Cairo and Rust don’t anymore. I’ll have to check the other tracks later.
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Alright, how about we orient the table vertically then since we’re only dealing with one RNA sequence at a time?
For example, the RNA strand “AUGUUUUCU” is translated like this:
| Codon | Amino Acid |
| ------ | ---------- |
| AUG | Methionine |
| UUU | Phenylalanine |
| UCU | Serine |
and
For example, AUGUUUUCUUAAAUG contains a STOP codon, so ignore any subsequent codons:
| Codon | Amino Acid |
| ----- | ---------- |
| AUG | Methionine |
| UUU | Phenylalanine |
| UCU | Serine |
| UAA | STOPPED |
| AUG | STOPPED |
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Works for me
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Thank you @IsaacG , I heard this earlier. What I tried to do here was include what (I had had the impression) had already been agreed on earlier, rather than splitting it, since the hard work of agreeing (I had thought) had already been done. The part that wasn’t agreed, I split out. I didn’t think it made sense to start again from scratch. If that is what had been proposed, I missed it.
Any update, @BNAndras ?
I like this except for “STOPPED” since it seems to imply somewhat that it’s a literal value. Is everyone OK with “(stopped)” instead? And @IsaacG , could you weigh in this vertical table suggestion and my “(stopped)” tweak, before I make another summary of changes?
And @BNAndras and @SleeplessByte, could you weigh in on @IsaacG 's suggestion, before I make another summary of changes:
Personally, to me, it flows better having the before and after. Without it, the table abruptly breaks the flow. But flow or not, I like the “here’s the broad idea” (which most people hopefully will get), followed by an explicit table, followed by an “in other words” (which, in anyone is lost still after seeing the table, should make it abundantly clear; those who aren’t lost can easily skip/skim thanks to the “in other words” preface). However, I welcome others now to weigh in.
Or if everyone wants, I can split just these two things into new threads. If someone wants to split every original suggestion into a new thread, be my guest. Thanks!
One person making a suggestion isn’t quite the same as everyone agreeing. As the number of changes grow, there are more specifics to clarify and it’s much harder for everyone to agree on all the points. People also miss bits of what is changing as the number of changes grow. Splitting things into smaller changes will make things easier for everyone. Seriously.
I’ve worked at Google for years. At Google, “small changes” was a well established guideline for changes. Large changes got automatic feedback telling people to make small changes. Large changes took much more time and effort to get through. Large changes needed a lot of justification explaining why they needed to be large.
See the Google recommendation for small changes.
I highly recommend taking specific parts that are widely agreed upon and making those into small changes, working through the changes incrementally. Trying to gather everything into one large chance is not the best option. It doesn’t simplify things. I’m pretty sure things thread would have been wrapped up by now if the chances were done in small increments.
See also
The vertical table sounds good to me.
I thought the whole point here was to use STOPPED uniformly. Now I’m not sure what you’re suggesting we use and if it’s going to be uniform or not.
Can we focus on one change at a time? Juggling so many changes is confusing and makes it hard to understand what’s being proposed/changed. I’m not sure what I’m agreeing to anymore without seeing all the changes.
I already acknowledged this general strategy and will definitely do so going forward — I am not arguing this as a general approach. This was about what to do with this one. And here, I had already summarized these changes a few times, with nobody objecting to most of the summary. So I only separated out the part where there had been disagreement.
Thanks.
No, it was to use STOP (all caps, no quotes) uniformly as the interpretation of a codon in isolation, not STOPPED as an interpretation of what the program has done during the processing of a sequence of codons. Hence my suggestion: These are different contexts, and to me, STOPPED gives a moment’s pause due to the conflation it presents, whereas (stopped) gives a clearly distinct meaning appropriate to the context.
We are down to 2 changes, thanks to your agreement about the vertical table. I actually had asked if I should open new threads about them. But then we juggled anyway. So below is an updated proposal, thanks to your assent regarding the vertical tables. Hopefully this is manageable. If not, I will open 2 other threads then come back here with the final proposal.
Updated proposal.
Full summary of changes:
- Active voice
- Use vertical tables, with the original sequence kept in preceding ¶ text, with the program run sequence using (stopped) instead of STOPPED, to distinguish from STOP and avoid conflating contexts
- Remove unexplained reference to ribosomes
- Clarify wording following STOP codon example
- Standardize
STOP codon(prioritizing ease of maintenance, not correctness) - Still mention 64 codons for now, but: cut unclear message about expanding the test suite (only applicable to offline users), cut untrue message about the program working for all codons if it works for one codon, and fix grammatical mistake (use “not all are important” instead of “all are not important”)
- Remove redundant “after” (given “subsequent”)
Preview render:
Description
Translate RNA sequences into proteins.
You can break an RNA strand into three-nucleotide sequences called codons and then translate them into amino acids to make a protein.
For example, the RNA strand “AUGUUUUCU” is translated like this:
| Codon | Amino Acid |
|---|---|
| AUG | Methionine |
| UUU | Phenylalanine |
| UCU | Serine |
There are also three STOP codons. If you encounter any of these codons, ignore the rest of the sequence — the protein is complete.
For example, AUGUUUUCUUAAAUG contains a STOP codon, so ignore any subsequent codons:
| Codon | Amino Acid |
|---|---|
| AUG | Methionine |
| UUU | Phenylalanine |
| UCU | Serine |
| UAA | (stopped) |
| AUG | (stopped) |
In other words, the latter AUG is not translated into another methionine here because it’s preceded by a STOP codon.
There are 64 codons which in turn correspond to 20 amino acids; however, not all codons will be used in this exercise. Below are the codons and resulting amino acids needed for the exercise.
| Codon | Amino Acid |
|---|---|
| AUG | Methionine |
| UUU, UUC | Phenylalanine |
| UUA, UUG | Leucine |
| UCU, UCC, UCA, UCG | Serine |
| UAU, UAC | Tyrosine |
| UGU, UGC | Cysteine |
| UGG | Tryptophan |
| UAA, UAG, UGA | STOP |
Learn more about protein translation on Wikipedia.
I’m not a fan of using STOP in one table and (stopped) in the other.
I’m in favor of this, which I see as in conflict with using (stopped).
Followed by a list of 7 changes 
I’m not sure how that’s 2 changes.
Since there is a new summary, I’ll reiterate my preference for not having a table interrupt the flow of an example.
This discussion has probably gone on too long now, and has got too complex to ever get to a conclusion, so I’m tip-toeing to try and get it over the line.
I’ve read through the latest draft and the objectives, and this is my suggested version, which I think deals with all the various changes people want. I’ve simplified things down to one table, which I’ve put earlier (three tables made it actively more confusing in my eyes). I’ve simplified the english a bit. I’ve gone through a couple of proof-reading iterations with LLMs.
If this is considered significantly better than what exists currently, and has nothing actively harmfully wrong, can I suggest we merge this, and then any further suggests can be address as individual items.
If @codingthat @IsaacG, @BNAndras and @SleeplessByte are in agreement (as you three seem to still be active in the thread), can I suggest that @codingthat creates a PR with this in? If anyone else would like to object, please do so, but I worry we’re in the weeds a litle right now!
Rendered Preview:
Description
Your job is to translate RNA sequences into proteins.
RNA strands are made up of three-nucleotide sequences called codons. Each codon translates to an amino acid. When joined together, those amino acids make a protein.
In the real world, there are 64 codons, which in turn correspond to 20 amino acids. However, for this exercise, you’ll only use a few of the possible 64. They are listed below:
| Codon | Amino Acid |
|---|---|
| AUG | Methionine |
| UUU, UUC | Phenylalanine |
| UUA, UUG | Leucine |
| UCU, UCC, UCA, UCG | Serine |
| UAU, UAC | Tyrosine |
| UGU, UGC | Cysteine |
| UGG | Tryptophan |
| UAA, UAG, UGA | STOP |
For example, the RNA string “AUGUUUUCU” has three codons: “AUG”, “UUU” and “UCU”. These map to Methionine, Phenylalanine, and Serine.
“STOP” Codons
You’ll note from the table above that there are three “STOP” codons. If you encounter any of these codons, ignore the rest of the sequence — the protein is complete.
For example, “AUGUUUUCUUAAAUG” contains a STOP codon (“UAA”). Once we reach that point, we stop processing. We therefore only consider the part before it (i.e. “AUGUUUUCU”), not any further codons after it (i.e. “AUG”).
4 Likes
Sounds good to me,
Re: consistent (Done)STOP, should the Stop Codons header by STOP Codons?
2 Likes
LGTM
(Post must be at least 10 characters)
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Looks GTM.
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Looks good to me.
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Thanks @iHiD for the cleanup and sidestepping. One minor request is to re-standardize a term, since the proposed now has three ways of referring to the stop codons: “STOP” codons, “STOP codons,” and STOP codon (without quotes). I’d love to make all three simply STOP codon(s) (without quotes) as earlier agreed upon. If not, I am otherwise in favour of PRing your version and willing to do so. Thanks again.
Given that the proposed changed is all signed off on, how about just pushing that change as is then circling back for further refinements? If you make a PR using the approved change, you should be able to get it merged pretty fast. Once that’s done, any future changes should be small and simple.
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None of the 65 tracks (including Cairo and Rust) implement additional codons at the moment.
2 Likes
I’ve edited the first bit of text in the section to be consistent with the title.
I think the STOP should be in quotes because otherwise it looks like someone is shouting “STOP [the] codons” in the same way someone might shout “STOP [the] thief!”. It needs to be clear that it’s a term we’re introducting. Once it’s been defined it then doesn’t need the quotes any more
LGTM!
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Ah yeah, you’re right, that would’ve made sense.
Thanks, that’s a good point.
PR’d at Rewrite per discussion by codingthat · Pull Request #2570 · exercism/problem-specifications · GitHub
Thanks, everyone! 
1 Like