Talk:Silent mutation

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This is an interesting article addressing why silent mutations might not be so silent. [[1]]

If there are parrallel codes in genomic sequences then altering one base pair, while not changing the actual amino acid, might impact other lines of coded information; possibly information pertaining to gene regulation, splicing of pre-mRNA. The more we learn about DNA the more amazing it becomes. --jorgekluney

Hello author of article, You might want to link some of the studies that have been finding dual-coding genes. Talk about exciting! Further research showing that there might be alternate reading-frames in the same genetic segment (overlapping genes *in the same segment* that code for multiple proteins-wow). --jorgekluney

On the other hand, the degree of evolutionary sequence conservation is higher for proteins than for the DNA encoding them, indicating that many or most silent mutations within reading frames are, in fact, silent.

Proposed Plan for Article Improvement[edit]

The article is an important topic in molecular biology and genetics, and thus should be expanded to further introduce and explain the topic. Expansion to the introductory section is planned including refining what is already submitted, including adding an image to better illustrate the definition of "silent mutation", and adding further background or history as applicable. Current discoveries or research updates will be added as well to illustrate the relevance of the topic. A more comprehensive tie in with the degeneracy of the genetic code can help to further develop the topic along with discussing the role of silent mutations in protein structure, folding, and function from the primary level up to tertiary and quaternary levels. The role of silent mutations in disease will be expanded with additional examples given. Finally, the experimental use of silent mutations in research and biotechnilogical advancements will be examined. Awotawa1 (talk) 03:00, 14 March 2013 (UTC)

Our group has begun our initial substantial contributions to improving this article. We've re-structured some of the main topic headings, while adding others and meaningful content within the body of the article from a number of different sources and perspectives. Any feedback on further improvements or opinions on current edits are much appreciated. Awotawa1 (talk) 03:17, 5 April 2013 (UTC)
Our group has taken into consideration and implemented several of the suggestions of the reviewers who have been courteous enough to review the article and offer their feedback. Many thanks! The introductory section has been restructured to improve grammar and flow of information. The section on silent mutations and the genetic code has been expanded and edited for grammar and usage. The tRNA section has been edited and refined for improved readability. Some inline citations have been corrected in regard to placement and usage as well as correct citing standards. There are still several reference sources that will be included as inline citations to conform to the rest of the article. Additionally, at least images for silent mutation examples and tRNA molecules and silent mutations will be included in the final version of the article, and other sections not previously mentioned will be expanded. It is still a work in progress, but a little more refined than before. Please keep the great feedback coming! Awotawa1 (talk) 04:24, 26 April 2013 (UTC)

Comments from Jberendt[edit]

So far, good contributions to this article. I would like to suggest cutting your lead section down. The first paragraph does a nice job summing up the article and I think the second paragraph adds some good information as well that could be kept. However, the second paragraph (if you want) and definitely the third could be made into their own sections if you had more to add to it. A section on studies performed such as what you mentioned about molecular cloning would be a great addition or you could simply add this to your examples section.

Another good contribution to this article would be visuals. An image of codons and the wobble position would be good in the section on silent mutations and genetic code. Also a chart of codon synonyms would be a good display of your content here.

Sources need to be cited in the tRNA section as well as in the examples section. I am confused by your references list at the bottom. Maybe these are what are supposed to be the sources for the two sections but it does not follow the format that allows readers to know exactly where your information came from.

Also, the nonsynonymous link does not exist in the examples section. There is a nonsynonymous substitution article you could link. However, you will notice that this is also a stub article so a better choice may be more appropriate. Jberendt (talk) 03:14, 11 April 2013 (UTC)

Thanks for the comments, Jamie. We do plan to add some images to aid in visualizing what is explained in the text. Also, the suggestion for the introductory section is appreciated.Awotawa1 (talk) 16:29, 14 April 2013 (UTC)
Amy, your lead section flows better with your recent editing and good use of wiki links! Jberendt (talk) 03:52, 26 April 2013 (UTC)
Thanks, Jamie. It's always easier to go back and improve with the help of great review comments and just a second or third look by oneself. Hope all is well with your group and project. Awotawa1 (talk) 03:55, 26 April 2013 (UTC)
Nice image at the start of the article! This definitely adds to the overall quality. Best of luck with wrapping up your project! Jberendt (talk) 02:00, 10 May 2013 (UTC)

Comments from Jakodak[edit]

Since all of these articles are in their infancy essentially, it seems rather unhelpful to critique the lack of detail or precise syntax. I understand the authors already know this. Therefore, my critique focuses on providing feedback concerning definitions, focus, and structure.

Generally, I like the way this article is structured. My sampling of the references indicated they are properly placed and lend great credibility to the assertions made. Although this article currently has no image or cartoon demonstrating the concept of a silent mutation, some concepts simply are not very amenable to pictorial representation. Pictures can sometimes confuse more than they teach and that may be the case with silent mutation. I have just one major critique of this article and because any advice regarding structure is somewhat dependent on how the authors respond to it, I will await the response.

There is one basic definitional problem within this article that needs to be clearly resolved in order to avoid confusion going forward. The authors point out that the term ‘silent mutation’ is used broadly to encompass non-consequential mutations as well as synonymous mutations. I do not doubt this is the case, but the authors have to be wary of maintaining this distinction. For instance, in the first sentence of the lead section silent mutation means one of two things: either a synonymous point mutation or an actual substitution with no discernible consequence. However, in the section further down titled ‘Structural Consequences of Silent Mutations’, silent mutation means only the former.

This distinction might be clear in the authors' heads, but I was confused when I first encountered the last sentence of the lead section. If the definition of a silent mutation is essentially any mutation with no discernible consequence, then a mutation with a definite and measurable affect should not be a gradation or a subset of a silent mutation. After reviewing the footnotes provided for this sentence, I understood the source of my confusion. The Beckman reference is using the synonymous mutation definition of silent mutation, a narrower definition than the wiki article lead. Beckman defines silent mutation strictly as a point mutation with no change in amino acid sequence. With this narrower definition, it makes sense to say that a silent mutation is not necessarily so silent if, in fact, there are still consequences. On the other hand, using the broader definition offered by the wiki article lead section creates a fundamental contradiction. The wiki article might very well be correct in describing the term’s use more broadly, but if so, the different senses of ‘silent mutation’ need to be carefully distinguished early on to avoid any confusion.Jakodak (talk) 15:36, 11 April 2013 (UTC)

Thanks for the useful feedback, James. I appreciate you pointing out the discrepancy with the range of the definitions. As you said, because this was clear to me when contributing to the article, I really didn't notice it at all until now. Great point!Awotawa1 (talk) 16:29, 14 April 2013 (UTC)

Review by Keilana[edit]

Hi guys, I've got a full review but I need to make something very clear before I start. Plagiarism (or as we call it here, copyright violation) is totally and completely unacceptable. I found three separate instances of blatant plagiarism in this article and removed them all. I've asked you in the review below to rewrite that information without copying it. Plagiarizing here is not just an issue of academic integrity, it is a very serious legal issue for Wikipedia, and besides, continuing to plagiarize can get you blocked. Please be more careful in the future. With that said, here's a full review. Keilana|Parlez ici 21:59, 19 April 2013 (UTC)

  • Don't bold "do" and "do not", or anything else in the lead, besides the first instance of "silent mutations".
  • Is it the final amino acid behavior or the final protein product's behavior? Please clarify.
  • You don't need citations in the lead if the information is covered elsewhere in the article (and except for rare cases, it should be).
  • Link isoleucine and leucine.
  • Footnote 2 needs a full citation template with all of the information so it's formatted correctly. This source could also be used throughout the article.
  • Don't capitalize after the first word in section headings (this is just weird Wikipedia house style, different from academic writing).
  • Either gloss or link degeneracy of the genetic code.
  • Put footnotes after the period throughout and remove spaces between the two footnotes.
  • I removed most of the first section because it was directly plagiarized from the sources. Please rewrite that information with a new source, as a USMLE prep book is in no way an acceptable source for a Wikipedia article.
  • That said, the first section of "Silent mutations and the genetic code" needs citations.
  • The section on tRNA needs to be written in a more encyclopedic tone, it also needs citations.
  • Use section headings (equals signs) for the subsections in "Structural consequences"
  • Mention that nonsense mutations are the premature insertion of a stop codon.
  • The last sentence of "Primary structure" needs a citation.
  • Explain complementary bonding.
  • You don't need to duplicate footnote 8, remove the first one.
  • Citation 5 needs to be formatted properly.
  • Check your use of "effect" and "affect".
  • I removed more plagiarism in "tertiary structure". Rewrite the stuff from source 9.
  • The Examples section needs citations throughout.
  • Examples also needs to be rewritten with a more encyclopedic tone and less acronyms. Also check your capitalization throughout.
  • All of the sources at the end need to be inline citations. I'm not sure what they're doing there.

Thank you Keilana, we will be more cautious and will avoid all plagiarism . Tbrownc1 (talk) 02:36, 25 April 2013 (UTC)
Thanks Keilana for your more than thorough review. As for the accusations of plagiarism, I assure you that anything resembling plagiarism on content that has been added by our group has been completely inadvertent. We will work to ensure that there is no hint of plagiarism in the article and I have been unaware of any copying that occurred as you put it. We will take all of your points into account when continuing to refine our work on the article. Thanks again. Awotawa1 (talk) 03:08, 25 April 2013 (UTC)
Just so you're aware, here is the edit where I removed the plagiarism so you know what it was. [2] Let me know if you have any questions. Keilana|Parlez ici 03:55, 25 April 2013 (UTC)
Thanks, Keilana. We will rewrite the portions of these sections we would still like to include in the article. Thanks for pointing them out. Awotawa1 (talk) 04:08, 25 April 2013 (UTC)
Awesome, best of luck. Keilana|Parlez ici 04:15, 25 April 2013 (UTC)

Comments from Jbmontgomery24[edit]

Awotawa1 and Tbrownc1, your article is starting to come together quite well and has a nice flow to it. Wonderful job! I look forward to seeing the final product next week! With that being said, please see my suggestions listed below, and do not feel obligated to make these changes.

  • I would like to echo on Jberendt's comment about visuals. I believe visuals with contribute to your article immensely. Perhaps, an image can be added to the lead section to catch the reader's eye on this interesting topic?
  • When trying to emphasize a word, do not bold it. Instead, Wikipedia prefers emphasis to a particular word to be italicized. Don't worry - our group did the same, but this was a suggestion from our OA. Please see the following link:Wikipedia:Manual_of_Style/Text_formatting#Emphasis.
  • Under "Silent mutations and the genetic code", link the word reading frame.
  • Under the "Structural consequences of silent mutations" header, I would change the primary, secondary, and tertiary structure sections from header sections (3 equal signs on each side of the title) to subcategories (2 equal signs on each side of the title) under the main header of "Structural consequences of silent mutations". It will make the article look more cohesive since those potential subcategories appear to go under that main header.
  • For the "Transfer RNA" section, link ribosome.
  • Unlink "nonsynonymous" since it is in red in the article - linked page does not exist for that word.
  • All of the references appear to be in an orderly fashion, but the last five references (11-15) are not numbered and linked to the corresponding parts of the article.

I look forward to the final contributions next week. If either of you have any questions and/or comments that I can help you both with, please feel free to let me know. Good luck! Jbmontgomery24 (talk) 18:12, 1 May 2013 (UTC)

Thanks Jbmontgomery24, all of your suggestions were very helpful and we will look into implementing them into our article. Tbrownc1 (talk) 00:03, 3 May 2013 (UTC)
Not a problem! Please feel free to let me know if you have any other questions and/or need any insights on anything else. Keep up the great work! Jbmontgomery24 (talk) 00:47, 3 May 2013 (UTC)
Great suggestions Jbmontgomery24! I agree with all of them. Thanks! Awotawa1 (talk) 01:55, 3 May 2013 (UTC)
Awotawa1, I'm glad you agree with the suggestions. Hopefully, they will only contribute to this wonderful article that you both have established. Also, I liked the suggestions that laurenwking mentioned, so with these final edits, your group should be in great shape! Look forward to seeing it next week! Cheers! Jbmontgomery24 (talk) 14:22, 3 May 2013 (UTC)
Awotawa1 and Tbrownc1, I had the number of equal signs backwards on the bulletin that I had listed about changing the primary, secondary, and tertiary structures as subcategories. Headers have 2 equal sings after each side of the title, whereas subcategories have 3 equal signs after each side of the title. I'm sure you both would have figured this out, but I wanted to give you a heads up my minor error in my main review. Hope this helps clarify any potential confusion. Good luck! Jbmontgomery24 (talk) 17:15, 4 May 2013 (UTC)
I wanted to also give you both a heads up that your first word of the article, "Silent mutation" can be in bold; however, the remaining body of the article cannot be in bold or italic per the suggestion I got from our OA (Keilana). Hope this helps! Jbmontgomery24 (talk) 17:52, 7 May 2013 (UTC)

Comments from laurenwking[edit]

Hi guys, Overall I think that the article is good. I agree with everything that jbmontgomery24 says. I think that it flows pretty well but it definitely needs images. I really like the Examples section, but I don't think I like that title. I saw the title and thought I was going to see examples of silent mutations. Maybe name it Effects of Silent mutations or something like that? My only suggestion that hasn't been touched on by others is in regards to the "Tertiary structure" section. I know we are all walking a fine line between too little and too much information on our pages. This section seems light to me. Another sentence or two, or even an example will help. I look forward to seeing the final product next week! Laurenwking (talk) 03:34, 3 May 2013 (UTC)

Thanks, Laurenwking. I like your suggestions. I agree with your comments on the subsection of tertiary structure. Awotawa1 (talk) 05:30, 3 May 2013 (UTC)
I appreciate the feedback Lauren. We are in the process of finding more images but it has been a somewhat difficult task. Tbrownc1 (talk) 16:48, 9 May 2013 (UTC)