Tweak language and formatting in `protein-translation/description.md`

Exercism Support
,
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  • Remove extraneous => for consistency
  • Remove redundant “after” (given “subsequent”)
  • Wikipedia just calls them “stop codons,” not “STOP codons,” but I italicized instead as a way to introduce a new term
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We ask that all changes to Exercism are discussed on our Community Forum before being opened on GitHub.

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Would the test case descriptions referencing STOP codons need to be updated as well for consistency? I’d rather not reimplement all those tests.

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What I like:

  • The removal of the => at the end of the line.
    IMHO the => at the beginning of the line is enough

I’m not sure about the other changes:

  • The removal of “(by the ribosome)”
  • The removal of the empty line between the explanation of stop codons and the examples.

Edit: The “fat arrow” is used across the whole file to describe some sort of sequence of steps or a transformation process.

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The => shows up elsewhere in the file. Removing it in one place does not make the file consistent.

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You’re right. I’ll edit my comment.

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Sorry about that. My habits are embarrassingly ingrained sometimes!

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You might want to back this out and reconsider what needs updating, if anything here, and propose a change without any PRs involved to discuss :slight_smile:

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It’s actually already just called “stop codon” later in the description. The fact that “STOP” is an expected test value isn’t really indicated by the current text. But I figure it doesn’t need to be—same way error messages are often not specified up front.

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Looking a bit closer, my change makes it consistent with the other uses in the file (and right next to it): one fat arrow per line, never 2.

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I appreciate your comment, but I’m confused, won’t this just be a new thread with the same discussion about the same proposed changes? Or do you mean I should have a separate thread for each change? Or one big thread but discussing the changes sequentially?

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Sorry, I forgot to mention “by the ribosome.” I removed that too since the word “ribosome” isn’t used anywhere else in the description, so this seems confusing at best for those who aren’t familiar with it. “By the program” would be more consistent with the rest of the description, but it’s also redundant. Hence the removal.

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The tests don’t check for a STOP value. It’s up to the student how they want to handle it as long as translation stops and the sequence is returned. That’s the behavior the tests related to stop codons are checking.

I was instead referring to the test descriptions in the canonical test data since it was unclear if we should update those as well so “STOP codon” is “stop codon”. Generally, the descriptions get reused in a track’s test suite in one form or another so that’d also be public-facing. However, we can’t just update the test descriptions for existing tests so new tests re-implementing the old tests but with updated descriptions would be needed. Then maintainers know they have tests to update and can do so. Not all tracks have generators so that’ll take up maintainer time.

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Oh — that must be specific to Elixir:

    @tag :pending
    test "identifies stop codons" do
      assert ProteinTranslation.of_codon("UAA") == {:ok, "STOP"}
      assert ProteinTranslation.of_codon("UAG") == {:ok, "STOP"}
      assert ProteinTranslation.of_codon("UGA") == {:ok, "STOP"}
    end

In fact, in the Elixir test descriptions it’s already “stop codon” almost everywhere, except in one.

Anyway thanks @BNAndras I see your point. I can remove that part of the PR (or rather, change the other instance of “stop codon” in the description to “STOP codon”) if that’s the final answer. :heavy_check_mark:

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Rather than using PRs to convey intended changes, can you update this forum thread with the latest proposed change(s) for discussion/approval?

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Sure, sorry, I didn’t mean I’d put in a new PR until everything was agreed. Here’s where I believe we’re at:

  • Remove extraneous => for consistency
  • Change 'STOP' codon and stop codon to both be STOP codon (caps but no quotes) to avoid extra test maintenance.
  • Remove “(by the ribosome)” for consistency and accessibility.
  • Remove redundant “after” (given “subsequent”)
  • Remove the empty line just before the redundant “after” because it heavily depends on the previous line, so makes more sense in the same ¶ rather than as a new idea.

^^ @siebenschlaefer sorry, I missed explaining that last one too earlier. I believe what probably happened is that it used to say “after a STOP codon.” But I think what I propose (removing “after” and also the newline) is both more concise and more readable.

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The fat arrow sequence section is difficult for me to parse mentally since the info after each => rephrases what the previous transformation is. So I’m going forward in the sequence when I hit the => and expecting the next transformation, but instead I’m seeing the previous transformation rephrased.

I’d suggest we show the steps like this:

RNA => Three-letter codons => proteins
"AUGUUUUCU" => "AUG", "UUU", "UCU" => "Methionine", "Phenylalanine", "Serine"
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There are 64 codons which in turn correspond to 20 amino acids; however, all of the codon sequences and resulting amino acids are not important in this exercise. If it works for one codon, the program should work for all of them. However, feel free to expand the list in the test suite to include them all.

That should read not all codon sequences and resulting amino acids are important. However, we should rephrase this since only CLI users would be in a place to run modified tests locally. That whole section ca be shortened to:

There are 64 codons which in turn correspond to 20 amino acids; however, not all codons will be used in this exercise.

We later provide a table of the relevant codons so perhaps we don’t even need this line.

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Just as an FYI, I did some work on this here: website/bootcamp_content/projects/string-puzzles/exercises/protein-translation/introduction.md at 00934f71f43f8efb5cb28d256bf8b46c99b218a7 · exercism/website · GitHub

(I don’t have brainspace to engage with the discussion, but maybe there’s something there that’s useful?)

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Thanks @BNAndras , I agree with both those proposals, except I now see that “proteins” should be “amino acids” for the third step. Could I make it into a horizontal table to align the corresponding elements? (It’d fit a standard 80-char terminal still even for people reading unrendered Markdown that way.)

RNA Three-letter codons Amino acids
“AUGUUUUCU” “AUG”, “UUU”, “UCU” “Methionine”, “Phenylalanine”, “Serine”

And thanks @iHiD , that’s helpful, I’m seeing ideas we can pull from your changes and make consistent (like active voice):

RNA can be broken into three-nucleotide sequences called codons, and then translated to a protein like so:

becomes

You can break an RNA strand into three-nucleotide sequences called codons and then translate them into amino acids to make a protein like so:

and

There are also three terminating codons (also known as ‘STOP’ codons); if any of these codons are encountered (by the ribosome), all translation ends and the protein is terminated.

All subsequent codons after are ignored, like this:

becomes

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, UAA is a STOP codon, so ignore any subsequent codons:
… (similar table here) …
(Note that the latter AUG is not translated into another methionine.)