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Here are three experiments to illustrate when the different approaches to statistics are appropriate. In the first experiment, you are testing a plant extract on rabbits to see if it will lower their blood pressure. You already know that the plant extract is a diuretic (makes the rabbits pee more) and you already know that diuretics tend to lower blood pressure, so you think there's a good chance it will work. If it does work, you'll do more low-cost animal tests on it before you do expensive, potentially risky human trials. Your prior expectation is that the null hypothesis (that the plant extract has no effect) has a good chance of being false, and the cost of a false positive is fairly low. So you should do frequentist hypothesis testing, with a significance level of 0.05.

A Bayesian would insist that you put in numbers just how likely you think the null hypothesis and various values of the alternative hypothesis are, before you do the experiment, and I'm not sure how that is supposed to work in practice for most experimental biology. But the general concept is a valuable one: as Carl Sagan summarized it, "Extraordinary claims require extraordinary evidence."

You must choose your significance level before you collect the data, of course. If you choose to use a different significance level than the conventional 0.05, people will be skeptical; you must be able to justify your choice. **Throughout this handbook, I will always use P** If you are doing an experiment where the cost of a false positive is a lot greater or smaller than the cost of a false negative, or an experiment where you think it is unlikely that the alternative hypothesis will be true, you should consider using a different significance level.

The significance level you choose should also depend on how likely you think it is that your alternative hypothesis will be true, a prediction that you make *before* you do the experiment. This is the foundation of Bayesian statistics, as explained below.

The significance level (also known as the "critical value" or "alpha") you should use depends on the costs of different kinds of errors. With a significance level of 0.05, you have a 5% chance of rejecting the null hypothesis, even if it is true. If you try 100 different treatments on your chickens, and none of them really change the sex ratio, 5% of your experiments will give you data that are significantly different from a 1:1 sex ratio, just by chance. In other words, 5% of your experiments will give you a false positive. If you use a higher significance level than the conventional 0.05, such as 0.10, you will increase your chance of a false positive to 0.10 (therefore increasing your chance of an embarrassingly wrong conclusion), but you will also decrease your chance of a false negative (increasing your chance of detecting a subtle effect). If you use a lower significance level than the conventional 0.05, such as 0.01, you decrease your chance of an embarrassing false positive, but you also make it less likely that you'll detect a real deviation from the null hypothesis if there is one.

The null hypothesis is a statement that you want to test. In general, the null hypothesis is that things are the same as each other, or the same as a theoretical expectation. For example, if you measure the size of the feet of male and female chickens, the null hypothesis could be that the average foot size in male chickens is the same as the average foot size in female chickens. If you count the number of male and female chickens born to a set of hens, the null hypothesis could be that the ratio of males to females is equal to a theoretical expectation of a 1:1 ratio.

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However, if both samples are not large, and both populations are normallydistributed, and both population standard deviations are not known, then you mayuse one of two "t" test that depends upon whether the populationvariances are equal or not. In either case the the standardized test statisticis given below.

The alternative hypothesis is that things are different from each other, or different from a theoretical expectation. For example, one alternative hypothesis would be that male chickens have a different average foot size than female chickens; another would be that the sex ratio is different from 1:1.

Usually, the null hypothesis is boring and the alternative hypothesis is interesting. For example, let's say you feed chocolate to a bunch of chickens, then look at the sex ratio in their offspring. If you get more females than males, it would be a tremendously exciting discovery: it would be a fundamental discovery about the mechanism of sex determination, female chickens are more valuable than male chickens in egg-laying breeds, and you'd be able to publish your result in *Science* or *Nature*. Lots of people have spent a lot of time and money trying to change the sex ratio in chickens, and if you're successful, you'll be rich and famous. But if the chocolate doesn't change the sex ratio, it would be an extremely boring result, and you'd have a hard time getting it published in the *Eastern Delaware Journal of Chickenology*. It's therefore tempting to look for patterns in your data that support the exciting alternative hypothesis. For example, you might look at 48 offspring of chocolate-fed chickens and see 31 females and only 17 males. This looks promising, but before you get all happy and start buying formal wear for the Nobel Prize ceremony, you need to ask "What's the probability of getting a deviation from the null expectation that large, just by chance, if the boring null hypothesis is really true?" Only when that probability is low can you reject the null hypothesis. The goal of statistical hypothesis testing is to estimate the probability of getting your observed results under the null hypothesis.

Suppose you are testing a claim that the percentage of all women with varicose veins is 25%, and your sample of 100 women had 20% with varicose veins. Then the sample proportion p=0.20. The standard error for your sample percentage is the square root of p(1-p)/n which equals 0.04 or 4%. You find the test statistic by taking the proportion in the sample with varicose veins, 0.20, subtracting the claimed proportion of all women with varicose veins, 0.25, and then dividing the result by the standard error, 0.04. These calculations give you a test statistic (standard score) of –0.05 divided by 0.04 = –1.25. This tells you that your sample results and the population claim in H_{0} are 1.25 standard errors apart; in particular, your sample results are 1.25 standard errors below the claim.

It is important to distinguish between *biological* null and alternative hypotheses and *statistical* null and alternative hypotheses. "Sexual selection by females has caused male chickens to evolve bigger feet than females" is a biological alternative hypothesis; it says something about biological processes, in this case sexual selection. "Male chickens have a different average foot size than females" is a statistical alternative hypothesis; it says something about the numbers, but nothing about what caused those numbers to be different. The biological null and alternative hypotheses are the first that you should think of, as they describe something interesting about biology; they are two possible answers to the biological question you are interested in ("What affects foot size in chickens?"). The statistical null and alternative hypotheses are statements about the data that should follow from the biological hypotheses: if sexual selection favors bigger feet in male chickens (a biological hypothesis), then the average foot size in male chickens should be larger than the average in females (a statistical hypothesis). If you reject the statistical null hypothesis, you then have to decide whether that's enough evidence that you can reject your biological null hypothesis. For example, if you don't find a significant difference in foot size between male and female chickens, you could conclude "There is no significant evidence that sexual selection has caused male chickens to have bigger feet." If you do find a statistically significant difference in foot size, that might not be enough for you to conclude that sexual selection caused the bigger feet; it might be that males eat more, or that the bigger feet are a developmental byproduct of the roosters' combs, or that males run around more and the exercise makes their feet bigger. When there are multiple biological interpretations of a statistical result, you need to think of additional experiments to test the different possibilities.

There are different ways of doing statistics. The technique used by the vast majority of biologists, and the technique that most of this handbook describes, is sometimes called "frequentist" or "classical" statistics. It involves testing a null hypothesis by comparing the data you observe in your experiment with the predictions of a null hypothesis. You estimate what the probability would be of obtaining the observed results, or something more extreme, if the null hypothesis were true. If this estimated probability (the *P* value) is small enough (below the significance value), then you conclude that it is unlikely that the null hypothesis is true; you reject the null hypothesis and accept an alternative hypothesis.

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