Biology IA · A · Unity and diversity · topic 3 of 25
Build a tree from protein sequences · IB Biology IA idea: guide, sample graph and step-by-step plan
a classic. test it, don't just repeat itFossils and anatomy give one family tree; protein sequences give another. Do they agree, and for how long does the 'molecular clock' keep ticking?
- ✓ you like evolution and data
- ✓ you can work from a computer
- ✓ you want to test a famous idea
The big idea
← this is your RQ hook!Mutations build up in a gene over time, so species that split long ago should have more differences in a shared protein. That is the idea behind the molecular clock, and cytochrome c is a classic test. You gather aligned sequences for a set of species, count differences against humans, and compare with the divergence times in a published tree. Real data rarely fall on a straight line, so ask why the pattern bends. One protein is a limited guide, and saying exactly how limited is where the best marks come from.
Make it yours: pick one twist
Copying a classic won't show your choices. Pick one of these (or invent your own) and your IA becomes yours.
Swipe for more twists →
Repeat with a protein that evolves faster or slower (for example haemoglobin or histone H4) for the same species.
→ Compares rates between proteins. Your graph has two sets of points, and your analysis compares gradients.Use the difference counts to build a simple tree and compare its branching with a published one.
→ Moves from correlation to cladistics. Your analysis is about whether the branching order matches, not a line fit.Express differences as a percentage of the aligned length instead of a count.
→ Makes proteins of different length comparable. Your calculations and axis labels change.Choose one group, such as mammals, and sample many species within it.
→ Narrows the time range so the relationship is easier to see, but you lose the long timescale where the pattern bends.Compare the rate for two separate branches to ask whether the clock ticks at the same speed.
→ A harder question that asks whether the model holds, not just whether a trend exists.Your Biology IA research question: run the check
Write your own question first. Then make sure it ticks every box:
- Names the protein, the sequence source and the range of divergence times (in millions of years).
- Says what counts as a difference (substitutions only, or gaps too) and how sequences are aligned and trimmed.
- Says where divergence times come from and that they carry their own uncertainty.
- Says how many species you will use and how you choose them.
- Says which statistic you will use, and what pattern would make you reject a simple clock.
The workflow
A database and simulation investigation has no apparatus, so the 'set-up' is your data pipeline. Draw your own version, with the real tools and filters, for the Method section.
How your Biology IA could be laid out
The usual order for a topic like this, what each part needs to show, and roughly how much of your 3,000 words it takes. The words are all yours.
Your question; why sequence differences might measure time; what you expect and why.
Mutation, selection and the molecular clock; what cytochrome c does; the shape you expect the relationship to take (cite).
Independent and dependent variables, plus the controls that apply to a database (same protein, same tool, same length).
Which databases and tool; species list and how chosen; how you aligned, trimmed and counted; where dates come from; enough detail to repeat.
Short: screen use only, with credit given to database sources.
Table of species, accession numbers, divergence times and the difference counts, with the date accessed.
How differences were counted, the rule for gaps, any conversion to percent; one worked example per calculation type.
Differences against time, with the uncertainty of the dates marked; the statistic; whether the pattern is a line or bends.
Answer with values and a statistic; compare with published work on the molecular clock; keep your claim to the species and time span you used.
Weaknesses of the sample, the alignment and the dates; which matters most for your answer; limits of one protein; linked improvements.
Every database entry, tool and paper.
What your Biology IA graph could look like
date uncertainty on the x-axis ✓Made-up data, to show you the form of a strong graph, not the answer. Yours will look different. example only
- Horizontal bars show the uncertainty in the divergence dates, which is usually bigger than any counting error.
- Counting differences has no measurement error. Say that in your text, and explain what the bars represent.
- Two models drawn: a straight clock and one that levels off because the same position can mutate twice. See which one your data follow.
- Label every point with the species, so the reader can see which groups sit above or below the trend.
- Another graph to consider: plot difference per million years against time, to show whether the apparent rate changes.
Your game plan
do the trial run on 5 species firstTick steps off as you go. We'll remember on this device.
0 of 10 done
- Read and predictFind what the molecular clock claims and what is known about cytochrome c. Write down the pattern you predict, and whether you expect it to stay straight over long times.
- Trial run (1 lesson)Pick five species, download sequences, align them and count differences. Are all sequences the same length? What happens at the ends and at gaps? Fix your rules now.
- Choose species and sourceChoose species that cover a wide range of divergence times. Decide where the dates come from, and note that they have ranges.
- Write the counting rulesDecide how to trim, how to treat gaps, and whether to use a count or a percentage. Write down why for each choice.
- Collect the dataFill the spreadsheet straight from the database and the alignment. Record accession numbers, dates accessed and tool versions.
- Choose the statisticDecide whether a rank correlation or a fit is suitable for the pattern you see, and what each assumes.
- Process and graphCalculate the statistic and plot the data. Show the uncertainty in the dates and check whether the points follow a line or a curve.
- Compare with the clock ideaDoes the pattern follow the simple clock? By how much do the data leave it, and where? What could cause that?
- EvaluateRank the weaknesses by their effect on your answer. Make every improvement specific to a weakness you found.
- Check before your teacher's draftRun the checklist below, then get your RQ or draft checked. Your teacher reads one draft only, so make it count.
Biology you'll need
Traps to avoid in this Biology IA
- Counting differences without a proper alignment: shifted sequences give meaningless numbers.
- Using too few species, so no pattern can be seen, or all from one close group.
- Fitting a straight line through the origin to data that clearly bend.
- Ignoring the uncertainty in the divergence dates.
- Mixing sequences from different versions of the protein, or of different lengths.
- Treating one protein as if it told the whole story of the species.
More Biology IA ideas like this
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This guide shows how a topic like this is usually approached. It is not an IA. Your question, choices, data, analysis and words must be your own: change something, tell your teacher where the idea came from, and follow your school's rules on outside help.