what is an alternative hypothesis biology

The mean number of cavities per person does not differ between the flossing group (µ ) and the non-flossing group (µ ) in the population; µ = µ .

There is no relationship between the amount of text highlighted and exam scores in the population; β = 0.

The proportion of people with depression in the daily-meditation group ( ) is greater than or equal to the no-meditation group ( ) in the population; ≥ .

The mean number of cavities per person differs between the flossing group (µ ) and the non-flossing group (µ ) in the population; µ ≠ µ .

There is a relationship between the amount of text highlighted and exam scores in the population; β ≠ 0.

The proportion of people with depression in the daily-meditation group ( ) is less than the no-meditation group ( ) in the population; < .

with two groups

9.1 Null and Alternative Hypotheses

The actual test begins by considering two hypotheses . They are called the null hypothesis and the alternative hypothesis . These hypotheses contain opposing viewpoints.

H 0 , the — null hypothesis: a statement of no difference between sample means or proportions or no difference between a sample mean or proportion and a population mean or proportion. In other words, the difference equals 0.

H a —, the alternative hypothesis: a claim about the population that is contradictory to H 0 and what we conclude when we reject H 0 .

Since the null and alternative hypotheses are contradictory, you must examine evidence to decide if you have enough evidence to reject the null hypothesis or not. The evidence is in the form of sample data.

After you have determined which hypothesis the sample supports, you make a decision. There are two options for a decision. They are reject H 0 if the sample information favors the alternative hypothesis or do not reject H 0 or decline to reject H 0 if the sample information is insufficient to reject the null hypothesis.

Mathematical Symbols Used in H 0 and H a :

H 0 always has a symbol with an equal in it. H a never has a symbol with an equal in it. The choice of symbol depends on the wording of the hypothesis test. However, be aware that many researchers use = in the null hypothesis, even with > or < as the symbol in the alternative hypothesis. This practice is acceptable because we only make the decision to reject or not reject the null hypothesis.

Example 9.1

H 0 : No more than 30 percent of the registered voters in Santa Clara County voted in the primary election. p ≤ 30 H a : More than 30 percent of the registered voters in Santa Clara County voted in the primary election. p > 30

A medical trial is conducted to test whether or not a new medicine reduces cholesterol by 25 percent. State the null and alternative hypotheses.

Example 9.2

We want to test whether the mean GPA of students in American colleges is different from 2.0 (out of 4.0). The null and alternative hypotheses are the following: H 0 : μ = 2.0 H a : μ ≠ 2.0

We want to test whether the mean height of eighth graders is 66 inches. State the null and alternative hypotheses. Fill in the correct symbol (=, ≠, ≥, <, ≤, >) for the null and alternative hypotheses.

• H 0 : μ __ 66
• H a : μ __ 66

Example 9.3

We want to test if college students take fewer than five years to graduate from college, on the average. The null and alternative hypotheses are the following: H 0 : μ ≥ 5 H a : μ < 5

We want to test if it takes fewer than 45 minutes to teach a lesson plan. State the null and alternative hypotheses. Fill in the correct symbol ( =, ≠, ≥, <, ≤, >) for the null and alternative hypotheses.

• H 0 : μ __ 45
• H a : μ __ 45

Example 9.4

An article on school standards stated that about half of all students in France, Germany, and Israel take advanced placement exams and a third of the students pass. The same article stated that 6.6 percent of U.S. students take advanced placement exams and 4.4 percent pass. Test if the percentage of U.S. students who take advanced placement exams is more than 6.6 percent. State the null and alternative hypotheses. H 0 : p ≤ 0.066 H a : p > 0.066

On a state driver’s test, about 40 percent pass the test on the first try. We want to test if more than 40 percent pass on the first try. Fill in the correct symbol (=, ≠, ≥, <, ≤, >) for the null and alternative hypotheses.

• H 0 : p __ 0.40
• H a : p __ 0.40

Collaborative Exercise

Bring to class a newspaper, some news magazines, and some internet articles. In groups, find articles from which your group can write null and alternative hypotheses. Discuss your hypotheses with the rest of the class.

This book may not be used in the training of large language models or otherwise be ingested into large language models or generative AI offerings without OpenStax's permission.

Want to cite, share, or modify this book? This book uses the Creative Commons Attribution License and you must attribute Texas Education Agency (TEA). The original material is available at: https://www.texasgateway.org/book/tea-statistics . Changes were made to the original material, including updates to art, structure, and other content updates.

Access for free at https://openstax.org/books/statistics/pages/1-introduction

• Authors: Barbara Illowsky, Susan Dean
• Publisher/website: OpenStax
• Book title: Statistics
• Publication date: Mar 27, 2020
• Location: Houston, Texas
• Book URL: https://openstax.org/books/statistics/pages/1-introduction
• Section URL: https://openstax.org/books/statistics/pages/9-1-null-and-alternative-hypotheses

© Apr 16, 2024 Texas Education Agency (TEA). The OpenStax name, OpenStax logo, OpenStax book covers, OpenStax CNX name, and OpenStax CNX logo are not subject to the Creative Commons license and may not be reproduced without the prior and express written consent of Rice University.

8.1 – The null and alternative hypotheses

• Introduction

Statistical Inference in the NHST Framework

Nhst workflow, null hypothesis, alternative hypothesis, alternative hypothesis often may be the research hypothesis, how to interpret the results of a statistical test, outcomes of an experiment, chapter 8 contents.

• a calculated test statistic
• degrees of freedom associated with the calculation of the test statistic
• Recall from our previous discussion (Chapter 8.2) that this is not strictly the interpretation of p-value, but a short-hand for how likely the data fit the null hypothesis. P-value alone can’t tell us about “truth.”
• in the event we reject the null hypothesis, we provisionally accept the alternative hypothesis .

By inference we mean to imply some formal process by which a conclusion is reached from data analysis of outcomes of an experiment. The process at its best leads to conclusions based on evidence. In statistics, evidence comes about from the careful and reasoned application of statistical procedures and the evaluation of probability (Abelson 1995).

Formally, statistics is rich in inference process. We begin by defining the  classical frequentist,  aka Neyman-Pearson approach, to inference, which involves the pairing of two kinds of statistical hypotheses: the null hypothesis (H O ) and the alternate hypothesis (H A ). Whether we accept the hull hypothesis or not is evaluated against a decision criterion, a fixed statistical significance level  (Lehmann 1992). Significance level refers to the setting of a  p-value threshold before testing is done. The threshold is often set to Type I error of 5% (Cowles & Davis 1982), but researchers should always consider whether this threshold is appropriate for their work (Benjamin et al 2017).

This inference process is referred to as Null Hypothesis Significance Testing, NHST. Additionally, a probability value will be obtained for the test outcome or test statistic value. In the Fisherian likelihood tradition, the magnitude of this statistic value can be associated with a probability value, the p-value, of how likely the result is given the null hypothesis is “true”. (Again, keep in mind that this is not strictly the interpretation of p-value, it’s a short-hand for how likely the data fit the null hypothesis. P-value alone can’t tell us about “truth”, per our  discussion, Chapter 8.2 .)

About -logP . P-values are traditionally reported as a decimal, like 0.000134, in the closed (set) interval (0,1) — p-values can never be exactly zero or one. The smaller the value, the less the chance our data agree with the null prediction. Small numbers like this can be confusing, particularly if many p-values are reported, like in many genomics works, e.g., GWAS studies. Instead of reporting vanishingly small p-values, studies may report the negative log 10 p-value , or -logP . Instead of small numbers, large numbers are reported, the larger, the more against the null hypothesis. Thus, our p-value becomes 3.87 -logP.

Why log 10 and not some other base transform? Just that log 10 is convenience — powers of 10.

The antilog of 3.87 returns our p-value

For convenience, a partial p-value -logP transform table

On your own, complete the table up to -logP 5 – 10. See Question 7 below .

We presented in the introduction to Chapter 8 without discussion a simple flow chart to illustrate the process of decision (Figure 1). Here, we repeat the flow chart diagram and follow with descriptions of the elements.

Figure 1. Flow chart of inductive statistical reasoning.

What’s missing from the flow chart is the very necessary caveat that interpretation of the null hypothesis is associated with two kinds of error, Type I error and Type II error. These points and others are discussed in the following sections.

We start with the hypothesis statements. For illustration we discuss hypotheses in terms of comparisons involving just two groups, also called two sample tests . One sample tests in contrast refer to scenarios where you compare a sample statistic to a population value. Extending these concepts to more than two samples is straight-forward, but we leave that discussion to Chapters 12 – 18.

By far the most common application of the null hypothesis testing paradigm involves the comparisons of different treatment groups on some outcome variable. These kinds of null hypotheses are the subject of Chapters 8 through 12.

The  Null hypothesis  (H O ) is a statement about the comparisons, e.g., between a sample statistic and the population, or between two treatment groups. The former is referred to as a one tailed test whereas the latter is called a two-tailed test . The null hypothesis is typically “no statistical difference” between the comparisons.

For example, a one sample, two tailed null hypothesis.

and we read it as “there is no statistical difference between our sample mean and the population mean.” For the more likely case in which no population mean is available, we provide another example, a two sample, two tailed null hypothesis.

Here, we read the statement as “there is no difference between our two sample means.” Equivalently, we interpret the statement as both sample means estimate the same population mean.

Under the Neyman-Pearson approach to inference we have two hypotheses: the null hypothesis and the alternate hypothesis. The hull hypothesis was defined above.

Tails of a test are discussed further in chapter 8.4 .

Alternative hypothesis  (H A ): If we conclude that the null hypothesis is false, or rather and more precisely, we find that we provisionally fail to reject the null hypothesis, then we provisionally accept the alternative hypothesis . The view then is that something other than random chance has influenced the sample observations. Note that the pairing of null and alternative hypotheses covers all possible outcomes. We do not, however, say that we have evidence for the alternative hypothesis under this statistical regimen (Abelson 1995). We tested the null hypothesis, not the alternative hypothesis. Thus, it is incorrect to write that, having found a statistical difference between two drug treatments, say aspirin and acetaminophen for relief of migraine symptoms, it is not correct to conclude that we have proven the case that acetaminophen improves improves symptoms of migraine sufferers.

For the one sample, two tailed null hypothesis, the alternative hypothesis is

and we read it as “there is a statistical difference between our sample mean and the population mean.” For the two sample, two tailed null hypothesis, the alternative hypothesis would be

and we read it as “there is a statistical difference between our two sample means.”

It may be helpful to distinguish between technical hypotheses, scientific hypothesis, or the equality of different kinds of treatments. Tests of technical hypotheses include the testing of statistical assumptions like normality assumption (see Chapter 13.3 ) and homogeneity of variances ( Chapter 13.4 ). The results of inferences about technical hypotheses are used by the statistician to justify selection of parametric statistical tests ( Chapter 13 ). The testing of some scientific hypothesis like whether or not there is a positive link between lifespan and insulin-like growth factor levels in humans (Fontana et al 2008), like the link between lifespan and IGFs in other organisms (Holtzenberger et al 2003), can be further advanced by considering multiple hypotheses and a test of nested hypotheses and evaluated either in Bayesian or likelihood approaches ( Chapter 16 and Chapter 17 ).

Any number of statistical tests may be used to calculate the value of the  test statistic . For example, a one sample t-test may be used to evaluate the difference between the sample mean and the population mean ( Chapter 8.5 ) or the independent sample t-test may be used to evaluate the difference between means of the control group and the treatment group ( Chapter 10 ). The test statistic is the particular value of the outcome of our evaluation of the hypothesis and it is associated with the p-value. In other words, given the assumption of a particular probability distribution, in this case the t-distribution, we can associate a probability, the p-value, that we observed the particular value of the test statistic and the null hypothesis is true in the reference population.

By convention, we determine  statistical significance  (Cox 1982; Whitley & Ball 2002) by assigning ahead of time a decision probability called the  Type I error rate , often given the symbol  α  (alpha). The practice is to look up the  critical value  that corresponds to the outcome of the test with degrees of freedom like your experiment and at the Type I error rate that you selected. The  Degrees of Freedom  (DF, df, or sometimes noted by the symbol  v ), are the number of independent pieces of information available to you. Knowing the degrees of freedom is a crucial piece of information for making the correct tests. Each statistical test has a specific formula for obtaining the independent information available for the statistical test. We first were introduced to DF when we calculated the sample variance with the Bessel correction , n – 1, instead of dividing through by n. With the df in hand, the value of the test statistic is compared to the critical value for our null hypothesis. If the test statistic is smaller than the critical value, we fail to reject the null hypothesis. If, however, the test statistic is greater than the critical value, then we provisionally reject the null hypothesis. This critical value comes from a probability distribution appropriate for the kind of sampling and properties of the measurement we are using. In other words, the rejection criterion for the null hypothesis is set to a critical value, which corresponds to a known probability, the Type I error rate.

Before proceeding with yet another interpretation, and hopefully less technical discussion about test statistics and critical values, we need to discuss the two types of statistical errors. The Type I error rate is the statistical error assigned to the probability that we may reject a null hypothesis as a result of our evaluation of our data when in fact in the reference population, the null hypothesis is, in fact, true. In Biology we generally use Type I error α = 0.05 level of significance. We say that the probability of obtaining the observed value AND H O  is true is 1 in 20 (5%) if α = 0.05. Put another way, we are willing to reject the Null Hypothesis when there is only a 5% chance that the observations could occur and the Null hypothesis is still true. Our test statistic is associated with the p-value; the critical value is associated with the Type I error rate. If and only if the test statistic value equals the critical value will the p-value equal the Type I error rate.

The second error type associated with hypothesis testing is, β, the  Type II statistical error rate . This is the case where we accept or fail to reject a null hypothesis based on our data, but in the reference population, the situation is that indeed, the null hypothesis is actually false.

Thus, we end with a concept that may take you a while to come to terms with — there are four, not two possible outcomes of an experiment.

What are the possible outcomes of a comparative experiment\? We have two treatments, one in which subjects are given a treatment and the other, subjects receive a placebo. Subjects are followed and an outcome is measured. We calculate the descriptive statistics aka summary statistics, means, standard deviations, and perhaps other statistics, and then ask whether there is a difference between the statistics for the groups. So, two possible outcomes of the experiment, correct\? If the treatment has no effect, then we would expect the two groups to have roughly the same values for means, etc., in other words, any difference between the groups is due to chance fluctuations in the measurements and not because of any systematic effect due to the treatment received. Conversely, then if there is a difference due to the treatment, we expect to see a large enough difference in the statistics so that we would notice the systematic effect due to the treatment.

Actually, there are four, not two, possible outcomes of an experiment, just as there were four and not two conclusions about the results of a clinical assay. The four possible outcomes of a test of a statistical null hypothesis are illustrated in Table 1.

Table 1. When conducting hypothesis testing, four outcomes are possible.

In the actual population, a thing happens or it doesn’t. The null hypothesis is either true or it is not. But we don’t have access to the reference population, we don’t have a census. In other words, there is truth, but we don’t have access to the truth. We can weight, assigned as a probability or p-value,  our decisions by how likely our results are given the assumption that the truth is indeed “no difference.”

If you recall, we’ve seen a table like Table 1 before in our discussion of conditional probability and risk analysis ( Chapter 7.3 ). We made the point that statistical inference and the interpretation of clinical tests are similar (Browner and Newman 1987). From the perspective of ordering a diagnostic test , the proper null hypothesis would be the patient does not have the disease. For your review, here’s that table (Table 2).

Table 2. Interpretations of results of a diagnostic or clinical test.

Thus, a positive diagnostic test result is interpreted as rejecting the null hypothesis. If the person actually does not have the disease, then the positive diagnostic test is a false positive.

• Match the corresponding entries in the two tables. For example, which outcome from the inference/hypothesis table matches  specificity of the test\ ?
• Find three sources on the web for definitions of the p-value. Write out these definitions in your notes and compare them.
• In your own words distinguish between the test statistic and the critical value.
• Can the p-value associated with the test statistic ever be zero\? Explain.
• Since the p-value is associated with the test statistic and the null hypothesis is true, what value must the p-value be for us to provisionally reject the null hypothesis\?
• All of our discussions have been about testing the null hypothesis, about accepting or rejecting, provisionally, the null hypothesis. If we reject the null hypothesis, can we say that we have evidence for the alternate hypothesis\?
• What are the p-values for -logP of 5, 6, 7, 8, 9, and 10\? Complete the p-value -logP transform table .
• Instead of log 10 transform, create a similar table but for negative natural log transform. Which is more convenient? Hint: log(x, base=exp(1))
• The null and alternative hypotheses
• The controversy over proper hypothesis testing
• Sampling distribution and hypothesis testing
• Tails of a test
• One sample t-test
• Confidence limits for the estimate of population mean
• References and suggested readings

If you could change one thing about college, what would it be?

Graduate faster

Better quality online classes

Flexible schedule

Access to top-rated instructors

Null vs. Alternative Hypothesis

04.28.2023 • 5 min read

Sarah Thomas

Subject Matter Expert

Learn about a null versus alternative hypothesis and what they show with examples for each. Also go over the main differences and similarities between them.

In This Article

What Is a Null Hypothesis?

What is an alternative hypothesis, outcomes of a hypothesis test.

Main Differences Between Null & Alternative Hypothesis

Similarities Between Null & Alternative Hypothesis

Hypothesis Testing & Errors

In statistics, you’ll draw insights or “inferences” about population parameters using data from a sample. This process is called inferential statistics.

To make statistical inferences, you need to determine if you have enough evidence to support a certain hypothesis about the population. This is where null and alternative hypotheses come into play!

In this article, we’ll explain the differences between these two types of hypotheses, and we’ll explain the role they play in hypothesis testing.

Imagine you want to know what percent of Americans are vegetarians. You find a Gallup poll claiming ‌5% of the population was vegetarian in 2018, but your intuition tells you vegetarianism is on the rise and that ‌far more than 5% of Americans are vegetarian today.

To investigate further, you collect your own sample data by surveying 1,000 randomly selected Americans. You’ll use this random sample to determine whether it’s likely ‌the true population proportion of vegetarians is, in fact, 5% (as the Gallup data suggests) or whether it could be the case that the percentage of vegetarians is now higher.

Notice ‌that your investigation involves two rival hypotheses about the population. One hypothesis is that the proportion of vegetarians is 5%. The other hypothesis is that the proportion of vegetarians is greater than 5%. In statistics, we would call the first hypothesis the null hypothesis, and the second hypothesis the alternative hypothesis. The null hypothesis ( H 0 H_0 H 0 ​ ) represents the status quo or what is assumed to be true about the population at the start of your investigation.

Null Hypothesis

In hypothesis testing, the null hypothesis ( H 0 H_0 H 0 ​ ) is the default hypothesis.

It's what the status quo assumes to be true about the population.

The alternative hypothesis ( H a H_a H a ​ or H 1 H_1 H 1 ​ ) is the hypothesis that stands contrary to the null hypothesis. The alternative hypothesis ‌represents the research hypothesis—what you as the statistician are trying to prove with your data .

In medical studies, where scientists are trying to demonstrate whether a treatment has a significant effect on patient outcomes, the alternative hypothesis represents the hypothesis that the treatment does have an effect, while the null hypothesis represents the assumption that the treatment has no effect.

Alternative Hypothesis

The alternative hypothesis ( H a H_a H a ​ or H 1 H_1 H 1 ​ ) is the hypothesis being proposed in opposition to the null hypothesis.

Examples of Null and Alternative Hypotheses

In a hypothesis test, the null and alternative hypotheses must be mutually exclusive statements, meaning both hypotheses cannot be true at the same time. For example, if the null hypothesis includes an equal sign, the alternative hypothesis must state that the values being mentioned are “not equal” in some way.

Your hypotheses will also depend on the formulation of your test—are you running a one-sample T-test, a two-sample T-test, F-test for ANOVA , or a Chi-squared test? It also matters whether you are conducting a directional one-tailed test or a nondirectional two-tailed test.

Example 1: Two-Tailed T-test

Null Hypothesis: The population mean is equal to some number, x. 𝝁 = x

Alternative Hypothesis: The population mean is not equal to x. 𝝁 ≠ x

Example 2: One-tailed T-test (Right-Tailed)

Null Hypothesis: The population mean is less than or equal to some number, x. 𝝁 ≤ x Alternative Hypothesis: The population mean is greater than x. 𝝁 > x

Example 3: One-tailed T-test (Left-Tailed)

Null Hypothesis: The population mean is greater than or equal to some number, x. 𝝁 ≥ x

Alternative Hypothesis: The population mean is less than x. 𝝁 < x

By the end of a hypothesis test, you will have reached one of two conclusions.

You will run into either 2 outcomes:

Fail to reject the null hypothesis on the grounds that there's insufficient evidence to move away from the null hypothesis

Reject the null hypothesis in favor of the alternative.

If you’re ‌confused about the outcomes of a hypothesis test, a good analogy is a jury trial. In a jury trial, the defendant is innocent until proven guilty. To reach a verdict of guilt, the jury must find strong evidence (beyond a reasonable doubt) that the defendant committed the crime.

This is analogous to a statistician who must assume the null hypothesis is true unless they can uncover strong evidence ( a p-value less than or equal to the significance level) in support of the alternative hypothesis.

Notice also, that a jury never concludes a defendant is innocent—only that the defendant is guilty or not guilty. This is similar to how we never conclude that the null hypothesis is true. In a hypothesis test, we never conclude ‌that the null hypothesis is true. We can only “reject” the null hypothesis or “fail to reject” it.

In this video, let’s look at the jury example again, the reasoning behind hypothesis testing, and how to form a test. It starts by stating your null and alternative hypotheses.

Main Differences Between Null and Alternative Hypothesis

Here is a summary of the key differences between the null and the alternative hypothesis test.

The null hypothesis represents the status quo; the alternative hypothesis represents an alternative statement about the population.

The null and the alternative are mutually exclusive statements, meaning both statements cannot be true at the same time.

In a medical study, the null hypothesis represents the assumption that a treatment has no statistically significant effect on the outcome being studied. The alternative hypothesis represents the belief that the treatment does have an effect.

The null hypothesis is denoted by H_0 ; the alternative hypothesis is denoted by H_a H_1

You “fail to reject” the null hypothesis when the p-value is larger than the significance level. You “reject” the null hypothesis in favor of the alternative hypothesis when the p-value is less than or equal to your test’s significance level.

Similarities Between Null and Alternative Hypothesis

The similarities between the null and alternative hypotheses are as follows.

Both the null and the alternative are statements about the same underlying data.

Both statements provide a possible answer to a statistician’s research question.

The same hypothesis test will provide evidence for or against the null and alternative hypotheses.

Hypothesis Testing and Errors

Always remember that statistical inference provides you with inferences based on probability rather than hard truths. Anytime you conduct a hypothesis test, there is a chance that you’ll reach the wrong conclusion about your data.

In statistics, we categorize these wrong conclusions into two types of errors:

Type I Errors

Type II Errors

Type I Error (ɑ)

A Type I error occurs when you reject the null hypothesis when, in fact, the null hypothesis is true. This is sometimes called a false positive and is analogous to a jury that falsely convicts an innocent defendant. The probability of making this type of error is represented by alpha, ɑ.

Type II Error (ꞵ)

A Type II error occurs when you fail to reject the null hypothesis when, in fact, the null hypothesis is false. This is sometimes called a false negative and is analogous to a jury that reaches a verdict of “not guilty,” when, in fact, the defendant has committed the crime. The probability of making this type of error is represented by beta, ꞵ.

Explore Outlier's Award-Winning For-Credit Courses

Outlier (from the co-founder of MasterClass) has brought together some of the world's best instructors, game designers, and filmmakers to create the future of online college.

Check out these related courses:

Intro to Statistics

How data describes our world.

Intro to Microeconomics

Why small choices have big impact.

Intro to Macroeconomics

How money moves our world.

Intro to Psychology

The science of the mind.

Related Articles

Degrees of Freedom In Statistics

Explore degrees of freedom. Learn about their importance, calculation methods, and two test types. Plus dive into solved examples for better understanding.

What Is Standard Error? Statistics Calculation and Overview

Learn what is standard error in statistics. This overview explains the definition, the process, the difference with standard deviation, and includes examples.

What Are Quartiles? Statistics 101

Learn what quartiles are and how they work in statistics. Understand how to calculate them and why even learn them.

Further Reading

What is the second derivative test [full guide], how to find derivatives in 3 steps, test statistics: definition, formulas & examples, what is the product rule [with examples], understanding math probability - definition, formula & how to find it, what is a residual in stats.

This page has been archived and is no longer updated

Genetics and Statistical Analysis

Once you have performed an experiment, how can you tell if your results are significant? For example, say that you are performing a genetic cross in which you know the genotypes of the parents. In this situation, you might hypothesize that the cross will result in a certain ratio of phenotypes in the offspring . But what if your observed results do not exactly match your expectations? How can you tell whether this deviation was due to chance? The key to answering these questions is the use of statistics , which allows you to determine whether your data are consistent with your hypothesis.

Forming and Testing a Hypothesis

The first thing any scientist does before performing an experiment is to form a hypothesis about the experiment's outcome. This often takes the form of a null hypothesis , which is a statistical hypothesis that states there will be no difference between observed and expected data. The null hypothesis is proposed by a scientist before completing an experiment, and it can be either supported by data or disproved in favor of an alternate hypothesis.

Let's consider some examples of the use of the null hypothesis in a genetics experiment. Remember that Mendelian inheritance deals with traits that show discontinuous variation, which means that the phenotypes fall into distinct categories. As a consequence, in a Mendelian genetic cross, the null hypothesis is usually an extrinsic hypothesis ; in other words, the expected proportions can be predicted and calculated before the experiment starts. Then an experiment can be designed to determine whether the data confirm or reject the hypothesis. On the other hand, in another experiment, you might hypothesize that two genes are linked. This is called an intrinsic hypothesis , which is a hypothesis in which the expected proportions are calculated after the experiment is done using some information from the experimental data (McDonald, 2008).

How Math Merged with Biology

But how did mathematics and genetics come to be linked through the use of hypotheses and statistical analysis? The key figure in this process was Karl Pearson, a turn-of-the-century mathematician who was fascinated with biology. When asked what his first memory was, Pearson responded by saying, "Well, I do not know how old I was, but I was sitting in a high chair and I was sucking my thumb. Someone told me to stop sucking it and said that if I did so, the thumb would wither away. I put my two thumbs together and looked at them a long time. ‘They look alike to me,' I said to myself, ‘I can't see that the thumb I suck is any smaller than the other. I wonder if she could be lying to me'" (Walker, 1958). As this anecdote illustrates, Pearson was perhaps born to be a scientist. He was a sharp observer and intent on interpreting his own data. During his career, Pearson developed statistical theories and applied them to the exploration of biological data. His innovations were not well received, however, and he faced an arduous struggle in convincing other scientists to accept the idea that mathematics should be applied to biology. For instance, during Pearson's time, the Royal Society, which is the United Kingdom's academy of science, would accept papers that concerned either mathematics or biology, but it refused to accept papers than concerned both subjects (Walker, 1958). In response, Pearson, along with Francis Galton and W. F. R. Weldon, founded a new journal called Biometrika in 1901 to promote the statistical analysis of data on heredity. Pearson's persistence paid off. Today, statistical tests are essential for examining biological data.

Pearson's Chi-Square Test for Goodness-of-Fit

One of Pearson's most significant achievements occurred in 1900, when he developed a statistical test called Pearson's chi-square (Χ 2 ) test, also known as the chi-square test for goodness-of-fit (Pearson, 1900). Pearson's chi-square test is used to examine the role of chance in producing deviations between observed and expected values. The test depends on an extrinsic hypothesis, because it requires theoretical expected values to be calculated. The test indicates the probability that chance alone produced the deviation between the expected and the observed values (Pierce, 2005). When the probability calculated from Pearson's chi-square test is high, it is assumed that chance alone produced the difference. Conversely, when the probability is low, it is assumed that a significant factor other than chance produced the deviation.

In 1912, J. Arthur Harris applied Pearson's chi-square test to examine Mendelian ratios (Harris, 1912). It is important to note that when Gregor Mendel studied inheritance, he did not use statistics, and neither did Bateson, Saunders, Punnett, and Morgan during their experiments that discovered genetic linkage . Thus, until Pearson's statistical tests were applied to biological data, scientists judged the goodness of fit between theoretical and observed experimental results simply by inspecting the data and drawing conclusions (Harris, 1912). Although this method can work perfectly if one's data exactly matches one's predictions, scientific experiments often have variability associated with them, and this makes statistical tests very useful.

The chi-square value is calculated using the following formula:

Using this formula, the difference between the observed and expected frequencies is calculated for each experimental outcome category. The difference is then squared and divided by the expected frequency . Finally, the chi-square values for each outcome are summed together, as represented by the summation sign (Σ).

Pearson's chi-square test works well with genetic data as long as there are enough expected values in each group. In the case of small samples (less than 10 in any category) that have 1 degree of freedom, the test is not reliable. (Degrees of freedom, or df, will be explained in full later in this article.) However, in such cases, the test can be corrected by using the Yates correction for continuity, which reduces the absolute value of each difference between observed and expected frequencies by 0.5 before squaring. Additionally, it is important to remember that the chi-square test can only be applied to numbers of progeny , not to proportions or percentages.

Now that you know the rules for using the test, it's time to consider an example of how to calculate Pearson's chi-square. Recall that when Mendel crossed his pea plants, he learned that tall (T) was dominant to short (t). You want to confirm that this is correct, so you start by formulating the following null hypothesis: In a cross between two heterozygote (Tt) plants, the offspring should occur in a 3:1 ratio of tall plants to short plants. Next, you cross the plants, and after the cross, you measure the characteristics of 400 offspring. You note that there are 305 tall pea plants and 95 short pea plants; these are your observed values. Meanwhile, you expect that there will be 300 tall plants and 100 short plants from the Mendelian ratio.

You are now ready to perform statistical analysis of your results, but first, you have to choose a critical value at which to reject your null hypothesis. You opt for a critical value probability of 0.01 (1%) that the deviation between the observed and expected values is due to chance. This means that if the probability is less than 0.01, then the deviation is significant and not due to chance, and you will reject your null hypothesis. However, if the deviation is greater than 0.01, then the deviation is not significant and you will not reject the null hypothesis.

So, should you reject your null hypothesis or not? Here's a summary of your observed and expected data: