1 Chapter 1: Nature of Science

Anastasia Chouvalova and Joshua Reid

Learning Objectives

By the end of this section, students will be able to:

1.1 Differentiate between observations and inference.

1.2 Distinguish between different methods of scientific investigation

1.3 Explain why science is described as a social process and the role of peer-review in science.

1.4 Explain how scientific knowledge is both durable and tentative in light of new evidence.


Science is a very specific way of learning, or knowing, about the world. Humans have used the process of science to learn a huge amount about the way the natural world works. Science is responsible for amazing innovations in medicine, hygiene, and technology. There are however, areas of knowledge and human experience that the methods of science cannot be applied to. These include such things as answering purely moral questions, aesthetic questions, or what can be generally categorized as spiritual questions. Science cannot investigate these areas because they are outside the realm of material phenomena, the phenomena of matter and energy, and cannot be observed and measured.

Here are some examples of questions that can be answered using science:

  • What is the optimum humidity for the growth and proliferation of the giant puffball fungus (Calvatia gigantea)? If you want to learn more about this cool fungus, visit the following link: https://www.nps.gov/articles/species-spotlight-puffballs.htm
  • Are birds attracted to other birds of a specific coloration?
  • What virus causes a certain disease in a population of sheep?
  • What dose of the antibiotic amoxicillin is optimal for treating pneumonia in an 80 year old?

On the other hand, here are some examples of questions that CANNOT be answered using science:

  • How mean is the Grinch compared to Santa Claus?
  • Where do ghosts live?
  • How ethical is it to genetically engineer human embryos? To learn more about designer babies, visit the following link: https://www.nature.com/articles/d41586-019-00673-1
  • What is the effect of fairies on Texan woodland ecosystems?

Take some time to reflect on each of these questions in order to understand why they can or cannot be answered through the use of science.

Reading Question #1

Which of the following questions COULD be answered using science?

A. What is Santa Claus’ favorite treat?

B.  Which sushi roll is better: avocado maki or crunchy california roll?

C. Should abortion be legal or illegal?

D. What is the effect of Purina cat food on cats’ fur quality?

 Because this is a biology class, we will be focusing on questions that can be answered scientifically. A scientific question is one that can be answered by using the process of science (testing hypotheses, making observations about the natural world, designing experiments).

Sometimes you will directly make observations yourself about the natural world that lead you to ask scientific questions, other times you might hear or read something that leads you to ask a question. Regardless of how you make your initial observation, you will want to do research about your topic before you start setting up an experiment. When you’re learning about a topic, it’s important to use credible sources of information.

Observations vs. Inferences

The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Remember that science is very good at answering questions having to do with observations about the natural world, but is very bad at answering questions having to do with morals, ethics, or personal opinions. Think back to the questions in Reading Question #1. If you see a question that had to do with an opinion or an ethically-complex matter, it is likely not answerable using science. However, a question that involves observation and data collection, as well as the use of quantitative measures, is likely answerable using science.

Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: “Why is the classroom so warm?”

Now, let’s get back to contrasting observations and inferences. Students will frequently get confused between these two. An observation is obtained usually from a primary source – this is a source that directly witnessed or experienced a certain event. In other words, an observation is easily seen. For instance, if you are a polar bear researcher who is observing the behavior and dietary tendencies of a polar bear from an observatory in Greenland, you are likely to notice that a polar bear consumes meat exclusively. Then, you may infer that the polar bear has a jaw morphology optimized for chewing on meat and a digestive tract optimized for digesting it. However, you cannot scrutinize the jaw morphology or the digestive tract well enough (unlike the polar bear’s dietary tendency, which is more evident to you), so this is still an inference rather than an observation. An inference is a conclusion that is drawn based on logical reasoning as well as evidence that is observed. Thus, observations are required to make an inference but they are still distinct.

Existing knowledge is critical to providing oneself with evidence to make an inference. For example, a biology student’s prior knowledge may tell them that mammals are viviparous (i.e., they give birth to their offspring). However, as often occurs in science, there are noteworthy exceptions to most rules. This is why science is fun! For example, the duck-billed platypus, echidna, and five monotreme species lay eggs, instead of giving birth to their offspring.

Reading Question #2

Which of the following describes the relationship between an observation and inference?

A. An inference constitutes a type of evidence needed to reach an observation.

B. An observation constitutes a type of evidence needed to reach an inference.

C. An observation and inference are interchangeable terms.

D. There is truly no relationship between an observation and inference.

Methods of Scientific Investigation and Scientific Inquiry

One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. Two methods of logical thinking are used: inductive reasoning and deductive reasoning.

Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data can be qualitative (descriptive) or quantitative (consisting of numbers), and the raw data can be supplemented with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data. Brain studies often work this way. Many brains are observed while people are doing a task. The part of the brain that lights up, indicating activity, is then demonstrated to be the part controlling the response to that task.

Deductive reasoning or deduction is the type of logic used in hypothesis-based science. Recall what a hypothesisis. In deductive reasoning, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a general principle or law to forecast specific results. From those general principles, a scientist can extrapolate and predict the specific results that would be valid as long as the general principles are valid. For example, a prediction would be that if the climate is becoming warmer in a region, the distribution of plants and animals should change. Comparisons have been made between distributions in the past and the present, and the many changes that have been found are consistent with a warming climate. Finding the change in distribution is evidence that the climate change conclusion is a valid one.

Deductive and inductive reasoning are related to the two main pathways of scientific study, that is, descriptive science and hypothesis-based science. Descriptive (or discovery) science aims to observe, explore, and discover, while hypothesis-based science begins with a specific question or problem and a potential answer or solution that can be tested. The boundary between these two forms of study is often blurred, because most scientific endeavors combine both approaches. Observations lead to questions, questions lead to forming a hypothesis as a possible answer to those questions, and then the hypothesis is tested. Thus, descriptive science and hypothesis-based science are in continuous dialogue.

Testing hypotheses

Biologists study the living world by posing questions about it and seeking science-based responses. This approach is common to other sciences as well and is often referred to as the scientific method. The scientific method was used even in ancient times, but it was first documented by England’s Sir Francis Bacon (Figure 1.1)  (1561–1626), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost anything as a logical problem-solving method.

Figure 1.1 Presumably, Sir Francis Bacon is the first philosopher documented to utilize the scientific method.

The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: “Why is the classroom so warm?”

Recall that a hypothesis is a suggested explanation that can be tested. To solve a problem, several hypotheses may be proposed. For example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.” But there could be other responses to the question, and therefore other hypotheses may be proposed. A second hypothesis might be, “The classroom is warm because there is a power failure, and so the air conditioning doesn’t work.”

Once a hypothesis has been selected, a prediction may be made. A prediction is similar to a hypothesis but it typically has the format “If . . . then . . . .” For example, the prediction for the first hypothesis might be, “If the student turns on the air conditioning, then the classroom will no longer be too warm.”

A hypothesis must be testable to ensure that it is valid. For example, a hypothesis that depends on what a bear thinks is not testable, because it can never be known what a bear thinks. It should also be falsifiable, meaning that it can be disproven by experimental results. An example of an unfalsifiable hypothesis is “Botticelli’s Birth of Venus is beautiful.” There is no experiment that might show this statement to be false. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. This is important. A hypothesis can be disproven, or eliminated, but it can never be proven. Science does not deal in proofs like mathematics. If an experiment fails to disprove a hypothesis, then we find support for that explanation, but this is not to say that down the road a better explanation will not be found, or a more carefully designed experiment will be found to falsify the hypothesis.

Each experiment will have one or more variables and one or more controls. A variable is any part of the experiment that can vary or change during the experiment. A control is a part of the experiment that does not change. Look for the variables and controls in the example that follows. As a simple example, an experiment might be conducted to test the hypothesis that phosphate limits the growth of algae in freshwater ponds. A series of artificial ponds are filled with water and half of them are treated by adding phosphate each week, while the other half are treated by adding a salt that is known not to be used by algae. The variable here is the phosphate (or lack of phosphate), the experimental or treatment cases are the ponds with added phosphate and the control ponds are those with something inert added, such as the salt. Just adding something is also a control against the possibility that adding extra matter to the pond has an effect. If the treated ponds show lesser growth of algae, then we have found support for our hypothesis. If they do not, then we reject our hypothesis. Be aware that rejecting one hypothesis does not determine whether or not the other hypotheses can be accepted; it simply eliminates one hypothesis that is not valid . Using the scientific method (Figure 1.2), the hypotheses that are inconsistent with experimental data are rejected.

Figure 1.2 The scientific method is a sequential series of steps, ranging from an observation and typically concluding in the reporting of results. If the acquired data does NOT support a given hypothesis, alternative hypotheses should be considered and tested again. Thus, this is often an iterative process. Persistence is key! The limitations of the scientific method as depicted above will be discussed in further detail below. Do not be fooled – this linear method does not accurately reflect how scientists and researchers conduct their work.

In the example below, the scientific method is used to solve an everyday problem. Which part in the example below is the hypothesis? Which is the prediction? Based on the results of the experiment, is the hypothesis supported? If it is not supported, propose some alternative hypotheses.

  1. My toaster doesn’t toast my bread.
  2. Why doesn’t my toaster work?
  3. There is something wrong with the electrical outlet.
  4. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
  5. I plug my coffeemaker into the outlet.
  6. My coffeemaker works.

In practice, the scientific method is not as rigid and structured as it might at first appear. Sometimes an experiment leads to conclusions that favor a change in approach; often, an experiment brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion; instead, scientists continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests.

Please refer to this link to gain an appreciation for why the scientific method is not truly the basic and in some senses, boring process as it is communicated to be in many scientific textbooks. Pay particular attention to the illustrated flowcharts.

Reading Question #3

Biology students are trying to describe the coloration of male cardinals in the Canadian province of Ontario. They find that across three regions, male cardinals are red. Of the following, which best exemplifies INDUCTIVE reasoning?

A. They conclude that all male cardinals in Ontario are red.

B. They predict that in the next regions they will survey, male cardinals will be red.

C. They predict that in the next regions they will survey, female cardinals will also be red.

D. Both A and B.

The importance of peer-review in science

Whether scientific research is basic science or applied science, scientists must share their findings in order for other researchers to expand and build upon their discoveries. Collaboration with other scientists—when planning, conducting, and analyzing results—is important for scientific research. For this reason, important aspects of a scientist’s work are communicating with peers and disseminating results to peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the select few who are present. Instead, most scientists present their results in peer-reviewed manuscripts that are published in scientific journals. Peer-reviewed manuscripts are scientific papers that a scientist’s colleagues or peers review. Scholarly work is checked by a group of experts in the same field to make sure it meets the journal standards before it is accepted or published. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings.

You’ve probably done a writing assignment or other project during which you have participated in a peer review process. During this process, your project was critiqued and evaluated by people of similar competence to yourself (your peers). This gave you feedback on which to improve your work. Scientific articles typically go through a peer review process before they are published in an academic journal, including conference journals. In this case, the peers who are reviewing the article are other experts in the specific field about which the paper is written. This allows other scientists to critique experimental design, data, and conclusions before that information is published in an academic journal. Often, the scientists who did the experiment and who are trying to publish it are required to do additional work or edit their paper before it is published. The goal of the scientific peer review process is to ensure that published primary articles contain the best possible science.

There are many journals and the popular press that do not use a peer-review system. A large number of online open-access journals, journals with articles available without cost, are now available many of which use rigorous peer-review systems, but some of which do not. Results of any studies published in these forums without peer review are not reliable and should not form the basis for other scientific work. In one exception, journals may allow a researcher to cite a personal communication from another researcher about unpublished results with the cited author’s permission.

The peer-review process for oral communications and poster presentations at scientific conferences is a little less gruelling than for journals, although, a peer-review process is still applied before the work is accepted by conference organisers. Although many scientists will grimace at the mention of ‘peer-review’, it is through this process that we increase the likelihood that valid science (and not pseudoscience) is shared with the world. Peer review is an essential part of the scientific process, to make important economic and health-related decisions that affect the future prosperity of humanity.

As with all forms of communication, scientific research articles, oral communications and poster presentations need to be prepared and delivered according to specific guidelines and using particular language. It is important that student scientists begin to understand these guidelines and are given opportunities to practice these forms of communication. This chapter provides a roadmap for preparing and delivering these important modes of scientific communication.

Reading Question #4

Imagine you are publishing a paper investigating the immune system’s involvement in multiple sclerosis (MS), a condition where the immune system attacks the myelin covering of neurons. Who is MOST qualified to conduct the peer-reviewing in a peer review process and is most likely to provide the highest-quality and most helpful peer review?

A. A family member who knows someone with MS.

B. A graduate student studying MS.

C. An immunologist who specializes in researching MS.

D. A professor with several publications about genetic disorders.

Reading Question #5

When are peer reviews warranted?

A. Grant proposals

B. Publication of journal articles

C. Publication of conference articles

D. All of the above


Adapted from Clark, M.A., Douglas, M., and Choi, J. (2018). Biology 2e. OpenStax. Retrieved from https://openstax.org/books/biology-2e/pages/1-introduction

Adapted from Bartee, L., Shriner, W., and Creech C. (n.d.) Principles of Biology. Pressbooks. Retrieved from


Molnar, C., & Gair, J. (2015). Concepts of Biology – 1st Canadian Edition. BCcampus. Retrieved from https://opentextbc.ca/biology/



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Introductory Biology 2 Copyright © 2023 by Anastasia Chouvalova and Joshua Reid is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License, except where otherwise noted.

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