectives

  • Identify aspects and misconceptions regarding the nature of science and scientific inquiry.
  • Explain how the commonly taught “scientific method” aligns with the setup of a research paper.
  • Describe the processes of science.
  • Identify scientific research questions.
  • Explain and make scientific observations and inferences.
  •  Describe the main parts of a scientific argument.
  • Given a description of an investigation, describe the type of study, the research question, and control and experimental variables, when appropriate.

An Introduction to the Nature of Science

To understand what is, just look around you. What do you see? Perhaps your hand on the mouse, a computer screen, papers, ballpoint pens, the family cat, the sun shining through the window, etc. Science is, in one sense, our knowledge of all that: all the stuff that is in the universe from the tiniest subatomic particles in a single atom of the metal in your computer’s circuits to the nuclear reactions that formed the immense ball of gas that is our sun, to the complex chemical interactions and electrical fluctuations within your own body that allow you to read and understand these words. But just as importantly, science is also a reliable process by which we learn about all that stuff in the universe. However, science is different from many other ways of learning because of the way it is done. Science relies on ideas with gathered from the .

Given the way that science is often taught—memorizing facts from a thick textbook based on research done decades ago and completing lab activities in which there is one known answer—many students have about what science is and how it works. Complete the following interactive to learn more about the real side of science!


Scientific Practices


article with text represented as lines into separate sections and an unlabeled graph
Graphic of a scientific article.

The above quiz mentioned that there really is no one scientific method. So why is “the scientific method” so often taught?

Simply put, it is easier to follow something in an organized, familiar format than to follow along the actual process of any given investigation. This is why the standard setup of a scientific article is organized in a similar way as “the scientific method” and likely why it is often taught in grade school (and even college).

See the chapter “Information Communication” to learn more about scientific articles.

Science Flowchart

As you learned from the activity above, scientists do not follow one Scientific Method. Rather, science is complex, but some shared practices among scientists (not just biologists, but all scientists) can be represented as a flowchart. Notice in the flowchart below, for instance,

  • it is non-linear; every study is unpredictable and follows a different path,
  • the research is not “done” after one investigation. Results often lead to new questions or new ways to investigate a similar question, and
  • one of the main elements is “Community Analysis and Feedback.” Science is a social endeavor and scientists talk to each other about their research before, during, and after an investigation is done and even published.


At first glance, scientific practices, as demonstrated in the science flowchart, might seem overwhelming. Even within the scope of a single investigation, science may involve many different people engaged in all sorts of different activities in different orders and at different points in time—it is simply much more dynamic, flexible, unpredictable, and rich than many other representations. Let’s break it down by looking at an example. The video below explains how an investigation of past climate change fits into the elements of the science flow chart.

For closed captioning or to view the full transcript see the video on YouTube. or click on the “YouTube” link in the video.

Testable Research Questions

What makes something science? The checklist below provides a guide for which sorts of activities are encompassed by science, but because the boundaries of science are not clearly defined, the list should not be interpreted as all-or-nothing. Some of these characteristics are particularly important to science (e.g., all of science must ultimately rely on evidence), but others are less central. For example, some perfectly scientific investigations may run into a dead-end and not lead to ongoing research. Use this checklist as a reminder of the usual features of science. If something doesn’t meet most of these characteristics, it shouldn’t be treated as science.

  • Science focuses on the natural world
  • Science aims to explain the natural world
  • Science uses testable ideas
  • Science relies on evidence
  • Science involves the scientific community
  • Science leads to ongoing research
  • Science benefits from scientific behavior


Most of us have probably wondered how other animals think and experience the world (e.g., is Fido really happy to see me or does he just want a treat), but can that curiosity be satisfied by science? After all, how could we ever test an idea about how another animal thinks? In the 1940s, psychologist Edward Tolman investigated a related question using the methods of science. He wanted to know how rats successfully navigate their surroundings—for example, a maze containing a hidden reward. Tolman suspected that rats would build mental maps of the maze as they investigated it (forming a mental picture of the layout of the maze), but many of his colleagues thought that rats would learn to navigate the maze through stimulus-response, associating particular cues with particular outcomes (e.g., taking this tunnel means I get a piece of cheese) without forming any big picture of the maze.

Do rats use a mental map to navigate? Image is of a mouse with a thought bubble of cheese at the end of a maze.
Do rats use a mental map to navigate?

Here’s how Tolman’s investigation measures up against our checklist:

So is it science? Though less stereotypically scientific than splitting atoms, this psychological research is very much within the realm of science.


As seen in the above exercise, only that are regarding the are within the purview of science.

Additional Example

Some topics initially appear to be scientific, but actually are not. For example, the Intelligent Design movement promotes the idea that many aspects of life are too complex to have evolved without the intervention of an intelligent cause—assumed by most proponents to be a being, like God. Promoters of this idea are interested in explaining what we observe in the natural world (the features of living things), which aligns well with science aims. However, because Intelligent Design relies on the action of an unspecified “intelligent cause,” it is not a . The Understanding Science website has more information.

Observations and Inferences

Figure. A collage of examples of how scientists can make observations. Hover over each image for a description. All images from pexels.com

We typically think of observations as having been seen “with our own eyes,” but in science, , humans cannot directly sense many of the phenomena that science investigates (no amount of staring at this computer screen will ever let you see the atoms that make it up or the UV radiation that it emits).

What are raw data? Raw data are unaltered observations. For example, an investigation of the evolutionary relationships among crustaceans, insects, millipedes, spiders, and their relatives might tell us the genetic sequence of a particular gene for each organism. This is raw data, but what does it mean? A long series of the As, Ts, Gs, and Cs that make up genetic sequences don’t, by themselves, do not tell us whether insects are more closely related to crustaceans or to spiders. Instead, that data must be analyzed through statistical calculations, tabulations, and/or visual representations. In this case, a biologist might begin to analyze the genetic data by aligning the different sequences, highlighting similarities and differences, and performing calculations to compare the different sequences. Only then can she interpret the results and figure out whether or not they support the hypothesis that insects are more closely related to crustaceans than to spiders.

What do we do once we have these observations? The next thing is to infer what those observations could mean concerning our research question. This is where prior knowledge and creativity can come into play. What we believe the observations mean is called an “inference.”


Try this exercise to practice identifying observations, inferring what those observations mean, and developing conclusions. Although the “investigation” is not science-based, the skills that you will practice model what scientists do.

Scientific Arguments

We can extend this idea of observations and inferences to .

In this case, the term argument refers not to a disagreement between two people, but to an evidence-based line of reasoning; so scientific arguments are more like the closing argument in a court case (a logical description of what we think and why we think it) than they are like the fights you may have had with siblings.

There are three main components to a scientific argument:

In the figure above, click on the information (“i”) icon to learn more about the main components of a scientific argument.


Below is an article with the parts of the argument labeled.

See caption for link to accessible PDF
This article titled “Odors Help Fruit Flies Escape Parasitoid Wasps” is a synopsis of a full research article. This image has the claim, evidence, and justification labeled. For an accessible version, see the PDF version of this image.

Testing Ideas

Ultimately, scientific ideas must not only be testable but must actually be tested—preferably with many different lines of by many different people. This characteristic is at the heart of all science. Now that we have learned about the complexity of science as a process, let’s explore some of the common ways in which scientists test ideas.

The table below describes some general aspects of the selected types of study: , , and . “Experiment” is broken down into three main types: true experiments, quasi-experiments, and natural experiments. One of the main aspects that distinguish true experiments from all other studies is having an ) and a ).

Types of Research Studies

Type of Study Does it follow the nature of science tenants explained in this chapter (e.g., science is somewhat subjective)? Does it examine possible treatment effects? Does the investigator perform some type of manipulation (e.g., introduce an experimental variable)? Does it use both a control group and experimental group(s)? Does it test for cause and effect relationships? Is the goal of the study to describe a sample's characteristics? Will the results and/or conclusion include images or drawings? Example_Research_Questions
True Experiment Yes Yes Yes Yes It may No It may How does the presence of a cowbird (brood parasite) affect foraging behavior of yellow warbler parents? Place a taxidermy cowbird near some yellow warbler nests; observe behavior of birds with and without the cowbird.
Quasi-Experiment Yes Yes Yes No It may No It may How does temperature affect honey production in honeybees? (create treatment groups exposed to different temperatures, keeping everything else constant)
Natural Experiment Yes Yes No It may have a control It may No It may How does the size of an island affect the number of plant species? (examine islands with similar environments)
Observational Study Yes No No No No It may It may How has biodiversity of coral reefs changed in the last 100 years (compare data collected across multiple decades)
Modeling Study Yes No No No Yes No It may How are wildcat species evolutionarily related to each other (use programs to compare genomes and create a phylogenetic tree)

A list of different types of research studies and their corresponding characteristics.

To learn more about these types of studies, click on the headings below:


Ideally, investigations also involve keeping as many other factors as as possible to better explain the outcome. This is particularly true in experiments. In experiments, ideally, just one variable will vary between the groups (the experimental variable), and everything else will remain constant (often referred to as “controlled variables”). For instance, if investigating the effects of temperature on honey bees, then the rest of the environment, such as the amount of space or sunlight, should remain the same across the groups. In a natural experiment, though, this is not possible for all variables and this lack of control needs to be considered when examining the results of the study (one of the downfalls of a natural experiment).

In modeling studies, the model is not an exact replica of the system of interest. Rather, it only focuses on the possible causes of the observed phenomenon (i.e., the effects of interest). Although the aspects of the system that are considered irrelevant are not true “controlled variables,” it is, nonetheless, important to consider when developing models.

Controlling variables during an observational study is usually not possible, or even desired as the intention is to describe relationships or patterns.

Are model organisms scientific models?

A  is a non-human species that has been widely studied, usually because it is easy to maintain and breed in a laboratory setting and has particular experimental advantages. For example, they may have particularly robust embryos that are easily studied and manipulated in the lab, which is useful for scientists studying development. Or, they may occupy a pivotal position in the evolutionary tree; this is useful for scientists studying evolution.

If a study uses a model organism, is it a modeling study? The answer may seem like an obvious “yes”, but consider how modeling organisms are used. For instance, what if the modeling organism is used in an experimental design in which some individuals are part of an and others are in a . The purpose of doing the research may be ultimately to predict how the treatment may affect humans, but what is the research question? The research question is “how does treatment x affect this model species?” Scientists then use that information to how the treatment might affect humans, but it cannot by itself actually answer the question of how humans will be impacted. Instead, it is inferred that humans may be impacted by prior research that connects physiological similarities and differences between the model species and humans.

Therefore, when asking if a study is a modeling study, do not assume it is because it is using a model species. Rather, consider what the research question is, not just the general purpose of doing the research.


Now try applying what you have learned about scientific research to an investigation!

For closed captioning or to view the full transcript see the video on YouTube. Or click on the “YouTube” link in the video.


This chapter is a modified derivative of the following articles:

Understanding Science. 2020. University of California Museum of Paleontology. 11 June 2020 <http://www.understandingscience.org>.

What are Model Organisms?” by Yourgenome, Genome Research Limited is licensed under CC BY 4.0 License.


Icon for the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

Nature of Science Copyright © 2021 by Andrea Bierema is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, except where otherwise noted.

Share This Book