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Six Steps of the Scientific Method

Learn What Makes Each Stage Important

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The scientific method is a systematic way of learning about the world around us and answering questions. The key difference between the scientific method and other ways of acquiring knowledge are forming a hypothesis and then testing it with an experiment.

The Six Steps

The number of steps can vary from one description to another (which mainly happens when data and analysis are separated into separate steps), however, this is a fairly standard list of the six scientific method steps that you are expected to know for any science class:

• Purpose/Question Ask a question.
• Research Conduct background research. Write down your sources so you can cite your references. In the modern era, a lot of your research may be conducted online. Scroll to the bottom of articles to check the references. Even if you can't access the full text of a published article, you can usually view the abstract to see the summary of other experiments. Interview experts on a topic. The more you know about a subject, the easier it will be to conduct your investigation.
• Hypothesis Propose a hypothesis . This is a sort of educated guess about what you expect. It is a statement used to predict the outcome of an experiment. Usually, a hypothesis is written in terms of cause and effect. Alternatively, it may describe the relationship between two phenomena. One type of hypothesis is the null hypothesis or the no-difference hypothesis. This is an easy type of hypothesis to test because it assumes changing a variable will have no effect on the outcome. In reality, you probably expect a change but rejecting a hypothesis may be more useful than accepting one.
• Experiment Design and perform an experiment to test your hypothesis. An experiment has an independent and dependent variable. You change or control the independent variable and record the effect it has on the dependent variable . It's important to change only one variable for an experiment rather than try to combine the effects of variables in an experiment. For example, if you want to test the effects of light intensity and fertilizer concentration on the growth rate of a plant, you're really looking at two separate experiments.
• Data/Analysis Record observations and analyze the meaning of the data. Often, you'll prepare a table or graph of the data. Don't throw out data points you think are bad or that don't support your predictions. Some of the most incredible discoveries in science were made because the data looked wrong! Once you have the data, you may need to perform a mathematical analysis to support or refute your hypothesis.
• Conclusion Conclude whether to accept or reject your hypothesis. There is no right or wrong outcome to an experiment, so either result is fine. Accepting a hypothesis does not necessarily mean it's correct! Sometimes repeating an experiment may give a different result. In other cases, a hypothesis may predict an outcome, yet you might draw an incorrect conclusion. Communicate your results. The results may be compiled into a lab report or formally submitted as a paper. Whether you accept or reject the hypothesis, you likely learned something about the subject and may wish to revise the original hypothesis or form a new one for a future experiment.

When Are There Seven Steps?

Sometimes the scientific method is taught with seven steps instead of six. In this model, the first step of the scientific method is to make observations. Really, even if you don't make observations formally, you think about prior experiences with a subject in order to ask a question or solve a problem.

Formal observations are a type of brainstorming that can help you find an idea and form a hypothesis. Observe your subject and record everything about it. Include colors, timing, sounds, temperatures, changes, behavior, and anything that strikes you as interesting or significant.

When you design an experiment, you are controlling and measuring variables. There are three types of variables:

• Controlled Variables:  You can have as many  controlled variables  as you like. These are parts of the experiment that you try to keep constant throughout an experiment so that they won't interfere with your test. Writing down controlled variables is a good idea because it helps make your experiment  reproducible , which is important in science! If you have trouble duplicating results from one experiment to another, there may be a controlled variable that you missed.
• Independent Variable:  This is the variable you control.
• Dependent Variable:  This is the variable you measure. It is called the dependent variable because it  depends  on the independent variable.
• Examples of Independent and Dependent Variables
• Null Hypothesis Examples
• Difference Between Independent and Dependent Variables
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• Understanding Simple vs Controlled Experiments
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• Null Hypothesis Definition and Examples
• Independent Variable Definition and Examples
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Steps of the Scientific Method 2

The scientific method is a system scientists and other people use to ask and answer questions about the natural world. In a nutshell, the scientific method works by making observations, asking a question or identifying a problem, and then designing and analyzing an experiment to test a prediction of what you expect will happen. It’s a powerful analytical tool because once you draw conclusions, you may be able to answer a question and make predictions about future events.

These are the steps of the scientific method:

• Make observations.

Sometimes this step is omitted in the list, but you always make observations before asking a question, whether you recognize it or not. You always have some background information about a topic. However, it’s a good idea to be systematic about your observations and to record them in a lab book or another way. Often, these initial observations can help you identify a question. Later on, this information may help you decide on another area of investigation of a topic.

• Ask a question, identify a problem, or state an objective.

There are various forms of this step. Sometimes you may want to state an objective and a problem and then phrase it in the form of a question. The reason it’s good to state a question is because it’s easiest to design an experiment to answer a question. A question helps you form a hypothesis, which focuses your study.

• Research the topic.

You should conduct background research on your topic to learn as much as you can about it. This can occur both before and after you state an objective and form a hypothesis. In fact, you may find yourself researching the topic throughout the entire process.

• Formulate a hypothesis.

A hypothesis is a formal prediction. There are two forms of a hypothesis that are particularly easy to test. One is to state the hypothesis as an “if, then” statement. An example of an if-then hypothesis is: “If plants are grown under red light, then they will be taller than plants grown under white light.” Another good type of hypothesis is what is called a “ null hypothesis ” or “no difference” hypothesis. An example of a null hypothesis is: “There is no difference in the rate of growth of plants grown under red light compared with plants grown under white light.”

• Design and perform an experiment to test the hypothesis.

Once you have a hypothesis, you need to find a way to test it. This involves an experiment . There are many ways to set up an experiment. A basic experiment contains variables, which are factors you can measure. The two main variables are the independent variable (the one you control or change) and the dependent variable (the one you measure to see if it is affected when you change the independent variable).

• Record and analyze the data you obtain from the experiment.

It’s a good idea to record notes alongside your data, stating anything unusual or unexpected. Once you have the data, draw a chart, table, or graph to present your results. Next, analyze the results to understand what it all means.

• Determine whether you accept or reject the hypothesis.

Do the results support the hypothesis or not? Keep in mind, it’s okay if the hypothesis is not supported, especially if you are testing a null hypothesis. Sometimes excluding an explanation answers your question! There is no “right” or “wrong” here. However, if you obtain an unexpected result, you might want to perform another experiment.

• Draw a conclusion and report the results of the experiment.

What good is knowing something if you keep it to yourself? You should report the outcome of the experiment, even if it’s just in a notebook. What did you learn from the experiment?

How Many Steps Are There?

You may be asked to list the 5 steps of the scientific method or the 6 steps of the method or some other number. There are different ways of grouping together the steps outlined here, so it’s a good idea to learn the way an instructor wants you to list the steps. No matter how many steps there are, the order is always the same.

Related Posts

2 thoughts on “ steps of the scientific method ”.

You raise a valid point, but peer review has its limitations. Consider the case of Galileo, for example.

That’s a good point too. But that was a rare limitation due to religion, and scientific consensus prevailed in the end. It’s nowhere near a reason to doubt scientific consensus in general. I’m thinking about issues such as climate change where so many people are skeptical despite 97% consensus among climate scientists. I was just surprised to see that this is not included as an important part of the process.

Comments are closed.

What Are The Steps Of The Scientific Method?

Julia Simkus

Editor at Simply Psychology

BA (Hons) Psychology, Princeton University

Julia Simkus is a graduate of Princeton University with a Bachelor of Arts in Psychology. She is currently studying for a Master's Degree in Counseling for Mental Health and Wellness in September 2023. Julia's research has been published in peer reviewed journals.

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On This Page:

Science is not just knowledge. It is also a method for obtaining knowledge. Scientific understanding is organized into theories.

The scientific method is a step-by-step process used by researchers and scientists to determine if there is a relationship between two or more variables. Psychologists use this method to conduct psychological research, gather data, process information, and describe behaviors.

It involves careful observation, asking questions, formulating hypotheses, experimental testing, and refining hypotheses based on experimental findings.

How it is Used

The scientific method can be applied broadly in science across many different fields, such as chemistry, physics, geology, and psychology. In a typical application of this process, a researcher will develop a hypothesis, test this hypothesis, and then modify the hypothesis based on the outcomes of the experiment.

The process is then repeated with the modified hypothesis until the results align with the observed phenomena. Detailed steps of the scientific method are described below.

Keep in mind that the scientific method does not have to follow this fixed sequence of steps; rather, these steps represent a set of general principles or guidelines.

7 Steps of the Scientific Method

Psychology uses an empirical approach.

Empiricism (founded by John Locke) states that the only source of knowledge comes through our senses – e.g., sight, hearing, touch, etc.

Empirical evidence does not rely on argument or belief. Thus, empiricism is the view that all knowledge is based on or may come from direct observation and experience.

The empiricist approach of gaining knowledge through experience quickly became the scientific approach and greatly influenced the development of physics and chemistry in the 17th and 18th centuries.

Step 1: Make an Observation (Theory Construction)

Every researcher starts at the very beginning. Before diving in and exploring something, one must first determine what they will study – it seems simple enough!

By making observations, researchers can establish an area of interest. Once this topic of study has been chosen, a researcher should review existing literature to gain insight into what has already been tested and determine what questions remain unanswered.

This assessment will provide helpful information about what has already been comprehended about the specific topic and what questions remain, and if one can go and answer them.

Specifically, a literature review might implicate examining a substantial amount of documented material from academic journals to books dating back decades. The most appropriate information gathered by the researcher will be shown in the introduction section or abstract of the published study results.

The background material and knowledge will help the researcher with the first significant step in conducting a psychology study, which is formulating a research question.

This is the inductive phase of the scientific process. Observations yield information that is used to formulate theories as explanations. A theory is a well-developed set of ideas that propose an explanation for observed phenomena.

Inductive reasoning moves from specific premises to a general conclusion. It starts with observations of phenomena in the natural world and derives a general law.

Step 2: Ask a Question

Once a researcher has made observations and conducted background research, the next step is to ask a scientific question. A scientific question must be defined, testable, and measurable.

A useful approach to develop a scientific question is: “What is the effect of…?” or “How does X affect Y?”

To answer an experimental question, a researcher must identify two variables: the independent and dependent variables.

The independent variable is the variable manipulated (the cause), and the dependent variable is the variable being measured (the effect).

An example of a research question could be, “Is handwriting or typing more effective for retaining information?” Answering the research question and proposing a relationship between the two variables is discussed in the next step.

Step 3: Form a Hypothesis (Make Predictions)

A hypothesis is an educated guess about the relationship between two or more variables. A hypothesis is an attempt to answer your research question based on prior observation and background research. Theories tend to be too complex to be tested all at once; instead, researchers create hypotheses to test specific aspects of a theory.

For example, a researcher might ask about the connection between sleep and educational performance. Do students who get less sleep perform worse on tests at school?

It is crucial to think about different questions one might have about a particular topic to formulate a reasonable hypothesis. It would help if one also considered how one could investigate the causalities.

It is important that the hypothesis is both testable against reality and falsifiable. This means that it can be tested through an experiment and can be proven wrong.

The falsification principle, proposed by Karl Popper , is a way of demarcating science from non-science. It suggests that for a theory to be considered scientific, it must be able to be tested and conceivably proven false.

To test a hypothesis, we first assume that there is no difference between the populations from which the samples were taken. This is known as the null hypothesis and predicts that the independent variable will not influence the dependent variable.

Examples of “if…then…” Hypotheses:

• If one gets less than 6 hours of sleep, then one will do worse on tests than if one obtains more rest.
• If one drinks lots of water before going to bed, one will have to use the bathroom often at night.
• If one practices exercising and lighting weights, then one’s body will begin to build muscle.

The research hypothesis is often called the alternative hypothesis and predicts what change(s) will occur in the dependent variable when the independent variable is manipulated.

It states that the results are not due to chance and that they are significant in terms of supporting the theory being investigated.

Although one could state and write a scientific hypothesis in many ways, hypotheses are usually built like “if…then…” statements.

Step 4: Run an Experiment (Gather Data)

The next step in the scientific method is to test your hypothesis and collect data. A researcher will design an experiment to test the hypothesis and gather data that will either support or refute the hypothesis.

The exact research methods used to examine a hypothesis depend on what is being studied. A psychologist might utilize two primary forms of research, experimental research, and descriptive research.

The scientific method is objective in that researchers do not let preconceived ideas or biases influence the collection of data and is systematic in that experiments are conducted in a logical way.

Experimental Research

Experimental research is used to investigate cause-and-effect associations between two or more variables. This type of research systematically controls an independent variable and measures its effect on a specified dependent variable.

Experimental research involves manipulating an independent variable and measuring the effect(s) on the dependent variable. Repeating the experiment multiple times is important to confirm that your results are accurate and consistent.

One of the significant advantages of this method is that it permits researchers to determine if changes in one variable cause shifts in each other.

While experiments in psychology typically have many moving parts (and can be relatively complex), an easy investigation is rather fundamental. Still, it does allow researchers to specify cause-and-effect associations between variables.

Most simple experiments use a control group, which involves those who do not receive the treatment, and an experimental group, which involves those who do receive the treatment.

An example of experimental research would be when a pharmaceutical company wants to test a new drug. They give one group a placebo (control group) and the other the actual pill (experimental group).

Descriptive Research

Descriptive research is generally used when it is challenging or even impossible to control the variables in question. Examples of descriptive analysis include naturalistic observation, case studies , and correlation studies .

One example of descriptive research includes phone surveys that marketers often use. While they typically do not allow researchers to identify cause and effect, correlational studies are quite common in psychology research. They make it possible to spot associations between distinct variables and measure the solidity of those relationships.

Step 5: Analyze the Data and Draw Conclusions

Once a researcher has designed and done the investigation and collected sufficient data, it is time to inspect this gathered information and judge what has been found. Researchers can summarize the data, interpret the results, and draw conclusions based on this evidence using analyses and statistics.

Upon completion of the experiment, you can collect your measurements and analyze the data using statistics. Based on the outcomes, you will either reject or confirm your hypothesis.

Analyze the Data

So, how does a researcher determine what the results of their study mean? Statistical analysis can either support or refute a researcher’s hypothesis and can also be used to determine if the conclusions are statistically significant.

When outcomes are said to be “statistically significant,” it is improbable that these results are due to luck or chance. Based on these observations, investigators must then determine what the results mean.

An experiment will support a hypothesis in some circumstances, but sometimes it fails to be truthful in other cases.

What occurs if the developments of a psychology investigation do not endorse the researcher’s hypothesis? It does mean that the study was worthless. Simply because the findings fail to defend the researcher’s hypothesis does not mean that the examination is not helpful or instructive.

This kind of research plays a vital role in supporting scientists in developing unexplored questions and hypotheses to investigate in the future. After decisions have been made, the next step is to communicate the results with the rest of the scientific community.

This is an integral part of the process because it contributes to the general knowledge base and can assist other scientists in finding new research routes to explore.

If the hypothesis is not supported, a researcher should acknowledge the experiment’s results, formulate a new hypothesis, and develop a new experiment.

We must avoid any reference to results proving a theory as this implies 100% certainty, and there is always a chance that evidence may exist that could refute a theory.

Draw Conclusions and Interpret the Data

When the empirical observations disagree with the hypothesis, a number of possibilities must be considered. It might be that the theory is incorrect, in which case it needs altering, so it fully explains the data.

Alternatively, it might be that the hypothesis was poorly derived from the original theory, in which case the scientists were expecting the wrong thing to happen.

It might also be that the research was poorly conducted, or used an inappropriate method, or there were factors in play that the researchers did not consider. This will begin the process of the scientific method again.

If the hypothesis is supported, the researcher can find more evidence to support their hypothesis or look for counter-evidence to strengthen their hypothesis further.

In either scenario, the researcher should share their results with the greater scientific community.

Step 6: Share Your Results

One of the final stages of the research cycle involves the publication of the research. Once the report is written, the researcher(s) may submit the work for publication in an appropriate journal.

Usually, this is done by writing up a study description and publishing the article in a professional or academic journal. The studies and conclusions of psychological work can be seen in peer-reviewed journals such as  Developmental Psychology , Psychological Bulletin, the  Journal of Social Psychology, and numerous others.

Scientists should report their findings by writing up a description of their study and any subsequent findings. This enables other researchers to build upon the present research or replicate the results.

As outlined by the American Psychological Association (APA), there is a typical structure of a journal article that follows a specified format. In these articles, researchers:

• Supply a brief narrative and background on previous research
• Give their hypothesis
• Specify who participated in the study and how they were chosen
• Provide operational definitions for each variable
• Explain the measures and methods used to collect data
• Describe how the data collected was interpreted
• Discuss what the outcomes mean

A detailed record of psychological studies and all scientific studies is vital to clearly explain the steps and procedures used throughout the study. So that other researchers can try this experiment too and replicate the results.

The editorial process utilized by academic and professional journals guarantees that each submitted article undergoes a thorough peer review to help assure that the study is scientifically sound. Once published, the investigation becomes another piece of the current puzzle of our knowledge “base” on that subject.

This last step is important because all results, whether they supported or did not support the hypothesis, can contribute to the scientific community. Publication of empirical observations leads to more ideas that are tested against the real world, and so on. In this sense, the scientific process is circular.

The editorial process utilized by academic and professional journals guarantees that each submitted article undergoes a thorough peer review to help assure that the study is scientifically sound.

Once published, the investigation becomes another piece of the current puzzle of our knowledge “base” on that subject.

By replicating studies, psychologists can reduce errors, validate theories, and gain a stronger understanding of a particular topic.

Step 7: Repeat the Scientific Method (Iteration)

Now, if one’s hypothesis turns out to be accurate, find more evidence or find counter-evidence. If one’s hypothesis is false, create a new hypothesis or try again.

One may wish to revise their first hypothesis to make a more niche experiment to design or a different specific question to test.

The amazingness of the scientific method is that it is a comprehensive and straightforward process that scientists, and everyone, can utilize over and over again.

So, draw conclusions and repeat because the scientific method is never-ending, and no result is ever considered perfect.

The scientific method is a process of:

• Making an observation.
• Forming a hypothesis.
• Making a prediction.
• Experimenting to test the hypothesis.

The procedure of repeating the scientific method is crucial to science and all fields of human knowledge.

Further Information

• Karl Popper – Falsification
• Thomas – Kuhn Paradigm Shift
• Positivism in Sociology: Definition, Theory & Examples
• Is Psychology a Science?
• Psychology as a Science (PDF)

List the 6 steps of the scientific methods in order

• Make an observation (theory construction)
• Ask a question. A scientific question must be defined, testable, and measurable.
• Form a hypothesis (make predictions)
• Run an experiment to test the hypothesis (gather data)
• Analyze the data and draw conclusions
• Share your results so that other researchers can make new hypotheses

What is the first step of the scientific method?

The first step of the scientific method is making an observation. This involves noticing and describing a phenomenon or group of phenomena that one finds interesting and wishes to explain.

Observations can occur in a natural setting or within the confines of a laboratory. The key point is that the observation provides the initial question or problem that the rest of the scientific method seeks to answer or solve.

What is the scientific method?

The scientific method is a step-by-step process that investigators can follow to determine if there is a causal connection between two or more variables.

Psychologists and other scientists regularly suggest motivations for human behavior. On a more casual level, people judge other people’s intentions, incentives, and actions daily.

While our standard assessments of human behavior are subjective and anecdotal, researchers use the scientific method to study psychology objectively and systematically.

All utilize a scientific method to study distinct aspects of people’s thinking and behavior. This process allows scientists to analyze and understand various psychological phenomena, but it also provides investigators and others a way to disseminate and debate the results of their studies.

The outcomes of these studies are often noted in popular media, which leads numerous to think about how or why researchers came to the findings they did.

Why Use the Six Steps of the Scientific Method

The goal of scientists is to understand better the world that surrounds us. Scientific research is the most critical tool for navigating and learning about our complex world.

Without it, we would be compelled to rely solely on intuition, other people’s power, and luck. We can eliminate our preconceived concepts and superstitions through methodical scientific research and gain an objective sense of ourselves and our world.

All psychological studies aim to explain, predict, and even control or impact mental behaviors or processes. So, psychologists use and repeat the scientific method (and its six steps) to perform and record essential psychological research.

So, psychologists focus on understanding behavior and the cognitive (mental) and physiological (body) processes underlying behavior.

In the real world, people use to understand the behavior of others, such as intuition and personal experience. The hallmark of scientific research is evidence to support a claim.

Scientific knowledge is empirical, meaning it is grounded in objective, tangible evidence that can be observed repeatedly, regardless of who is watching.

The scientific method is crucial because it minimizes the impact of bias or prejudice on the experimenter. Regardless of how hard one tries, even the best-intentioned scientists can’t escape discrimination. can’t

It stems from personal opinions and cultural beliefs, meaning any mortal filters data based on one’s experience. Sadly, this “filtering” process can cause a scientist to favor one outcome over another.

For an everyday person trying to solve a minor issue at home or work, succumbing to these biases is not such a big deal; in fact, most times, it is important.

But in the scientific community, where results must be inspected and reproduced, bias or discrimination must be avoided.

When to Use the Six Steps of the Scientific Method ?

One can use the scientific method anytime, anywhere! From the smallest conundrum to solving global problems, it is a process that can be applied to any science and any investigation.

Even if you are not considered a “scientist,” you will be surprised to know that people of all disciplines use it for all kinds of dilemmas.

Try to catch yourself next time you come by a question and see how you subconsciously or consciously use the scientific method.

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Scientific Method Steps in Psychology Research

Steps, Uses, and Key Terms

Kendra Cherry, MS, is a psychosocial rehabilitation specialist, psychology educator, and author of the "Everything Psychology Book."

Emily is a board-certified science editor who has worked with top digital publishing brands like Voices for Biodiversity, Study.com, GoodTherapy, Vox, and Verywell.

Verywell / Theresa Chiechi

How do researchers investigate psychological phenomena? They utilize a process known as the scientific method to study different aspects of how people think and behave.

When conducting research, the scientific method steps to follow are:

• Observe what you want to investigate
• Ask a research question and make predictions
• Test the hypothesis and collect data
• Examine the results and draw conclusions
• Report and share the results 

This process not only allows scientists to investigate and understand different psychological phenomena but also provides researchers and others a way to share and discuss the results of their studies.

Generally, there are five main steps in the scientific method, although some may break down this process into six or seven steps. An additional step in the process can also include developing new research questions based on your findings.

What Is the Scientific Method?

What is the scientific method and how is it used in psychology?

The scientific method consists of five steps. It is essentially a step-by-step process that researchers can follow to determine if there is some type of relationship between two or more variables.

By knowing the steps of the scientific method, you can better understand the process researchers go through to arrive at conclusions about human behavior.

Scientific Method Steps

While research studies can vary, these are the basic steps that psychologists and scientists use when investigating human behavior.

The following are the scientific method steps:

Step 1. Make an Observation

Before a researcher can begin, they must choose a topic to study. Once an area of interest has been chosen, the researchers must then conduct a thorough review of the existing literature on the subject. This review will provide valuable information about what has already been learned about the topic and what questions remain to be answered.

A literature review might involve looking at a considerable amount of written material from both books and academic journals dating back decades.

The relevant information collected by the researcher will be presented in the introduction section of the final published study results. This background material will also help the researcher with the first major step in conducting a psychology study: formulating a hypothesis.

Step 2. Ask a Question

Once a researcher has observed something and gained some background information on the topic, the next step is to ask a question. The researcher will form a hypothesis, which is an educated guess about the relationship between two or more variables

For example, a researcher might ask a question about the relationship between sleep and academic performance: Do students who get more sleep perform better on tests at school?

In order to formulate a good hypothesis, it is important to think about different questions you might have about a particular topic.

You should also consider how you could investigate the causes. Falsifiability is an important part of any valid hypothesis. In other words, if a hypothesis was false, there needs to be a way for scientists to demonstrate that it is false.

Step 3. Test Your Hypothesis and Collect Data

Once you have a solid hypothesis, the next step of the scientific method is to put this hunch to the test by collecting data. The exact methods used to investigate a hypothesis depend on exactly what is being studied. There are two basic forms of research that a psychologist might utilize: descriptive research or experimental research.

Descriptive research is typically used when it would be difficult or even impossible to manipulate the variables in question. Examples of descriptive research include case studies, naturalistic observation , and correlation studies. Phone surveys that are often used by marketers are one example of descriptive research.

Correlational studies are quite common in psychology research. While they do not allow researchers to determine cause-and-effect, they do make it possible to spot relationships between different variables and to measure the strength of those relationships. 

Experimental research is used to explore cause-and-effect relationships between two or more variables. This type of research involves systematically manipulating an independent variable and then measuring the effect that it has on a defined dependent variable .

One of the major advantages of this method is that it allows researchers to actually determine if changes in one variable actually cause changes in another.

While psychology experiments are often quite complex, a simple experiment is fairly basic but does allow researchers to determine cause-and-effect relationships between variables. Most simple experiments use a control group (those who do not receive the treatment) and an experimental group (those who do receive the treatment).

Step 4. Examine the Results and Draw Conclusions

Once a researcher has designed the study and collected the data, it is time to examine this information and draw conclusions about what has been found.  Using statistics , researchers can summarize the data, analyze the results, and draw conclusions based on this evidence.

So how does a researcher decide what the results of a study mean? Not only can statistical analysis support (or refute) the researcher’s hypothesis; it can also be used to determine if the findings are statistically significant.

When results are said to be statistically significant, it means that it is unlikely that these results are due to chance.

Based on these observations, researchers must then determine what the results mean. In some cases, an experiment will support a hypothesis, but in other cases, it will fail to support the hypothesis.

So what happens if the results of a psychology experiment do not support the researcher's hypothesis? Does this mean that the study was worthless?

Just because the findings fail to support the hypothesis does not mean that the research is not useful or informative. In fact, such research plays an important role in helping scientists develop new questions and hypotheses to explore in the future.

After conclusions have been drawn, the next step is to share the results with the rest of the scientific community. This is an important part of the process because it contributes to the overall knowledge base and can help other scientists find new research avenues to explore.

Step 5. Report the Results

The final step in a psychology study is to report the findings. This is often done by writing up a description of the study and publishing the article in an academic or professional journal. The results of psychological studies can be seen in peer-reviewed journals such as  Psychological Bulletin , the  Journal of Social Psychology ,  Developmental Psychology , and many others.

The structure of a journal article follows a specified format that has been outlined by the  American Psychological Association (APA) . In these articles, researchers:

• Provide a brief history and background on previous research
• Present their hypothesis
• Identify who participated in the study and how they were selected
• Provide operational definitions for each variable
• Describe the measures and procedures that were used to collect data
• Explain how the information collected was analyzed
• Discuss what the results mean

Why is such a detailed record of a psychological study so important? By clearly explaining the steps and procedures used throughout the study, other researchers can then replicate the results. The editorial process employed by academic and professional journals ensures that each article that is submitted undergoes a thorough peer review, which helps ensure that the study is scientifically sound.

Once published, the study becomes another piece of the existing puzzle of our knowledge base on that topic.

Before you begin exploring the scientific method steps, here's a review of some key terms and definitions that you should be familiar with:

• Falsifiable : The variables can be measured so that if a hypothesis is false, it can be proven false
• Hypothesis : An educated guess about the possible relationship between two or more variables
• Variable : A factor or element that can change in observable and measurable ways
• Operational definition : A full description of exactly how variables are defined, how they will be manipulated, and how they will be measured

Uses for the Scientific Method

The  goals of psychological studies  are to describe, explain, predict and perhaps influence mental processes or behaviors. In order to do this, psychologists utilize the scientific method to conduct psychological research. The scientific method is a set of principles and procedures that are used by researchers to develop questions, collect data, and reach conclusions.

Goals of Scientific Research in Psychology

Researchers seek not only to describe behaviors and explain why these behaviors occur; they also strive to create research that can be used to predict and even change human behavior.

Psychologists and other social scientists regularly propose explanations for human behavior. On a more informal level, people make judgments about the intentions, motivations , and actions of others on a daily basis.

While the everyday judgments we make about human behavior are subjective and anecdotal, researchers use the scientific method to study psychology in an objective and systematic way. The results of these studies are often reported in popular media, which leads many to wonder just how or why researchers arrived at the conclusions they did.

Examples of the Scientific Method

Now that you're familiar with the scientific method steps, it's useful to see how each step could work with a real-life example.

Say, for instance, that researchers set out to discover what the relationship is between psychotherapy and anxiety .

• Step 1. Make an observation : The researchers choose to focus their study on adults ages 25 to 40 with generalized anxiety disorder.
• Step 2. Ask a question : The question they want to answer in their study is: Do weekly psychotherapy sessions reduce symptoms in adults ages 25 to 40 with generalized anxiety disorder?
• Step 3. Test your hypothesis : Researchers collect data on participants' anxiety symptoms . They work with therapists to create a consistent program that all participants undergo. Group 1 may attend therapy once per week, whereas group 2 does not attend therapy.
• Step 4. Examine the results : Participants record their symptoms and any changes over a period of three months. After this period, people in group 1 report significant improvements in their anxiety symptoms, whereas those in group 2 report no significant changes.
• Step 5. Report the results : Researchers write a report that includes their hypothesis, information on participants, variables, procedure, and conclusions drawn from the study. In this case, they say that "Weekly therapy sessions are shown to reduce anxiety symptoms in adults ages 25 to 40."

Of course, there are many details that go into planning and executing a study such as this. But this general outline gives you an idea of how an idea is formulated and tested, and how researchers arrive at results using the scientific method.

Erol A. How to conduct scientific research ? Noro Psikiyatr Ars . 2017;54(2):97-98. doi:10.5152/npa.2017.0120102

University of Minnesota. Psychologists use the scientific method to guide their research .

Shaughnessy, JJ, Zechmeister, EB, & Zechmeister, JS. Research Methods In Psychology . New York: McGraw Hill Education; 2015.

By Kendra Cherry, MSEd Kendra Cherry, MS, is a psychosocial rehabilitation specialist, psychology educator, and author of the "Everything Psychology Book."

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Mechanics (Essentials) - Class 11th

Course: mechanics (essentials) - class 11th   >   unit 2.

• Introduction to physics
• What is physics?

The scientific method

• Models and Approximations in Physics

Introduction

• Make an observation.
• Ask a question.
• Form a hypothesis , or testable explanation.
• Make a prediction based on the hypothesis.
• Test the prediction.
• Iterate: use the results to make new hypotheses or predictions.

Scientific method example: Failure to toast

1. make an observation..

• Observation: the toaster won't toast.

2. Ask a question.

• Question: Why won't my toaster toast?

3. Propose a hypothesis.

• Hypothesis: Maybe the outlet is broken.

4. Make predictions.

• Prediction: If I plug the toaster into a different outlet, then it will toast the bread.

5. Test the predictions.

• Test of prediction: Plug the toaster into a different outlet and try again.
• If the toaster does toast, then the hypothesis is supported—likely correct.
• If the toaster doesn't toast, then the hypothesis is not supported—likely wrong.

Logical possibility

Practical possibility, building a body of evidence, 6. iterate..

• Iteration time!
• If the hypothesis was supported, we might do additional tests to confirm it, or revise it to be more specific. For instance, we might investigate why the outlet is broken.
• If the hypothesis was not supported, we would come up with a new hypothesis. For instance, the next hypothesis might be that there's a broken wire in the toaster.

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Scientific Method

Science is an enormously successful human enterprise. The study of scientific method is the attempt to discern the activities by which that success is achieved. Among the activities often identified as characteristic of science are systematic observation and experimentation, inductive and deductive reasoning, and the formation and testing of hypotheses and theories. How these are carried out in detail can vary greatly, but characteristics like these have been looked to as a way of demarcating scientific activity from non-science, where only enterprises which employ some canonical form of scientific method or methods should be considered science (see also the entry on science and pseudo-science ). Others have questioned whether there is anything like a fixed toolkit of methods which is common across science and only science. Some reject privileging one view of method as part of rejecting broader views about the nature of science, such as naturalism (Dupré 2004); some reject any restriction in principle (pluralism).

Scientific method should be distinguished from the aims and products of science, such as knowledge, predictions, or control. Methods are the means by which those goals are achieved. Scientific method should also be distinguished from meta-methodology, which includes the values and justifications behind a particular characterization of scientific method (i.e., a methodology) — values such as objectivity, reproducibility, simplicity, or past successes. Methodological rules are proposed to govern method and it is a meta-methodological question whether methods obeying those rules satisfy given values. Finally, method is distinct, to some degree, from the detailed and contextual practices through which methods are implemented. The latter might range over: specific laboratory techniques; mathematical formalisms or other specialized languages used in descriptions and reasoning; technological or other material means; ways of communicating and sharing results, whether with other scientists or with the public at large; or the conventions, habits, enforced customs, and institutional controls over how and what science is carried out.

While it is important to recognize these distinctions, their boundaries are fuzzy. Hence, accounts of method cannot be entirely divorced from their methodological and meta-methodological motivations or justifications, Moreover, each aspect plays a crucial role in identifying methods. Disputes about method have therefore played out at the detail, rule, and meta-rule levels. Changes in beliefs about the certainty or fallibility of scientific knowledge, for instance (which is a meta-methodological consideration of what we can hope for methods to deliver), have meant different emphases on deductive and inductive reasoning, or on the relative importance attached to reasoning over observation (i.e., differences over particular methods.) Beliefs about the role of science in society will affect the place one gives to values in scientific method.

The issue which has shaped debates over scientific method the most in the last half century is the question of how pluralist do we need to be about method? Unificationists continue to hold out for one method essential to science; nihilism is a form of radical pluralism, which considers the effectiveness of any methodological prescription to be so context sensitive as to render it not explanatory on its own. Some middle degree of pluralism regarding the methods embodied in scientific practice seems appropriate. But the details of scientific practice vary with time and place, from institution to institution, across scientists and their subjects of investigation. How significant are the variations for understanding science and its success? How much can method be abstracted from practice? This entry describes some of the attempts to characterize scientific method or methods, as well as arguments for a more context-sensitive approach to methods embedded in actual scientific practices.

1. Overview and organizing themes

2. historical review: aristotle to mill, 3.1 logical constructionism and operationalism, 3.2. h-d as a logic of confirmation, 3.3. popper and falsificationism, 3.4 meta-methodology and the end of method, 4. statistical methods for hypothesis testing, 5.1 creative and exploratory practices.

• 5.2 Computer methods and the ‘new ways’ of doing science

6.1 “The scientific method” in science education and as seen by scientists

6.2 privileged methods and ‘gold standards’, 6.3 scientific method in the court room, 6.4 deviating practices, 7. conclusion, other internet resources, related entries.

This entry could have been given the title Scientific Methods and gone on to fill volumes, or it could have been extremely short, consisting of a brief summary rejection of the idea that there is any such thing as a unique Scientific Method at all. Both unhappy prospects are due to the fact that scientific activity varies so much across disciplines, times, places, and scientists that any account which manages to unify it all will either consist of overwhelming descriptive detail, or trivial generalizations.

The choice of scope for the present entry is more optimistic, taking a cue from the recent movement in philosophy of science toward a greater attention to practice: to what scientists actually do. This “turn to practice” can be seen as the latest form of studies of methods in science, insofar as it represents an attempt at understanding scientific activity, but through accounts that are neither meant to be universal and unified, nor singular and narrowly descriptive. To some extent, different scientists at different times and places can be said to be using the same method even though, in practice, the details are different.

Whether the context in which methods are carried out is relevant, or to what extent, will depend largely on what one takes the aims of science to be and what one’s own aims are. For most of the history of scientific methodology the assumption has been that the most important output of science is knowledge and so the aim of methodology should be to discover those methods by which scientific knowledge is generated.

Science was seen to embody the most successful form of reasoning (but which form?) to the most certain knowledge claims (but how certain?) on the basis of systematically collected evidence (but what counts as evidence, and should the evidence of the senses take precedence, or rational insight?) Section 2 surveys some of the history, pointing to two major themes. One theme is seeking the right balance between observation and reasoning (and the attendant forms of reasoning which employ them); the other is how certain scientific knowledge is or can be.

Section 3 turns to 20 th century debates on scientific method. In the second half of the 20 th century the epistemic privilege of science faced several challenges and many philosophers of science abandoned the reconstruction of the logic of scientific method. Views changed significantly regarding which functions of science ought to be captured and why. For some, the success of science was better identified with social or cultural features. Historical and sociological turns in the philosophy of science were made, with a demand that greater attention be paid to the non-epistemic aspects of science, such as sociological, institutional, material, and political factors. Even outside of those movements there was an increased specialization in the philosophy of science, with more and more focus on specific fields within science. The combined upshot was very few philosophers arguing any longer for a grand unified methodology of science. Sections 3 and 4 surveys the main positions on scientific method in 20 th century philosophy of science, focusing on where they differ in their preference for confirmation or falsification or for waiving the idea of a special scientific method altogether.

In recent decades, attention has primarily been paid to scientific activities traditionally falling under the rubric of method, such as experimental design and general laboratory practice, the use of statistics, the construction and use of models and diagrams, interdisciplinary collaboration, and science communication. Sections 4–6 attempt to construct a map of the current domains of the study of methods in science.

As these sections illustrate, the question of method is still central to the discourse about science. Scientific method remains a topic for education, for science policy, and for scientists. It arises in the public domain where the demarcation or status of science is at issue. Some philosophers have recently returned, therefore, to the question of what it is that makes science a unique cultural product. This entry will close with some of these recent attempts at discerning and encapsulating the activities by which scientific knowledge is achieved.

Attempting a history of scientific method compounds the vast scope of the topic. This section briefly surveys the background to modern methodological debates. What can be called the classical view goes back to antiquity, and represents a point of departure for later divergences. [ 1 ]

We begin with a point made by Laudan (1968) in his historical survey of scientific method:

Perhaps the most serious inhibition to the emergence of the history of theories of scientific method as a respectable area of study has been the tendency to conflate it with the general history of epistemology, thereby assuming that the narrative categories and classificatory pigeon-holes applied to the latter are also basic to the former. (1968: 5)

To see knowledge about the natural world as falling under knowledge more generally is an understandable conflation. Histories of theories of method would naturally employ the same narrative categories and classificatory pigeon holes. An important theme of the history of epistemology, for example, is the unification of knowledge, a theme reflected in the question of the unification of method in science. Those who have identified differences in kinds of knowledge have often likewise identified different methods for achieving that kind of knowledge (see the entry on the unity of science ).

Different views on what is known, how it is known, and what can be known are connected. Plato distinguished the realms of things into the visible and the intelligible ( The Republic , 510a, in Cooper 1997). Only the latter, the Forms, could be objects of knowledge. The intelligible truths could be known with the certainty of geometry and deductive reasoning. What could be observed of the material world, however, was by definition imperfect and deceptive, not ideal. The Platonic way of knowledge therefore emphasized reasoning as a method, downplaying the importance of observation. Aristotle disagreed, locating the Forms in the natural world as the fundamental principles to be discovered through the inquiry into nature ( Metaphysics Z , in Barnes 1984).

Aristotle is recognized as giving the earliest systematic treatise on the nature of scientific inquiry in the western tradition, one which embraced observation and reasoning about the natural world. In the Prior and Posterior Analytics , Aristotle reflects first on the aims and then the methods of inquiry into nature. A number of features can be found which are still considered by most to be essential to science. For Aristotle, empiricism, careful observation (but passive observation, not controlled experiment), is the starting point. The aim is not merely recording of facts, though. For Aristotle, science ( epistêmê ) is a body of properly arranged knowledge or learning—the empirical facts, but also their ordering and display are of crucial importance. The aims of discovery, ordering, and display of facts partly determine the methods required of successful scientific inquiry. Also determinant is the nature of the knowledge being sought, and the explanatory causes proper to that kind of knowledge (see the discussion of the four causes in the entry on Aristotle on causality ).

In addition to careful observation, then, scientific method requires a logic as a system of reasoning for properly arranging, but also inferring beyond, what is known by observation. Methods of reasoning may include induction, prediction, or analogy, among others. Aristotle’s system (along with his catalogue of fallacious reasoning) was collected under the title the Organon . This title would be echoed in later works on scientific reasoning, such as Novum Organon by Francis Bacon, and Novum Organon Restorum by William Whewell (see below). In Aristotle’s Organon reasoning is divided primarily into two forms, a rough division which persists into modern times. The division, known most commonly today as deductive versus inductive method, appears in other eras and methodologies as analysis/​synthesis, non-ampliative/​ampliative, or even confirmation/​verification. The basic idea is there are two “directions” to proceed in our methods of inquiry: one away from what is observed, to the more fundamental, general, and encompassing principles; the other, from the fundamental and general to instances or implications of principles.

The basic aim and method of inquiry identified here can be seen as a theme running throughout the next two millennia of reflection on the correct way to seek after knowledge: carefully observe nature and then seek rules or principles which explain or predict its operation. The Aristotelian corpus provided the framework for a commentary tradition on scientific method independent of science itself (cosmos versus physics.) During the medieval period, figures such as Albertus Magnus (1206–1280), Thomas Aquinas (1225–1274), Robert Grosseteste (1175–1253), Roger Bacon (1214/1220–1292), William of Ockham (1287–1347), Andreas Vesalius (1514–1546), Giacomo Zabarella (1533–1589) all worked to clarify the kind of knowledge obtainable by observation and induction, the source of justification of induction, and best rules for its application. [ 2 ] Many of their contributions we now think of as essential to science (see also Laudan 1968). As Aristotle and Plato had employed a framework of reasoning either “to the forms” or “away from the forms”, medieval thinkers employed directions away from the phenomena or back to the phenomena. In analysis, a phenomena was examined to discover its basic explanatory principles; in synthesis, explanations of a phenomena were constructed from first principles.

During the Scientific Revolution these various strands of argument, experiment, and reason were forged into a dominant epistemic authority. The 16 th –18 th centuries were a period of not only dramatic advance in knowledge about the operation of the natural world—advances in mechanical, medical, biological, political, economic explanations—but also of self-awareness of the revolutionary changes taking place, and intense reflection on the source and legitimation of the method by which the advances were made. The struggle to establish the new authority included methodological moves. The Book of Nature, according to the metaphor of Galileo Galilei (1564–1642) or Francis Bacon (1561–1626), was written in the language of mathematics, of geometry and number. This motivated an emphasis on mathematical description and mechanical explanation as important aspects of scientific method. Through figures such as Henry More and Ralph Cudworth, a neo-Platonic emphasis on the importance of metaphysical reflection on nature behind appearances, particularly regarding the spiritual as a complement to the purely mechanical, remained an important methodological thread of the Scientific Revolution (see the entries on Cambridge platonists ; Boyle ; Henry More ; Galileo ).

In Novum Organum (1620), Bacon was critical of the Aristotelian method for leaping from particulars to universals too quickly. The syllogistic form of reasoning readily mixed those two types of propositions. Bacon aimed at the invention of new arts, principles, and directions. His method would be grounded in methodical collection of observations, coupled with correction of our senses (and particularly, directions for the avoidance of the Idols, as he called them, kinds of systematic errors to which naïve observers are prone.) The community of scientists could then climb, by a careful, gradual and unbroken ascent, to reliable general claims.

Bacon’s method has been criticized as impractical and too inflexible for the practicing scientist. Whewell would later criticize Bacon in his System of Logic for paying too little attention to the practices of scientists. It is hard to find convincing examples of Bacon’s method being put in to practice in the history of science, but there are a few who have been held up as real examples of 16 th century scientific, inductive method, even if not in the rigid Baconian mold: figures such as Robert Boyle (1627–1691) and William Harvey (1578–1657) (see the entry on Bacon ).

It is to Isaac Newton (1642–1727), however, that historians of science and methodologists have paid greatest attention. Given the enormous success of his Principia Mathematica and Opticks , this is understandable. The study of Newton’s method has had two main thrusts: the implicit method of the experiments and reasoning presented in the Opticks, and the explicit methodological rules given as the Rules for Philosophising (the Regulae) in Book III of the Principia . [ 3 ] Newton’s law of gravitation, the linchpin of his new cosmology, broke with explanatory conventions of natural philosophy, first for apparently proposing action at a distance, but more generally for not providing “true”, physical causes. The argument for his System of the World ( Principia , Book III) was based on phenomena, not reasoned first principles. This was viewed (mainly on the continent) as insufficient for proper natural philosophy. The Regulae counter this objection, re-defining the aims of natural philosophy by re-defining the method natural philosophers should follow. (See the entry on Newton’s philosophy .)

To his list of methodological prescriptions should be added Newton’s famous phrase “ hypotheses non fingo ” (commonly translated as “I frame no hypotheses”.) The scientist was not to invent systems but infer explanations from observations, as Bacon had advocated. This would come to be known as inductivism. In the century after Newton, significant clarifications of the Newtonian method were made. Colin Maclaurin (1698–1746), for instance, reconstructed the essential structure of the method as having complementary analysis and synthesis phases, one proceeding away from the phenomena in generalization, the other from the general propositions to derive explanations of new phenomena. Denis Diderot (1713–1784) and editors of the Encyclopédie did much to consolidate and popularize Newtonianism, as did Francesco Algarotti (1721–1764). The emphasis was often the same, as much on the character of the scientist as on their process, a character which is still commonly assumed. The scientist is humble in the face of nature, not beholden to dogma, obeys only his eyes, and follows the truth wherever it leads. It was certainly Voltaire (1694–1778) and du Chatelet (1706–1749) who were most influential in propagating the latter vision of the scientist and their craft, with Newton as hero. Scientific method became a revolutionary force of the Enlightenment. (See also the entries on Newton , Leibniz , Descartes , Boyle , Hume , enlightenment , as well as Shank 2008 for a historical overview.)

Not all 18 th century reflections on scientific method were so celebratory. Famous also are George Berkeley’s (1685–1753) attack on the mathematics of the new science, as well as the over-emphasis of Newtonians on observation; and David Hume’s (1711–1776) undermining of the warrant offered for scientific claims by inductive justification (see the entries on: George Berkeley ; David Hume ; Hume’s Newtonianism and Anti-Newtonianism ). Hume’s problem of induction motivated Immanuel Kant (1724–1804) to seek new foundations for empirical method, though as an epistemic reconstruction, not as any set of practical guidelines for scientists. Both Hume and Kant influenced the methodological reflections of the next century, such as the debate between Mill and Whewell over the certainty of inductive inferences in science.

The debate between John Stuart Mill (1806–1873) and William Whewell (1794–1866) has become the canonical methodological debate of the 19 th century. Although often characterized as a debate between inductivism and hypothetico-deductivism, the role of the two methods on each side is actually more complex. On the hypothetico-deductive account, scientists work to come up with hypotheses from which true observational consequences can be deduced—hence, hypothetico-deductive. Because Whewell emphasizes both hypotheses and deduction in his account of method, he can be seen as a convenient foil to the inductivism of Mill. However, equally if not more important to Whewell’s portrayal of scientific method is what he calls the “fundamental antithesis”. Knowledge is a product of the objective (what we see in the world around us) and subjective (the contributions of our mind to how we perceive and understand what we experience, which he called the Fundamental Ideas). Both elements are essential according to Whewell, and he was therefore critical of Kant for too much focus on the subjective, and John Locke (1632–1704) and Mill for too much focus on the senses. Whewell’s fundamental ideas can be discipline relative. An idea can be fundamental even if it is necessary for knowledge only within a given scientific discipline (e.g., chemical affinity for chemistry). This distinguishes fundamental ideas from the forms and categories of intuition of Kant. (See the entry on Whewell .)

Clarifying fundamental ideas would therefore be an essential part of scientific method and scientific progress. Whewell called this process “Discoverer’s Induction”. It was induction, following Bacon or Newton, but Whewell sought to revive Bacon’s account by emphasising the role of ideas in the clear and careful formulation of inductive hypotheses. Whewell’s induction is not merely the collecting of objective facts. The subjective plays a role through what Whewell calls the Colligation of Facts, a creative act of the scientist, the invention of a theory. A theory is then confirmed by testing, where more facts are brought under the theory, called the Consilience of Inductions. Whewell felt that this was the method by which the true laws of nature could be discovered: clarification of fundamental concepts, clever invention of explanations, and careful testing. Mill, in his critique of Whewell, and others who have cast Whewell as a fore-runner of the hypothetico-deductivist view, seem to have under-estimated the importance of this discovery phase in Whewell’s understanding of method (Snyder 1997a,b, 1999). Down-playing the discovery phase would come to characterize methodology of the early 20 th century (see section 3 ).

Mill, in his System of Logic , put forward a narrower view of induction as the essence of scientific method. For Mill, induction is the search first for regularities among events. Among those regularities, some will continue to hold for further observations, eventually gaining the status of laws. One can also look for regularities among the laws discovered in a domain, i.e., for a law of laws. Which “law law” will hold is time and discipline dependent and open to revision. One example is the Law of Universal Causation, and Mill put forward specific methods for identifying causes—now commonly known as Mill’s methods. These five methods look for circumstances which are common among the phenomena of interest, those which are absent when the phenomena are, or those for which both vary together. Mill’s methods are still seen as capturing basic intuitions about experimental methods for finding the relevant explanatory factors ( System of Logic (1843), see Mill entry). The methods advocated by Whewell and Mill, in the end, look similar. Both involve inductive generalization to covering laws. They differ dramatically, however, with respect to the necessity of the knowledge arrived at; that is, at the meta-methodological level (see the entries on Whewell and Mill entries).

3. Logic of method and critical responses

The quantum and relativistic revolutions in physics in the early 20 th century had a profound effect on methodology. Conceptual foundations of both theories were taken to show the defeasibility of even the most seemingly secure intuitions about space, time and bodies. Certainty of knowledge about the natural world was therefore recognized as unattainable. Instead a renewed empiricism was sought which rendered science fallible but still rationally justifiable.

Analyses of the reasoning of scientists emerged, according to which the aspects of scientific method which were of primary importance were the means of testing and confirming of theories. A distinction in methodology was made between the contexts of discovery and justification. The distinction could be used as a wedge between the particularities of where and how theories or hypotheses are arrived at, on the one hand, and the underlying reasoning scientists use (whether or not they are aware of it) when assessing theories and judging their adequacy on the basis of the available evidence. By and large, for most of the 20 th century, philosophy of science focused on the second context, although philosophers differed on whether to focus on confirmation or refutation as well as on the many details of how confirmation or refutation could or could not be brought about. By the mid-20 th century these attempts at defining the method of justification and the context distinction itself came under pressure. During the same period, philosophy of science developed rapidly, and from section 4 this entry will therefore shift from a primarily historical treatment of the scientific method towards a primarily thematic one.

Advances in logic and probability held out promise of the possibility of elaborate reconstructions of scientific theories and empirical method, the best example being Rudolf Carnap’s The Logical Structure of the World (1928). Carnap attempted to show that a scientific theory could be reconstructed as a formal axiomatic system—that is, a logic. That system could refer to the world because some of its basic sentences could be interpreted as observations or operations which one could perform to test them. The rest of the theoretical system, including sentences using theoretical or unobservable terms (like electron or force) would then either be meaningful because they could be reduced to observations, or they had purely logical meanings (called analytic, like mathematical identities). This has been referred to as the verifiability criterion of meaning. According to the criterion, any statement not either analytic or verifiable was strictly meaningless. Although the view was endorsed by Carnap in 1928, he would later come to see it as too restrictive (Carnap 1956). Another familiar version of this idea is operationalism of Percy William Bridgman. In The Logic of Modern Physics (1927) Bridgman asserted that every physical concept could be defined in terms of the operations one would perform to verify the application of that concept. Making good on the operationalisation of a concept even as simple as length, however, can easily become enormously complex (for measuring very small lengths, for instance) or impractical (measuring large distances like light years.)

Carl Hempel’s (1950, 1951) criticisms of the verifiability criterion of meaning had enormous influence. He pointed out that universal generalizations, such as most scientific laws, were not strictly meaningful on the criterion. Verifiability and operationalism both seemed too restrictive to capture standard scientific aims and practice. The tenuous connection between these reconstructions and actual scientific practice was criticized in another way. In both approaches, scientific methods are instead recast in methodological roles. Measurements, for example, were looked to as ways of giving meanings to terms. The aim of the philosopher of science was not to understand the methods per se , but to use them to reconstruct theories, their meanings, and their relation to the world. When scientists perform these operations, however, they will not report that they are doing them to give meaning to terms in a formal axiomatic system. This disconnect between methodology and the details of actual scientific practice would seem to violate the empiricism the Logical Positivists and Bridgman were committed to. The view that methodology should correspond to practice (to some extent) has been called historicism, or intuitionism. We turn to these criticisms and responses in section 3.4 . [ 4 ]

Positivism also had to contend with the recognition that a purely inductivist approach, along the lines of Bacon-Newton-Mill, was untenable. There was no pure observation, for starters. All observation was theory laden. Theory is required to make any observation, therefore not all theory can be derived from observation alone. (See the entry on theory and observation in science .) Even granting an observational basis, Hume had already pointed out that one could not deductively justify inductive conclusions without begging the question by presuming the success of the inductive method. Likewise, positivist attempts at analyzing how a generalization can be confirmed by observations of its instances were subject to a number of criticisms. Goodman (1965) and Hempel (1965) both point to paradoxes inherent in standard accounts of confirmation. Recent attempts at explaining how observations can serve to confirm a scientific theory are discussed in section 4 below.

The standard starting point for a non-inductive analysis of the logic of confirmation is known as the Hypothetico-Deductive (H-D) method. In its simplest form, a sentence of a theory which expresses some hypothesis is confirmed by its true consequences. As noted in section 2 , this method had been advanced by Whewell in the 19 th century, as well as Nicod (1924) and others in the 20 th century. Often, Hempel’s (1966) description of the H-D method, illustrated by the case of Semmelweiss’ inferential procedures in establishing the cause of childbed fever, has been presented as a key account of H-D as well as a foil for criticism of the H-D account of confirmation (see, for example, Lipton’s (2004) discussion of inference to the best explanation; also the entry on confirmation ). Hempel described Semmelsweiss’ procedure as examining various hypotheses explaining the cause of childbed fever. Some hypotheses conflicted with observable facts and could be rejected as false immediately. Others needed to be tested experimentally by deducing which observable events should follow if the hypothesis were true (what Hempel called the test implications of the hypothesis), then conducting an experiment and observing whether or not the test implications occurred. If the experiment showed the test implication to be false, the hypothesis could be rejected. If the experiment showed the test implications to be true, however, this did not prove the hypothesis true. The confirmation of a test implication does not verify a hypothesis, though Hempel did allow that “it provides at least some support, some corroboration or confirmation for it” (Hempel 1966: 8). The degree of this support then depends on the quantity, variety and precision of the supporting evidence.

Another approach that took off from the difficulties with inductive inference was Karl Popper’s critical rationalism or falsificationism (Popper 1959, 1963). Falsification is deductive and similar to H-D in that it involves scientists deducing observational consequences from the hypothesis under test. For Popper, however, the important point was not the degree of confirmation that successful prediction offered to a hypothesis. The crucial thing was the logical asymmetry between confirmation, based on inductive inference, and falsification, which can be based on a deductive inference. (This simple opposition was later questioned, by Lakatos, among others. See the entry on historicist theories of scientific rationality. )

Popper stressed that, regardless of the amount of confirming evidence, we can never be certain that a hypothesis is true without committing the fallacy of affirming the consequent. Instead, Popper introduced the notion of corroboration as a measure for how well a theory or hypothesis has survived previous testing—but without implying that this is also a measure for the probability that it is true.

Popper was also motivated by his doubts about the scientific status of theories like the Marxist theory of history or psycho-analysis, and so wanted to demarcate between science and pseudo-science. Popper saw this as an importantly different distinction than demarcating science from metaphysics. The latter demarcation was the primary concern of many logical empiricists. Popper used the idea of falsification to draw a line instead between pseudo and proper science. Science was science because its method involved subjecting theories to rigorous tests which offered a high probability of failing and thus refuting the theory.

A commitment to the risk of failure was important. Avoiding falsification could be done all too easily. If a consequence of a theory is inconsistent with observations, an exception can be added by introducing auxiliary hypotheses designed explicitly to save the theory, so-called ad hoc modifications. This Popper saw done in pseudo-science where ad hoc theories appeared capable of explaining anything in their field of application. In contrast, science is risky. If observations showed the predictions from a theory to be wrong, the theory would be refuted. Hence, scientific hypotheses must be falsifiable. Not only must there exist some possible observation statement which could falsify the hypothesis or theory, were it observed, (Popper called these the hypothesis’ potential falsifiers) it is crucial to the Popperian scientific method that such falsifications be sincerely attempted on a regular basis.

The more potential falsifiers of a hypothesis, the more falsifiable it would be, and the more the hypothesis claimed. Conversely, hypotheses without falsifiers claimed very little or nothing at all. Originally, Popper thought that this meant the introduction of ad hoc hypotheses only to save a theory should not be countenanced as good scientific method. These would undermine the falsifiabililty of a theory. However, Popper later came to recognize that the introduction of modifications (immunizations, he called them) was often an important part of scientific development. Responding to surprising or apparently falsifying observations often generated important new scientific insights. Popper’s own example was the observed motion of Uranus which originally did not agree with Newtonian predictions. The ad hoc hypothesis of an outer planet explained the disagreement and led to further falsifiable predictions. Popper sought to reconcile the view by blurring the distinction between falsifiable and not falsifiable, and speaking instead of degrees of testability (Popper 1985: 41f.).

From the 1960s on, sustained meta-methodological criticism emerged that drove philosophical focus away from scientific method. A brief look at those criticisms follows, with recommendations for further reading at the end of the entry.

Thomas Kuhn’s The Structure of Scientific Revolutions (1962) begins with a well-known shot across the bow for philosophers of science:

History, if viewed as a repository for more than anecdote or chronology, could produce a decisive transformation in the image of science by which we are now possessed. (1962: 1)

The image Kuhn thought needed transforming was the a-historical, rational reconstruction sought by many of the Logical Positivists, though Carnap and other positivists were actually quite sympathetic to Kuhn’s views. (See the entry on the Vienna Circle .) Kuhn shares with other of his contemporaries, such as Feyerabend and Lakatos, a commitment to a more empirical approach to philosophy of science. Namely, the history of science provides important data, and necessary checks, for philosophy of science, including any theory of scientific method.

The history of science reveals, according to Kuhn, that scientific development occurs in alternating phases. During normal science, the members of the scientific community adhere to the paradigm in place. Their commitment to the paradigm means a commitment to the puzzles to be solved and the acceptable ways of solving them. Confidence in the paradigm remains so long as steady progress is made in solving the shared puzzles. Method in this normal phase operates within a disciplinary matrix (Kuhn’s later concept of a paradigm) which includes standards for problem solving, and defines the range of problems to which the method should be applied. An important part of a disciplinary matrix is the set of values which provide the norms and aims for scientific method. The main values that Kuhn identifies are prediction, problem solving, simplicity, consistency, and plausibility.

An important by-product of normal science is the accumulation of puzzles which cannot be solved with resources of the current paradigm. Once accumulation of these anomalies has reached some critical mass, it can trigger a communal shift to a new paradigm and a new phase of normal science. Importantly, the values that provide the norms and aims for scientific method may have transformed in the meantime. Method may therefore be relative to discipline, time or place

Feyerabend also identified the aims of science as progress, but argued that any methodological prescription would only stifle that progress (Feyerabend 1988). His arguments are grounded in re-examining accepted “myths” about the history of science. Heroes of science, like Galileo, are shown to be just as reliant on rhetoric and persuasion as they are on reason and demonstration. Others, like Aristotle, are shown to be far more reasonable and far-reaching in their outlooks then they are given credit for. As a consequence, the only rule that could provide what he took to be sufficient freedom was the vacuous “anything goes”. More generally, even the methodological restriction that science is the best way to pursue knowledge, and to increase knowledge, is too restrictive. Feyerabend suggested instead that science might, in fact, be a threat to a free society, because it and its myth had become so dominant (Feyerabend 1978).

An even more fundamental kind of criticism was offered by several sociologists of science from the 1970s onwards who rejected the methodology of providing philosophical accounts for the rational development of science and sociological accounts of the irrational mistakes. Instead, they adhered to a symmetry thesis on which any causal explanation of how scientific knowledge is established needs to be symmetrical in explaining truth and falsity, rationality and irrationality, success and mistakes, by the same causal factors (see, e.g., Barnes and Bloor 1982, Bloor 1991). Movements in the Sociology of Science, like the Strong Programme, or in the social dimensions and causes of knowledge more generally led to extended and close examination of detailed case studies in contemporary science and its history. (See the entries on the social dimensions of scientific knowledge and social epistemology .) Well-known examinations by Latour and Woolgar (1979/1986), Knorr-Cetina (1981), Pickering (1984), Shapin and Schaffer (1985) seem to bear out that it was social ideologies (on a macro-scale) or individual interactions and circumstances (on a micro-scale) which were the primary causal factors in determining which beliefs gained the status of scientific knowledge. As they saw it therefore, explanatory appeals to scientific method were not empirically grounded.

A late, and largely unexpected, criticism of scientific method came from within science itself. Beginning in the early 2000s, a number of scientists attempting to replicate the results of published experiments could not do so. There may be close conceptual connection between reproducibility and method. For example, if reproducibility means that the same scientific methods ought to produce the same result, and all scientific results ought to be reproducible, then whatever it takes to reproduce a scientific result ought to be called scientific method. Space limits us to the observation that, insofar as reproducibility is a desired outcome of proper scientific method, it is not strictly a part of scientific method. (See the entry on reproducibility of scientific results .)

By the close of the 20 th century the search for the scientific method was flagging. Nola and Sankey (2000b) could introduce their volume on method by remarking that “For some, the whole idea of a theory of scientific method is yester-year’s debate …”.

Despite the many difficulties that philosophers encountered in trying to providing a clear methodology of conformation (or refutation), still important progress has been made on understanding how observation can provide evidence for a given theory. Work in statistics has been crucial for understanding how theories can be tested empirically, and in recent decades a huge literature has developed that attempts to recast confirmation in Bayesian terms. Here these developments can be covered only briefly, and we refer to the entry on confirmation for further details and references.

Statistics has come to play an increasingly important role in the methodology of the experimental sciences from the 19 th century onwards. At that time, statistics and probability theory took on a methodological role as an analysis of inductive inference, and attempts to ground the rationality of induction in the axioms of probability theory have continued throughout the 20 th century and in to the present. Developments in the theory of statistics itself, meanwhile, have had a direct and immense influence on the experimental method, including methods for measuring the uncertainty of observations such as the Method of Least Squares developed by Legendre and Gauss in the early 19 th century, criteria for the rejection of outliers proposed by Peirce by the mid-19 th century, and the significance tests developed by Gosset (a.k.a. “Student”), Fisher, Neyman & Pearson and others in the 1920s and 1930s (see, e.g., Swijtink 1987 for a brief historical overview; and also the entry on C.S. Peirce ).

These developments within statistics then in turn led to a reflective discussion among both statisticians and philosophers of science on how to perceive the process of hypothesis testing: whether it was a rigorous statistical inference that could provide a numerical expression of the degree of confidence in the tested hypothesis, or if it should be seen as a decision between different courses of actions that also involved a value component. This led to a major controversy among Fisher on the one side and Neyman and Pearson on the other (see especially Fisher 1955, Neyman 1956 and Pearson 1955, and for analyses of the controversy, e.g., Howie 2002, Marks 2000, Lenhard 2006). On Fisher’s view, hypothesis testing was a methodology for when to accept or reject a statistical hypothesis, namely that a hypothesis should be rejected by evidence if this evidence would be unlikely relative to other possible outcomes, given the hypothesis were true. In contrast, on Neyman and Pearson’s view, the consequence of error also had to play a role when deciding between hypotheses. Introducing the distinction between the error of rejecting a true hypothesis (type I error) and accepting a false hypothesis (type II error), they argued that it depends on the consequences of the error to decide whether it is more important to avoid rejecting a true hypothesis or accepting a false one. Hence, Fisher aimed for a theory of inductive inference that enabled a numerical expression of confidence in a hypothesis. To him, the important point was the search for truth, not utility. In contrast, the Neyman-Pearson approach provided a strategy of inductive behaviour for deciding between different courses of action. Here, the important point was not whether a hypothesis was true, but whether one should act as if it was.

Similar discussions are found in the philosophical literature. On the one side, Churchman (1948) and Rudner (1953) argued that because scientific hypotheses can never be completely verified, a complete analysis of the methods of scientific inference includes ethical judgments in which the scientists must decide whether the evidence is sufficiently strong or that the probability is sufficiently high to warrant the acceptance of the hypothesis, which again will depend on the importance of making a mistake in accepting or rejecting the hypothesis. Others, such as Jeffrey (1956) and Levi (1960) disagreed and instead defended a value-neutral view of science on which scientists should bracket their attitudes, preferences, temperament, and values when assessing the correctness of their inferences. For more details on this value-free ideal in the philosophy of science and its historical development, see Douglas (2009) and Howard (2003). For a broad set of case studies examining the role of values in science, see e.g. Elliott & Richards 2017.

In recent decades, philosophical discussions of the evaluation of probabilistic hypotheses by statistical inference have largely focused on Bayesianism that understands probability as a measure of a person’s degree of belief in an event, given the available information, and frequentism that instead understands probability as a long-run frequency of a repeatable event. Hence, for Bayesians probabilities refer to a state of knowledge, whereas for frequentists probabilities refer to frequencies of events (see, e.g., Sober 2008, chapter 1 for a detailed introduction to Bayesianism and frequentism as well as to likelihoodism). Bayesianism aims at providing a quantifiable, algorithmic representation of belief revision, where belief revision is a function of prior beliefs (i.e., background knowledge) and incoming evidence. Bayesianism employs a rule based on Bayes’ theorem, a theorem of the probability calculus which relates conditional probabilities. The probability that a particular hypothesis is true is interpreted as a degree of belief, or credence, of the scientist. There will also be a probability and a degree of belief that a hypothesis will be true conditional on a piece of evidence (an observation, say) being true. Bayesianism proscribes that it is rational for the scientist to update their belief in the hypothesis to that conditional probability should it turn out that the evidence is, in fact, observed (see, e.g., Sprenger & Hartmann 2019 for a comprehensive treatment of Bayesian philosophy of science). Originating in the work of Neyman and Person, frequentism aims at providing the tools for reducing long-run error rates, such as the error-statistical approach developed by Mayo (1996) that focuses on how experimenters can avoid both type I and type II errors by building up a repertoire of procedures that detect errors if and only if they are present. Both Bayesianism and frequentism have developed over time, they are interpreted in different ways by its various proponents, and their relations to previous criticism to attempts at defining scientific method are seen differently by proponents and critics. The literature, surveys, reviews and criticism in this area are vast and the reader is referred to the entries on Bayesian epistemology and confirmation .

5. Method in Practice

Attention to scientific practice, as we have seen, is not itself new. However, the turn to practice in the philosophy of science of late can be seen as a correction to the pessimism with respect to method in philosophy of science in later parts of the 20 th century, and as an attempted reconciliation between sociological and rationalist explanations of scientific knowledge. Much of this work sees method as detailed and context specific problem-solving procedures, and methodological analyses to be at the same time descriptive, critical and advisory (see Nickles 1987 for an exposition of this view). The following section contains a survey of some of the practice focuses. In this section we turn fully to topics rather than chronology.

A problem with the distinction between the contexts of discovery and justification that figured so prominently in philosophy of science in the first half of the 20 th century (see section 2 ) is that no such distinction can be clearly seen in scientific activity (see Arabatzis 2006). Thus, in recent decades, it has been recognized that study of conceptual innovation and change should not be confined to psychology and sociology of science, but are also important aspects of scientific practice which philosophy of science should address (see also the entry on scientific discovery ). Looking for the practices that drive conceptual innovation has led philosophers to examine both the reasoning practices of scientists and the wide realm of experimental practices that are not directed narrowly at testing hypotheses, that is, exploratory experimentation.

Examining the reasoning practices of historical and contemporary scientists, Nersessian (2008) has argued that new scientific concepts are constructed as solutions to specific problems by systematic reasoning, and that of analogy, visual representation and thought-experimentation are among the important reasoning practices employed. These ubiquitous forms of reasoning are reliable—but also fallible—methods of conceptual development and change. On her account, model-based reasoning consists of cycles of construction, simulation, evaluation and adaption of models that serve as interim interpretations of the target problem to be solved. Often, this process will lead to modifications or extensions, and a new cycle of simulation and evaluation. However, Nersessian also emphasizes that

creative model-based reasoning cannot be applied as a simple recipe, is not always productive of solutions, and even its most exemplary usages can lead to incorrect solutions. (Nersessian 2008: 11)

Thus, while on the one hand she agrees with many previous philosophers that there is no logic of discovery, discoveries can derive from reasoned processes, such that a large and integral part of scientific practice is

the creation of concepts through which to comprehend, structure, and communicate about physical phenomena …. (Nersessian 1987: 11)

Similarly, work on heuristics for discovery and theory construction by scholars such as Darden (1991) and Bechtel & Richardson (1993) present science as problem solving and investigate scientific problem solving as a special case of problem-solving in general. Drawing largely on cases from the biological sciences, much of their focus has been on reasoning strategies for the generation, evaluation, and revision of mechanistic explanations of complex systems.

Addressing another aspect of the context distinction, namely the traditional view that the primary role of experiments is to test theoretical hypotheses according to the H-D model, other philosophers of science have argued for additional roles that experiments can play. The notion of exploratory experimentation was introduced to describe experiments driven by the desire to obtain empirical regularities and to develop concepts and classifications in which these regularities can be described (Steinle 1997, 2002; Burian 1997; Waters 2007)). However the difference between theory driven experimentation and exploratory experimentation should not be seen as a sharp distinction. Theory driven experiments are not always directed at testing hypothesis, but may also be directed at various kinds of fact-gathering, such as determining numerical parameters. Vice versa , exploratory experiments are usually informed by theory in various ways and are therefore not theory-free. Instead, in exploratory experiments phenomena are investigated without first limiting the possible outcomes of the experiment on the basis of extant theory about the phenomena.

The development of high throughput instrumentation in molecular biology and neighbouring fields has given rise to a special type of exploratory experimentation that collects and analyses very large amounts of data, and these new ‘omics’ disciplines are often said to represent a break with the ideal of hypothesis-driven science (Burian 2007; Elliott 2007; Waters 2007; O’Malley 2007) and instead described as data-driven research (Leonelli 2012; Strasser 2012) or as a special kind of “convenience experimentation” in which many experiments are done simply because they are extraordinarily convenient to perform (Krohs 2012).

5.2 Computer methods and ‘new ways’ of doing science

The field of omics just described is possible because of the ability of computers to process, in a reasonable amount of time, the huge quantities of data required. Computers allow for more elaborate experimentation (higher speed, better filtering, more variables, sophisticated coordination and control), but also, through modelling and simulations, might constitute a form of experimentation themselves. Here, too, we can pose a version of the general question of method versus practice: does the practice of using computers fundamentally change scientific method, or merely provide a more efficient means of implementing standard methods?

Because computers can be used to automate measurements, quantifications, calculations, and statistical analyses where, for practical reasons, these operations cannot be otherwise carried out, many of the steps involved in reaching a conclusion on the basis of an experiment are now made inside a “black box”, without the direct involvement or awareness of a human. This has epistemological implications, regarding what we can know, and how we can know it. To have confidence in the results, computer methods are therefore subjected to tests of verification and validation.

The distinction between verification and validation is easiest to characterize in the case of computer simulations. In a typical computer simulation scenario computers are used to numerically integrate differential equations for which no analytic solution is available. The equations are part of the model the scientist uses to represent a phenomenon or system under investigation. Verifying a computer simulation means checking that the equations of the model are being correctly approximated. Validating a simulation means checking that the equations of the model are adequate for the inferences one wants to make on the basis of that model.

A number of issues related to computer simulations have been raised. The identification of validity and verification as the testing methods has been criticized. Oreskes et al. (1994) raise concerns that “validiation”, because it suggests deductive inference, might lead to over-confidence in the results of simulations. The distinction itself is probably too clean, since actual practice in the testing of simulations mixes and moves back and forth between the two (Weissart 1997; Parker 2008a; Winsberg 2010). Computer simulations do seem to have a non-inductive character, given that the principles by which they operate are built in by the programmers, and any results of the simulation follow from those in-built principles in such a way that those results could, in principle, be deduced from the program code and its inputs. The status of simulations as experiments has therefore been examined (Kaufmann and Smarr 1993; Humphreys 1995; Hughes 1999; Norton and Suppe 2001). This literature considers the epistemology of these experiments: what we can learn by simulation, and also the kinds of justifications which can be given in applying that knowledge to the “real” world. (Mayo 1996; Parker 2008b). As pointed out, part of the advantage of computer simulation derives from the fact that huge numbers of calculations can be carried out without requiring direct observation by the experimenter/​simulator. At the same time, many of these calculations are approximations to the calculations which would be performed first-hand in an ideal situation. Both factors introduce uncertainties into the inferences drawn from what is observed in the simulation.

For many of the reasons described above, computer simulations do not seem to belong clearly to either the experimental or theoretical domain. Rather, they seem to crucially involve aspects of both. This has led some authors, such as Fox Keller (2003: 200) to argue that we ought to consider computer simulation a “qualitatively different way of doing science”. The literature in general tends to follow Kaufmann and Smarr (1993) in referring to computer simulation as a “third way” for scientific methodology (theoretical reasoning and experimental practice are the first two ways.). It should also be noted that the debates around these issues have tended to focus on the form of computer simulation typical in the physical sciences, where models are based on dynamical equations. Other forms of simulation might not have the same problems, or have problems of their own (see the entry on computer simulations in science ).

In recent years, the rapid development of machine learning techniques has prompted some scholars to suggest that the scientific method has become “obsolete” (Anderson 2008, Carrol and Goodstein 2009). This has resulted in an intense debate on the relative merit of data-driven and hypothesis-driven research (for samples, see e.g. Mazzocchi 2015 or Succi and Coveney 2018). For a detailed treatment of this topic, we refer to the entry scientific research and big data .

6. Discourse on scientific method

Despite philosophical disagreements, the idea of the scientific method still figures prominently in contemporary discourse on many different topics, both within science and in society at large. Often, reference to scientific method is used in ways that convey either the legend of a single, universal method characteristic of all science, or grants to a particular method or set of methods privilege as a special ‘gold standard’, often with reference to particular philosophers to vindicate the claims. Discourse on scientific method also typically arises when there is a need to distinguish between science and other activities, or for justifying the special status conveyed to science. In these areas, the philosophical attempts at identifying a set of methods characteristic for scientific endeavors are closely related to the philosophy of science’s classical problem of demarcation (see the entry on science and pseudo-science ) and to the philosophical analysis of the social dimension of scientific knowledge and the role of science in democratic society.

One of the settings in which the legend of a single, universal scientific method has been particularly strong is science education (see, e.g., Bauer 1992; McComas 1996; Wivagg & Allchin 2002). [ 5 ] Often, ‘the scientific method’ is presented in textbooks and educational web pages as a fixed four or five step procedure starting from observations and description of a phenomenon and progressing over formulation of a hypothesis which explains the phenomenon, designing and conducting experiments to test the hypothesis, analyzing the results, and ending with drawing a conclusion. Such references to a universal scientific method can be found in educational material at all levels of science education (Blachowicz 2009), and numerous studies have shown that the idea of a general and universal scientific method often form part of both students’ and teachers’ conception of science (see, e.g., Aikenhead 1987; Osborne et al. 2003). In response, it has been argued that science education need to focus more on teaching about the nature of science, although views have differed on whether this is best done through student-led investigations, contemporary cases, or historical cases (Allchin, Andersen & Nielsen 2014)

Although occasionally phrased with reference to the H-D method, important historical roots of the legend in science education of a single, universal scientific method are the American philosopher and psychologist Dewey’s account of inquiry in How We Think (1910) and the British mathematician Karl Pearson’s account of science in Grammar of Science (1892). On Dewey’s account, inquiry is divided into the five steps of

(i) a felt difficulty, (ii) its location and definition, (iii) suggestion of a possible solution, (iv) development by reasoning of the bearing of the suggestions, (v) further observation and experiment leading to its acceptance or rejection. (Dewey 1910: 72)

Similarly, on Pearson’s account, scientific investigations start with measurement of data and observation of their correction and sequence from which scientific laws can be discovered with the aid of creative imagination. These laws have to be subject to criticism, and their final acceptance will have equal validity for “all normally constituted minds”. Both Dewey’s and Pearson’s accounts should be seen as generalized abstractions of inquiry and not restricted to the realm of science—although both Dewey and Pearson referred to their respective accounts as ‘the scientific method’.

Occasionally, scientists make sweeping statements about a simple and distinct scientific method, as exemplified by Feynman’s simplified version of a conjectures and refutations method presented, for example, in the last of his 1964 Cornell Messenger lectures. [ 6 ] However, just as often scientists have come to the same conclusion as recent philosophy of science that there is not any unique, easily described scientific method. For example, the physicist and Nobel Laureate Weinberg described in the paper “The Methods of Science … And Those By Which We Live” (1995) how

The fact that the standards of scientific success shift with time does not only make the philosophy of science difficult; it also raises problems for the public understanding of science. We do not have a fixed scientific method to rally around and defend. (1995: 8)

Interview studies with scientists on their conception of method shows that scientists often find it hard to figure out whether available evidence confirms their hypothesis, and that there are no direct translations between general ideas about method and specific strategies to guide how research is conducted (Schickore & Hangel 2019, Hangel & Schickore 2017)

Reference to the scientific method has also often been used to argue for the scientific nature or special status of a particular activity. Philosophical positions that argue for a simple and unique scientific method as a criterion of demarcation, such as Popperian falsification, have often attracted practitioners who felt that they had a need to defend their domain of practice. For example, references to conjectures and refutation as the scientific method are abundant in much of the literature on complementary and alternative medicine (CAM)—alongside the competing position that CAM, as an alternative to conventional biomedicine, needs to develop its own methodology different from that of science.

Also within mainstream science, reference to the scientific method is used in arguments regarding the internal hierarchy of disciplines and domains. A frequently seen argument is that research based on the H-D method is superior to research based on induction from observations because in deductive inferences the conclusion follows necessarily from the premises. (See, e.g., Parascandola 1998 for an analysis of how this argument has been made to downgrade epidemiology compared to the laboratory sciences.) Similarly, based on an examination of the practices of major funding institutions such as the National Institutes of Health (NIH), the National Science Foundation (NSF) and the Biomedical Sciences Research Practices (BBSRC) in the UK, O’Malley et al. (2009) have argued that funding agencies seem to have a tendency to adhere to the view that the primary activity of science is to test hypotheses, while descriptive and exploratory research is seen as merely preparatory activities that are valuable only insofar as they fuel hypothesis-driven research.

In some areas of science, scholarly publications are structured in a way that may convey the impression of a neat and linear process of inquiry from stating a question, devising the methods by which to answer it, collecting the data, to drawing a conclusion from the analysis of data. For example, the codified format of publications in most biomedical journals known as the IMRAD format (Introduction, Method, Results, Analysis, Discussion) is explicitly described by the journal editors as “not an arbitrary publication format but rather a direct reflection of the process of scientific discovery” (see the so-called “Vancouver Recommendations”, ICMJE 2013: 11). However, scientific publications do not in general reflect the process by which the reported scientific results were produced. For example, under the provocative title “Is the scientific paper a fraud?”, Medawar argued that scientific papers generally misrepresent how the results have been produced (Medawar 1963/1996). Similar views have been advanced by philosophers, historians and sociologists of science (Gilbert 1976; Holmes 1987; Knorr-Cetina 1981; Schickore 2008; Suppe 1998) who have argued that scientists’ experimental practices are messy and often do not follow any recognizable pattern. Publications of research results, they argue, are retrospective reconstructions of these activities that often do not preserve the temporal order or the logic of these activities, but are instead often constructed in order to screen off potential criticism (see Schickore 2008 for a review of this work).

Philosophical positions on the scientific method have also made it into the court room, especially in the US where judges have drawn on philosophy of science in deciding when to confer special status to scientific expert testimony. A key case is Daubert vs Merrell Dow Pharmaceuticals (92–102, 509 U.S. 579, 1993). In this case, the Supreme Court argued in its 1993 ruling that trial judges must ensure that expert testimony is reliable, and that in doing this the court must look at the expert’s methodology to determine whether the proffered evidence is actually scientific knowledge. Further, referring to works of Popper and Hempel the court stated that

ordinarily, a key question to be answered in determining whether a theory or technique is scientific knowledge … is whether it can be (and has been) tested. (Justice Blackmun, Daubert v. Merrell Dow Pharmaceuticals; see Other Internet Resources for a link to the opinion)

But as argued by Haack (2005a,b, 2010) and by Foster & Hubner (1999), by equating the question of whether a piece of testimony is reliable with the question whether it is scientific as indicated by a special methodology, the court was producing an inconsistent mixture of Popper’s and Hempel’s philosophies, and this has later led to considerable confusion in subsequent case rulings that drew on the Daubert case (see Haack 2010 for a detailed exposition).

The difficulties around identifying the methods of science are also reflected in the difficulties of identifying scientific misconduct in the form of improper application of the method or methods of science. One of the first and most influential attempts at defining misconduct in science was the US definition from 1989 that defined misconduct as

fabrication, falsification, plagiarism, or other practices that seriously deviate from those that are commonly accepted within the scientific community . (Code of Federal Regulations, part 50, subpart A., August 8, 1989, italics added)

However, the “other practices that seriously deviate” clause was heavily criticized because it could be used to suppress creative or novel science. For example, the National Academy of Science stated in their report Responsible Science (1992) that it

wishes to discourage the possibility that a misconduct complaint could be lodged against scientists based solely on their use of novel or unorthodox research methods. (NAS: 27)

This clause was therefore later removed from the definition. For an entry into the key philosophical literature on conduct in science, see Shamoo & Resnick (2009).

The question of the source of the success of science has been at the core of philosophy since the beginning of modern science. If viewed as a matter of epistemology more generally, scientific method is a part of the entire history of philosophy. Over that time, science and whatever methods its practitioners may employ have changed dramatically. Today, many philosophers have taken up the banners of pluralism or of practice to focus on what are, in effect, fine-grained and contextually limited examinations of scientific method. Others hope to shift perspectives in order to provide a renewed general account of what characterizes the activity we call science.

One such perspective has been offered recently by Hoyningen-Huene (2008, 2013), who argues from the history of philosophy of science that after three lengthy phases of characterizing science by its method, we are now in a phase where the belief in the existence of a positive scientific method has eroded and what has been left to characterize science is only its fallibility. First was a phase from Plato and Aristotle up until the 17 th century where the specificity of scientific knowledge was seen in its absolute certainty established by proof from evident axioms; next was a phase up to the mid-19 th century in which the means to establish the certainty of scientific knowledge had been generalized to include inductive procedures as well. In the third phase, which lasted until the last decades of the 20 th century, it was recognized that empirical knowledge was fallible, but it was still granted a special status due to its distinctive mode of production. But now in the fourth phase, according to Hoyningen-Huene, historical and philosophical studies have shown how “scientific methods with the characteristics as posited in the second and third phase do not exist” (2008: 168) and there is no longer any consensus among philosophers and historians of science about the nature of science. For Hoyningen-Huene, this is too negative a stance, and he therefore urges the question about the nature of science anew. His own answer to this question is that “scientific knowledge differs from other kinds of knowledge, especially everyday knowledge, primarily by being more systematic” (Hoyningen-Huene 2013: 14). Systematicity can have several different dimensions: among them are more systematic descriptions, explanations, predictions, defense of knowledge claims, epistemic connectedness, ideal of completeness, knowledge generation, representation of knowledge and critical discourse. Hence, what characterizes science is the greater care in excluding possible alternative explanations, the more detailed elaboration with respect to data on which predictions are based, the greater care in detecting and eliminating sources of error, the more articulate connections to other pieces of knowledge, etc. On this position, what characterizes science is not that the methods employed are unique to science, but that the methods are more carefully employed.

Another, similar approach has been offered by Haack (2003). She sets off, similar to Hoyningen-Huene, from a dissatisfaction with the recent clash between what she calls Old Deferentialism and New Cynicism. The Old Deferentialist position is that science progressed inductively by accumulating true theories confirmed by empirical evidence or deductively by testing conjectures against basic statements; while the New Cynics position is that science has no epistemic authority and no uniquely rational method and is merely just politics. Haack insists that contrary to the views of the New Cynics, there are objective epistemic standards, and there is something epistemologically special about science, even though the Old Deferentialists pictured this in a wrong way. Instead, she offers a new Critical Commonsensist account on which standards of good, strong, supportive evidence and well-conducted, honest, thorough and imaginative inquiry are not exclusive to the sciences, but the standards by which we judge all inquirers. In this sense, science does not differ in kind from other kinds of inquiry, but it may differ in the degree to which it requires broad and detailed background knowledge and a familiarity with a technical vocabulary that only specialists may possess.

• Aikenhead, G.S., 1987, “High-school graduates’ beliefs about science-technology-society. III. Characteristics and limitations of scientific knowledge”, Science Education , 71(4): 459–487.
• Allchin, D., H.M. Andersen and K. Nielsen, 2014, “Complementary Approaches to Teaching Nature of Science: Integrating Student Inquiry, Historical Cases, and Contemporary Cases in Classroom Practice”, Science Education , 98: 461–486.
• Anderson, C., 2008, “The end of theory: The data deluge makes the scientific method obsolete”, Wired magazine , 16(7): 16–07
• Arabatzis, T., 2006, “On the inextricability of the context of discovery and the context of justification”, in Revisiting Discovery and Justification , J. Schickore and F. Steinle (eds.), Dordrecht: Springer, pp. 215–230.
• Barnes, J. (ed.), 1984, The Complete Works of Aristotle, Vols I and II , Princeton: Princeton University Press.
• Barnes, B. and D. Bloor, 1982, “Relativism, Rationalism, and the Sociology of Knowledge”, in Rationality and Relativism , M. Hollis and S. Lukes (eds.), Cambridge: MIT Press, pp. 1–20.
• Bauer, H.H., 1992, Scientific Literacy and the Myth of the Scientific Method , Urbana: University of Illinois Press.
• Bechtel, W. and R.C. Richardson, 1993, Discovering complexity , Princeton, NJ: Princeton University Press.
• Berkeley, G., 1734, The Analyst in De Motu and The Analyst: A Modern Edition with Introductions and Commentary , D. Jesseph (trans. and ed.), Dordrecht: Kluwer Academic Publishers, 1992.
• Blachowicz, J., 2009, “How science textbooks treat scientific method: A philosopher’s perspective”, The British Journal for the Philosophy of Science , 60(2): 303–344.
• Bloor, D., 1991, Knowledge and Social Imagery , Chicago: University of Chicago Press, 2 nd edition.
• Boyle, R., 1682, New experiments physico-mechanical, touching the air , Printed by Miles Flesher for Richard Davis, bookseller in Oxford.
• Bridgman, P.W., 1927, The Logic of Modern Physics , New York: Macmillan.
• –––, 1956, “The Methodological Character of Theoretical Concepts”, in The Foundations of Science and the Concepts of Science and Psychology , Herbert Feigl and Michael Scriven (eds.), Minnesota: University of Minneapolis Press, pp. 38–76.
• Burian, R., 1997, “Exploratory Experimentation and the Role of Histochemical Techniques in the Work of Jean Brachet, 1938–1952”, History and Philosophy of the Life Sciences , 19(1): 27–45.
• –––, 2007, “On microRNA and the need for exploratory experimentation in post-genomic molecular biology”, History and Philosophy of the Life Sciences , 29(3): 285–311.
• Carnap, R., 1928, Der logische Aufbau der Welt , Berlin: Bernary, transl. by R.A. George, The Logical Structure of the World , Berkeley: University of California Press, 1967.
• –––, 1956, “The methodological character of theoretical concepts”, Minnesota studies in the philosophy of science , 1: 38–76.
• Carrol, S., and D. Goodstein, 2009, “Defining the scientific method”, Nature Methods , 6: 237.
• Churchman, C.W., 1948, “Science, Pragmatics, Induction”, Philosophy of Science , 15(3): 249–268.
• Cooper, J. (ed.), 1997, Plato: Complete Works , Indianapolis: Hackett.
• Darden, L., 1991, Theory Change in Science: Strategies from Mendelian Genetics , Oxford: Oxford University Press
• Dewey, J., 1910, How we think , New York: Dover Publications (reprinted 1997).
• Douglas, H., 2009, Science, Policy, and the Value-Free Ideal , Pittsburgh: University of Pittsburgh Press.
• Dupré, J., 2004, “Miracle of Monism ”, in Naturalism in Question , Mario De Caro and David Macarthur (eds.), Cambridge, MA: Harvard University Press, pp. 36–58.
• Elliott, K.C., 2007, “Varieties of exploratory experimentation in nanotoxicology”, History and Philosophy of the Life Sciences , 29(3): 311–334.
• Elliott, K. C., and T. Richards (eds.), 2017, Exploring inductive risk: Case studies of values in science , Oxford: Oxford University Press.
• Falcon, Andrea, 2005, Aristotle and the science of nature: Unity without uniformity , Cambridge: Cambridge University Press.
• Feyerabend, P., 1978, Science in a Free Society , London: New Left Books
• –––, 1988, Against Method , London: Verso, 2 nd edition.
• Fisher, R.A., 1955, “Statistical Methods and Scientific Induction”, Journal of The Royal Statistical Society. Series B (Methodological) , 17(1): 69–78.
• Foster, K. and P.W. Huber, 1999, Judging Science. Scientific Knowledge and the Federal Courts , Cambridge: MIT Press.
• Fox Keller, E., 2003, “Models, Simulation, and ‘computer experiments’”, in The Philosophy of Scientific Experimentation , H. Radder (ed.), Pittsburgh: Pittsburgh University Press, 198–215.
• Gilbert, G., 1976, “The transformation of research findings into scientific knowledge”, Social Studies of Science , 6: 281–306.
• Gimbel, S., 2011, Exploring the Scientific Method , Chicago: University of Chicago Press.
• Goodman, N., 1965, Fact , Fiction, and Forecast , Indianapolis: Bobbs-Merrill.
• Haack, S., 1995, “Science is neither sacred nor a confidence trick”, Foundations of Science , 1(3): 323–335.
• –––, 2003, Defending science—within reason , Amherst: Prometheus.
• –––, 2005a, “Disentangling Daubert: an epistemological study in theory and practice”, Journal of Philosophy, Science and Law , 5, Haack 2005a available online . doi:10.5840/jpsl2005513
• –––, 2005b, “Trial and error: The Supreme Court’s philosophy of science”, American Journal of Public Health , 95: S66-S73.
• –––, 2010, “Federal Philosophy of Science: A Deconstruction-and a Reconstruction”, NYUJL & Liberty , 5: 394.
• Hangel, N. and J. Schickore, 2017, “Scientists’ conceptions of good research practice”, Perspectives on Science , 25(6): 766–791
• Harper, W.L., 2011, Isaac Newton’s Scientific Method: Turning Data into Evidence about Gravity and Cosmology , Oxford: Oxford University Press.
• Hempel, C., 1950, “Problems and Changes in the Empiricist Criterion of Meaning”, Revue Internationale de Philosophie , 41(11): 41–63.
• –––, 1951, “The Concept of Cognitive Significance: A Reconsideration”, Proceedings of the American Academy of Arts and Sciences , 80(1): 61–77.
• –––, 1965, Aspects of scientific explanation and other essays in the philosophy of science , New York–London: Free Press.
• –––, 1966, Philosophy of Natural Science , Englewood Cliffs: Prentice-Hall.
• Holmes, F.L., 1987, “Scientific writing and scientific discovery”, Isis , 78(2): 220–235.
• Howard, D., 2003, “Two left turns make a right: On the curious political career of North American philosophy of science at midcentury”, in Logical Empiricism in North America , G.L. Hardcastle & A.W. Richardson (eds.), Minneapolis: University of Minnesota Press, pp. 25–93.
• Hoyningen-Huene, P., 2008, “Systematicity: The nature of science”, Philosophia , 36(2): 167–180.
• –––, 2013, Systematicity. The Nature of Science , Oxford: Oxford University Press.
• Howie, D., 2002, Interpreting probability: Controversies and developments in the early twentieth century , Cambridge: Cambridge University Press.
• Hughes, R., 1999, “The Ising Model, Computer Simulation, and Universal Physics”, in Models as Mediators , M. Morgan and M. Morrison (eds.), Cambridge: Cambridge University Press, pp. 97–145
• Hume, D., 1739, A Treatise of Human Nature , D. Fate Norton and M.J. Norton (eds.), Oxford: Oxford University Press, 2000.
• Humphreys, P., 1995, “Computational science and scientific method”, Minds and Machines , 5(1): 499–512.
• ICMJE, 2013, “Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals”, International Committee of Medical Journal Editors, available online , accessed August 13 2014
• Jeffrey, R.C., 1956, “Valuation and Acceptance of Scientific Hypotheses”, Philosophy of Science , 23(3): 237–246.
• Kaufmann, W.J., and L.L. Smarr, 1993, Supercomputing and the Transformation of Science , New York: Scientific American Library.
• Knorr-Cetina, K., 1981, The Manufacture of Knowledge , Oxford: Pergamon Press.
• Krohs, U., 2012, “Convenience experimentation”, Studies in History and Philosophy of Biological and BiomedicalSciences , 43: 52–57.
• Kuhn, T.S., 1962, The Structure of Scientific Revolutions , Chicago: University of Chicago Press
• Latour, B. and S. Woolgar, 1986, Laboratory Life: The Construction of Scientific Facts , Princeton: Princeton University Press, 2 nd edition.
• Laudan, L., 1968, “Theories of scientific method from Plato to Mach”, History of Science , 7(1): 1–63.
• Lenhard, J., 2006, “Models and statistical inference: The controversy between Fisher and Neyman-Pearson”, The British Journal for the Philosophy of Science , 57(1): 69–91.
• Leonelli, S., 2012, “Making Sense of Data-Driven Research in the Biological and the Biomedical Sciences”, Studies in the History and Philosophy of the Biological and Biomedical Sciences , 43(1): 1–3.
• Levi, I., 1960, “Must the scientist make value judgments?”, Philosophy of Science , 57(11): 345–357
• Lindley, D., 1991, Theory Change in Science: Strategies from Mendelian Genetics , Oxford: Oxford University Press.
• Lipton, P., 2004, Inference to the Best Explanation , London: Routledge, 2 nd edition.
• Marks, H.M., 2000, The progress of experiment: science and therapeutic reform in the United States, 1900–1990 , Cambridge: Cambridge University Press.
• Mazzochi, F., 2015, “Could Big Data be the end of theory in science?”, EMBO reports , 16: 1250–1255.
• Mayo, D.G., 1996, Error and the Growth of Experimental Knowledge , Chicago: University of Chicago Press.
• McComas, W.F., 1996, “Ten myths of science: Reexamining what we think we know about the nature of science”, School Science and Mathematics , 96(1): 10–16.
• Medawar, P.B., 1963/1996, “Is the scientific paper a fraud”, in The Strange Case of the Spotted Mouse and Other Classic Essays on Science , Oxford: Oxford University Press, 33–39.
• Mill, J.S., 1963, Collected Works of John Stuart Mill , J. M. Robson (ed.), Toronto: University of Toronto Press
• NAS, 1992, Responsible Science: Ensuring the integrity of the research process , Washington DC: National Academy Press.
• Nersessian, N.J., 1987, “A cognitive-historical approach to meaning in scientific theories”, in The process of science , N. Nersessian (ed.), Berlin: Springer, pp. 161–177.
• –––, 2008, Creating Scientific Concepts , Cambridge: MIT Press.
• Newton, I., 1726, Philosophiae naturalis Principia Mathematica (3 rd edition), in The Principia: Mathematical Principles of Natural Philosophy: A New Translation , I.B. Cohen and A. Whitman (trans.), Berkeley: University of California Press, 1999.
• –––, 1704, Opticks or A Treatise of the Reflections, Refractions, Inflections & Colors of Light , New York: Dover Publications, 1952.
• Neyman, J., 1956, “Note on an Article by Sir Ronald Fisher”, Journal of the Royal Statistical Society. Series B (Methodological) , 18: 288–294.
• Nickles, T., 1987, “Methodology, heuristics, and rationality”, in Rational changes in science: Essays on Scientific Reasoning , J.C. Pitt (ed.), Berlin: Springer, pp. 103–132.
• Nicod, J., 1924, Le problème logique de l’induction , Paris: Alcan. (Engl. transl. “The Logical Problem of Induction”, in Foundations of Geometry and Induction , London: Routledge, 2000.)
• Nola, R. and H. Sankey, 2000a, “A selective survey of theories of scientific method”, in Nola and Sankey 2000b: 1–65.
• –––, 2000b, After Popper, Kuhn and Feyerabend. Recent Issues in Theories of Scientific Method , London: Springer.
• –––, 2007, Theories of Scientific Method , Stocksfield: Acumen.
• Norton, S., and F. Suppe, 2001, “Why atmospheric modeling is good science”, in Changing the Atmosphere: Expert Knowledge and Environmental Governance , C. Miller and P. Edwards (eds.), Cambridge, MA: MIT Press, 88–133.
• O’Malley, M., 2007, “Exploratory experimentation and scientific practice: Metagenomics and the proteorhodopsin case”, History and Philosophy of the Life Sciences , 29(3): 337–360.
• O’Malley, M., C. Haufe, K. Elliot, and R. Burian, 2009, “Philosophies of Funding”, Cell , 138: 611–615.
• Oreskes, N., K. Shrader-Frechette, and K. Belitz, 1994, “Verification, Validation and Confirmation of Numerical Models in the Earth Sciences”, Science , 263(5147): 641–646.
• Osborne, J., S. Simon, and S. Collins, 2003, “Attitudes towards science: a review of the literature and its implications”, International Journal of Science Education , 25(9): 1049–1079.
• Parascandola, M., 1998, “Epidemiology—2 nd -Rate Science”, Public Health Reports , 113(4): 312–320.
• Parker, W., 2008a, “Franklin, Holmes and the Epistemology of Computer Simulation”, International Studies in the Philosophy of Science , 22(2): 165–83.
• –––, 2008b, “Computer Simulation through an Error-Statistical Lens”, Synthese , 163(3): 371–84.
• Pearson, K. 1892, The Grammar of Science , London: J.M. Dents and Sons, 1951
• Pearson, E.S., 1955, “Statistical Concepts in Their Relation to Reality”, Journal of the Royal Statistical Society , B, 17: 204–207.
• Pickering, A., 1984, Constructing Quarks: A Sociological History of Particle Physics , Edinburgh: Edinburgh University Press.
• Popper, K.R., 1959, The Logic of Scientific Discovery , London: Routledge, 2002
• –––, 1963, Conjectures and Refutations , London: Routledge, 2002.
• –––, 1985, Unended Quest: An Intellectual Autobiography , La Salle: Open Court Publishing Co..
• Rudner, R., 1953, “The Scientist Qua Scientist Making Value Judgments”, Philosophy of Science , 20(1): 1–6.
• Rudolph, J.L., 2005, “Epistemology for the masses: The origin of ‘The Scientific Method’ in American Schools”, History of Education Quarterly , 45(3): 341–376
• Schickore, J., 2008, “Doing science, writing science”, Philosophy of Science , 75: 323–343.
• Schickore, J. and N. Hangel, 2019, “‘It might be this, it should be that…’ uncertainty and doubt in day-to-day science practice”, European Journal for Philosophy of Science , 9(2): 31. doi:10.1007/s13194-019-0253-9
• Shamoo, A.E. and D.B. Resnik, 2009, Responsible Conduct of Research , Oxford: Oxford University Press.
• Shank, J.B., 2008, The Newton Wars and the Beginning of the French Enlightenment , Chicago: The University of Chicago Press.
• Shapin, S. and S. Schaffer, 1985, Leviathan and the air-pump , Princeton: Princeton University Press.
• Smith, G.E., 2002, “The Methodology of the Principia”, in The Cambridge Companion to Newton , I.B. Cohen and G.E. Smith (eds.), Cambridge: Cambridge University Press, 138–173.
• Snyder, L.J., 1997a, “Discoverers’ Induction”, Philosophy of Science , 64: 580–604.
• –––, 1997b, “The Mill-Whewell Debate: Much Ado About Induction”, Perspectives on Science , 5: 159–198.
• –––, 1999, “Renovating the Novum Organum: Bacon, Whewell and Induction”, Studies in History and Philosophy of Science , 30: 531–557.
• Sober, E., 2008, Evidence and Evolution. The logic behind the science , Cambridge: Cambridge University Press
• Sprenger, J. and S. Hartmann, 2019, Bayesian philosophy of science , Oxford: Oxford University Press.
• Steinle, F., 1997, “Entering New Fields: Exploratory Uses of Experimentation”, Philosophy of Science (Proceedings), 64: S65–S74.
• –––, 2002, “Experiments in History and Philosophy of Science”, Perspectives on Science , 10(4): 408–432.
• Strasser, B.J., 2012, “Data-driven sciences: From wonder cabinets to electronic databases”, Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences , 43(1): 85–87.
• Succi, S. and P.V. Coveney, 2018, “Big data: the end of the scientific method?”, Philosophical Transactions of the Royal Society A , 377: 20180145. doi:10.1098/rsta.2018.0145
• Suppe, F., 1998, “The Structure of a Scientific Paper”, Philosophy of Science , 65(3): 381–405.
• Swijtink, Z.G., 1987, “The objectification of observation: Measurement and statistical methods in the nineteenth century”, in The probabilistic revolution. Ideas in History, Vol. 1 , L. Kruger (ed.), Cambridge MA: MIT Press, pp. 261–285.
• Waters, C.K., 2007, “The nature and context of exploratory experimentation: An introduction to three case studies of exploratory research”, History and Philosophy of the Life Sciences , 29(3): 275–284.
• Weinberg, S., 1995, “The methods of science… and those by which we live”, Academic Questions , 8(2): 7–13.
• Weissert, T., 1997, The Genesis of Simulation in Dynamics: Pursuing the Fermi-Pasta-Ulam Problem , New York: Springer Verlag.
• William H., 1628, Exercitatio Anatomica de Motu Cordis et Sanguinis in Animalibus , in On the Motion of the Heart and Blood in Animals , R. Willis (trans.), Buffalo: Prometheus Books, 1993.
• Winsberg, E., 2010, Science in the Age of Computer Simulation , Chicago: University of Chicago Press.
• Wivagg, D. & D. Allchin, 2002, “The Dogma of the Scientific Method”, The American Biology Teacher , 64(9): 645–646

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• Scientific Method at philpapers. Darrell Rowbottom (ed.).
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What is the Scientific Method: How does it work and why is it important?

The scientific method is a systematic process involving steps like defining questions, forming hypotheses, conducting experiments, and analyzing data. It minimizes biases and enables replicable research, leading to groundbreaking discoveries like Einstein's theory of relativity, penicillin, and the structure of DNA. This ongoing approach promotes reason, evidence, and the pursuit of truth in science.

Updated on November 18, 2023

Beginning in elementary school, we are exposed to the scientific method and taught how to put it into practice. As a tool for learning, it prepares children to think logically and use reasoning when seeking answers to questions.

Rather than jumping to conclusions, the scientific method gives us a recipe for exploring the world through observation and trial and error. We use it regularly, sometimes knowingly in academics or research, and sometimes subconsciously in our daily lives.

In this article we will refresh our memories on the particulars of the scientific method, discussing where it comes from, which elements comprise it, and how it is put into practice. Then, we will consider the importance of the scientific method, who uses it and under what circumstances.

What is the scientific method?

The scientific method is a dynamic process that involves objectively investigating questions through observation and experimentation . Applicable to all scientific disciplines, this systematic approach to answering questions is more accurately described as a flexible set of principles than as a fixed series of steps.

The following representations of the scientific method illustrate how it can be both condensed into broad categories and also expanded to reveal more and more details of the process. These graphics capture the adaptability that makes this concept universally valuable as it is relevant and accessible not only across age groups and educational levels but also within various contexts.

Steps in the scientific method

While the scientific method is versatile in form and function, it encompasses a collection of principles that create a logical progression to the process of problem solving:

• Define a question : Constructing a clear and precise problem statement that identifies the main question or goal of the investigation is the first step. The wording must lend itself to experimentation by posing a question that is both testable and measurable.
• Gather information and resources : Researching the topic in question to find out what is already known and what types of related questions others are asking is the next step in this process. This background information is vital to gaining a full understanding of the subject and in determining the best design for experiments. 
• Form a hypothesis : Composing a concise statement that identifies specific variables and potential results, which can then be tested, is a crucial step that must be completed before any experimentation. An imperfection in the composition of a hypothesis can result in weaknesses to the entire design of an experiment.
• Perform the experiments : Testing the hypothesis by performing replicable experiments and collecting resultant data is another fundamental step of the scientific method. By controlling some elements of an experiment while purposely manipulating others, cause and effect relationships are established.
• Analyze the data : Interpreting the experimental process and results by recognizing trends in the data is a necessary step for comprehending its meaning and supporting the conclusions. Drawing inferences through this systematic process lends substantive evidence for either supporting or rejecting the hypothesis.
• Report the results : Sharing the outcomes of an experiment, through an essay, presentation, graphic, or journal article, is often regarded as a final step in this process. Detailing the project's design, methods, and results not only promotes transparency and replicability but also adds to the body of knowledge for future research.
• Retest the hypothesis : Repeating experiments to see if a hypothesis holds up in all cases is a step that is manifested through varying scenarios. Sometimes a researcher immediately checks their own work or replicates it at a future time, or another researcher will repeat the experiments to further test the hypothesis.

Where did the scientific method come from?

Oftentimes, ancient peoples attempted to answer questions about the unknown by:

• Making simple observations
• Discussing the possibilities with others deemed worthy of a debate
• Drawing conclusions based on dominant opinions and preexisting beliefs

For example, take Greek and Roman mythology. Myths were used to explain everything from the seasons and stars to the sun and death itself.

However, as societies began to grow through advancements in agriculture and language, ancient civilizations like Egypt and Babylonia shifted to a more rational analysis for understanding the natural world. They increasingly employed empirical methods of observation and experimentation that would one day evolve into the scientific method . 

In the 4th century, Aristotle, considered the Father of Science by many, suggested these elements , which closely resemble the contemporary scientific method, as part of his approach for conducting science:

• Study what others have written about the subject.
• Look for the general consensus about the subject.
• Perform a systematic study of everything even partially related to the topic.

By continuing to emphasize systematic observation and controlled experiments, scholars such as Al-Kindi and Ibn al-Haytham helped expand this concept throughout the Islamic Golden Age . 

In his 1620 treatise, Novum Organum , Sir Francis Bacon codified the scientific method, arguing not only that hypotheses must be tested through experiments but also that the results must be replicated to establish a truth. Coming at the height of the Scientific Revolution, this text made the scientific method accessible to European thinkers like Galileo and Isaac Newton who then put the method into practice.

As science modernized in the 19th century, the scientific method became more formalized, leading to significant breakthroughs in fields such as evolution and germ theory. Today, it continues to evolve, underpinning scientific progress in diverse areas like quantum mechanics, genetics, and artificial intelligence.

Why is the scientific method important?

The history of the scientific method illustrates how the concept developed out of a need to find objective answers to scientific questions by overcoming biases based on fear, religion, power, and cultural norms. This still holds true today.

By implementing this standardized approach to conducting experiments, the impacts of researchers’ personal opinions and preconceived notions are minimized. The organized manner of the scientific method prevents these and other mistakes while promoting the replicability and transparency necessary for solid scientific research.

The importance of the scientific method is best observed through its successes, for example: 

• “ Albert Einstein stands out among modern physicists as the scientist who not only formulated a theory of revolutionary significance but also had the genius to reflect in a conscious and technical way on the scientific method he was using.” Devising a hypothesis based on the prevailing understanding of Newtonian physics eventually led Einstein to devise the theory of general relativity .
• Howard Florey “Perhaps the most useful lesson which has come out of the work on penicillin has been the demonstration that success in this field depends on the development and coordinated use of technical methods.” After discovering a mold that prevented the growth of Staphylococcus bacteria, Dr. Alexander Flemimg designed experiments to identify and reproduce it in the lab, thus leading to the development of penicillin .
• James D. Watson “Every time you understand something, religion becomes less likely. Only with the discovery of the double helix and the ensuing genetic revolution have we had grounds for thinking that the powers held traditionally to be the exclusive property of the gods might one day be ours. . . .” By using wire models to conceive a structure for DNA, Watson and Crick crafted a hypothesis for testing combinations of amino acids, X-ray diffraction images, and the current research in atomic physics, resulting in the discovery of DNA’s double helix structure .

Final thoughts

As the cases exemplify, the scientific method is never truly completed, but rather started and restarted. It gave these researchers a structured process that was easily replicated, modified, and built upon. 

While the scientific method may “end” in one context, it never literally ends. When a hypothesis, design, methods, and experiments are revisited, the scientific method simply picks up where it left off. Each time a researcher builds upon previous knowledge, the scientific method is restored with the pieces of past efforts.

By guiding researchers towards objective results based on transparency and reproducibility, the scientific method acts as a defense against bias, superstition, and preconceived notions. As we embrace the scientific method's enduring principles, we ensure that our quest for knowledge remains firmly rooted in reason, evidence, and the pursuit of truth.

The AJE Team

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Science and the scientific method: Definitions and examples

Here's a look at the foundation of doing science — the scientific method.

The scientific method

Hypothesis, theory and law, a brief history of science, additional resources, bibliography.

Science is a systematic and logical approach to discovering how things in the universe work. It is also the body of knowledge accumulated through the discoveries about all the things in the universe. 

The word "science" is derived from the Latin word "scientia," which means knowledge based on demonstrable and reproducible data, according to the Merriam-Webster dictionary . True to this definition, science aims for measurable results through testing and analysis, a process known as the scientific method. Science is based on fact, not opinion or preferences. The process of science is designed to challenge ideas through research. One important aspect of the scientific process is that it focuses only on the natural world, according to the University of California, Berkeley . Anything that is considered supernatural, or beyond physical reality, does not fit into the definition of science.

When conducting research, scientists use the scientific method to collect measurable, empirical evidence in an experiment related to a hypothesis (often in the form of an if/then statement) that is designed to support or contradict a scientific theory .

"As a field biologist, my favorite part of the scientific method is being in the field collecting the data," Jaime Tanner, a professor of biology at Marlboro College, told Live Science. "But what really makes that fun is knowing that you are trying to answer an interesting question. So the first step in identifying questions and generating possible answers (hypotheses) is also very important and is a creative process. Then once you collect the data you analyze it to see if your hypothesis is supported or not."

The steps of the scientific method go something like this, according to Highline College :

• Make an observation or observations.
• Form a hypothesis — a tentative description of what's been observed, and make predictions based on that hypothesis.
• Test the hypothesis and predictions in an experiment that can be reproduced.
• Analyze the data and draw conclusions; accept or reject the hypothesis or modify the hypothesis if necessary.
• Reproduce the experiment until there are no discrepancies between observations and theory. "Replication of methods and results is my favorite step in the scientific method," Moshe Pritsker, a former post-doctoral researcher at Harvard Medical School and CEO of JoVE, told Live Science. "The reproducibility of published experiments is the foundation of science. No reproducibility — no science."

Some key underpinnings to the scientific method:

• The hypothesis must be testable and falsifiable, according to North Carolina State University . Falsifiable means that there must be a possible negative answer to the hypothesis.
• Research must involve deductive reasoning and inductive reasoning . Deductive reasoning is the process of using true premises to reach a logical true conclusion while inductive reasoning uses observations to infer an explanation for those observations.
• An experiment should include a dependent variable (which does not change) and an independent variable (which does change), according to the University of California, Santa Barbara .
• An experiment should include an experimental group and a control group. The control group is what the experimental group is compared against, according to Britannica .

The process of generating and testing a hypothesis forms the backbone of the scientific method. When an idea has been confirmed over many experiments, it can be called a scientific theory. While a theory provides an explanation for a phenomenon, a scientific law provides a description of a phenomenon, according to The University of Waikato . One example would be the law of conservation of energy, which is the first law of thermodynamics that says that energy can neither be created nor destroyed. 

A law describes an observed phenomenon, but it doesn't explain why the phenomenon exists or what causes it. "In science, laws are a starting place," said Peter Coppinger, an associate professor of biology and biomedical engineering at the Rose-Hulman Institute of Technology. "From there, scientists can then ask the questions, 'Why and how?'"

Laws are generally considered to be without exception, though some laws have been modified over time after further testing found discrepancies. For instance, Newton's laws of motion describe everything we've observed in the macroscopic world, but they break down at the subatomic level.

This does not mean theories are not meaningful. For a hypothesis to become a theory, scientists must conduct rigorous testing, typically across multiple disciplines by separate groups of scientists. Saying something is "just a theory" confuses the scientific definition of "theory" with the layperson's definition. To most people a theory is a hunch. In science, a theory is the framework for observations and facts, Tanner told Live Science.

The earliest evidence of science can be found as far back as records exist. Early tablets contain numerals and information about the solar system , which were derived by using careful observation, prediction and testing of those predictions. Science became decidedly more "scientific" over time, however.

1200s: Robert Grosseteste developed the framework for the proper methods of modern scientific experimentation, according to the Stanford Encyclopedia of Philosophy. His works included the principle that an inquiry must be based on measurable evidence that is confirmed through testing.

1400s: Leonardo da Vinci began his notebooks in pursuit of evidence that the human body is microcosmic. The artist, scientist and mathematician also gathered information about optics and hydrodynamics.

1500s: Nicolaus Copernicus advanced the understanding of the solar system with his discovery of heliocentrism. This is a model in which Earth and the other planets revolve around the sun, which is the center of the solar system.

1600s: Johannes Kepler built upon those observations with his laws of planetary motion. Galileo Galilei improved on a new invention, the telescope, and used it to study the sun and planets. The 1600s also saw advancements in the study of physics as Isaac Newton developed his laws of motion.

1700s: Benjamin Franklin discovered that lightning is electrical. He also contributed to the study of oceanography and meteorology. The understanding of chemistry also evolved during this century as Antoine Lavoisier, dubbed the father of modern chemistry , developed the law of conservation of mass.

1800s: Milestones included Alessandro Volta's discoveries regarding electrochemical series, which led to the invention of the battery. John Dalton also introduced atomic theory, which stated that all matter is composed of atoms that combine to form molecules. The basis of modern study of genetics advanced as Gregor Mendel unveiled his laws of inheritance. Later in the century, Wilhelm Conrad Röntgen discovered X-rays , while George Ohm's law provided the basis for understanding how to harness electrical charges.

1900s: The discoveries of Albert Einstein , who is best known for his theory of relativity, dominated the beginning of the 20th century. Einstein's theory of relativity is actually two separate theories. His special theory of relativity, which he outlined in a 1905 paper, " The Electrodynamics of Moving Bodies ," concluded that time must change according to the speed of a moving object relative to the frame of reference of an observer. His second theory of general relativity, which he published as " The Foundation of the General Theory of Relativity ," advanced the idea that matter causes space to curve.

In 1952, Jonas Salk developed the polio vaccine , which reduced the incidence of polio in the United States by nearly 90%, according to Britannica . The following year, James D. Watson and Francis Crick discovered the structure of DNA , which is a double helix formed by base pairs attached to a sugar-phosphate backbone, according to the National Human Genome Research Institute .

2000s: The 21st century saw the first draft of the human genome completed, leading to a greater understanding of DNA. This advanced the study of genetics, its role in human biology and its use as a predictor of diseases and other disorders, according to the National Human Genome Research Institute .

• This video from City University of New York delves into the basics of what defines science.
• Learn about what makes science science in this book excerpt from Washington State University .
• This resource from the University of Michigan — Flint explains how to design your own scientific study.

Merriam-Webster Dictionary, Scientia. 2022. https://www.merriam-webster.com/dictionary/scientia

University of California, Berkeley, "Understanding Science: An Overview." 2022. ​​ https://undsci.berkeley.edu/article/0_0_0/intro_01  

Highline College, "Scientific method." July 12, 2015. https://people.highline.edu/iglozman/classes/astronotes/scimeth.htm  

North Carolina State University, "Science Scripts." https://projects.ncsu.edu/project/bio183de/Black/science/science_scripts.html  

University of California, Santa Barbara. "What is an Independent variable?" October 31,2017. http://scienceline.ucsb.edu/getkey.php?key=6045  

Encyclopedia Britannica, "Control group." May 14, 2020. https://www.britannica.com/science/control-group  

The University of Waikato, "Scientific Hypothesis, Theories and Laws." https://sci.waikato.ac.nz/evolution/Theories.shtml  

Stanford Encyclopedia of Philosophy, Robert Grosseteste. May 3, 2019. https://plato.stanford.edu/entries/grosseteste/  

Encyclopedia Britannica, "Jonas Salk." October 21, 2021. https://www.britannica.com/ biography /Jonas-Salk

National Human Genome Research Institute, "​Phosphate Backbone." https://www.genome.gov/genetics-glossary/Phosphate-Backbone  

National Human Genome Research Institute, "What is the Human Genome Project?" https://www.genome.gov/human-genome-project/What  

‌ Live Science contributor Ashley Hamer updated this article on Jan. 16, 2022.

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September 8, 2021

Explaining How Research Works

We’ve heard “follow the science” a lot during the pandemic. But it seems science has taken us on a long and winding road filled with twists and turns, even changing directions at times. That’s led some people to feel they can’t trust science. But when what we know changes, it often means science is working.

Explaining the scientific process may be one way that science communicators can help maintain public trust in science. Placing research in the bigger context of its field and where it fits into the scientific process can help people better understand and interpret new findings as they emerge. A single study usually uncovers only a piece of a larger puzzle.

Questions about how the world works are often investigated on many different levels. For example, scientists can look at the different atoms in a molecule, cells in a tissue, or how different tissues or systems affect each other. Researchers often must choose one or a finite number of ways to investigate a question. It can take many different studies using different approaches to start piecing the whole picture together.

Sometimes it might seem like research results contradict each other. But often, studies are just looking at different aspects of the same problem. Researchers can also investigate a question using different techniques or timeframes. That may lead them to arrive at different conclusions from the same data.

Using the data available at the time of their study, scientists develop different explanations, or models. New information may mean that a novel model needs to be developed to account for it. The models that prevail are those that can withstand the test of time and incorporate new information. Science is a constantly evolving and self-correcting process.

Scientists gain more confidence about a model through the scientific process. They replicate each other’s work. They present at conferences. And papers undergo peer review, in which experts in the field review the work before it can be published in scientific journals. This helps ensure that the study is up to current scientific standards and maintains a level of integrity. Peer reviewers may find problems with the experiments or think different experiments are needed to justify the conclusions. They might even offer new ways to interpret the data.

It’s important for science communicators to consider which stage a study is at in the scientific process when deciding whether to cover it. Some studies are posted on preprint servers for other scientists to start weighing in on and haven’t yet been fully vetted. Results that haven't yet been subjected to scientific scrutiny should be reported on with care and context to avoid confusion or frustration from readers.

We’ve developed a one-page guide, "How Research Works: Understanding the Process of Science" to help communicators put the process of science into perspective. We hope it can serve as a useful resource to help explain why science changes—and why it’s important to expect that change. Please take a look and share your thoughts with us by sending an email to  [email protected].

Below are some additional resources:

• Discoveries in Basic Science: A Perfectly Imperfect Process
• When Clinical Research Is in the News
• What is Basic Science and Why is it Important?
• ​ What is a Research Organism?
• What Are Clinical Trials and Studies?
• Basic Research – Digital Media Kit
• Decoding Science: How Does Science Know What It Knows? (NAS)
• Can Science Help People Make Decisions ? (NAS)

Connect with Us

• More Social Media from NIH

TODAY'S HOURS:

Research Process

• Select a Topic
• Find Background Info
• Focus Topic
• List Keywords
• Search for Sources
• Evaluate & Integrate Sources
• Cite and Track Sources

What is Scientific Research?

Research study design, natural vs. social science, qualitative vs. quantitative research, more information on qualitative research in the social sciences, acknowledgements.

Thank you to Julie Miller, reference intern, for helping to create this page.

Some people use the term research loosely, for example:

• People will say they are researching different online websites to find the best place to buy a new appliance or locate a lawn care service.
• TV news may talk about conducting research when they conduct a viewer poll on current event topic such as an upcoming election.
• Undergraduate students working on a term paper or project may say they are researching the internet to find information.
• Private sector companies may say they are conducting research to find a solution for a supply chain holdup.

However, none of the above is considered “scientific research” unless:

• The research contributes to a body of science by providing new information through ethical study design or
• The research follows the scientific method, an iterative process of observation and inquiry.

The Scientific Method

• Make an observation: notice a phenomenon in your life or in society or find a gap in the already published literature.
• Ask a question about what you have observed.
• Hypothesize about a potential answer or explanation.
• Make predictions if our hypothesis is correct.
• Design an experiment or study that will test your prediction.
• Test the prediction by conducting an experiment or study; report the outcomes of your study.
• Iterate! Was your prediction correct? Was the outcome unexpected? Did it lead to new observations?

The scientific method is not separate from the Research Process as described in the rest of this guide, in fact the Research Process is directly related to the observation stage of the scientific method. Understanding what other scientists and researchers have already studied will help you focus your area of study and build on their knowledge.

Designing your experiment or study is important for both natural and social scientists. Sage Research Methods (SRM) has an excellent "Project Planner" that guides you through the basic stages of research design. SRM also has excellent explanations of qualitative and quantitative research methods for the social sciences.

For the natural sciences, Springer Nature Experiments and Protocol Exchange have guidance on quantitative research methods.

Books, journals, reference books, videos, podcasts, data-sets, and case studies on social science research methods.

Sage Research Methods includes over 2,000 books, reference books, journal articles, videos, datasets, and case studies on all aspects of social science research methodology. Browse the methods map or the list of methods to identify a social science method to pursue further. Includes a project planning tool and the "Which Stats Test" tool to identify the best statistical method for your project. Includes the notable "little green book" series (Quantitative Applications in the Social Sciences) and the "little blue book" series (Qualitative Research Methods).

Platform connecting researchers with protocols and methods.

Springer Nature Experiments has been designed to help users/researchers find and evaluate relevant protocols and methods across the whole Springer Nature protocols and methods portfolio using one search. This database includes:

• Nature Protocols
• Nature Reviews Methods Primers
• Nature Methods
• Springer Protocols

Open repository for sharing scientific research protocols. These protocols are posted directly on the Protocol Exchange by authors and are made freely available to the scientific community for use and comment.

Includes these topics:

• Biochemistry
• Biological techniques
• Chemical biology
• Chemical engineering
• Cheminformatics
• Climate science
• Computational biology and bioinformatics
• Drug discovery
• Electronics
• Energy sciences
• Environmental sciences
• Materials science
• Molecular biology
• Molecular medicine
• Neuroscience
• Organic chemistry
• Planetary science

Qualitative research is primarily exploratory. It is used to gain an understanding of underlying reasons, opinions, and motivations. Qualitative research is also used to uncover trends in thought and opinions and to dive deeper into a problem by studying an individual or a group.

Qualitative methods usually use unstructured or semi-structured techniques. The sample size is typically smaller than in quantitative research.

Example: interviews and focus groups.

Quantitative research is characterized by the gathering of data with the aim of testing a hypothesis. The data generated are numerical, or, if not numerical, can be transformed into useable statistics.

Quantitative data collection methods are more structured than qualitative data collection methods and sample sizes are usually larger.

Example: survey

Note: The above descriptions of qualitative and quantitative research are mainly for research in the Social Sciences, rather than for Natural Sciences as most natural sciences rely on quantitative methods for their experiments.

Qualitative research is approaching the world in its natural setting and in a way that reveals the particularities rather than doing studies in a controlled setting. It aims to understand, describe, and sometimes explain social phenomena in a number of different ways:

• Experiences of individuals or groups
• Interactions and communications
• Documents (texts, images, film, or sounds, and digital documents)
• Experiences or interactions

Qualitative researchers seek to understand how people conceptualize the world around them, what they are doing, how they are doing it or what is happening to them in terms that are significant and that offer meaningful learnings.

Qualitative researchers develop and refine concepts (or hypotheses, if they are used) in the process of research and of collecting data. Cases (its history and complexity) are an important context for understanding the issue that is studied. A major part of qualitative research is based on text and writing – from field notes and transcripts to descriptions and interpretations and finally to the presentation of the findings and of the research as a whole.

For more information, see:

• << Previous: Cite and Track Sources
• Last Updated: May 21, 2024 1:45 PM
• URL: https://libguides.umflint.edu/research

Psychological Research

The Scientific Process

Learning objectives.

• Explain the steps of the scientific method
• Differentiate between theories and hypotheses

The goal of all scientists is to better understand the world around them. Psychologists focus their attention on understanding behavior, as well as the cognitive (mental) and physiological (body) processes that underlie behavior. In contrast to other methods that people use to understand the behavior of others, such as intuition and personal experience, the hallmark of scientific research is that there is evidence to support a claim. Scientific knowledge is empirical : It is grounded in objective, tangible evidence that can be observed time and time again, regardless of who is observing.

While behavior is observable, the mind is not. If someone is crying, we can see the behavior. However, the reason for the behavior is more difficult to determine. Is the person crying due to being sad, in pain, or happy? Sometimes we can learn the reason for someone’s behavior by simply asking a question, like “Why are you crying?” However, there are situations in which an individual is either uncomfortable or unwilling to answer the question honestly, or is incapable of answering. For example, infants would not be able to explain why they are crying. In such circumstances, the psychologist must be creative in finding ways to better understand behavior. This module explores how scientific knowledge is generated, and how important that knowledge is in forming decisions in our personal lives and in the public domain.

Process of Scientific Research

Scientific knowledge is advanced through a process known as the scientific method. Basically, ideas (in the form of theories and hypotheses) are tested against the real world (in the form of empirical observations), and those empirical observations lead to more ideas that are tested against the real world, and so on.

The basic steps in the scientific method are:

• Observe a natural phenomenon and define a question about it
• Make a hypothesis, or potential solution to the question
• Test the hypothesis
• If the hypothesis is true, find more evidence or find counter-evidence
• If the hypothesis is false, create a new hypothesis or try again
• Draw conclusions and repeat–the scientific method is never-ending, and no result is ever considered perfect

In order to ask an important question that may improve our understanding of the world, a researcher must first observe natural phenomena. By making observations, a researcher can define a useful question. After finding a question to answer, the researcher can then make a prediction (a hypothesis) about what he or she thinks the answer will be. This prediction is usually a statement about the relationship between two or more variables. After making a hypothesis, the researcher will then design an experiment to test his or her hypothesis and evaluate the data gathered. These data will either support or refute the hypothesis. Based on the conclusions drawn from the data, the researcher will then find more evidence to support the hypothesis, look for counter-evidence to further strengthen the hypothesis, revise the hypothesis and create a new experiment, or continue to incorporate the information gathered to answer the research question.

Basic Principles of the Scientific Method

Two key concepts in the scientific approach are theory and hypothesis. A theory is a well-developed set of ideas that propose an explanation for observed phenomena that can be used to make predictions about future observations. A hypothesis is a testable prediction that is arrived at logically from a theory. It is often worded as an if-then statement (e.g., if I study all night, I will get a passing grade on the test). The hypothesis is extremely important because it bridges the gap between the realm of ideas and the real world. As specific hypotheses are tested, theories are modified and refined to reflect and incorporate the result of these tests.

Other key components in following the scientific method include verifiability, predictability, falsifiability, and fairness. Verifiability means that an experiment must be replicable by another researcher. To achieve verifiability, researchers must make sure to document their methods and clearly explain how their experiment is structured and why it produces certain results.

Predictability in a scientific theory implies that the theory should enable us to make predictions about future events. The precision of these predictions is a measure of the strength of the theory.

Falsifiability refers to whether a hypothesis can be disproved. For a hypothesis to be falsifiable, it must be logically possible to make an observation or do a physical experiment that would show that there is no support for the hypothesis. Even when a hypothesis cannot be shown to be false, that does not necessarily mean it is not valid. Future testing may disprove the hypothesis. This does not mean that a hypothesis has to be shown to be false, just that it can be tested.

To determine whether a hypothesis is supported or not supported, psychological researchers must conduct hypothesis testing using statistics. Hypothesis testing is a type of statistics that determines the probability of a hypothesis being true or false. If hypothesis testing reveals that results were “statistically significant,” this means that there was support for the hypothesis and that the researchers can be reasonably confident that their result was not due to random chance. If the results are not statistically significant, this means that the researchers’ hypothesis was not supported.

Fairness implies that all data must be considered when evaluating a hypothesis. A researcher cannot pick and choose what data to keep and what to discard or focus specifically on data that support or do not support a particular hypothesis. All data must be accounted for, even if they invalidate the hypothesis.

Applying the Scientific Method

To see how this process works, let’s consider a specific theory and a hypothesis that might be generated from that theory. As you’ll learn in a later module, the James-Lange theory of emotion asserts that emotional experience relies on the physiological arousal associated with the emotional state. If you walked out of your home and discovered a very aggressive snake waiting on your doorstep, your heart would begin to race and your stomach churn. According to the James-Lange theory, these physiological changes would result in your feeling of fear. A hypothesis that could be derived from this theory might be that a person who is unaware of the physiological arousal that the sight of the snake elicits will not feel fear.

Remember that a good scientific hypothesis is falsifiable, or capable of being shown to be incorrect. Recall from the introductory module that Sigmund Freud had lots of interesting ideas to explain various human behaviors (Figure 3). However, a major criticism of Freud’s theories is that many of his ideas are not falsifiable; for example, it is impossible to imagine empirical observations that would disprove the existence of the id, the ego, and the superego—the three elements of personality described in Freud’s theories. Despite this, Freud’s theories are widely taught in introductory psychology texts because of their historical significance for personality psychology and psychotherapy, and these remain the root of all modern forms of therapy.

In contrast, the James-Lange theory does generate falsifiable hypotheses, such as the one described above. Some individuals who suffer significant injuries to their spinal columns are unable to feel the bodily changes that often accompany emotional experiences. Therefore, we could test the hypothesis by determining how emotional experiences differ between individuals who have the ability to detect these changes in their physiological arousal and those who do not. In fact, this research has been conducted and while the emotional experiences of people deprived of an awareness of their physiological arousal may be less intense, they still experience emotion (Chwalisz, Diener, & Gallagher, 1988).

Link to Learning

Want to participate in a study? Visit this Psychological Research on the Net website and click on a link that sounds interesting to you in order to participate in online research.

Why the Scientific Method Is Important for Psychology

The use of the scientific method is one of the main features that separates modern psychology from earlier philosophical inquiries about the mind. Compared to chemistry, physics, and other “natural sciences,” psychology has long been considered one of the “social sciences” because of the subjective nature of the things it seeks to study. Many of the concepts that psychologists are interested in—such as aspects of the human mind, behavior, and emotions—are subjective and cannot be directly measured. Psychologists often rely instead on behavioral observations and self-reported data, which are considered by some to be illegitimate or lacking in methodological rigor. Applying the scientific method to psychology, therefore, helps to standardize the approach to understanding its very different types of information.

The scientific method allows psychological data to be replicated and confirmed in many instances, under different circumstances, and by a variety of researchers. Through replication of experiments, new generations of psychologists can reduce errors and broaden the applicability of theories. It also allows theories to be tested and validated instead of simply being conjectures that could never be verified or falsified. All of this allows psychologists to gain a stronger understanding of how the human mind works.

Scientific articles published in journals and psychology papers written in the style of the American Psychological Association (i.e., in “APA style”) are structured around the scientific method. These papers include an Introduction, which introduces the background information and outlines the hypotheses; a Methods section, which outlines the specifics of how the experiment was conducted to test the hypothesis; a Results section, which includes the statistics that tested the hypothesis and state whether it was supported or not supported, and a Discussion and Conclusion, which state the implications of finding support for, or no support for, the hypothesis. Writing articles and papers that adhere to the scientific method makes it easy for future researchers to repeat the study and attempt to replicate the results.

CC licensed content, Original

• Modification and adaptation. Provided by : Lumen Learning. License : CC BY-SA: Attribution-ShareAlike

CC licensed content, Shared previously

• Why is Research Important?. Authored by : OpenStax College. Located at : https://openstax.org/books/psychology-2e/pages/2-1-why-is-research-important . License : CC BY: Attribution . License Terms : Download for free at https://openstax.org/books/psychology-2e/pages/1-introduction
• Psychology and the Scientific Method: From Theory to Conclusion, content on the scientific method principles. Provided by : Boundless. Located at : https://www.boundless.com/psychology/textbooks/boundless-psychology-textbook/researching-psychology-2/the-scientific-method-26/psychology-and-the-scientific-method-from-theory-to-conclusion-123-12658/images/the-scientific-method/ . License : CC BY-SA: Attribution-ShareAlike

grounded in objective, tangible evidence that can be observed time and time again, regardless of who is observing

well-developed set of ideas that propose an explanation for observed phenomena

(plural: hypotheses) tentative and testable statement about the relationship between two or more variables

an experiment must be replicable by another researcher

implies that a theory should enable us to make predictions about future events

able to be disproven by experimental results

implies that all data must be considered when evaluating a hypothesis

General Psychology Copyright © by OpenStax and Lumen Learning is licensed under a Creative Commons Attribution 4.0 International License , except where otherwise noted.

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Module 1: Introduction: What is Research?

Learning Objectives

By the end of this module, you will be able to:

• Explain how the scientific method is used to develop new knowledge
• Describe why it is important to follow a research plan

The Scientific Method consists of observing the world around you and creating a  hypothesis  about relationships in the world. A hypothesis is an informed and educated prediction or explanation about something. Part of the research process involves testing the  hypothesis , and then examining the results of these tests as they relate to both the hypothesis and the world around you. When a researcher forms a hypothesis, this acts like a map through the research study. It tells the researcher which factors are important to study and how they might be related to each other or caused by a  manipulation  that the researcher introduces (e.g. a program, treatment or change in the environment). With this map, the researcher can interpret the information he/she collects and can make sound conclusions about the results.

Research can be done with human beings, animals, plants, other organisms and inorganic matter. When research is done with human beings and animals, it must follow specific rules about the treatment of humans and animals that have been created by the U.S. Federal Government. This ensures that humans and animals are treated with dignity and respect, and that the research causes minimal harm.

No matter what topic is being studied, the value of the research depends on how well it is designed and done. Therefore, one of the most important considerations in doing good research is to follow the design or plan that is developed by an experienced researcher who is called the  Principal Investigator  (PI). The PI is in charge of all aspects of the research and creates what is called a  protocol  (the research plan) that all people doing the research must follow. By doing so, the PI and the public can be sure that the results of the research are real and useful to other scientists.

Module 1: Discussion Questions

• How is a hypothesis like a road map?
• Who is ultimately responsible for the design and conduct of a research study?
• How does following the research protocol contribute to informing public health practices?

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What is Scientific Research and How Can it be Done?

Scientific researches are studies that should be systematically planned before performing them. In this review, classification and description of scientific studies, planning stage randomisation and bias are explained.

Research conducted for the purpose of contributing towards science by the systematic collection, interpretation and evaluation of data and that, too, in a planned manner is called scientific research: a researcher is the one who conducts this research. The results obtained from a small group through scientific studies are socialised, and new information is revealed with respect to diagnosis, treatment and reliability of applications. The purpose of this review is to provide information about the definition, classification and methodology of scientific research.

Before beginning the scientific research, the researcher should determine the subject, do planning and specify the methodology. In the Declaration of Helsinki, it is stated that ‘the primary purpose of medical researches on volunteers is to understand the reasons, development and effects of diseases and develop protective, diagnostic and therapeutic interventions (method, operation and therapies). Even the best proven interventions should be evaluated continuously by investigations with regard to reliability, effectiveness, efficiency, accessibility and quality’ ( 1 ).

The questions, methods of response to questions and difficulties in scientific research may vary, but the design and structure are generally the same ( 2 ).

Classification of Scientific Research

Scientific research can be classified in several ways. Classification can be made according to the data collection techniques based on causality, relationship with time and the medium through which they are applied.

• Observational
• Experimental
• Descriptive
• Retrospective
• Prospective
• Cross-sectional
• Social descriptive research ( 3 )

Another method is to classify the research according to its descriptive or analytical features. This review is written according to this classification method.

I. Descriptive research

• Case series
• Surveillance studies

II. Analytical research

• Observational studies: cohort, case control and cross- sectional research
• Interventional research: quasi-experimental and clinical research
• Case Report: it is the most common type of descriptive study. It is the examination of a single case having a different quality in the society, e.g. conducting general anaesthesia in a pregnant patient with mucopolysaccharidosis.
• Case Series: it is the description of repetitive cases having common features. For instance; case series involving interscapular pain related to neuraxial labour analgesia. Interestingly, malignant hyperthermia cases are not accepted as case series since they are rarely seen during historical development.
• Surveillance Studies: these are the results obtained from the databases that follow and record a health problem for a certain time, e.g. the surveillance of cross-infections during anaesthesia in the intensive care unit.

Moreover, some studies may be experimental. After the researcher intervenes, the researcher waits for the result, observes and obtains data. Experimental studies are, more often, in the form of clinical trials or laboratory animal trials ( 2 ).

Analytical observational research can be classified as cohort, case-control and cross-sectional studies.

Firstly, the participants are controlled with regard to the disease under investigation. Patients are excluded from the study. Healthy participants are evaluated with regard to the exposure to the effect. Then, the group (cohort) is followed-up for a sufficient period of time with respect to the occurrence of disease, and the progress of disease is studied. The risk of the healthy participants getting sick is considered an incident. In cohort studies, the risk of disease between the groups exposed and not exposed to the effect is calculated and rated. This rate is called relative risk. Relative risk indicates the strength of exposure to the effect on the disease.

Cohort research may be observational and experimental. The follow-up of patients prospectively is called a prospective cohort study . The results are obtained after the research starts. The researcher’s following-up of cohort subjects from a certain point towards the past is called a retrospective cohort study . Prospective cohort studies are more valuable than retrospective cohort studies: this is because in the former, the researcher observes and records the data. The researcher plans the study before the research and determines what data will be used. On the other hand, in retrospective studies, the research is made on recorded data: no new data can be added.

In fact, retrospective and prospective studies are not observational. They determine the relationship between the date on which the researcher has begun the study and the disease development period. The most critical disadvantage of this type of research is that if the follow-up period is long, participants may leave the study at their own behest or due to physical conditions. Cohort studies that begin after exposure and before disease development are called ambidirectional studies . Public healthcare studies generally fall within this group, e.g. lung cancer development in smokers.

• Case-Control Studies: these studies are retrospective cohort studies. They examine the cause and effect relationship from the effect to the cause. The detection or determination of data depends on the information recorded in the past. The researcher has no control over the data ( 2 ).

Cross-sectional studies are advantageous since they can be concluded relatively quickly. It may be difficult to obtain a reliable result from such studies for rare diseases ( 2 ).

Cross-sectional studies are characterised by timing. In such studies, the exposure and result are simultaneously evaluated. While cross-sectional studies are restrictedly used in studies involving anaesthesia (since the process of exposure is limited), they can be used in studies conducted in intensive care units.

• Quasi-Experimental Research: they are conducted in cases in which a quick result is requested and the participants or research areas cannot be randomised, e.g. giving hand-wash training and comparing the frequency of nosocomial infections before and after hand wash.
• Clinical Research: they are prospective studies carried out with a control group for the purpose of comparing the effect and value of an intervention in a clinical case. Clinical study and research have the same meaning. Drugs, invasive interventions, medical devices and operations, diets, physical therapy and diagnostic tools are relevant in this context ( 6 ).

Clinical studies are conducted by a responsible researcher, generally a physician. In the research team, there may be other healthcare staff besides physicians. Clinical studies may be financed by healthcare institutes, drug companies, academic medical centres, volunteer groups, physicians, healthcare service providers and other individuals. They may be conducted in several places including hospitals, universities, physicians’ offices and community clinics based on the researcher’s requirements. The participants are made aware of the duration of the study before their inclusion. Clinical studies should include the evaluation of recommendations (drug, device and surgical) for the treatment of a disease, syndrome or a comparison of one or more applications; finding different ways for recognition of a disease or case and prevention of their recurrence ( 7 ).

Clinical Research

In this review, clinical research is explained in more detail since it is the most valuable study in scientific research.

Clinical research starts with forming a hypothesis. A hypothesis can be defined as a claim put forward about the value of a population parameter based on sampling. There are two types of hypotheses in statistics.

• H 0 hypothesis is called a control or null hypothesis. It is the hypothesis put forward in research, which implies that there is no difference between the groups under consideration. If this hypothesis is rejected at the end of the study, it indicates that a difference exists between the two treatments under consideration.
• H 1 hypothesis is called an alternative hypothesis. It is hypothesised against a null hypothesis, which implies that a difference exists between the groups under consideration. For example, consider the following hypothesis: drug A has an analgesic effect. Control or null hypothesis (H 0 ): there is no difference between drug A and placebo with regard to the analgesic effect. The alternative hypothesis (H 1 ) is applicable if a difference exists between drug A and placebo with regard to the analgesic effect.

The planning phase comes after the determination of a hypothesis. A clinical research plan is called a protocol . In a protocol, the reasons for research, number and qualities of participants, tests to be applied, study duration and what information to be gathered from the participants should be found and conformity criteria should be developed.

The selection of participant groups to be included in the study is important. Inclusion and exclusion criteria of the study for the participants should be determined. Inclusion criteria should be defined in the form of demographic characteristics (age, gender, etc.) of the participant group and the exclusion criteria as the diseases that may influence the study, age ranges, cases involving pregnancy and lactation, continuously used drugs and participants’ cooperation.

The next stage is methodology. Methodology can be grouped under subheadings, namely, the calculation of number of subjects, blinding (masking), randomisation, selection of operation to be applied, use of placebo and criteria for stopping and changing the treatment.

I. Calculation of the Number of Subjects

The entire source from which the data are obtained is called a universe or population . A small group selected from a certain universe based on certain rules and which is accepted to highly represent the universe from which it is selected is called a sample and the characteristics of the population from which the data are collected are called variables. If data is collected from the entire population, such an instance is called a parameter . Conducting a study on the sample rather than the entire population is easier and less costly. Many factors influence the determination of the sample size. Firstly, the type of variable should be determined. Variables are classified as categorical (qualitative, non-numerical) or numerical (quantitative). Individuals in categorical variables are classified according to their characteristics. Categorical variables are indicated as nominal and ordinal (ordered). In nominal variables, the application of a category depends on the researcher’s preference. For instance, a female participant can be considered first and then the male participant, or vice versa. An ordinal (ordered) variable is ordered from small to large or vice versa (e.g. ordering obese patients based on their weights-from the lightest to the heaviest or vice versa). A categorical variable may have more than one characteristic: such variables are called binary or dichotomous (e.g. a participant may be both female and obese).

If the variable has numerical (quantitative) characteristics and these characteristics cannot be categorised, then it is called a numerical variable. Numerical variables are either discrete or continuous. For example, the number of operations with spinal anaesthesia represents a discrete variable. The haemoglobin value or height represents a continuous variable.

Statistical analyses that need to be employed depend on the type of variable. The determination of variables is necessary for selecting the statistical method as well as software in SPSS. While categorical variables are presented as numbers and percentages, numerical variables are represented using measures such as mean and standard deviation. It may be necessary to use mean in categorising some cases such as the following: even though the variable is categorical (qualitative, non-numerical) when Visual Analogue Scale (VAS) is used (since a numerical value is obtained), it is classified as a numerical variable: such variables are averaged.

Clinical research is carried out on the sample and generalised to the population. Accordingly, the number of samples should be correctly determined. Different sample size formulas are used on the basis of the statistical method to be used. When the sample size increases, error probability decreases. The sample size is calculated based on the primary hypothesis. The determination of a sample size before beginning the research specifies the power of the study. Power analysis enables the acquisition of realistic results in the research, and it is used for comparing two or more clinical research methods.

Because of the difference in the formulas used in calculating power analysis and number of samples for clinical research, it facilitates the use of computer programs for making calculations.

It is necessary to know certain parameters in order to calculate the number of samples by power analysis.

• Type-I (α) and type-II (β) error levels
• Difference between groups (d-difference) and effect size (ES)
• Distribution ratio of groups
• Direction of research hypothesis (H1)

a. Type-I (α) and Type-II (β) Error (β) Levels

Two types of errors can be made while accepting or rejecting H 0 hypothesis in a hypothesis test. Type-I error (α) level is the probability of finding a difference at the end of the research when there is no difference between the two applications. In other words, it is the rejection of the hypothesis when H 0 is actually correct and it is known as α error or p value. For instance, when the size is determined, type-I error level is accepted as 0.05 or 0.01.

Another error that can be made during a hypothesis test is a type-II error. It is the acceptance of a wrongly hypothesised H 0 hypothesis. In fact, it is the probability of failing to find a difference when there is a difference between the two applications. The power of a test is the ability of that test to find a difference that actually exists. Therefore, it is related to the type-II error level.

Since the type-II error risk is expressed as β, the power of the test is defined as 1–β. When a type-II error is 0.20, the power of the test is 0.80. Type-I (α) and type-II (β) errors can be intentional. The reason to intentionally make such an error is the necessity to look at the events from the opposite perspective.

b. Difference between Groups and ES

ES is defined as the state in which statistical difference also has clinically significance: ES≥0.5 is desirable. The difference between groups is the absolute difference between the groups compared in clinical research.

c. Allocation Ratio of Groups

The allocation ratio of groups is effective in determining the number of samples. If the number of samples is desired to be determined at the lowest level, the rate should be kept as 1/1.

d. Direction of Hypothesis (H1)

The direction of hypothesis in clinical research may be one-sided or two-sided. While one-sided hypotheses hypothesis test differences in the direction of size, two-sided hypotheses hypothesis test differences without direction. The power of the test in two-sided hypotheses is lower than one-sided hypotheses.

After these four variables are determined, they are entered in the appropriate computer program and the number of samples is calculated. Statistical packaged software programs such as Statistica, NCSS and G-Power may be used for power analysis and calculating the number of samples. When the samples size is calculated, if there is a decrease in α, difference between groups, ES and number of samples, then the standard deviation increases and power decreases. The power in two-sided hypothesis is lower. It is ethically appropriate to consider the determination of sample size, particularly in animal experiments, at the beginning of the study. The phase of the study is also important in the determination of number of subjects to be included in drug studies. Usually, phase-I studies are used to determine the safety profile of a drug or product, and they are generally conducted on a few healthy volunteers. If no unacceptable toxicity is detected during phase-I studies, phase-II studies may be carried out. Phase-II studies are proof-of-concept studies conducted on a larger number (100–500) of volunteer patients. When the effectiveness of the drug or product is evident in phase-II studies, phase-III studies can be initiated. These are randomised, double-blinded, placebo or standard treatment-controlled studies. Volunteer patients are periodically followed-up with respect to the effectiveness and side effects of the drug. It can generally last 1–4 years and is valuable during licensing and releasing the drug to the general market. Then, phase-IV studies begin in which long-term safety is investigated (indication, dose, mode of application, safety, effectiveness, etc.) on thousands of volunteer patients.

II. Blinding (Masking) and Randomisation Methods

When the methodology of clinical research is prepared, precautions should be taken to prevent taking sides. For this reason, techniques such as randomisation and blinding (masking) are used. Comparative studies are the most ideal ones in clinical research.

Blinding Method

A case in which the treatments applied to participants of clinical research should be kept unknown is called the blinding method . If the participant does not know what it receives, it is called a single-blind study; if even the researcher does not know, it is called a double-blind study. When there is a probability of knowing which drug is given in the order of application, when uninformed staff administers the drug, it is called in-house blinding. In case the study drug is known in its pharmaceutical form, a double-dummy blinding test is conducted. Intravenous drug is given to one group and a placebo tablet is given to the comparison group; then, the placebo tablet is given to the group that received the intravenous drug and intravenous drug in addition to placebo tablet is given to the comparison group. In this manner, each group receives both the intravenous and tablet forms of the drug. In case a third party interested in the study is involved and it also does not know about the drug (along with the statistician), it is called third-party blinding.

Randomisation Method

The selection of patients for the study groups should be random. Randomisation methods are used for such selection, which prevent conscious or unconscious manipulations in the selection of patients ( 8 ).

No factor pertaining to the patient should provide preference of one treatment to the other during randomisation. This characteristic is the most important difference separating randomised clinical studies from prospective and synchronous studies with experimental groups. Randomisation strengthens the study design and enables the determination of reliable scientific knowledge ( 2 ).

The easiest method is simple randomisation, e.g. determination of the type of anaesthesia to be administered to a patient by tossing a coin. In this method, when the number of samples is kept high, a balanced distribution is created. When the number of samples is low, there will be an imbalance between the groups. In this case, stratification and blocking have to be added to randomisation. Stratification is the classification of patients one or more times according to prognostic features determined by the researcher and blocking is the selection of a certain number of patients for each stratification process. The number of stratification processes should be determined at the beginning of the study.

As the number of stratification processes increases, performing the study and balancing the groups become difficult. For this reason, stratification characteristics and limitations should be effectively determined at the beginning of the study. It is not mandatory for the stratifications to have equal intervals. Despite all the precautions, an imbalance might occur between the groups before beginning the research. In such circumstances, post-stratification or restandardisation may be conducted according to the prognostic factors.

The main characteristic of applying blinding (masking) and randomisation is the prevention of bias. Therefore, it is worthwhile to comprehensively examine bias at this stage.

Bias and Chicanery

While conducting clinical research, errors can be introduced voluntarily or involuntarily at a number of stages, such as design, population selection, calculating the number of samples, non-compliance with study protocol, data entry and selection of statistical method. Bias is taking sides of individuals in line with their own decisions, views and ideological preferences ( 9 ). In order for an error to lead to bias, it has to be a systematic error. Systematic errors in controlled studies generally cause the results of one group to move in a different direction as compared to the other. It has to be understood that scientific research is generally prone to errors. However, random errors (or, in other words, ‘the luck factor’-in which bias is unintended-do not lead to bias ( 10 ).

Another issue, which is different from bias, is chicanery. It is defined as voluntarily changing the interventions, results and data of patients in an unethical manner or copying data from other studies. Comparatively, bias may not be done consciously.

In case unexpected results or outliers are found while the study is analysed, if possible, such data should be re-included into the study since the complete exclusion of data from a study endangers its reliability. In such a case, evaluation needs to be made with and without outliers. It is insignificant if no difference is found. However, if there is a difference, the results with outliers are re-evaluated. If there is no error, then the outlier is included in the study (as the outlier may be a result). It should be noted that re-evaluation of data in anaesthesiology is not possible.

Statistical evaluation methods should be determined at the design stage so as not to encounter unexpected results in clinical research. The data should be evaluated before the end of the study and without entering into details in research that are time-consuming and involve several samples. This is called an interim analysis . The date of interim analysis should be determined at the beginning of the study. The purpose of making interim analysis is to prevent unnecessary cost and effort since it may be necessary to conclude the research after the interim analysis, e.g. studies in which there is no possibility to validate the hypothesis at the end or the occurrence of different side effects of the drug to be used. The accuracy of the hypothesis and number of samples are compared. Statistical significance levels in interim analysis are very important. If the data level is significant, the hypothesis is validated even if the result turns out to be insignificant after the date of the analysis.

Another important point to be considered is the necessity to conclude the participants’ treatment within the period specified in the study protocol. When the result of the study is achieved earlier and unexpected situations develop, the treatment is concluded earlier. Moreover, the participant may quit the study at its own behest, may die or unpredictable situations (e.g. pregnancy) may develop. The participant can also quit the study whenever it wants, even if the study has not ended ( 7 ).

In case the results of a study are contrary to already known or expected results, the expected quality level of the study suggesting the contradiction may be higher than the studies supporting what is known in that subject. This type of bias is called confirmation bias. The presence of well-known mechanisms and logical inference from them may create problems in the evaluation of data. This is called plausibility bias.

Another type of bias is expectation bias. If a result different from the known results has been achieved and it is against the editor’s will, it can be challenged. Bias may be introduced during the publication of studies, such as publishing only positive results, selection of study results in a way to support a view or prevention of their publication. Some editors may only publish research that extols only the positive results or results that they desire.

Bias may be introduced for advertisement or economic reasons. Economic pressure may be applied on the editor, particularly in the cases of studies involving drugs and new medical devices. This is called commercial bias.

In recent years, before beginning a study, it has been recommended to record it on the Web site www.clinicaltrials.gov for the purpose of facilitating systematic interpretation and analysis in scientific research, informing other researchers, preventing bias, provision of writing in a standard format, enhancing contribution of research results to the general literature and enabling early intervention of an institution for support. This Web site is a service of the US National Institutes of Health.

The last stage in the methodology of clinical studies is the selection of intervention to be conducted. Placebo use assumes an important place in interventions. In Latin, placebo means ‘I will be fine’. In medical literature, it refers to substances that are not curative, do not have active ingredients and have various pharmaceutical forms. Although placebos do not have active drug characteristic, they have shown effective analgesic characteristics, particularly in algology applications; further, its use prevents bias in comparative studies. If a placebo has a positive impact on a participant, it is called the placebo effect ; on the contrary, if it has a negative impact, it is called the nocebo effect . Another type of therapy that can be used in clinical research is sham application. Although a researcher does not cure the patient, the researcher may compare those who receive therapy and undergo sham. It has been seen that sham therapies also exhibit a placebo effect. In particular, sham therapies are used in acupuncture applications ( 11 ). While placebo is a substance, sham is a type of clinical application.

Ethically, the patient has to receive appropriate therapy. For this reason, if its use prevents effective treatment, it causes great problem with regard to patient health and legalities.

Before medical research is conducted with human subjects, predictable risks, drawbacks and benefits must be evaluated for individuals or groups participating in the study. Precautions must be taken for reducing the risk to a minimum level. The risks during the study should be followed, evaluated and recorded by the researcher ( 1 ).

After the methodology for a clinical study is determined, dealing with the ‘Ethics Committee’ forms the next stage. The purpose of the ethics committee is to protect the rights, safety and well-being of volunteers taking part in the clinical research, considering the scientific method and concerns of society. The ethics committee examines the studies presented in time, comprehensively and independently, with regard to ethics and science; in line with the Declaration of Helsinki and following national and international standards concerning ‘Good Clinical Practice’. The method to be followed in the formation of the ethics committee should be developed without any kind of prejudice and to examine the applications with regard to ethics and science within the framework of the ethics committee, Regulation on Clinical Trials and Good Clinical Practice ( www.iku.com ). The necessary documents to be presented to the ethics committee are research protocol, volunteer consent form, budget contract, Declaration of Helsinki, curriculum vitae of researchers, similar or explanatory literature samples, supporting institution approval certificate and patient follow-up form.

Only one sister/brother, mother, father, son/daughter and wife/husband can take charge in the same ethics committee. A rector, vice rector, dean, deputy dean, provincial healthcare director and chief physician cannot be members of the ethics committee.

Members of the ethics committee can work as researchers or coordinators in clinical research. However, during research meetings in which members of the ethics committee are researchers or coordinators, they must leave the session and they cannot sign-off on decisions. If the number of members in the ethics committee for a particular research is so high that it is impossible to take a decision, the clinical research is presented to another ethics committee in the same province. If there is no ethics committee in the same province, an ethics committee in the closest settlement is found.

Thereafter, researchers need to inform the participants using an informed consent form. This form should explain the content of clinical study, potential benefits of the study, alternatives and risks (if any). It should be easy, comprehensible, conforming to spelling rules and written in plain language understandable by the participant.

This form assists the participants in taking a decision regarding participation in the study. It should aim to protect the participants. The participant should be included in the study only after it signs the informed consent form; the participant can quit the study whenever required, even when the study has not ended ( 7 ).

Peer-review: Externally peer-reviewed.

Author Contributions: Concept - C.Ö.Ç., A.D.; Design - C.Ö.Ç.; Supervision - A.D.; Resource - C.Ö.Ç., A.D.; Materials - C.Ö.Ç., A.D.; Analysis and/or Interpretation - C.Ö.Ç., A.D.; Literature Search - C.Ö.Ç.; Writing Manuscript - C.Ö.Ç.; Critical Review - A.D.; Other - C.Ö.Ç., A.D.

Conflict of Interest: No conflict of interest was declared by the authors.

Financial Disclosure: The authors declared that this study has received no financial support.

The Scientific Method

Introduction.

There are many scientific disciplines that address topics from medicine and astrophysics to agriculture and zoology. In each discipline, modern scientists use a process called the "Scientific Method" to advance their knowledge and understanding. This publication describes the method scientists use to conduct research and describe and explain nature, ultimately trying prove or disprove theories.

Scientists all over the world conduct research using the Scientific Method. The University of Nevada Cooperative Extension exists to provide unbiased, research-based information on topics important and relevant to society. The scientific research efforts, analyses, and subsequent information disseminated by Cooperative Extension is driven by careful review and synthesis of relevant scientific research. Cooperative Extension presents useful information based on the best science available, and today that science is based on knowledge obtained by application of the Scientific Method.

The Scientific Method – What it’s Not

The Scientific Method is a process for explaining the world we see. It is:

• Not a formula

The Scientific Method – What is it?

The Scientific Method is a process used to validate observations while minimizing observer bias. Its goal is for research to be conducted in a fair, unbiased and repeatable manner.

Long ago, people viewed the workings of nature and believed that the events and phenomena they observed were associated with the intrinsic nature of the beings or things being observed (Ackoff 1962, Wilson 1937). Today we view events and phenomena as having been caused , and science has evolved as a process to ask how and why things and events happen. Scientists seek to understand the relationships and intricacies between cause and effect in order to predict outcomes of future or similar events. To answer these questions and to help predict future happenings, scientists use the Scientific Method - a series of steps that lead to answers that accurately describe the things we observe, or at least improve our understanding of them.

The Scientific Method is not the only way, but is the best-known way to discover how and why the world works, without our knowledge being tainted by religious, political, or philosophical values. This method provides a means to formulate questions about general observations and devise theories of explanation. The approach lends itself to answering questions in fair and unbiased statements, as long as questions are posed correctly, in a hypothetical form that can be tested.

Definitions

It is important to understand three important terms before describing the Scientific Method.

This is a statement made by a researcher that is a working assumption to be tested and proven. It is something "considered true for the purpose of investigation" (Webster’s Dictionary 1995). An example might be “The earth is round.”

general principles drawn from facts that explain observations and can be used to predict new events. An example would be Newton’s theory of gravitation or Einstein’s theory of relativity. Each is based on falsifiable hypotheses of phenomenon we observe.

Falsifiable/ Null Hypothesis

to prove to be false (Webster’s Dictionary 1995). The hypothesis that is generated must be able to be tested, and either accepted or rejected. Scientists make hypotheses that they want to disprove in order that they may prove the working assumption describing the observed phenomena. This is done by declaring the statement or hypothesis as falsifiable . So, we would state the above hypothesis as “the earth is not round,” or “the earth is square” making it a working statement to be disproved.

The Scientific Method is not a formula, but rather a process with a number of sequential steps designed to create an explainable outcome that increases our knowledge base. This process is as follows:

STEP 1. Make an OBSERVATION

gather and assimilate information about an event, phenomenon, process, or an exception to a previous observation, etc.

STEP 2. Define the PROBLEM

ask questions about the observation that are relevant and testable. Define the null hypothesis to provide unbiased results.

STEP 3: Form the HYPOTHESIS

create an explanation, or educated guess, for the observation that is testable and falsifiable.

STEP 4: Conduct the EXPERIMENT

devise and perform an experiment to test the hypothesis.

STEP 5: Derive a THEORY

create a statement based in the outcome of the experiment that explains the observation(s) and predicts the likelihood of future observations.

Replication

Using the Scientific Method to answer questions about events or phenomena we observe can be repeated to fine-tune our theories. For example, if we conduct research using the Scientific Method and think we have answered a question, but different results occur the next time we make an observation, we may have to ask new questions and formulate new hypotheses that are tested by another experiment. Sometimes scientists must perform many experiments over many years or even decades using the Scientific Method to prove or disprove theories that are generated from one initial question. Numerous studies are often necessary to fully test the broad range of results that occur in order that scientists can formulate theories that truly account for the variation we see in our natural environment.

The Scientific Method – Is it worth all the effort?

Scientific knowledge can only advance when all scientists systematically use the same process to discover and disseminate new information. The advantage of all scientific research using the Scientific Method is that the experiments are repeatable by anyone, anywhere. When similar results occur in each experiment, these facts make the case for the theory stronger. If the same experiment is performed many times in many different locations, under a broad range of conditions, then the theory derived from these experiments is considered strong and widely applicable. If the questions are posed as testable hypotheses that rely on inductive reasoning and empiricism – that is, observations and data collection – then experiments can be devised to generate logical theories that explain the things we see. If we understand why the observed results occur, then we can accurately apply concepts derived from the experiment to other situations.

What do we need to consider when using the Scientific Method?

The Scientific Method requires that we ask questions and perform experiments to prove or disprove questions in ways that will lead to unbiased answers. Experiments must be well designed to provide accurate and repeatable (precise) results. If we test hypotheses correctly, then we can prove the cause of a phenomenon and determine the likelihood (probability) of the events to happen again. This provides predictive power. The Scientific Method enables us to test a hypothesis and distinguish between the correlation of two or more things happening in association with each other and the actual cause of the phenomenon we observe.

Correlation of two variables cannot explain the cause and effect of their relationship. Scientists design experiments using a number of methods to ensure the results reveal the likelihood of the observation happening (probability). Controlled experiments are used to analyze these relationships and develop cause and effect relationships. Statistical analysis is used to determine whether differences between treatments can be attributed to the treatment applied, if they are artifacts of the experimental design, or of natural variation.

In summary, the Scientific Method produces answers to questions posed in the form of a working hypothesis that enables us to derive theories about what we observe in the world around us. Its power lies in its ability to be repeated, providing unbiased answers to questions to derive theories. This information is powerful and offers opportunity to predict future events and phenomena.

Bibliography

• Ackoff, R. 1962. Scientific Method, Optimizing Applied Research Decisions. Wiley and Sons, New York, NY.
• Wilson, F. 1937. The Logic and Methodology of Science in Early Modern Thought. University of Toronto Press. Buffalo, NY.
• Committee on Science, Engineering, and Public Policy. Experimental Error. 1995. From: On Being a Scientist: Responsible Conduct in Research. Second Edition.
• The Gale Group. The Scientific Method. 2001. Gale Encyclopedia of Psychology. Second Edition.

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Also of Interest:

An EEO/AA Institution. Copyright © 2024 , University of Nevada Cooperative Extension. A partnership of Nevada counties; University of Nevada, Reno; and the U.S. Department of Agriculture

Scientific Methods

What is scientific method.

The Scientific method is a process with the help of which scientists try to investigate, verify, or construct an accurate and reliable version of any natural phenomena. They are done by creating an objective framework for the purpose of scientific inquiry and analysing the results scientifically to come to a conclusion that either supports or contradicts the observation made at the beginning.

Scientific Method Steps

The aim of all scientific methods is the same, that is, to analyse the observation made at the beginning. Still, various steps are adopted per the requirement of any given observation. However, there is a generally accepted sequence of steps in scientific methods.

• Observation and formulation of a question:  This is the first step of a scientific method. To start one, an observation has to be made into any observable aspect or phenomena of the universe, and a question needs to be asked about that aspect. For example, you can ask, “Why is the sky black at night? or “Why is air invisible?”
• Data Collection and Hypothesis:  The next step involved in the scientific method is to collect all related data and formulate a hypothesis based on the observation. The hypothesis could be the cause of the phenomena, its effect, or its relation to any other phenomena.
• Testing the hypothesis:  After the hypothesis is made, it needs to be tested scientifically. Scientists do this by conducting experiments. The aim of these experiments is to determine whether the hypothesis agrees with or contradicts the observations made in the real world. The confidence in the hypothesis increases or decreases based on the result of the experiments.
• Analysis and Conclusion:  This step involves the use of proper mathematical and other scientific procedures to determine the results of the experiment. Based on the analysis, the future course of action can be determined. If the data found in the analysis is consistent with the hypothesis, it is accepted. If not, then it is rejected or modified and analysed again.

It must be remembered that a hypothesis cannot be proved or disproved by doing one experiment. It needs to be done repeatedly until there are no discrepancies in the data and the result. When there are no discrepancies and the hypothesis is proved, it is accepted as a ‘theory’.

Scientific Method Examples

Following is an example of the scientific method:

Growing bean plants:

• What is the purpose: The main purpose of this experiment is to know where the bean plant should be kept inside or outside to check the growth rate and also set the time frame as four weeks.
• Construction of hypothesis: The hypothesis used is that the bean plant can grow anywhere if the scientific methods are used.
• Executing the hypothesis and collecting the data: Four bean plants are planted in identical pots using the same soil. Two are placed inside, and the other two are placed outside. Parameters like the amount of exposure to sunlight, and amount of water all are the same. After the completion of four weeks, all four plant sizes are measured.
• Analyse the data:  While analysing the data, the average height of plants should be taken into account from both places to determine which environment is more suitable for growing the bean plants.
• Conclusion:  The conclusion is drawn after analyzing the data.
• Results:  Results can be reported in the form of a tabular form.

Frequently Asked Questions – FAQs

What is scientific method, what is hypothesis, give an example of a simple hypothesis., define complex hypothesis., what are the steps of the scientific method, what is the aim of scientific methods, state true or false: observation and formulation of a question is the third step of scientific method, explain the step: analysis and conclusion., leave a comment cancel reply.

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• Published: 25 May 2024

Exploring the “gene–metabolite” network of ischemic stroke with blood stasis and toxin syndrome by integrated transcriptomics and metabolomics strategy

• Yue Liu 1   na1 ,
• Wenqiang Cui 1 , 3   na1 ,
• Hongxi Liu 1   na1 ,
• Mingjiang Yao 1 , 2 ,
• Wei Shen 1 ,
• Lina Miao 1 ,
• Jingjing Wei 1 ,
• Xiao Liang 1 &
• Yunling Zhang 1  

Scientific Reports volume  14 , Article number:  11947 ( 2024 ) Cite this article

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Metrics details

• Diseases of the nervous system

A research model combining a disease and syndrome can provide new ideas for the treatment of ischemic stroke. In the field of traditional Chinese medicine, blood stasis and toxin (BST) syndrome is considered an important syndrome seen in patients with ischemic stroke (IS). However, the biological basis of IS-BST syndrome is currently not well understood. Therefore, this study aimed to explore the biological mechanism of IS-BST syndrome. This study is divided into two parts: (1) establishment of an animal model of ischemic stroke disease and an animal model of BST syndrome in ischemic stroke; (2) use of omics methods to identify differentially expressed genes and metabolites in the models. We used middle cerebral artery occlusion (MCAO) surgery to establish the disease model, and utilized carrageenan combined with active dry yeast and MCAO surgery to construct the IS-BST syndrome model. Next, we used transcriptomics and metabolomics methods to explore the differential genes and metabolites in the disease model and IS-BST syndrome model. It is found that the IS-BST syndrome model exhibited more prominent characteristics of IS disease and syndrome features. Both the disease model and the IS-BST syndrome model share some common biological processes, such as thrombus formation, inflammatory response, purine metabolism, sphingolipid metabolism, and so on. Results of the “gene–metabolite” network revealed that the IS-BST syndrome model exhibited more pronounced features of complement-coagulation cascade reactions and amino acid metabolism disorders. Additionally, the “F2 (thrombin)–NMDAR/glutamate” pathway was coupled with the formation process of the blood stasis and toxin syndrome. This study reveals the intricate mechanism of IS-BST syndrome, offering a successful model for investigating the combination of disease and syndrome.

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Introduction.

Stroke, an illness characterized by a high rate of morbidity, mortality, and disability, is the second leading cause of death globally 1 . Ischemic Stroke (IS) accounts for 87% of all stroke incidences and is the outcome of blood flow disruption caused by thrombotic and embolic events 2 , 3 . The recombinant tissue plasminogen activator (rt-PA) is currently the only approved medical therapy for IS. However, its clinical applicability is limited to only a small proportion of stroke patients by the narrow time window in which it can be administered 4 , 5 . As a result, the development of novel therapeutic drugs or combination therapies for IS treatment is imperative. With few therapeutic options available, patients and healthcare workers are increasingly embracing traditional Chinese medicine (TCM), which has a unique theoretical system characterized by a holistic concept and syndrome differentiation and treatment principles 6 . According to research, combining TCM and Western medication is effective in symptom relief, neurological healing, and enhancing IS patients’ Quality of Life (QoL) 7 , 8 .

The TCM concept is based on the fact that different stages of disease occurrence and development could present varying symptoms and signs. Syndrome ( ZHENG in Chinese) comprises symptoms and signs that reflect the essence of a particular stage or type of disease. The various stages or types of syndromes intertwine and overlap, making up the entirety of the disease process. Developing a research model that integrates the “disease” concept in Western medicine with the “syndrome” concept in TCM theory is one of the future directions in Chinese integrative medicine. This approach aims to enhance our understanding of complex health conditions by harmonizing the perspectives of the two medical systems 9 . Blood stasis is an essential pathogenesis in TCM theory and clinical practice of IS, and the blood stasis syndrome ( Xueyu Zheng ) is the most common type of IS 10 . However, IS a dangerous condition that often progresses rapidly, and a single blood stasis theory may not comprehensively explain its complex pathogenic factors and processes 11 . The clinical IS manifestations caused by a sudden blood flow disruption are highly similar to those of diseases precipitated by ‘toxin’ in TCM. Illnesses caused by ‘toxin’ are often sudden and could even be fatal 12 . According to TCM, ‘toxins’ are formed by the accumulation and transformation of other pathogenic elements. Since blood stasis lasts for a long time, it could breed toxins. As a result, current IS practices stress the critical involvement of “blood stasis and toxin interaction” in its occurrence 13 . However, the biological mechanism underlying the Blood Stasis and Toxin (BST) syndrome remains unclear. Therefore, elucidating the biological basis of the IS-BST syndrome will undoubtedly promote advancements in the IS treatment methodology ( Supplementary Information ).

The Disease-Syndrome (DS) combination modeling is a crucial aspect of biomedical research 14 . According to the TCM basic theory, blood stasis could breed toxin, which in turn can consume body fluid, increasing blood viscosity and leading to blood stasis ultimately. Blood stasis and toxin accumulate in the body, leading to the occurrence of diseases. Modern medical research often explains this process as microcirculation disorder, abnormal hemorheology, enhanced platelet aggregation, inflammatory reactions, etc. Carrageenan (Ca) is considered to damage vascular endothelial cells and cause thrombosis, and is often used to prepare rodent thrombosis models 15 , 16 . Lipopolysaccharides (LPS) and active dry yeast (Yeast) acting on the body can induce the production of endogenous inflammatory factors and toxic substances, and are often used as tools in simulating the TCM concept of “toxin”. Our previous research utilized Ca to simulate the pathogenic factor of blood stasis, and used LPS and Yeast to simulate toxic pathogenic factors. We systematically compared BST models constructed using these three methods: simple Ca, Ca combined with LPS, and Ca combined with Yeast. We comprehensively evaluated syndrome characteristics, tail blood flow perfusion, whole blood viscosity, plasma viscosity, platelet aggregation rate, and plasma inflammatory factors, and ultimately found that the combination of Ca and Yeast models can present more stable BST syndrome characteristics. The BST model, established through the combination of Ca and Yeast, exhibited fever, a black tail phenomenon, reduced tail blood perfusion, elevated whole blood and plasma viscosity, increased platelet aggregation rate, and raised levels of the plasma inflammatory factor IL-6 17 . Based on these results, the present work aimed to establish a comprehensive animal model incorporating both the IS pathological characteristics and the BST syndrome characteristics. Specifically, we aim to create a fundamental tool for further studying the essence of IS and pharmacological mechanisms of Chinese herbal medicine. In other words, for a better understanding, it is important to conduct IS or syndrome-guided medication research on a mature DS combination model. However, diseases and syndromes are holistic concepts, and it is difficult to comprehensively describe the combination of diseases and syndromes using limited model evaluation indicators. As a solution to this drawback, omics technology has played an increasingly important role in life sciences in recent years, allowing the complexity of biological processes to be explained from multiple perspectives 18 . The application of “omics” in TCM research has attracted widespread attention, offering a technical platform for exploring the essence of the DS combination 19 , 20 , 21 .

Herein, we created a rat model incorporating both IS and the BST syndrome and designated it as the DS model. Transcriptomic and metabolomic approaches were used to investigate the biological basis of this model, yielding insights into the mechanisms underlying the IS-BST syndrome (Fig.  1 ). In addition to providing a scientific basis for TCM complexity, this study may discover new diagnostic biomarkers of the IS-BST syndrome, offering potential therapeutic targets for IS treatment.

The flowchart of modeling methods and transcriptomics and metabolomics research.

Materials and methods

Experimental animals.

Fourty-five male Specific Pathogen-Free (SPF) Sprague Dawley (SD) rats (weight = 230 ± 10 g) were purchased from Beijing Weitong Lihua Co., Ltd. [Beijing, China; Laboratory animal certificate number: SYXK (jing), 2018-0018]. These animals were housed in a controlled environment of 16 °C ± 2 °C and humidity of 55% ± 5% under a 12-h light/dark cycle and were allowed ad libitum access to food and water throughout the experiment. The Experimental Ethics Committee of Xiyuan Hospital ethically reviewed and approved this study’s research protocol.

Reagents and materials

Carrageenan was supplied by Shanghai Macklin Biochemical Co., Ltd. (Shanghai, China, Batch No: C14408398). Active dry yeast was purchased from Angel Yeast Co., Ltd. (Yichang, China; Batch No: HY2009R). The rat Interleukin-6 (IL-6) Enzyme-Linked Immunosorbent Assay (ELISA) kit was acquired from Cohesion Biosciences. (UK; Batch No: CEK1619). Nylon suture for Middle Cerebral Artery Occlusion (MCAO) surgery was purchased from Hebei Tiannong Biotechnology Co., Ltd. (Shijiazhuang, China; Batch No: 20210630).

Modeling and evaluation methods of disease and syndrome animal models

Modeling methods.

After 3 days of adaptive feeding, the rats were randomly divided into three groups (n = 15): normal control group (NC group), the disease model group (Disease group) and the disease-syndrome model group (DS group).

The DS group was intraperitoneally injected with 10 mg·kg −1 of carrageenan on the first day of modeling. On the second day, the Disease and DS groups underwent MCAO surgery. Notably, the DS group was subcutaneously injected with 2 g·kg −1 of active dry yeast into the back immediately after inserting the nylon suture into the middle cerebral artery. On the other hand, the NC group was fed normally and received no treatment.

The modified Longa method was used to induce MCAO surgery 22 . The animals in the Disease and DS groups were weighed and anesthetized with pentobarbital sodium (40 mg·kg −1 ) after 12 h of fasting (water allowed). Subsequently, the anesthetized rats were fixed on the operating table, and the right Common Carotid Artery (CCA) and the right External Carotid Artery (ECA) were separated through a longitudinal incision in the middle of the neck and ligated near the cardiac end. A loose knot was then tied approximately 0.5 cm above the ligature. The Internal Carotid Artery (ICA) was clamped with an arterial clamp, and a small incision was made between the sliding and dead nodes of the CCA. The ICA artery clamp was tied off once the nylon suture was inserted and made contact with the CCA bifurcation. The suture entered the ICA from the CCA up until it reached the initial area of the anterior cerebral artery. The insertion was stopped when a small amount of resistance was felt from the incision, at approximately 18 mm. After 1.5 h of ischemia, the suture was removed from the ICA to the CCA, followed by 22.5 h of reperfusion.

Model evaluation indicators and methods

Model evaluation was performed as follows:

General observations: Mental status, diet, movement, and body hair glossiness of three animal groups were observed and recorded. The characteristic manifestations of the rat syndromes were also observed.

Evaluation of neurological deficits: A validated five-point scale was used to quantify the neurological deficit scores for all rats at 24 h postoperatively 23 . Specifically, a rat with no neurological deficit symptoms received a score of 0, a rat failing to completely stretch the left fore paw received a score of 1, a rat circling to the left received a score of 2, a rat falling to the left or rolling on the ground received a score of 3, and a rat showing no spontaneous activity with consciousness disorder received a score of 4.

Tail blood flow perfusion detection: The PeriCam PSI system (Perimed, Sweden) was used to detect blood perfusion in the rats’ tail tips. We focused the cursor on the 1 cm point at the tip of the rat tail, and then observed and recorded the tail blood perfusion. The laser blood perfusion speckle image was generated, and then the average blood perfusion of the tail tip of each group of rats was analyzed using PIMSoft software along with the PeriCam PSI system.

Detection of Whole Blood Viscosity (WBV), Plasma Viscosity (PV), and platelet Aggregation Rate (AR): Blood samples were extracted from the abdominal aorta of rats. The blood was then collected into one heparin anticoagulant tube and one sodium citrate anticoagulant tube. Subsequently, WBV, PV, and platelet AR were detected in rats using a fully automatic hemorheological analyzer (Beijing Succeeder Technology Inc., China) and a PL-12 platelet function analyzer (SINNOWA Medical Science and Technology Co., Ltd., China).

Measurement of the cerebral infarction area: We performed 2,3,5-Triphenyltetrazolium Chloride (TTC, Sigma, USA) staining to visualize the ischemic infarction area. All rat brains were sliced into 2-mm-thick coronal sections before incubating each slice in a 0.1% TTC solution at 37 °C for 30 min. The slices were then fixed in 4% paraformaldehyde. The infarction area was quantified using Image J software.

Hematoxylin–eosin staining (HE): Brain samples were swiftly extracted from all rats, followed by overnight fixation in 4% paraformaldehyde. Subsequently, the brains were dehydrated using graded alcohol and encased in paraffin wax. The 5 μm thick-paraffin-embedded brain tissue sections were then processed with the HE kit to observe the neuronal pathological changes.

Enzyme-Linked Immunosorbent Assay (ELISA): Cortical tissue samples were extracted from the rats’ ischemic hemisphere and the corresponding side in the NC group. The tissue samples were then incubated with an appropriate lysis buffer volume and mechanically processed using a cold grinder. The mixture was allowed to settle before obtaining the supernatant by centrifuging it at 3000 rpm for 10 min at 4 °C. The interleukin-6 (IL-6) expression level in the rat brain tissue was determined using an ELISA kit per the recommended protocol.

Research on the biological basis of the disease-syndrome combination model through integrated transcriptomics and metabolomics analysis

Based on the established model, transcriptomic and metabolomic analyses were performed on the brain tissues of the three groups of rats to explore the biological mechanisms of the DS model.

RNA-seq-based transcriptomic study

Rna extraction, library construction and sequencing.

Total RNA was extracted from the ischemic cortical tissue of rats using the Trizol Reagent (Invitrogen Life Technologies). Four samples were processed per group. A NanoDrop spectrophotometer (Thermo Scientific) was used to assess the concentration, quality, and integrity of the extracted RNAs. Three micrograms of RNA were used as input material for RNA sample preparations.

The RNA library was completed by Shanghai Personal Biotechnology Co. Ltd. A total RNA of ≥ 1 μg was selected, and cDNA was synthesized using the NEBNext Ultra II RNA Library Prep Kit (Illumina). The AMPure XP beads were used to screen cDNA fragments of around 400–500 bp, perform PCR amplification, and purify the PCR product, resulting in a library. Sequencing was performed using the NovaSeq 6000 platform (Illumina) after completing the library quality inspection.

Differential gene expression analysis

The image file was obtained after sequencing the sample on the machine, and the sequencing platform generated the original FASTQ data (Raw data). Quality checks were performed on raw data using FastQC v0.11.8. Reads that met the quality control (QC) standards for the rat reference genome were mapped using the HISAT2 aligner v2.0.5. The read count of the original expression level of each gene was obtained using HTSeq. Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were used to normalize expression levels to ensure comparability of gene expression levels between different genes and samples. Transcriptomic analysis was performed through Principal Components Analysis (PCA). Differential Gene (DG) expression analysis was performed using the DESeq2 package, with P  < 0.05 and |log2FoldChange| > 1 as the screening conditions. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analyses of DGs were performed using the Database for Annotation Visualization and Integrated Discovery (DAVID).

Untargeted metabolomic study

Sample pretreatment.

Sample preparation and liquid chromatography—tandem mass spectrometry (LC–MS/MS) detection were completed by Shanghai Personal Biotechnology Co. Ltd. Eight ischemic cortical tissue samples per group were thawed gradually at 4 °C. Subsequently, 1 mL of precooling methyl alcohol/acetonitrile/water (2:2:1, v/v) was added, and the mixture was sufficiently vortexed. After 30 min of low-temperature ultrasonic breakdown, the samples were centrifuged at 14,000× g for 20 min at 4 °C to precipitate the protein. The supernatants were collected, vacuum-dried, and kept at − 80 °C, awaiting further experiments. The material was then resolved in 100 μL acetonitrile/water (1:1, v/v), sufficiently vortexed, and centrifuged at 14,000 rpm, for 15 min at 4 °C. Following that, the supernatants were subjected to LC–MS/MS analysis.

LC–MS/MS analysis

Chromatographic separation was performed using an ACQUITY UPLC BEH C18 column (100 mm × 2.1 mm, 1.7 μm, Waters, USA) with a column temperature of 40 °C and a flow rate of 0.3 mL/min. The mobile phase A consisted of water with 0.1% formic acid, while mobile phase B was acetonitrile. The metabolites were eluted using the following gradient: 0–0.5 min, 5%B; 0.5–1.0 min, 5%B; 1.0–9.0 min, 5–100%B; 9.0–12.0 min, 100%B; 12.0–15.0 min, 5%B. The sample injection volume for each sample was 5 μL. Throughout the analysis, samples were kept in an autosampler at 4 °C. To avoid any impact from instrument signal fluctuations, samples were analyzed in random order. Quality control (QC) samples were inserted after each group of samples in the sample queue to monitor and assess system stability and the reliability of experimental data.

The MS conditions were as follows: Ion source: electrospray ionization (ESI); Samples were detected in both ESI positive and negative modes. Mass spectrum parameters: Ion source gas1 (Gas1): 60; Ion source gas2 (Gas2): 60; Curtain gas: 30; Source temperature: 320 °C; Spray Voltage (V): 3500 (positive ion), − 3500 (negative ion). In MS only acquisition, the instrument was set to acquire over the m/z range 60–1000 Da, product ion scan m/z range 25–1000 Da, MS scan accumulation time 0.20 s/spectra, product ion scan accumulation time 0.05 s/spectra. MS/MS is acquired using information dependent acquisition (IDA) with high sensitivity mode selected. The collision energy (CE) was fixed at 35 eV with ± 15 eV. Declustering potential (DP) was set as ± 60 V. IDA was set as follows: Exclude isotopes within 4 Da; Candidate ions to monitor per cycle: 6.

Data preprocessing and statistical analysis

The acquired LC–MS/MS raw data were preprocessed by Compound Discoverer 3.0 (Thermo Fisher Scientific) software, including peak extraction, peak alignment, peak correction, and normalization. A three-dimensional data matrix composed of sample names, peak information (including retention time and molecular weight), and peak areas was output. The structural identification of metabolites was conducted by using accurate mass matching (< 25 ppm) and MS/MS spectral matching, and searching through the self-built database in the laboratory, as well as other online databases such as Bio cyc, HMDB, Metlin, HFMDB, and Lipidmaps.

In the extracted ion features, only the variables having more than 50% of the nonzero measurement values in at least one group were kept. SIMCA-P 14.1 (Umetrics, Umea, Sweden) was used for Orthogonal partial least-squares-discriminant analysis (OPLS-DA). The differential metabolites (DMs) between groups were screened based on a threshold of variable importance on the projection (VIP) values obtained from the OPLS-DA model, where metabolites with VIP > 1.0 and P  < 0.05 were considered DMs.

Gene–metabolite network construction

The DGs and DMs were entered into the “Network Analysis” module of the MetaboAnalyst platform to explore the transcriptome–metabolome biological connections. The Cytoscape software was utilized to visualize the “gene–metabolite” network.

Statistical methods

Data management and statistical analyses were performed using GraphPad Prism software (San Diego, CA). The results are presented as Mean (M) ± Standard Deviation (SD). The independent sample t -test or one-way ANOVA was utilized for data analysis. Results with P  < 0.05 were considered statistically significant, with P  < 0.01 showing a highly significant difference.

Ethical statement

The study was approved by Experimental Ethics Committee at Xiyuan hospital, China Academy of Chinese Medical Sciences (No. 2022XLC045-2), all methods were carried out in accordance with relevant guidelines and regulations. This study was carried out in compliance with the ARRIVE guidelines.

General information and characteristic manifestations of the syndrome

Zero, one, and one deaths were reported in the control, disease, and DS groups, respectively. The NC group animals had a normal diet, free movement, good mental state, and slightly rough hair before sampling. Rats in the disease and DS groups exhibited a significant decrease in activity, reduced food intake, loose and matte hair, decreased body mass, and decreased energy levels. In TCM theory, it is believed that blood stasis and toxin often damage body functions, leading to symptoms such as mental depression and fatigue. The DS group rats showed more significant mental distress, preferring to curl up in a corner with their hair in a ‘burst’ state, and were also less resistant when touched.

Furthermore, after modelling, the DS group animals showed swollen and black purple claw nails, as well as noticeable purple and dark auricular veins and a “black tail” state at the tail. The other rat groups showed no significant changes in characterization (Fig.  2 a). According to the TCM basic theory, the accumulation of blood stasis and toxin in the body can cause poor blood circulation, or even damage the blood vessels, leading to ecchymosis on the surface of the body, local tissue swelling or necrosis. Therefore, based on these manifestations, the DS group exhibited more obvious syndrome characteristics.

( a ) Syndrome characteristics of rats in each group after modeling. ( b ) Neurological score was measured 24 h postoperatively. ** p  < 0.01 against the NC group. ( c ) Measurement of the cerebral infarction area (n = 6/group). ** p  < 0.01 against the NC group. ( d ) Cerebral infarction area was assessed through TTC staining 24 h post-surgery.

Comparison of neurological deficits and the cerebral infarction areas

We evaluated the degree of neurological deficits in each group of rats 24 h post-surgery. The neurological function scores of the disease model and the DS model groups were significantly higher than those of the NC group ( P  < 0.01) (Fig.  2 b). On the other hand, the cerebral infarction area was assessed using TTC staining at 24 h postoperatively. The disease model and DS groups had a significantly greater infarction size than the NC group ( P  < 0.01) (Fig.  2 c,d). Furthermore, there was no significant difference between the disease and DS groups (Supplementary Information 1 ).

Comparison of tail blood flow perfusion

The blood perfusion at the tail end of rats usually refers to the blood flow in a specific area of the tail. A state of blood stasis may affect the blood perfusion at the tail of rats, causing it to decrease or be blocked. The number of warm tone pixels was positively correlated with the richness of blood flow per unit area in laser speckle imaging. The tail-end blood flow perfusion of the NC group was abundant compared to that of the DS group, which was significantly lower ( P  < 0.01). On the other hand, although the tail-end blood flow perfusion in the disease group exhibited a decreasing trend compared to the control group, there was no statistical significance (Fig.  3 a,b).

( a ) Representative images of tail blood flow perfusion in each rat group. ( b ) Comparison of tail blood flow perfusion in each rat group (n = 7). ** p  < 0.01 against the NC group. ## p  < 0.01 against the disease group.

Comparison of WBV, PV, and platelet AR

Abnormal changes in blood rheology such as fluidity and viscosity are important pathological mechanisms that progress from blood stasis to the coexistence of blood stasis and toxin. Blood rheology reflects the flow and viscosity of blood, serving as a crucial indicator of the body's blood stasis condition 24 . Compared to the NC group, the WBV at the median shear rate was significantly higher in the disease and DS groups ( P  < 0.05, P  < 0.01). Notably, the DS group had a significantly higher WBV at the low/median/high shear rate ( P  < 0.05, P  < 0.01). Consistent with the WBV results, the PV was markedly higher in the disease and DS groups than the NC group ( P  < 0.01). Furthermore, the DS group had a significantly higher PV than the disease group ( P  < 0.01). Additionally, the maximum and average platelet ARs were significantly higher in the disease and DS model groups than the control group ( P  < 0.01). However, there were no significant statistical differences between the disease and DS groups in platelet ARs. These findings show that the DS model rats exhibited more severe blood stasis state. These results are summarized in Tables 1 and 2 .

Comparison of IL-6 expression levels in brain tissue

Whether in the pathogenesis of cerebral infarction or in the formation process of BST syndrome, there will be an increase in inflammatory cytokines. The expression level of IL-6 was significantly higher in the brain tissue of rats in the disease and DS groups compared with the levels in the control group rats ( P  < 0.05, P  < 0.01). There was no significant differences between the disease and DS groups (Fig.  4 ).

ELISA was used to determine IL-6 expression in ischemic cortical tissue. * p  < 0.05, ** p  < 0.01 vs . the NC group.

Comparison of HE staining examination

Pathological and morphological changes in brain tissue were observed through HE staining. Neuronal cells in the cortex of the NC group rats were arranged neatly, with normal neuronal morphology (Fig.  5 ). There were no pathological changes such as degeneration or necrosis in the NC group. On the other hand, the disease and DS groups showed noticeable pathological alterations, including disordered cell arrangement, loose structure, common neuronal degeneration and necrosis, nuclear pyknosis, and glial cell proliferation.

Representative images of histopathological changes in the brain tissues in three rat groups captured under a 200× and 400× light microscope.

Transcriptomic characteristics of the IS-BST syndrome

PCA analysis revealed a clear distinction between the three groups along the first principal component with a 59% explained variance (Fig.  6 a). The FPKM density distribution can intuitively reflect the general patterns and characteristics of RNA seq data at the quantitative level. As shown in Fig.  6 b, the FPKM homogeneity was good across individual samples, suggesting that the quality of each sample was good and reliable.

( a ) Principal component analysis: The horizontal axis represents the first principal component, and the vertical axis represents the second principal component; Different colors represent different groups, and different shapes represent different samples. ( b ) FPKM density distribution. N the NC group, M the disease group, C the DS group.

In total, 782 DGs were identified between the disease group and NC groups, with 679 DGs upregulated and 103 DGs downregulated. The heat and volcano maps showed the expression of DGs between Disease group and NC group (Fig.  7 a,b). In addition, 2426 DGs were screened between the DS and NC groups, of which 1361 and 1065 DGs were upregulated and downregulated, respectively. Figure  7 c,d show the heatmap and volcano plot for all DGs, respectively (Supplementary Information 2 , 3 , 5 , 6 ).

( a ) Heat map of DGs between the NC and disease groups. ( b ) Volcano plot of DGs between the NC and disease groups. ( c ) Heat map of DGs between the NC and DS groups. ( d ) Volcano plot of DGs between the NC and DS groups. N the NC group, M the disease group, C the DS group.

Subsequently, the Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the DGs. The GO analysis comprises Biological Processes (BP), Cellular Components (CC), and Molecular Functions (MF). The top ten significant enrichment terms of BP, CC, and MF with the highest gene counts were visualized in a bar chart. Most of the enriched BP terms of the DGs in the disease model were mainly associated with response to stress, defense response, and inflammatory response. In the CC domain, the DGs of the disease model were mainly involved in the extracellular region, cell periphery, and extracellular space; further, a strong increase in the genes was mainly involved in protein binding, binding, and receptor binding (Fig.  8 a). The DGs of DS model were primarily enriched in regulation of multicellular organismal process, system development, multicellular organism development, and other biological processes; cell periphery, plasma membrane, intrinsic component of plasma membrane, and other cellular components; protein binding, receptor binding, binding, and other molecular functions (Fig.  8 b).

( a ) GO enrichment analysis of the DGs in disease group (red, green, and blue represent the CC, MF, and BP terms, respectively). ( b ) GO enrichment analysis of the DGs in DS group. ( c ) Bubble chart showing the top 20 pathways of DGs between the NC and disease groups. ( d ) Bubble chart showing the top 20 pathways of DGs between the NC and DS groups.

The bubble diagram showed the top 20 significant enrichment potential pathways with the highest gene counts. The results revealed that the DGs of disease group were mainly enriched in complement and coagulation cascades, TNF signaling pathway, NF-kappa B signaling pathway, cytokine-cytokine receptor interaction, etc. (Fig.  8 c). The DGs of DS group were mainly enriched in the TNF signaling pathway, the ECM-receptor interaction pathway, cancer pathways, the lipid and atherosclerosis pathway, and complement and coagulation cascades, among other pathways (Fig.  8 d).

Metabolomic characteristics of the IS-BST syndrome

Herein, 14,623 metabolites were discovered, of which 473 were annotated in the online databases and self-built database in the laboratory. The DMs were generated through OPLS-DA analysis using the SIMCA software, with VIP > 1 and P  < 0.05 as the screening conditions. The OPLS-DA score revealed that the NC, disease, and DS groups exhibited a clear trend of separation (Fig. 9 a,b). A total of 102 metabolites were identified between the disease group and NC groups, with 34 DMs upregulated and 68 DMs downregulated. These 102 metabolites are visualized by heat maps and volcano maps (Fig. 9 c,d). Compared with the NC group, 151 metabolites were altered in the DS group, of which 60 and 91 DMs were screened between the two groups and established to be upregulated and downregulated, respectively. Figure  9 e,f show the heatmap and volcano plot for all DGs, respectively (Supplementary Information 4 & 7 ).

( a ) OPLS-DA analysis of three groups: Positive ion mode. ( b ) OPLS-DA analysis of three groups: Negative ion mode. ( c ) Heat map of DGs between the NC and disease groups. ( d ) Volcano plot of DGs between the NC and disease groups. ( e ) Heat map of DGs between the NC and DS groups. ( f ) Volcano plot of DGs between the NC and DS groups. N the NC group, M the disease group, C the DS group.

Key pathways implicated in the disease model and the DS model were identified by metabolic pathway analysis. Several metabolic pathways related to disease group were identified, including central carbon metabolism in cancer, taste transduction, ABC transporters, GABA ergic synapse, and purine metabolism (Fig.  10 a). In addition, several metabolic pathways such as the taste transduction, purine metabolism pathway, central carbon metabolism in cancer, alanine, aspartate, and glutamate matabolism, valine, leucine and isoleucine biosynthesis, and so on were significantly associated with the DS group (Fig.  10 b).

( a ) Bubble chart showing the top 20 pathways of DMs between the NC and disease groups. ( b ) Bubble chart showing the top 20 pathways of DMs between the NC and DS groups.

DGs–DMs interaction analysis

By integrating transcriptomics and metabolomic data, we established a “gene–metabolite” network for the disease model and DS model. As shown in Fig.  11 a and Table 3 , the “gene–metabolite” network of the disease model comprised three mRNAs (C3, F2, and F7) and five metabolites (serotonin, gamma-aminobutyric acid, genistein, estradiol and l-proline). C3 was the most relevant gene with a degree and betweenness of 3 and 12.5, respectively. Estradiol was the metabolite most related to genes, with a degree and betweenness of 2 and 10, respectively.

( a ) The “gene–metabolite” network of the disease model. ( b ) The “gene–metabolite” network of the DS model.

Five mRNAs (F2, C3, F7, C5, and F3) and eight metabolites (serotonin, gamma-aminobutyric acid (GABA), estradiol, l-glutamic acid, l-lysine, genistein, uric acid (UA), and 4-guanidinobutanoic acid) made up the “gene–metabolite” network of the DS model. The most significant metabolite was serotonin, which had degrees and betweennesses of 4 and 25.5, respectively. F2 was the gene most closely associated with metabolites, with betweenness and degree of 6 and 38.67, respectively. Furthermore, F2 was linked to serotonin, l-glutamic acid, 4-guanidinobutanoic acid, l-lysine, GABA, and UA (Fig.  11 b and Table 4 ).

Ischemic Stroke (IS) is a common illness with profound health implications. In recent years, TCM, which has special benefits regarding IS treatment, has received substantial attention. Syndrome differentiation-based treatment is the fundamental principle of TCM in understanding and treating diseases 25 . Currently, the ‘disease-syndrome combination’ is not only a clinical stroke diagnosis and treatment approach, but also a highly consensus research model. The “disease-syndrome combination” animal model is a disease model-based animal model with good reliability and stability. At the same time, the introduction of the ‘syndrome’ concept in TCM has proven to be valuable in reflecting the phased and dynamic changes in disease characterizations in TCM. Specifically, it serves as a platform and conduit for researching clinical diseases in the field of TCM.

Herein, on the basis of our preliminary work, we used a multi-factor combination to construct an animal IS model with blood stasis and toxin syndrome, and explored the biological mechanisms underlying the model through transcriptomic and metabolomic analyses. Our findings hold academic significance as they contribute to the exploration of therapeutic principles underlying TCM formulae and the development of precision medicine for IS treatment.

Multiple evaluation indicators show that the combination of carrageenan and active dry yeast along with MCAO, can be used to successfully establish an IS-BST animal model

Motor dysfunction is one of the main IS manifestations. Herein, rats in both the disease and DS groups showed left limb hemiplegia, with decreased neurological function scores. The cerebral ischemic injury in rats was further confirmed by TTC staining. Compared to the disease model, the DS model included an additional TCM-BST syndrome based on motor dysfunction. The TCM basic theory posits that blood stasis and toxin damage the veins and collaterals, which in turn causes blood to overflow outside the veins and accumulate under the skin, resulting in bruises and ecchymosis on the skin. Therefore, apart from symptoms such as mental distress, decreased activity, reduced food intake, and rough hair, the characteristics of the DS group also included ecchymosis on rats’ ears and claws and thrombi in their tails. Additionally, rats in the DS group also showed a significant decrease in tail blood flow perfusion.

The BST syndrome consists of two syndrome elements: blood stasis and toxin. Pertinent modern studies often interpret blood stasis as abnormal hemorheology, aberrant platelet aggregation function, microcirculation disorders, and so on 26 . Inflammatory responses are often used as a common indicator for evaluating toxins and pathogens 11 . At the same time, thrombosis and inflammatory responses are highly connected mechanisms that promote neuronal damage after ischemia in the complex IS pathological process 27 . Our findings revealed that WBV (low, medium, and high shear), PV, and platelet AR were significantly higher in the DS group than the NC group. It is well-documented that IL-6 is an important inflammatory response marker post-IS 28 . In this study, the IL-6 expression levels in brain tissue were significantly increased in both the disease and DS model groups.

Histopathology can objectively reflect model establishment success and disease severity. Herein, the disease and DS groups showed severe pathological damage, but with no histopathological differences.

Based on the above-mentioned findings, we inferred that the DS group had more stable IS characteristics and the blood stasis and toxin syndrome, implying that it is a preferable standard for constructing an IS-related blood stasis and toxin accumulation animal model (Fig.  12 ).

+ denotes P  < 0.05 vs. NC group, ++ denotes P  < 0.01 vs. NC group. The DS group presents more severe disease and syndrome characteristics, making it the preferred standard for constructing the IS-BST syndrome model.

Transcriptomic and metabolomic strategies could reveal the biological basis of the IS-BST syndrome

Transcriptomics analysis and metabolomics analysis.

In the transcriptomics study, 782 mRNAs were identified as DGs for the disease. They were mainly enriched in complement and coagulation cascades, TNF signaling pathway, NF-kappa B signaling pathway, cytokine–cytokine receptor interaction, etc. A total of 2426 mRNAs were screened as DGs for the DS model. They were enriched in the TNF signaling pathway, the ECM-receptor interaction pathway, cancer pathways, the lipid and atherosclerosis pathway, and complement and coagulation cascades, etc.

In the enrichment analysis of differential genes between the disease and DS models, the top 20 enriched pathways indicate that atherosclerosis, thrombosis, and inflammatory response are the main relevant pathways. Lipid and atherosclerosis as well as fluid shear stress and atherosclerosis are two of the signal pathways linked to atherosclerosis. Thrombosis-related signaling mechanisms include coagulation cascades and complement. The TNF signaling pathway, NF-kappa B signaling pathway, MAPK signaling pathway, IL-17 signaling pathway, etc. are among the signal pathways linked to the inflammatory response.

In the metabonomics study, 102 metabolites were identified as DMs for the disease. They were enriched in the GABAergic synapse, purine metabolism, protein digestion and absorption, cAMP signaling pathway, etc. A total of 151 metabolites were identified as DMs for the DS model. They were enriched in the alanine, aspartate and glutamate metabolism, valine, leucine and isoleucine biosynthesis, sphingolipid signaling pathway, cAMP signaling pathway, etc. The DS model is established on the basis of the disease model, so there are also some common metabolic pathways between the DS model and the disease model, such as purine metabolism, sphingolipid metabolism, cAMP signaling pathway, and so on.

Gene–metabolite network analysis

Coagulation and complement cascade reaction and the is-bst syndrome.

However, single omics studies are difficult to comprehensively and systematically decipher the regulatory mechanisms of complex pathological processes. Herein, we integrated and analyzed the transcriptomic and metabolomic research findings to construct a “gene–metabolite” network. There are common signatures in the “gene–metabolite” network of the disease and DS models.

Prothrombin (F2), tissue factor (F3), and coagulation factor VII (F7) are the key coagulation elements in the coagulation system. Prothrombin (F2) is a thrombin precursor that exists in an inactive form in the bloodstream. A series of enzyme cascade reactions are triggered when blood vessels are injured, leading to the conversion of F2 into active thrombin. Active thrombin, as a strong activator, then converts fibrinogen into fibrin, promoting blood clot formation 29 . On the other hand, F3 mainly exists on the damaged vascular intima and tissue cells. It binds to F7 in the plasma when tissue damage occurs, triggering a coagulation cascade reaction 30 . Under the synergistic effect of F2, F3, and F7, blood stasis can cause endothelial damage and promote intravascular thrombosis. In this study, the levels of F2 and F7 were significantly elevated in the brain tissues of the disease model and DS model rats, and the levels of F3 were also significantly increased in the brain tissues of the DS model rats. This indicates that the IS-BST rats exhibit stronger coagulation features.

Various components of the complement system and coagulation system interact, activate, and regulate each to synergistically respond to host defense and damage repair. Complement component C3 (C3) is one of the most abundant components in the complement system, which can directly bind to platelets, fibrin, and molecules on the cell surface, thereby promote the coagulation process and thrombosis 31 , 32 . In addition, C3 is also a major participant in the initiation of inflammatory response in the central nervous system diseases 33 , 34 . Inhibiting C3 activity can alleviate the inflammatory response and decrease the volume of cerebral infarction in MCAO mice 35 . A significant increase in serum C3 levels in patients with ischemic stroke has been linked to poor clinical outcomes 36 . C5 is another key component of the complement system, which promotes the migration of neutrophils and monocytes to the injured site and enhances the release of inflammatory factors 37 , 38 . The expression of C5 was also upregulated in the brain after ischemic stroke, and the inhibition of C5 was found to significantly reduce infarct volumes and improve neurological scores 39 . In this study, C3 was significantly upregulated in the brain tissues of the disease model rats, while in the DS model, apart from upregulation of C3, C5 was also significantly upregulated, indicating a more pronounced inflammatory response in the IS-BST.

Although the complement and coagulation system are independent of each other, they closely function together, synergistically participating in key pathways such as thromboinflammatory response 40 , 41 . The “gene–metabolite” regulatory network diagram presented in this study indicates high correlation of these genes, especially in the DS model, suggesting that the biological basis for the interaction between blood stasis and toxin involves the complement and coagulation cascade reactions.

AA metabolism and IS-BST syndrome

In the “gene–metabolite” networks of the two models, there are some common metabolites, including serotonin, estradiol, gamma-aminobutyric acid (GABA), and genistein. Serotonin, also known as 5-hydroxytryptamine, is an indolamine with vasoconstrictive and aggregating properties. Researchers have demonstrated that serotonin can promote the development of platelets and increase procoagulant activity 42 . Researches indicate that acute ischemic stroke patients taking selective serotonin reuptake inhibitors can improve clinical recovery, with mechanisms including stimulating neurogenesis, anti-inflammation, and improving cerebral blood flow 43 , 44 . Estrogen is a lipophilic steroid hormone that exerts its functions by binding to estrogen receptors (ER). Estrogen receptors are present in various tissues, including brain parenchyma 45 . Research indicates that estrogen, especially estradiol, can mitigate brain damage caused by ischemic stroke by regulating immune cell responses 46 . GABA is considered as an inhibitory transmitter that can inhibit neuronal excitation and reduce neuronal damage caused by excitatory glutamate following cerebral ischemia 47 . In this study, serotonin was upregulated in the brain tissues of the disease model rats, while the levels of estradiol and GABA were downregulated.

In this study, l -proline is an unique metabolite in the disease model. A study has shown that five metabolites, including proline, are common in both animal models of ischemic stroke and clinical patients 48 . There may be a certain link between l -proline and ischemic stroke, but the specific mechanism of action still needs further research and exploration.

Studies have indicated that impaired amino acid metabolism is associated with the development of ischemic stroke and BST syndrome 13 , 49 . In the “gene–metabolite” regulatory network of DS model, the differential metabolites are mainly related to amino acid-related metabolism. In addition to serotonin and GABA, l-glutamic acid (Glu), l-lysine, and 4-guanidinobutyric acid also participate in amino acid metabolic pathways. Glu is the most abundant free amino acid in the brain and the main excitatory neurotransmitter in the brain. In cerebral ischemia, glu-mediated excitatory toxicity is an important mechanism leading to the occurrence of neuronal death and brain injury 50 . Lysine is an essential alkaline amino acid that can pass through the blood–brain barrier and provide the necessary energy for the repair and normal functioning of physiological activities of nerve cells. Oral administration of lysine was found to reduce the area of cerebral infarction in rats and alleviate brain edema 51 . 4-Guanidinobutyric acid is a metabolite in the process of converting arginine to GABA, and its reduced content may lead to a decrease in GABA 52 .

In brain tissue samples from the BST group, serotonin and l-glutamic acid were increased, while GABA and l-lysine were decreased. Moreover, the content of 4-Guanidinobutyric acid was observed to increase significantly. Regarding the inconsistent expression trends between 4-Guanidinobutyric acid and GABA, we hypothesized that the conversion of arginine to GABA involves multiple enzymatic reactions and intermediate products, with 4-guanidinobutyric acid being just one of them. Although changes in the content of 4-guanidinobutyric acid may affect the levels of its subsequent metabolites, it is not the sole factor determining the concentration of GABA. Furthermore, more replicated experiments are needed to verify the expression level of 4-guanidinobutyric acid in the brain tissue of DS model rats.

F2 (thrombin)-glutamate and blood stasis—toxin

From the DS model “gene–metabolite” regulatory network, we found that F2 is the core gene with the highest degree of correlation. Thrombin, a serine protease, is encoded by the F2 gene. During cerebral ischemia, thrombin levels are elevated, which positively correlate with the infarct size 53 , 54 . High levels of thrombin has been linked to the occurrence of neurotoxicity 55 . Thrombin can cause blood–brain barrier disruption, increase endothelial permeability and damage to the brain tissue 56 . It has been demonstrated that thrombin stimulates NMDAR potentiation by activating its receptor PAR-1 (protease activator receptor-1), inducing a glutamate-mediated excitotoxicity 57 , 58 . As shown in the “gene–metabolite” network, l-glutamic acid is one of the downstream metabolites of F2. As we mentioned earlier, prolonged blood stasis leads to the production of toxins. To some extent, there is a strong similarity between “F2 (thrombin)–NMDAR/glutamate” pathway and the process of blood stasis brewing poison (Fig.  13 ). Therefore, we we have reasons to believe that the DS model “gene–metabolite” network can not only explain the pathogenesis of the disease, but also elucidate the biological significance of BST syndrome to a certain extent. However, our findings are based on animal research, and hence they may be somewhat different from actual clinical observations. Future research is necessary to validate these findings on IS-BST syndrome clinical patients.

F2 (thrombin)-glutamate and blood stasis—toxin.

Conclusions

In this study, we constructed an animal model of IS-BST syndrome and established a model evaluation system that includes macroscopic characterization, microscopic indicators, and pathological morphology. It can be used to study conditions combining a disease and syndrome. By integrating transcriptomics and metabolomics research results, we found that IS-BST exhibits more prominent characteristics of coagulation and complement cascade reactions, as well as amino acid metabolism disorders. The “F2 (thrombin)-NMDAR/glutamate” pathway we inferred from the “gene–metabolite” regulatory network provides a clear direction for our subsequent pharmacological research. In conclusion, the IS-BST model aligns with TCM theories in understanding diseases and syndromes. It will help promote innovative research on “disease–syndrome therapy formula” and it is expected to provide an effective solution to address the limitations of ischemic stroke treatment.

Data availability

The data in this study are available from the corresponding author upon reasonable request.

Ajoolabady, A. et al. Targeting autophagy in ischemic stroke: From molecular mechanisms to clinical therapeutics. Pharmacol. Ther. 225 , 107848 (2021).

Article   CAS   PubMed   PubMed Central   Google Scholar  

Mozaffarian, D. et al. Heart disease and stroke statistics-2016 update: A Report From the American Heart Association. Circulation 133 (4), e38-360 (2016).

PubMed   Google Scholar  

Parvez, S. et al. Dodging blood brain barrier with “nano” warriors: Novel strategy against ischemic stroke. Theranostics 12 (2), 689–719 (2022).

Zhang, S. R., Phan, T. G. & Sobey, C. G. Targeting the immune system for ischemic stroke. Trends Pharmacol. Sci. 42 (2), 96–105 (2021).

Article   CAS   PubMed   Google Scholar  

Zhang, L., Zhang, Z. G. & Chopp, M. The neurovascular unit and combination treatment strategies for stroke. Trends Pharmacol. Sci. 33 (8), 415–422 (2012).

Yuan, H. et al. The traditional medicine and modern medicine from natural products. Molecules 21 (5), 559 (2016).

Article   PubMed   PubMed Central   Google Scholar  

Wu, B. et al. Meta-analysis of traditional Chinese patent medicine for ischemic stroke. Stroke 38 (6), 1973–1979 (2007).

Article   PubMed   Google Scholar  

Zhang, Y. et al. Efficacy of integrated rehabilitation techniques of traditional Chinese medicine for ischemic stroke: A randomized controlled trial. Am. J. Chin. Med. 41 (5), 971–981 (2013).

Article   ADS   PubMed   Google Scholar  

Chen, K. J. The treatment viewpoints and clinical practice of disease identification and syndrome typing. Zhongguo Zhong Xi Yi Jie He Za Zhi 31 (8), 1016–1017 (2011).

Wang, Y. et al. Investigation of invigorating qi and activating blood circulation prescriptions in treating qi deficiency and blood stasis syndrome of ischemic stroke patients: Study protocol for a randomized controlled trial. Front. Pharmacol. 11 , 892 (2020).

Xue, M. et al. Effect of Chinese drugs for activating blood circulation and detoxifying on indices of thrombosis, inflammatory reaction, and tissue damage in a rabbit model of toxin-heat and blood stasis syndrome. Chin. J. Integr. Med. 19 (1), 42–47 (2013).

Wang, J. & Zhang, J. P. A preliminary study of TCM stage-oriented treatment of atherosclerosis. J. Tradit. Chin. Med. 29 (3), 201–204 (2009).

Xu, J. J. et al. Elucidation of the mechanisms and effective substances of paeoniae radix rubra against toxic heat and blood stasis syndrome with a stage-oriented strategy. Front. Pharmacol. 13 , 842839 (2022).

Li, S. et al. Disease-syndrome combination modeling: Metabolomic strategy for the pathogenesis of chronic kidney disease. Sci. Rep. 7 (1), 8830 (2017).

Article   ADS   PubMed   PubMed Central   Google Scholar  

Yang, H. R. et al. Exploring the fibrin(ogen)olytic, anticoagulant, and antithrombotic activities of natural cysteine protease (ficin) with the κ-carrageenan-induced rat tail thrombosis model. Nutrients 14 (17), 3552 (2022).

Li, Q. et al. NaoXinTong capsule inhibits carrageenan-induced thrombosis in mice. J. Cardiovasc. Pharmacol. 72 (1), 49–59 (2018).

Article   MathSciNet   CAS   PubMed   Google Scholar  

Liu, Y. et al. Establishment and evaluation of animal models of combined blood stasis and toxin syndrome. Chin. J. Exp. Tradit. Med. Formulae 29 (13), 72–78 (2023).

Google Scholar  

Li, W. et al. Multi-omics research strategies in ischemic stroke: A multidimensional perspective. Ageing Res. Rev. 81 , 101730 (2022).

Guo, R. et al. Omics strategies decipher therapeutic discoveries of traditional Chinese medicine against different diseases at multiple layers molecular-level. Pharmacol. Res. 152 , 104627 (2020).

Zhu, X. et al. Multi-omics approaches for in-depth understanding of therapeutic mechanism for Traditional Chinese Medicine. Front. Pharmacol. 13 , 1031051 (2022).

Liu, T. et al. Multi-omics approaches for deciphering the complexity of traditional Chinese medicine syndromes in stroke: A systematic review. Front. Pharmacol. 13 , 980650 (2022).

Longa, E. Z. et al. Reversible middle cerebral artery occlusion without craniectomy in rats. Stroke 20 (1), 84–91 (1989).

Bederson, J. B. et al. Rat middle cerebral artery occlusion: Evaluation of the model and development of a neurologic examination. Stroke 17 (3), 472–476 (1986).

Zhang, Q. et al. UPLC-G2Si-HDMS untargeted metabolomics for identification of Yunnan Baiyao’s metabolic target in promoting blood circulation and removing blood Stasis. Molecules 27 (10), 3208 (2022).

Xu, H. et al. A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine. Acta Pharm. Sin. B 11 (6), 1379–1399 (2021).

Ma, X. J., Yin, H. J. & Chen, K. J. Research progress of correlation between blood-stasis syndrome and inflammation. Zhongguo Zhong Xi Yi Jie He Za Zhi 27 (7), 669–672 (2007).

De Meyer, S. F. et al. Thromboinflammation in brain ischemia: Recent updates and future perspectives. Stroke 53 (5), 1487–1499 (2022).

Su, J. H. et al. Interleukin-6: A novel target for cardio-cerebrovascular diseases. Front. Pharmacol. 12 , 745061 (2021).

Colucci, G. et al. Venous stasis and thrombin generation. J. Thromb. Haemost. 2 (6), 1008–1009 (2004).

Chi, L. et al. Characterization of a tissue factor/factor VIIa-dependent model of thrombosis in hypercholesterolemic rabbits. J. Thromb. Haemost. 2 (1), 85–92 (2004).

Manderson, A. P. et al. Continual low-level activation of the classical complement pathway. J. Exp. Med. 194 (6), 747–756 (2001).

King, R. J. et al. Fibrinogen interaction with complement C3: A potential therapeutic target to reduce thrombosis risk. Haematologica 106 (6), 1616–1623 (2021).

Zhang, L. Y. et al. Microglia exacerbate white matter injury via complement C3/C3aR pathway after hypoperfusion. Theranostics 10 (1), 74–90 (2020).

Guttikonda, S. R. et al. Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease. Nat. Neurosci. 24 (3), 343–354 (2021).

Ma, Y. et al. Significance of complement system in ischemic stroke: A comprehensive review. Aging Dis. 10 (2), 429–462 (2019).

Yang, P. et al. Increased serum complement C3 levels are associated with adverse clinical outcomes after ischemic stroke. Stroke 52 (3), 868–877 (2021).

Escamilla-Rivera, V. et al. Plasma protein adsorption on Fe(3)O(4)-PEG nanoparticles activates the complement system and induces an inflammatory response. Int. J. Nanomedicine 14 , 2055–2067 (2019).

Lu, W. et al. C5a aggravates dysfunction of the articular cartilage and synovial fluid in rats with knee joint immobilization. Mol. Med. Rep. 18 (2), 2110–2116 (2018).

CAS   PubMed   PubMed Central   Google Scholar  

Pavlovski, D. et al. Generation of complement component C5a by ischemic neurons promotes neuronal apoptosis. FASEB J. 26 (9), 3680–3690 (2012).

Pryzdial, E. L. G., Leatherdale, A. & Conway, E. M. Coagulation and complement: Key innate defense participants in a seamless web. Front. Immunol. 13 , 918775 (2022).

Pfeiler, S. et al. Propagation of thrombosis by neutrophils and extracellular nucleosome networks. Haematologica 102 (2), 206–213 (2017).

Lopez-Vilchez, I. et al. Serotonin enhances platelet procoagulant properties and their activation induced during platelet tissue factor uptake. Cardiovasc. Res. 84 (2), 309–316 (2009).

Siepmann, T. et al. Selective serotonin reuptake inhibitors to improve outcome in acute ischemic stroke: Possible mechanisms and clinical evidence. Brain Behav. 5 (10), e00373 (2015).

Espinera, A. R. et al. Citalopram enhances neurovascular regeneration and sensorimotor functional recovery after ischemic stroke in mice. Neuroscience 247 , 1–11 (2013).

Yang, M. et al. Dysfunction of estrogen-related receptor alpha-dependent hepatic vldl secretion contributes to sex disparity in Nafld/Nash development. Theranostics 10 (24), 10874–10891 (2020).

Zhong, X. et al. Immunomodulatory role of estrogen in ischemic stroke: Neuroinflammation and effect of sex. Front. Immunol. 14 , 1164258 (2023).

Michalettos, G. & Ruscher, K. Crosstalk between GABAergic neurotransmission and inflammatory cascades in the post-ischemic brain: Relevance for stroke recovery. Front. Cell. Neurosci. 16 , 807911 (2022).

Jia, J. et al. Application of metabolomics to the discovery of biomarkers for ischemic stroke in the murine model: A comparison with the clinical results. Mol. Neurobiol. 58 (12), 6415–6426 (2021).

Chen, X. et al. Effect of Gua Lou Gui Zhi decoction on focal cerebral ischemia-reperfusion injury through regulating the expression of excitatory amino acids and their receptors. Mol. Med. Rep. 10 (1), 248–254 (2014).

Shen, Z. et al. Glutamate excitotoxicity: Potential therapeutic target for ischemic stroke. Biomed. Pharmacother. 151 , 113125 (2022).

Kondoh, T. et al. Lysine and arginine reduce the effects of cerebral ischemic insults and inhibit glutamate-induced neuronal activity in rats. Front. Integr. Neurosci. 4 , 18 (2010).

PubMed   PubMed Central   Google Scholar  

Adkins, D. E. et al. Behavioral metabolomics analysis identifies novel neurochemical signatures in methamphetamine sensitization. Genes Brain Behav. 12 (8), 780–791 (2013).

Chen, B. et al. Thrombin activity associated with neuronal damage during acute focal ischemia. J. Neurosci. 32 (22), 7622–7631 (2012).

Bushi, D. et al. Quantitative detection of thrombin activity in an ischemic stroke model. J. Mol. Neurosci. 51 (3), 844–850 (2013).

Striggow, F. et al. The protease thrombin is an endogenous mediator of hippocampal neuroprotection against ischemia at low concentrations but causes degeneration at high concentrations. Proc. Natl. Acad. Sci. USA 97 (5), 2264–2269 (2000).

Article   ADS   CAS   PubMed   PubMed Central   Google Scholar  

Shavit-Stein, E. et al. Neurocoagulation from a mechanistic point of view in the central nervous system. Semin. Thromb. Hemost. 48 (3), 277–287 (2022).

Becker, D. et al. NMDA-receptor inhibition restores Protease-Activated Receptor 1 (PAR1) mediated alterations in homeostatic synaptic plasticity of denervated mouse dentate granule cells. Neuropharmacology 86 , 212–218 (2014).

Gingrich, M. B. et al. Potentiation of NMDA receptor function by the serine protease thrombin. J. Neurosci. 20 (12), 4582–4595 (2000).

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Acknowledgements

We thank the Shanghai Personal Biotechnology Cp. Ltd (Shanghai, China) for providing omics services. The authors would like to thank all the reviewers who participated in the review, as well as MJEditor ( https://www.mjeditor.com ) for providing English editing services during the preparation of this manuscript.

This research was funded by the Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine, grant number ZYYCXTD-C-202007, the China Academy of Chinese Medical Sciences Innovation Fund, grant numbers CI2021A01301 and CI2021A00911, the Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences, grant number CI2021B006, and the Fundamental Research Funds for the Central public welfare research institutes, grant number 2020YJSZX-3.

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These authors contributed equally: Yue Liu, Wenqiang Cui and Hongxi Liu.

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Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, China

Yue Liu, Wenqiang Cui, Hongxi Liu, Mingjiang Yao, Wei Shen, Lina Miao, Jingjing Wei, Xiao Liang & Yunling Zhang

Beijing Key Laboratory of Pharmacology of Chinese Materia Region, Institute of Basic Medical Sciences, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China

Mingjiang Yao

Department of Neurology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China

Wenqiang Cui

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Study concepts and design: Yunling Zhang, Yue Liu, Mingjiang Yao and Xiao Liang; Investigation, data curation, visualization, writing original draft: Yue Liu; Experimental operations: Yue Liu, Mingjiang Yao, Wenqiang Cui, and Hongxi Liu; Reagents, materials, and analysis tools: Yue Liu and Mingjiang Yao; Review and editing manuscript: Jingjing Wei, Wei Shen, and Lina Miao; Funding acquisition: Xiao Liang and Yunling Zhang. All authors approved the final manuscript after reading.

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Liu, Y., Cui, W., Liu, H. et al. Exploring the “gene–metabolite” network of ischemic stroke with blood stasis and toxin syndrome by integrated transcriptomics and metabolomics strategy. Sci Rep 14 , 11947 (2024). https://doi.org/10.1038/s41598-024-61633-y

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Improving models to study the human heart

by Olivia Dimmer, Northwestern University

Northwestern Medicine scientists have developed a new method to measure and optimize the maturation process of cultured heart muscle cells, an approach that has the potential to set the future standard for a common cell model in scientific research, according to details published in Cell Reports .

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are cultured heart muscle cell models widely used to study a variety of human heart disease and responses to experimental drugs. However, newly cultured cardiomyocytes don't accurately reflect mature heart muscle cells in adult humans, and previous methods of measuring maturation were not high throughput.

Differences in cellular maturity may affect the results of various experiments and studies done using the cells, so understanding when the cells are suitable is critical, said Paul Burridge, Ph.D., associate professor of Pharmacology and senior author of the study.

"The hiPSC-CM models don't perfectly match an adult cardiomyocyte," said Burridge, who is also a member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University.

"There are a number of ways you can make these cardiomyocytes more mature, but all of those techniques are time-consuming and not always compatible with the assays we perform, so we were really interested in what we could do to make these cardiomyocytes match an adult cardiomyocyte as much as possible."

In the study, Burridge and his collaborators cultured hiPSC-CMs and performed high-throughput assays to measure maturation of the cells. They found several factors could indicate when the cells are mature, including gene expression , mitochondrial function and electrical activity .

Building off this discovery, the investigators then developed cellular media—combinations of compounds and nutrients designed to support cultured cellular growth—and optimized it for the rapid maturation of the heart muscle cells.

The new measurement method and optimized cellular media will make it easier for scientists to study human heart cells, Burridge said.

"IPS cell-derived cardiomyocytes appear to be one of the most powerful applications of the IPS cell technology in drug screening," Burridge said. "The cells basically represent the heart cells of a patient. Whether we're interested in the effects of drugs, arrhythmia, or heart failure , we want to have the best models possible. Here, we have improved the fidelity of that model without making it more complex."

Moving forward, Burridge and his collaborators will continue to optimize the model to match human heart muscle cells as closely as possible, he said, and potentially reduce the need for animal models in scientific research.

"The better we can make this, the more work can be done in this cell culture model rather than in animal models such as mice, as it was done in the past," Burridge said. "By improving the quality of this model, that's going to get us a little bit closer."

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Traditional desalination methods, such as reverse osmosis and thermal techniques, have been critical in turning the ocean's vast waters into a drinkable resource.

Yet, these systems come at a steep ecological and energetic cost, consuming approximately 3 kilowatt-hours per cubic meter (kWh/m^3), impacting marine ecosystems, and incurring significant maintenance challenges due to membrane fouling and corrosion.

Enter the revolutionary thermodiffusion-based desalination. This novel method takes advantage of the natural phenomenon where salt migrates to the colder side of a temperature gradient, leaving the rest of the water at a reduced salinity. Research, led by Ph.D. candidate Shuqi Xu and chief investigator Professor Juan Felipe Torres, describes a process devoid of electricity, bypassing the need for membranes or phase change and reducing energy requirements by a staggering 80%.

The technology operates by pushing seawater through a narrow channel between heated and cooled plates. The fresh output from this system sees seawater salinity plunging from 30,000 parts per million (ppm) to a mere 500 ppm, a feat achieved through repeated cycles.

"To the best of our knowledge, thermodiffusive desalination is the first thermal desalination method that does not require a phase change," noted Professor Torres. "It's operated entirely in the liquid phase, and what's more important is that it does not require membranes or other types of ion-adsorbing materials to purify water."

Further amplifying its potential, this desalination approach champions the cause for rural and remote communities. Notably, the research team is in the process of constructing a larger, multi-channel device powered by a solar panel in Tonga, an island facing a critical drought. The system's low-grade heat requirement opens the door to utilizing environmental heat sources like sunlight or industrial byproducts, rendering it a highly adaptable and eco-friendly alternative.

The implications for military tech and politics enthusiasts are immense. Water security is a critical component of geopolitical stability, and advanced desalination methods can play a pivotal role in maintaining it. The strategic distribution of such technology can aid in humanitarian efforts, minimize conflict over water resources, and enhance the resilience of communities in arid regions or those affected by climate-induced water scarcity.

This breakthrough, published in Nature Communications, positions thermodiffusive desalination as a game-changer that could reconfigure the global water supply landscape. While still in the developmental stage, the method's scalability and energy efficiency herald a new chapter in the quest for sustainable freshwater solutions—a chapter that resonates powerfully with a world on the lookout for cutting-edge scientific advancements and climate-smart innovations.

Relevant articles: - New Desalination Method Cuts Energy Use By 80% , Electronics For You - New, electricity-free desalination method shows promise , Tech Xplore - Thermodiffusive desalination , Nature - New desalination method offers low-energy alternative to purify salty water , Penn State

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