Part F: A Closer Look at....

The Dilution Series and Statistics

Introduction
When you make a dilution series, the tube you start with contains approximately 10^6 cells/mL. From the earlier procedure you know that the suspension actually holds between 1 and 2 million cells/mL, but for now, suppose you have exactly 1 million cells/mL. Since the tube contains 2 mL, you should have 2 million cells. If you pipet out exactly 0.1 mL, how many cells will you get? You would expect to get 1/20 of the 2 million cells in the tube, 10^5 cells, but you probably won't because some extra cells could have been in the 0.1 mL you pulled out. This expected variation is called the standard deviation, and for our experiment is approximately the square root of the number of cells you expect to get. Thus, if you expect 105 cells you may only get within 300 cells of 10^5 (300=(10^5)).
Missing a hundred thousand by a mere 300 is not so bad, but notice what happens with the further dilutions. By the time you expect to get 100 cells, the standard deviation is 10, the square root of 100. So if you expect to get 100 cells on a plate and in fact you get 90, that is not necessarily due to poor technique. About 1/3 of the time you should expect to get a result outside the standard deviation; even getting 80, therefore, may not be the result of poor technique. Furthermore, just because you get 100 when you expect 100 does not mean you have great technique; you were also lucky. To develop and demonstrate good technique you must prepare many dilution series. Try to plate 100 cells 20 times. If your technique is good, you will get an average of 100 cells per plate, with 13-15 in the 90-110 range, and the rest outside it.

Rules:


  1. Expected number of cells = (Number in tube) x (fraction of volume withdrawn);
  2. Standard deviation = square root of expected number of cells;
  3. Number of plates outside 1 standard deviation 1/3.

Let's think about designing experiments with these rules in mind. How many cells should we aim to get on a plate? If we expect to get 100 then our result should be around 10010, while if we expect to get 10 then we should see around 103. The uncertainty looks smaller in the second case. But this is an illusion. 3 is 30% of 10 while 10 is only 10% of 100, so aiming for 100 is smarter than aiming for 10; the relative uncertainty is smaller. What about aiming for 1000 cells on a plate? Then we would expect around 1000+/-30, a 3% relative error. This is true, the statistical error is smaller, but it is very hard to count 1000 colonies accurately. Using so many cells introduces a large systematic error into the procedure. When designing an experiment you have to steer a course between the statistical errors that come with too few cells/plate and the systematic errors that come with too many cells, or even too many plates; people get tired and count inaccurately if there is too much to do.

Distributions

Each time you draw 0.1mL from the tube you get some number of cells that you spread on the plate and that grow up into colonies. We can imagine doing this very many times, creating a huge number of plates, all made with the same procedure. There are many plates with 100 cells, lots with 107, a few with 74, very few with 13, and so on. This imaginary population has a distribution of numbers of cells per plate, represented by stacks of plates in the figure below.

Figure 1:

Making a real plate is like pulling a plate out of this ghostly distribution: The plate will probably come from some where near the mean because there are many more plates there, but it may come from the wings, that is just less likely.

Real experiments

When we actually do an experiment we are not sure exactly how many cells/mL we have in suspension, we are not sure that we withdraw exactly 0.1 mL of the suspension, and we do not how many of the cells are viable (yeast cells eventually die of old age). Thus, although we do know that we are spreading roughly 100-200 cells on a plate we do not know exactly how many colonies we should expect. That is, we do not know what distribution our procedure is producing. We make control plates to figure this out. In the survival experiment, for example, we keep some plates unexposed to UV radiation. If they grow up to contain 120, 136, and 98 colonies then we can reasonably guess that our procedures have produced a distribution whose mean is (120+136+98)/3 = 118. The other plates that are exposed to the UV are made by the same procedures so we expect that before getting any radiation they also come from this distribution.

Some language from statistics The example of the dilution series illustrates a number of ideas from statistics, a widely applicable piece of mathematics. When we use a definite set of procedures to make the plates we create in our mind's eye a population of plates. The actual control plates are a sample drawn from the population. The job of statistics is to use the sample to learn things about the population. The population is characterized by parameters. In this example the mean number of cells/plate is the parameter we care about. We took our control plates, the sample, and used the mean of this sample to estimate the mean of the population. We say that the sample mean is an estimator of the population mean. Our estimation is better with larger samples. If we had made 10 control plates containing 101, 127, 113, 120, 126, 95, 130, 120, 136, 112 cells instead of the three above our sample size would be 10 instead of 3. We would still estimate the mean to be 118 as we did before but we would feel much more confident of our estimate. We will not go into the quantitative details of sample size and confidence levels.
The most important characteristics of a sample are its size, its mean and its standard deviation, or its variance. The size of the sample is usually obvious, and the sample mean is familiar: it is just the average. The standard deviation and variance of a sample are most easily explained by an example. Consider the sample of 3 plates above. The mean is 118 so the deviation of the first plate is 120-118, the deviation of the second is 136-118, and of the third is 98-118. The variance is

((120-118)^2+(136-118)^2+(98-118)^2)/3=242;

that is, the variance is the mean of the squares of the deviations. The standard deviation is just the square root of the variance, which gives it its other name: the root mean square deviation, or rms deviation. The standard deviation of a sample is an estimator of the standard deviation of the population, so in this example we estimate the standard deviation of the population to be (242) 16. This is not far from what we expect from the rule given above (Standard deviation = square root of expected number of cells): (118) 11. Why the difference? The rule gives the ideal standard deviation, to be expected if all procedures are perfectly carried out, which is not possible in real life. You should be able to get close to that ideal with lots of practice but real experiments will produce populations with bigger standard deviations than this ideal. Of course, real samples will sometimes, by chance, have a smaller standard deviation than this ideal! The sample deviation is just an estimator of the population deviation, it will sometimes be too big and sometimes too small.

More about distributions

We will discuss several examples of distributions in this section, but the normal distribution is the most common. (``Normal'' means a particular type of distribution, not an ``ordinary'' distribution.) This is the familiar bell-shaped distribution that describes many situations, from the number of cells on a plate to students' scores on an exam. It has two parameters, the mean = and the standard deviation = . The mean is the position of the maximum of the bell-shaped curve and the standard deviation determines the width of the peak. Consider the qualitative picture sketched below. Both of these distributions have the same mean, but in the distribution labeled (a) you are unlikely to get a number very far from the mean, while in the distribution labeled (b) you would not be surprised to get a number quite far from the mean.

Figure 2

Figure 3

Recall that the normal distribution that describes the ideal dilution series experiment done with perfect technique has standard deviation equal to the square root of the mean, but usually there are other sources of variation, such as variation in the amount of solution withdrawn for each plate, so the standard deviation is usually a separate parameter unrelated to the mean. The mathematical expression for the normal distribution is given below. We give it just for fun; you don't need to use it now. It uses some symbols you may not yet know, but your teacher, or your math teacher, can help. The number of plates having x colonies we call N(x) and

N(x)=(1/(2*pi )) exp(-(x- )^2/2^2)

One interesting feature of this expression should be noticed: it involves , the ratio of the circumference of a circle to its diameter. Why in the world should geometry have anything to do with growth of yeast cells? But it does. This is one of the amazing things about mathematics! The next important distribution in biology is called the Poisson distribution. It is named for a mathematician who used it. This distribution is involved when we consider mutations induced by radiation, or the probability of ``cross-over'' when DNA recombines. It also describes the probability of hearing a ``click'' when you hold a Geiger counter near a radioactive source and describes the probability of two callers ringing the same phone number at the same time. What all these situations have in common is that the probability of the interesting event is very low, but there are many opportunities for the event to occur: it is very unlikely that any particular cell will mutate, but there are very many cells; it is very unlikely that any particular radioactive nucleus will decay, but there are very many such nuclei; and so on. We will use the example of mutation by radiation to explain this distribution.
When you expose the yeast cells that normally make white colonies to UV radiation you occasionally find a red colony growing up. This can be the result of a mutation. We would like to know the probability that a single cell will mutate when exposed to this much radiation. Let's call this p. How can we measure this? The most straightforward idea is probably to expose a lot of plates, colonies the cells/plate, count the number of mutated cells, and then the number of mutations divided by the total number of cells exposed is p. So suppose your whole class makes one thousand plates, with 200 cells/plate, exposes them all to the same amount of radiation, lets the colonies grow up, and then starts looking for mutants. The result of such an experiment is sketched below.

Figure 4:

Figure 5:

The figure labeled (a) plots the number of plates having n mutations versus n; the figure labeled (b) plots the probability of having n mutations on a plate versus n. The connection is simple: there were 903 of the 1000 plates that had 0 mutants so the probability of getting 0 is 0.90, there were 89 that had 1 mutant so the probability of 1 is 0.09, and so on. We wanted to measure p, the probability that a single cell will mutate when exposed to this much radiation. The total number of mutants is 111 (89 plates with one means 89 mutants, 6 plates with two adds twelve, and so on) and the total number of cells is 1000 plates times 200 cells/plate. Thus we get p=111/200,000. So we have found out what we wanted to, but there is a little more we can learn. The dashed line in (b) is a Poisson distribution of the probability of getting n mutants, P(n), versus n. We can see that this is a pretty good description of the experimental results. The mathematical expression of the Poisson distribution is

P(n)=(exp - ) ^)n/n!

with

= (p) x (number of cells per plate)

where p is the parameter we wanted. This gives us a different way to determine p. All we need is P(0), the probability that there are zero mutations on a plate. Because this number is determined using lots of plates the relative error is small, so it is probably fairly accurate. Here is how to use P(0) to find "lambda" and then p. From the formula for the Poisson distribution we see that P(0) equals exp-, so = -ln P(0)= 0.10 and so p=/(number of cells per plate) = 0.10/200 =0.0005, just as we found before.
The last distribution we will discuss here is the binomial distribution. This gives the probability of having n successes in N tries. A typical situation is rolling dice or flipping a coin: the binomial distribution tells the probability of rolling 7 four times in 11 attempts, for example. A biological example is the mutation experiment we just discussed. We could call ``causing a mutation'' a success and the number of cells on a plate would be the number of tries: the radiation tries to mutate each cell and succeeds only with the few mutants.
The binomial distribution is characterized by one parameter, p, the probability of success on any single try. The mathematical expression of the binomial distribution is this. Let P(n,N) be the probability of having n successes in N tries. Then if p is the probability of success on any single try we have

P(n,N)=[N!/n!(N-n)!] x p^n x (1-p)^(N-n).

The quantity inside the square brackets is called "the binomial coefficient" or "N choose n." The latter name is used because it gives the number of ways to choose n objects from a set of N things. For example, if you roll two ordinary dice the probability of getting a 7 is 1/6 (can you figure out why this is so?) so the probability of rolling 7 four times in eleven attempts is (11 choose 4)(1/6)^4(5/6)^7 0.07.

There is a connection between the three distributions we have discussed. If N is very large then the binomial distribution is practically indistinguishable from the normal distribution with = Np and = Np(1-p); if N is very large and p is very small then the binomial distribution is practically indistinguishable from the Poisson distribution with =Np. This equivalence of Poisson and binomial distributions is the reason we could use the mutation experiment as an illustration of each of these distributions.

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Last updated Friday August 19 2005