I. Good Example: (partial write-up for phase I of problem #2)

Problem 2: Identify phage with compensating mutations

Rationale: Since the starting phage is a frameshift mutant, it will not form plaques on E. coli K. If I plate out large numbers of phage on K and observe viable plaques, these must either be: 1) contaminants, or 2) mutant derivatives of the parent that have undergone a genetic change that allows them to grow (revertants). Since the former don't occur in the simulation, the new phages must be double mutants that aquired a second mutation that is able to suppress the effects of the first mutation. This will be confirmed (control) by plating on E. coli B, which should result in small but not large plaques.

Observations:
- Plated a 1:10 dilution of phage #1 (the starting mutant) onto E. coli K. I observed 5 small plaques growing, and harvested these to the 'fridge (1-5).
In comparison (control), plating the same amount of phage on E. coli B results in complete lysis.
- To confirm the properties of phages 1-5 (being revertants), I plated each of them on E. coli B at a dilution of 1 in 10^4 and observed ~50 small plaques indicative of wild type phenotype.

Conclusions: The phages 1-5 in my fridge are most likely revertants containing the original mutation and a new mutations of the opposite because the phages grow (form plaques) on E coli K and form small plaques on E. coli B.
While it is possible that one or more of them are true revertants (original mutation restored to wild type sequence) this is unlikely since there are many, many different ways to restore the reading frame (i.e. any nearby -1 deletion should restore a +1 frameshift), whereas there is only a single change that will restore wild type sequence. For similar reasons, it is unlikely that any of the phage contain identical second mutations.

II. Bad Example:

In order to further delineate our expectations in terms of presenting your work, I asked a student, who has seen a lot of notebooks go by, to produce something shameful that incorporates some embarrassments to avoid. I edited the initial work, and our joint effort follows (Grader's comments are marked in red):

Rationale: To accomplish this goal, we will need to plate phage and harvest the plaques that are growing.  These will be the ones that are new mutations of the opposite sign.
Commentary: More of a protocol than principles... it gives the bottom line of what you have to do but misses all of the logic behind it. The logic (or the why) is what we are looking for

Here's Webster's II New College Dictionary on rationale:
1. The fundamental reasons for something: BASIS.
2. An exposition of the guiding principles or justifications.

Observations: Poured one plate of the starting mutant.  I observed some plaques growing and harvested them into the fridge.  To make sure that these were the new mutations of the opposite sign (like the ones discussed in the rationale) and not contaminants, I plated several control plates with higher dilution factors.  Since no plaques grew on these plates, I realized that there were no contaminants in the experiment and the ones of the main plate must have been new mutations of the opposite sign.
Commentary: Observations do not include critical information: dilution factor, B or K, an actual number of plaques, what kind of plaques were harvested, etc.
"Controls" were random tests at random dilutions.

Note, the point of a scientific write-up is that if you died suddenly, an alien could walk into the lab, pick up your notebook and resume your experiments.
While we will not be enforcing THAT level of completeness, we should be able to deduce the key features of the experiment at hand without re-animating your brain. Do NOT assume you are talking to someone who knows more than you do; EXPLAIN yourself.
Remember, few people complain about something being 'too clear' or having understood 'too well', myself and the T.A.s included!

Conclusions: The phage in my fridge numbered 3-7 contain new mutations of the opposite sign of the starting mutation.
Commentary: Conclusion is a one-sentence statement of the outcome and does not explain how it was arrived at (first person to comment on ending sentence in 'at' earns first -25 point notebook deduction!).

Final comment: Spellcheckers have been invented. Use it! Please do us the simple courtesy of spelling correctly; even if you can't, your computer can.