Title: InkBiology / Scientific method and quantitative biology
On every note of this deck, unless a note says otherwise:
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Front: DEFINE
Define: Reproducible.
Back: Somebody else, or the same person using different apparatus or a different method, gets the same results.

Front: DEFINE
Define: Degrees of freedom.
Back: A number derived from the size of the data set that decides which critical value you read from the table.

Front: DEFINE
Define: Significant figures.
Back: The digits in a measurement that carry information about its size, counted from the first non-zero digit.

Front: DEFINE
Define: Causation.
Back: A relationship in which changing one variable changes the other. It cannot be read off a scatter graph.

Front: DEFINE
Define: Precise.
Back: Repeat readings close to one another. Precision says nothing at all about being right.

Front: DEFINE
Define: Dependent variable.
Back: The quantity you measure, whose value depends on the independent variable. It goes on the vertical axis.

Front: DEFINE
Define: Confounding variable.
Back: A variable that changes with the independent variable and could itself explain the change in the dependent variable, so the two effects cannot be separated by the data collected.

Front: DEFINE
Define: Correlation.
Back: A relationship in which two variables tend to change together. It may be positive, negative or absent, and it makes no claim about which variable moved first.

Front: DEFINE
Define: Randomisation.
Back: Assigning subjects or sample positions by chance rather than by choice, so that variables nobody thought of tend to balance out between the groups on average.

Front: CHECK YOURSELF
A student investigates the effect of light intensity on the rate of photosynthesis by counting bubbles from pondweed, moving a bench lamp to five distances from the beaker. The bubble count rises steadily as the lamp is moved closer. Identify the independent, dependent and two control variables, identify one confounding variable, and state what the student may and may not conclude.
Back: Independent variable: the distance of the lamp from the beaker in centimetres, standing in for light intensity. Dependent variable: bubbles released per minute. Control variables include the mass of pondweed, the concentration of hydrogencarbonate solution supplying carbon dioxide, and the equilibration time before counting starts.
The confounding variable is temperature. A filament lamp warms the water, and warms it more as it comes closer, so light intensity and temperature rise together and these readings cannot separate them.
The student may conclude that bubble production increased as the lamp was brought closer, over the range of distances used, for this piece of pondweed. That is all the data supports.
The student may not conclude that light intensity caused the increase, because temperature changed with it; nor that the rate of photosynthesis rose, because bubble count assumes every bubble is the same size; nor anything about distances outside those tested.
The repair is a design change rather than more repeats: a water-filled flask between lamp and beaker as a heat filter, temperature reported at each distance, and a light meter so intensity is measured rather than inferred.

Front: DEFINE
Define: Resolution.
Back: The smallest change an instrument can register: 0.01 g on a three-decimal-place balance, 1 mm on a metre rule.

Front: DEFINE
Define: Control variable.
Back: A quantity held the same across every treatment, so that it cannot be the reason the dependent variable changed.

Front: DEFINE
Define: Median.
Back: The middle value when the readings are put in order. Unmoved by a single extreme value, which is why it is used for skewed data such as incomes, reaction times or the number of parasites per host.

Front: CHECK YOURSELF
Two groups of woodlice are given a choice chamber, one half humid and one half dry. Of 80 woodlice, 58 are found on the humid side and 22 on the dry side after ten minutes. State a null hypothesis, choose and carry out a suitable test, and write the conclusion. The critical value of chi-squared at p = 0.05 with 1 degree of freedom is 3.84.
Back: Test: chi-squared, because the data are counts of individuals in two categories against a ratio that can be predicted, since with no effect of humidity the woodlice would be spread 1:1.
Null hypothesis: there is no significant difference between the observed numbers of woodlice on the humid and dry sides and the numbers expected if humidity had no effect on their distribution.
Calculation: the expected values are 80 ÷ 2 = 40 on each side, both well above 5. Then (58 − 40)² ÷ 40 = 8.10 and (22 − 40)² ÷ 40 = 8.10, so chi-squared = 16.2. Degrees of freedom = 2 categories − 1 = 1, and the critical value is 3.84.
Conclusion: 16.2 is far greater than 3.84 at p = 0.05 with 1 degree of freedom, so the null hypothesis is rejected. Significantly more woodlice were found on the humid side than an even distribution would give.
Worth adding in an evaluation: the test shows the distribution was uneven, not why. Separating a kinesis, in which woodlice simply move less once they reach damp air and so accumulate, from a taxis, in which they move towards it directionally, needs individual paths tracked rather than a headcount at the end.

Front: DEFINE
Define: Significance level.
Back: The probability threshold, conventionally 0.05, below which the null hypothesis is rejected.

Front: DEFINE
Define: Trailing zeros after a decimal point.
Back: Always significant. 4.20 has three, and says the hundredths digit was measured.

Front: SPOT THE ERROR
Say what is wrong with this claim:
You give your answer to the same number of decimal places as the numbers in the question.
Back: Significant figures, not decimal places. A leaf measured at 43 mm has two significant figures; written as 0.043 m it has three decimal places and still two significant figures, because changing the unit cannot improve the ruler.

Front: DEFINE
Define: Leading zeros.
Back: Never significant. 0.0043 has two significant figures, because the zeros only locate the decimal point.

Front: DEFINE
Define: Repeatable.
Back: The same person, using the same method and the same apparatus, gets the same results again.

Front: SPOT THE ERROR
Say what is wrong with this claim:
If the error bars on two means do not overlap, the difference between them is significant.
Back: Non-overlapping bars are a hint, not a verdict, and what they support depends on what they show: one standard deviation, one standard error and a 95% confidence interval have different lengths on the same data. Only the test decides.

Front: DEFINE
Define: Null hypothesis.
Back: A statement that there is no significant difference, no significant association or no significant correlation between the variables, and that any difference observed is due to chance.

Front: DEFINE
Define: Accurate.
Back: Close to the true value.

Front: DEFINE
Define: Mode.
Back: The most common value. The only one of the three that works for categories such as blood group or flower colour.

Front: DEFINE
Define: Independent variable.
Back: The quantity you change on purpose, and the only one that should differ between your treatments. It goes on the horizontal axis.

Front: SPOT THE ERROR
Say what is wrong with this claim:
A control is the tube you leave the interesting thing out of, and every experiment has one.
Back: Two different things share the word. A control variable is a quantity held still; a control experiment is a whole extra run of the method. Plenty of sound investigations need no control tube at all: a potometer measuring uptake at five wind speeds has controlled variables everywhere and none.

Front: DEFINE
Define: Valid.
Back: A measurement is valid if it measures what it claims to measure; an investigation is valid if its design allows its conclusion to follow. A confounding variable destroys validity however careful the measuring was.

Front: DEFINE
Define: Control experiment.
Back: An extra run of the method, differing in one deliberate way, done to rule out an explanation the main runs cannot rule out on their own.

Front: CHECK YOURSELF
A student measures the length of the coleoptile of ten seedlings with a millimetre rule, before and after three days of growth in the dark. One seedling measures 18 mm at the start and 27 mm at the end. Calculate the percentage change in length, the mean growth rate in mm per day, and the percentage uncertainty in the percentage change. State the answers to a sensible number of significant figures.
Back: Percentage change: 27 − 18 = 9 mm, and 9 ÷ 18 × 100 = +50%, to two significant figures because both measurements carry two. Growth rate: 9 mm over 3 days = 3.0 mm per day, and the 3 days is counted rather than measured so it imposes no limit on the figures.
Uncertainty: a millimetre rule read at both ends gives ±1 mm on each length, so the difference of 9 mm carries ±2 mm, which is 2 ÷ 9 × 100 = 22%. The initial 18 mm carries 1 ÷ 18 × 100 = 5.6%. The two were divided, so the percentages add to about 28%.
The percentage change is therefore 50% ± 14 percentage points, somewhere between about 36% and 64%. That is a startlingly wide answer from two tidy-looking measurements, and it shows what to change: leaving the seedlings a week rather than three days gives a bigger difference and shrinks the percentage uncertainty without touching the ruler. Taking a mean of ten seedlings helps too, though it does nothing about a rule misread the same way every time.

Front: DEFINE
Define: Mean.
Back: The total divided by the number of readings. Uses every value, and is what almost every biological calculation wants.