Talk:Protein moonlighting

Text books notes
Paraphrased From the text book: "Many cells' flagellum consist of a single protein called flagellin." Caption of figure 1.14, page 13. Swmmr1928 (talk) 02:46, 16 March 2011 (UTC)

Sriram also said that we could talk, in our article, about diseases as a result of a deficiency of an enzyme. As a result of this deficiency, the doctors have trouble treating this because the symptoms are not what they would expect because of the multifunctions of that protein that the victim was deficient in. Swmmr1928 (talk) 02:59, 16 March 2011 (UTC)

From class textbook
For example, trees suck out protein from leaves before the leaves are let go. The protein makes bark.

Motor proteins can carry out mechanical activities.

Information of product design resides in the nucleic acids and the construction workers are normally proteins.

The chromosomal DNA of eukaryotes, unlike that of prokaryotes, is tightly associated with proteins to form a complex nuceloprotein material known as chromatin.

Movement of prokaryotic cell is accomplished by a thin protein filament called a flagellum which protrudes from the cell and rotates.

The genetic material of a virion is surrounded by a protein capsule or capsid.

Viruses have on their surface a protein that is able to bind to a particular surface component of its host cell.

Molecules of misscellaneous function include vitamins, which adjuncts to proteins.

Proteins are the macromolecules that carry out virtually all of a cell's activities they are the molecular tools and machines that make things happen.

Proteins can allow cell recognition. Proteins do DNA stuff like regulation and reproduction. Proteins allows cellular transport. Proteins contribute cell structure. Proteins allow motility which allows muscles to work. Proteins allow storage of nitrogen that is stable and will not degrade.

Proteins have more than one function. Crystallins cause refraction of light. Proteins with multiple functions are called moonlighting proteins.

You need to eat protein because humans cannot make all 20 amino acids.

As ezymes, protens vastly accelerate the rate of metabolc reactions. As structural cables proteins provide mechanical spport both within cells and outside their perimeters as hormoes, growth factors, and gene activators, proteins perform a wide variety of regulatory functions as membrance receptors and transporters. Proteins exhibit a high degree of specificity because proteins have shapes and surfaces that allow them to interact selectively.

The side chain or r group bonded to the a carbon is highly variable among the 20 building blocks and it is this variability that ulitmately gives proteins their diverse structures and activitites.

My sentence: "THe side chains can be separated into four groups, polar charged, polar uncharged, nonpolar" Protein Structure

Primary structure of a polypeptide is the specific linear sequence of amino acids that constitute the chain. The term conformation refers to the three dimensional arrangement of the atoms of a molecule, to their spacial organization. Secendary structure describes the conformation of portions of the polypeptide chain. Two conformation were preferred that provided the maximum possible number of hydrogen bonds. In the alpha helix, the backbone of the polypeptide was cylindlical. The backbone lies on the inside of the helix, and the side chains project outward. There are hydrogen bonds between the peptide bonds that give this structure strength. Every amino acid is close to the amino acid four amino acids above it and the carbonyl group will form a hydrogen bond with a imine group. Oxygen and hydrogen will form a hydrogen bond.

In the beta pleated sheet, several segments of a polypeptide lie side by side in a folded or pleated conformation. Side chains will alternate projecting upward and download.

Tertiary Structure describes the conformation of the entire polypeptide. Tertiary structure is stabilized by an array of noncovalent bonds between diverse side chains of the protein. Secondary structure is limited to 2 conformations, but tertiary structure is virtually limitless. Tertiary structure is determined using x-ray crystallography.

Protein Domain. Most eukaryotic proteins are composed of two or more spatially distinct modules or domains, that fold independent of one another. An enzyme can consist of four distinct domains. The different domains of a polypeptide often represent parts that function in a semi-independent manner. Proteins domains are often identified with a specific function.

Proteins composed of subunits are said to have Quaternary Structure. A protein composed of two identical subunits is described as a homodimer, whereas a protein composed of two nonidentical subunits is a geterodimer.

173.66.192.26 (talk) 00:16, 27 March 2011 (UTC)

Summary
This article focuses on moonlighting proteins which are proteins with more than one function. It first discusses the discovery of the moonlighting proteins and the theory behind moonlighting protein evolution. Next, it discusses the research techniques used to identify protein functions, specifically the use of mass spectrometry. The group then compares normal proteins and moonlighting proteins with regard to structure, function and method used to complete their functions. They sum up by examining the relevance of moonlighting proteins’ to modern science and how engineering aspects can be applied to the concept of moonlighting proteins.

Major Concerns
In the history section, talking about Piatagorski and Wistow and how they came about discovering moonlighting proteins in the 1980’s and expanding the ideas in the first paragraph could enhance this section. The 2nd paragraph touching on how moonlighting proteins were believed to come about through evolution is very logical and well put together. The links look good as well. It could be interested to talk about exactly when moonlighting proteins were accepted as truly existing (specific experiment, lab, date, etc.)

The techniques used to determine a protein’s function section could go into more detail about techniques other than mass spectrometry as well as going into more depth on the unknown function mentioned at the end of the last segment.

In the section titled “Comparing normal proteins and moonlight proteins,” explain and support the claim that moonlighting enzymes have two active sites, whereas a normal enzyme has just one active site. Much of the information under the structure section seems to fit better under the functions paragraph. To improve the structure section, look into different potential structures of moonlighting proteins and how they differ from one another. The Function paragraph seems to mainly focus on examples of enzymes instead of the actual functions themselves. Consider listing some common functions of moonlighting enzymes compared to the functions of non-moonlighting proteins. The final paragraph in this section seems to be a combination of the first two paragraphs. Maybe instead of having a separate “How they moonlight” section, the information could be split into the other two paragraphs, or most of the information could be moved and then the third paragraph could have specifically how an enzyme moonlights (do the two reactions occur at the same time, in what situations does the enzyme act as what substrate, what makes how moonlighting proteins work different from how normal enzymes work, etc.)

The scientific relevance paragraph seems to be disconnected. To improve the flow of this section, it would be useful to switch the order of sentences 2 and 3. Also, a lot of points could be elaborated. For instance, in the sentence that begins with “Such large numbers suggest that they are abundant…” explain what large numbers are being referred to. Overall, while this section is a strong start, it could definitely be more specific. The engineering proteins section needs to be elaborated. While the definition of protein engineering is important, how does this relate to moonlighting proteins? How do engineers plan on using the methods of protein engineering with moonlighting proteins?

Minor Concerns
In “Techniques used to determine a protein’s function”- consider word choice. The sentence beginning with “the manner in which scientists…” hurts the flow of information and should be considered for removal.

In the Scientific relevance section, this sentence: “The bacterium M. tuberculosis has a moonlighting protein in which one of its functions counteracts the effects of antibiotics” is a little unclear. Maybe try “One of the moonlight functions of the bacterium M. tuberculosis counteracts the effects of antibiotics.”

Overall citations and grammar look good. Look over some word choices.

Summary
The authors explain that a moonlighting protein is a protein that performs more than one function, such as enzymatic activity, cellular structure, or signal reception/transduction. They then describe techniques used to identify moonlighting proteins and then the primary ways in which moonlighting proteins are different from regular proteins. Following this, they discuss the operational aspects of moonlighting proteins. They conclude the article by discussing the wider implications and applications of moonlighting proteins.

Major Concerns
In the introductory paragraph, a specific example is given for structural functionality (lens crystallins) but not for any of the others. Consider adding examples for each of the functionalities mentioned or removing the one example. Including multiple functions but only one example makes the sentence read awkwardly.

In the “Techniques” section are there other techniques not mentioned? If so, include them and short descriptions, if not, retitling this section would be appropriate.

In the Structure section, “I-Amil maturase and PutA” are mentioned, but not elaborated upon. Identification of what these specific proteins are and do would be relevant and helpful (similar to how DegP’s function was explained when it was mentioned). If possible, an image displaying their crystalline structure would be useful as this section references said structure multiple times.

In the Functions section, the first two paragraphs are very vague and confusing. Enzymes ARE proteins that catalyze chemical reactions: should enzyme be protein? More discussion of the other functions proteins can moonlight would be helpful.

“Conserved”/”ancient proteins” are not explained at all, what exactly are they and how do they specifically relate to moonlighting proteins? The pyruvate carboxylase example is well done but it is not clear what two functions the E. coli protein performs, its function in DNA replication is explained but its antioxidant role is not.

In “How they moonlight,” the various ways moonlight occurs could be separated and explained individually, as in the case of differential localization. The other methods are all mentioned in one sentence and then explained together in a way makes distinguishing each method difficult.

The protein engineering section should either be expanded by including examples and further explanation or else eliminated altogether. Incorporating it with the scientific relevance section and connecting it to the tuberculosis example would improve both sections.

Minor Concerns
The final sentence of the introductory paragraph is not structured correctly, “functions of proteins include…to growth and motility.” Perhaps change to “to aid in growth and motility.”

In the sentence “these uni-functional proteins now had the ability to perform multiple functions” change ‘now had’ to gained.

Several examples of misused singular/plural forms (One example: “Other methods through which proteins may moonlight are by changing its oligomeric state”, “proteins” is plural, “its” is singular)

This is a purely organizational note, but it might make more sense to move the section discussing functional differences of moonlighting techniques BEFORE the practical identification (NMR) section, as the functional differences are more relevant to the purpose of the article.

Consider moving the table to the right side of the article, with the “structure,” “functions,” etc. sections to the left.

The headings of each section read more like sentences and should be condensed to one or two words (ie “Techniques used to…” could be shortened to “Practical Identification” or something similar.

References 16,17 and 18 are all cited previously (as 7, 3 and 3 respectively.) Should be condensed as 10-15 were. Otherwise, the references seem to be cited appropriately.

Dride (talk) 20:35, 13 April 2011 (UTC)

Merge
Gene sharing discusses the same topic and should be merged with Moonlighting protein. Quarl (talk) 06:02, 17 April 2011 (UTC)


 * Agreed. Boghog (talk) 12:34, 17 April 2011 (UTC)


 * I agree they should be merged, but I suggest Protein moonlighting is a better title. There's discussion at Wikipedia talk:WikiProject Molecular and Cellular Biology.  Adrian J. Hunter(talk•contribs) 13:28, 18 April 2011 (UTC)


 * The two articles are quite complementary, so an eventual merger is desirable. However, Moonlighting protein is the subject of a educational assignment that will end by May 15, 2011 (see talk page). Identifying student contributions and grading this assignment will be easier if Moonlighting protein is kept separate until that date. I can encourage the student group writing that article to merge them after this date. Any problems with this? 68.34.44.204 (talk) 02:56, 20 April 2011 (UTC)


 * That comment was by me -- I forgot to sign in before posting. UM BIOE120 Instructor (talk) 02:58, 20 April 2011 (UTC)


 * No complaints from me – as far as Wikipedia is concerned, there is no deadline. For now I've boldly removed the merge tags, as there's consensus the merge is appropriate and I can't imagine anyone opposing it. Apologies if my and others' edits will make grading harder, but the page was in article space, so I assumed it could be edited by anyone.  Kudos to you and your students for creating this, too – you've found a hole in Wikipedia's coverage, and added plenty of valuable and up-to-date information, and I think the final merged article is going to be excellent. Adrian J. Hunter(talk•contribs) 05:45, 20 April 2011 (UTC)


 * Thanks Adrian. The credit for the work rightfully goes to the student team who wrote it. UM BIOE120 Instructor (talk) 01:18, 22 April 2011 (UTC)

Recent edits
I have restored an earlier version and have selectively included some of the newer material. Please note that Wikipedia is an encyclopedia and its article should simply state facts. The restored lead is factual statement of what a moonlighting protein is. The reverted lead reads like an essay (e.g., "Biochemists do not know why") and therefore is not appropriate for an encyclopedia. In addition, the reverted material contained too many peacock terms (e.g., "result of groundbreaking research", "the archetype of a universal metabolic pathway", etc.). Boghog (talk) 03:26, 27 April 2011 (UTC)


 * Hello Boghog :) Thank you for taking interest in this article and I would gladly discuss some of your problems with my edits.   Instead of "Biochemists do not know why..." how about "There is still no accepted reason why..."
 * I would argue that "the archetype of a universal metabolic pathway" is not a peacock term. It is used to describe the same thing in the article on glycolysis.
 * What other issues do you have with my edits? Sw mmr1928  talk  15:04, 27 April 2011 (UTC)


 * Hi talk:Swmmr1928. Thank you for your response. You have added a lot of good material to the article, but I thought that your last edits were taking the article in the wrong direction. To expand on my previous explanation, the biggest concern I had was about the lead.  The lead should concisely define the subject and scope of the article as will as summarize the most important parts of the article.  The lead should also explain why the subject is important or notable.  While you did attempt to explain why the subject is notable, I think you over stated the case.


 * Yes. I was trying to include each heading in the lead. Sw mmr1928   talk  21:44, 27 April 2011 (UTC)


 * In particular, the statement "moonlighting activities of proteins are essential for the study of cellular function" raised some alarm bells. As discussed here, I and number of other contributors that are knowledgeable about proteins have never heard of the phrase "moonlighting protein" before. Furthermore, while searching for this term in PubMed did return ~110 citations, this is a very small fraction of the number of papers that have been published on protein function.  How can moonlighting activities be essential for the study of proteins when so few papers have been published about the subject?


 * "Because knowledge and cataloging of the moonlighting activities of proteins are essential for the study of cellular function and human physiology, we also review recently reported and recommended methods for the discovery of moonlighting activities." It does not matter how many people have never heard of the phrase "moonlighting protein" before or how many papers have been published about the subject.  WP is not a Democracy and I am quoting a peer reviewed journal (Sriram 2005). Sw mmr1928   talk  21:35, 27 April 2011 (UTC)
 * Now we have two problems. The first that I already mentioned is that Sriram has grossly overstated the case.  The second is that you have quoted the author verbatim from the abstract of the source without providing in-text attribution.  You can solve both problems by including in-text attribution. The fact that only a tiny fraction of protein research articles mention moonlighting strongly implies that moonlighting cannot be essential to the study of proteins.  To state that moonlighting is essential destroys the credibility of this article and is contrary to WP:NPOV.  On the other hand, stating that Sriram thinks moonlighting is essential is OK.  Boghog (talk) 04:12, 28 April 2011 (UTC)


 * How else could I provide an in-text attribution without stating that Sriram thinks moonlighting is essential?
 * There should be no problem stating that Sriram thinks moonlighting is essential. Alternatively you can rephrase what he wrote.


 * Also unsupported statements such as "biochemists do not know why proteins began moonlighting" are at best not very enlightening and at worst are misleading. Proteins began moonlighting because these additional functions were found by evolution to be advantageous to the organism.  There is no more mystery to a protein adopting  a second function as compared to its first function.  Both functions are a result of evolutionary pressure.


 * "There are two nonexclusive hypotheses about the existence of moonlighting activities: that these activities simply evolved and were not lost and that they offer definite advantages to the cell or organism (Jeffery 1999)."


 * "It has been speculated that moonlighting possibly evolves as a way to expand the functional capabilities of an organism without the burden of an expanding genome . However, this is not very likely as in many organisms large parts of the genome do not seem to have a function and thus there may be little selection pressure to limit genome size (Huberts 2010)."  Sw mmr1928   talk  21:37, 27 April 2011 (UTC)


 * An expanded version of this statement is OK, but perhaps it would be better to move this out of the lead. Boghog (talk) 04:12, 28 April 2011 (UTC)


 * "Biochemists thought that each protein had at most one function" – this statement is probably false. While I am not 100% certain, I think one could probably find at least a few examples of proteins serving more than one function published prior to 1988.


 * Yes this would improve the article if you knew when the discovery of multiple roles of proteins occured:) Sw mmr1928   talk  21:39, 27 April 2011 (UTC)


 * I need to do some more digging. Boghog (talk) 04:12, 28 April 2011 (UTC)


 * "archetype of a universal metabolic pathway" – Yes, I now see that that phrase is used in the glycolysis article, but even there, I think using this phrase is over done while in this article, it is off-topic. A simple wiki link to glycolysis should be sufficient.
 * Referring to scientists and biochemists, with the exception of the history section, is unnecessary. Just refer to the results of the research and not who did the research.
 * Again, I wanted to reiterate that I think that you have done a great job in expanding this article, but I think it needed a mid course correction. I look forward to more of your contributions.  Cheers.  Boghog (talk) 19:52, 27 April 2011 (UTC)


 * Can I make some of my edits again that you reverted that you have not brought up here. For example, you removed a citation. Sw mmr1928   talk  21:41, 27 April 2011 (UTC)


 * I would not object to including modified versions of your edits as discussed above. Boghog (talk) 04:12, 28 April 2011 (UTC)


 * I wish you had made incremental edits or created a discussion instead of undoing so much at once with no notice.
 * What are the problems with these edits?


 * http://en.wikipedia.org/w/index.php?title=Moonlighting_protein&action=historysubmit&diff=426136112&oldid=426136066
 * wiki link to very specialized term for which is it is unlikely an article that will ever be written. The way it was originally written in quotes IMHO is better.

Is 8531 results for differential localization not enough? Have you never heard of this term either? Sw mmr1928  talk  18:26, 28 April 2011 (UTC)
 * I immediately understood what the term meant and therefore I have no trouble including the term in the article in quotation marks. I only question whether it is appropriate to include a wiki link from a derived concept to an article that is not likely be created.  Furthermore while you are absolutely correct that a PubMed search for "differential" and "localization" produces 8531 hits, a search for  "differential localization" produces only 656 hits.  Hence this phrase is some times used in the literature, but not widely so. "Differential localization" is direct consequence of tissue or subcellular selective tissue distribution which in turn is measured by expression profiling.  Hence it might be appropriate to include a piped link from  "differential localization" to "expression profiling" (e.g.,  differential localization ). Boghog (talk) 19:38, 28 April 2011 (UTC)

expression profiling


 * http://en.wikipedia.org/w/index.php?title=Moonlighting_protein&action=historysubmit&diff=426136066&oldid=426135775
 * The use of the acronym "AO" for  "Peroxisomal Protein Alcohol Oxidase" is much less redundant and more efficient.  Also the section suffered from WP:OVERLINK.  Finally I selectively restored some of these links in this edit.

I will follow the advice from WP:OVERLINK from now on. Sw mmr1928  talk  18:28, 28 April 2011 (UTC)


 * I feel the history section should be broken into discovery and terminology section and an evolution section
 * http://en.wikipedia.org/w/index.php?title=Moonlighting_protein&diff=next&oldid=426051992
 * I have no issue with this edit.


 * The evolution section would be an ideal place to discuss theories on the evolution of moonlighting proteins.


 * For example this paragraph does not fit in the History section:
 * "It is believed that moonlighting proteins have existed for over a billion years and came about by means of evolution. Many moonlighting proteins are the result of a fusion of genes which originally coded for proteins with a single function.[4] Proteins are quite large compared to the active site of a protein, meaning a large majority of the protein is inactive. Through alterations of the active site or areas around the active site, it is believed that these uni-functional proteins now had the ability to perform multiple functions. These moonlighting proteins became evolutionarily favorable for a cell; the cell can produce less proteins if a single protein can do the job of multiple proteins.[5] As a result, the DNA needed for a cell is consolidated making the cell more efficient."


 * What problems do you have with this edit?
 * http://en.wikipedia.org/w/index.php?title=Moonlighting_protein&diff=next&oldid=426050712
 * unsourced

The term "Gene Sharing" is not wholly endorsed by the academic community. Specifically because it is ambiguous. Piatigorsky himself doesn't like "Moonlighting" because of it's connotations of illicit activity. However some argue that "Moonlighting" is more appropriate.(ref: Times Literary Supplement, February 29 2008, p.30). I suggest mentioning this in the article and adding a "Moonlighting (Genetics)" to the Moonlighting (disambiguation) page. --Kavrod (talk) 18:21, 4 September 2008 (UTC)

From http://en.wikipedia.org/wiki/Talk:Gene_sharing Sw mmr1928  talk  18:32, 28 April 2011 (UTC)
 * You undid this valuable edit I made:
 * http://en.wikipedia.org/w/index.php?title=Moonlighting_protein&diff=next&oldid=426133495
 * Minor edit that can be re-added.
 * You removed the source I provided in this edit:
 * http://en.wikipedia.org/w/index.php?title=Moonlighting_protein&diff=prev&oldid=426130622
 * Sriram_2005 was cited multiple times in the article and is still included the citation list in the reference section. It is trivial to re-add an in-line citation to this reference if needed.
 * You removed the source I provided in this edit:
 * http://en.wikipedia.org/w/index.php?title=Moonlighting_protein&diff=next&oldid=426132462
 * Huberts_2010 was cited multiple times in the article and is still part of the citation list in the reference section. Again, it is trivial to re-add an in-line citation to this reference if needed.


 * What in the world have you done to the reflist section? In this edit:
 * http://en.wikipedia.org/w/index.php?title=Moonlighting_protein&diff=next&oldid=426136112

Sw mmr1928  talk  13:07, 28 April 2011 (UTC)
 * Two things. First, I have sorted the citations alphabetically (Piatigorsk_1988 before Sriram_2005) and the Wikipedia diff function obscures this difference. There is no difference in the Piatigorsk_1988 citation.  The difference in the Sriram_2005 is a mistake that I corrected in this edit.  I apologize for that error.  Boghog (talk) 18:18, 28 April 2011 (UTC)

Suggestions
Hi. Thanks for responding to my comments and for your continued edits. The article is developing nicely.

I have a few suggestions. In the techniques section, a clearer distinction is needed between methods used to detect the presence of a protein and methods used to determine its structure. For example, real-time PCR is used to quantify mRNA and hence infer the presence of a particular protein which is encoded by the mRNA. Mass spec is mainly used to detect the presence of proteins but can also be used to determine the primary structure. X-ray crystallography and NMR can be used to determine the tertiary structure of a protein. Dual polarization interferometry may be used to measure changes in protein structure, but is not used to determine the protein structure itself. Systems biology is a rather fuzzy concept, but includes things like interactomics that gives clues to a proteins function based on what it interacts with. Boghog (talk) 06:24, 29 April 2011 (UTC)

Thanks thats really good. I added it :) Sw mmr1928   talk  14:46, 29 April 2011 (UTC)

2nd Review by Group 2
All of the major concerns of the first draft have been addressed. Overall the article reads much better than it did previously and flaws that distracted the reader from the article’s content have been removed. The section headings seem much more fitting overall. The ordering of the sections is excellent because it contributes to the ease of understanding each section. All of the previous terms that were unclear have been fully explained or turned into links to their respective Wikipedia articles to provide easy access to an explanation.

All other minor concerns that were problems in the previous draft have been corrected, and the grammatical errors have been fixed. Confusing and/or redundant wording has been revised, increasing the quality of the article as a whole. The table still disrupts the flow of the page to a certain extent but reorienting the table may prove too difficult or impossible for what it is worth.

There is only one new minor concern that seems as though a Wikipedia editor has already pointed out. In the Discovery section of the article, the last sentence is a type of statement that needs a citation to go along with it, or needs to be more specific, or should maybe be left out if the information to cite the statement is not available.

Overall it appears the authors paid attention to each part of the review and addressed all of the identified problems. The article has been significantly improved compared to the first draft. —Preceding unsigned comment added by Mcole123 (talk • contribs) 21:57, 3 May 2011 (UTC)

History
This section has been removed from the article and replaced by a “Discovery” part combined with a “Evolution” section that help to better clarify how moonlighting proteins were first discovered by Piatigorsky and Wistow and then proceeds to explain the evolutionary mechanisms that took place to create moonlighting proteins. These proteins are advantageous to the organism since they have multiple functions. There are no major concerns as the article definitively explains both the discovery and the evolution (or reason for them arising) of them well. A minor concern might be the last sentence in the Discovery paragraph with it needing a citation, but citations in general look good. Spelling, grammar, and punctuation also seem fine.

Techniques used to determine function
Good changes, and used my advice and added alternate techniques besides mass spectrometry. Problem still remains with how it looks and flows, because there is one bolded subdivision and although other methods are talked about they are glossed over, I think that this article in this section should either have separate bold titled techniques, or take the bolded title away all together and just meld the methods all under the one title (Techniques).

Comparing normal proteins and moonlighting proteins
This section seems to now be incorporated into the “Functions” section. A minor change suggestion is removing one “exhibit” from the first sentence of the second paragraph of this section. Add a comma after pathway in the same sentence as mentioned in the previous suggestion. “The function in AO import/assembly is fully independent of the enzyme activity of pyruvate carboxylase, because amino acid substitutions can be introduced that fully inactive the enzyme activity of pryuvate carboxylase...” - possibly change inactive to  deactivate?

Overall, this section of the article is much easier to read than before, and the table at the end is a nice touch. I also liked how the structure of the moonlighting proteins was mentioned.

Scientific Relevance
This section has been renamed “clinical significance.” This section is much clearer and more specific. All minor correction suggestions have been improved.

Engineering proteins
This section has been completely removed from the article

Hhuang1 (talk) 22:21, 3 May 2011 (UTC)

Protein engineering section
I second concerns raised by about the use of the table in the Protein engineering section. If it greatly added to the article, it would be worth reconstructing it using only the most important parts, but I don't think it's really relevant to the article — how does it aid the understanding of moonlighting proteins?  Jebus989 ✰ 08:10, 5 May 2011 (UTC)

Hello Jebus989

maybe i should copy our previous discussion on boghog's talk page and paste it here Sw mmr1928  talk  15:43, 5 May 2011 (UTC)


 * It's ok, I've just gone and read it. He questions why the table is useful here too, so that probably means it should be removed. Why, for example, is it relevant that vesicles hold fluids, similar to containers ...vesicles are primarily lipid (granted proteins may be involved) and it's giving one example of function, so it's not moonlighting; also the technology analogy also doesn't really add anything  Jebus989 ✰ 16:03, 5 May 2011 (UTC)


 * I agree with that it is difficult to see how this table relates to moonlighting and in addition, has copyright issues.  Hence I think the table should be removed. Please note that the first table in the functions section is merely a list of facts and therefore is permissible fair use while the second table in the protein engineering section contains analogies and therefore is more than a simple list of facts and hence it is not be appropriate to claim fair use. Finally it is important to note that the use of in-line attribution is only appropriate for short quotations, not lengthy tables. Boghog (talk) 16:41, 5 May 2011 (UTC)

Removing the table is OK. What do you have in mind to replace it? Sw mmr1928  talk  17:29, 5 May 2011 (UTC)


 * I was about to ask you the same question. Do you have any sources that discuss the implication of moonlighting to protein engineering that could be used to expand on the last sentence of the lead? Boghog (talk) 18:46, 5 May 2011 (UTC)


 * No, but reading this (the lead at least) makes it pretty clear that knowledge about proteins functions is invaluable to protein engineering. Isn't the statement I just made similar to my earlier statement that you disproved because there were not enough search results?? Sw mmr1928   talk  21:08, 5 May 2011 (UTC)


 * Undoubtedly knowledge about protein function is invaluable in protein engineering... that's like saying if you're going to build a car it's useful to understand how cars work — it goes without saying. If you have sources of where protein moonlighting specifically has been a consideration in protein engineering papers, it would be straightforward to incorporate them into a paragraph. A simple search for moonlighting+protein+engineering finds nothing immediately relevant (though there are some reviews and specific examples of moonlighting which could be used elsewhere in the article)  Jebus989 ✰ 22:03, 5 May 2011 (UTC)

Jebus989 are these suitable? Another And another Sw mmr1928  talk  23:12, 5 May 2011 (UTC)


 * These papers come close since they discuss why the study of protein evolution (A) is relevant to protein engineering (B), but none of the papers specifically mention moonlighting or gene sharing (C). The papers above support A → B, while A → C is already documented in this article.  But we still have no reliable source to support C → B. Boghog (talk) 23:58, 5 May 2011 (UTC)

EXACTLY! The amount of results of a search does not determine if a statement is true or not. Jebus989, specifically I am talking about this discussion with BOGHOG:


 * BOGHOG:"In particular, the statement "moonlighting activities of proteins are essential for the study of cellular function" raised some alarm bells. ...while searching for this term in PubMed did return ~110 citations, this is a very small fraction of the number of papers that have been published on protein function. How can moonlighting activities be essential for the study of proteins when so few papers have been published about the subject?


 * Me:"Because knowledge and cataloging of the moonlighting activities of proteins are essential for the study of cellular function and human physiology, we also review..." It does not matter how many people have never heard of the phrase "moonlighting protein" before or how many papers have been published about the subject. WP is not a Democracy and I am quoting a peer reviewed journal (Sriram 2005).Swmmr1928 talk 21:35, 27 April 2011 (UTC)

BOGHOG: I still think my sentence (moonlighting activities of proteins are essential for the study of cellular function) should be added because the amount of results of a search does not determine if a statement is true or not! Like Jebus989 said, "that's like saying if you're going to build a car it's useful to understand how cars work" — it goes without saying! What do you think Jebus989? Sw mmr1928  talk  22:32, 5 May 2011 (UTC)


 * Jebus989 already answered your question here. I agree with Jebus989 that this is an unnecessary statement. Boghog (talk) 22:46, 5 May 2011 (UTC)
 * If it goes without saying, why say it? Boghog (talk) 00:25, 6 May 2011 (UTC)
 * Boghog, your original argument is that "moonlighting activities cannot be essential for the study of proteins when so few papers have been published about the subject." Not the statement is unnecessary. Sw mmr1928   talk  22:57, 5 May 2011 (UTC)


 * An important point is that as far as we know, most protein do not moonlight. In processes where moonlighting proteins are involved by definition moonlighting will be critical to understanding those particular processes, but for many other processes that do not involve moonlighting proteins, moonlighting by definition is not relevant. Hence the statement "moonlighting activities of proteins are essential for the study of cellular function" is an exaggeration. These types of statements are often made in specialist review articles by authors that have spent years studying the subject and may not be completely objective.  In contrast, these types of peacock statements are not appropriate for an encyclopedia that strives to maintain a neutral point of view. Boghog (talk) 23:38, 5 May 2011 (UTC)


 * Jebus989, do you agree with the above? Sw mmr1928  talk  01:03, 6 May 2011 (UTC)

"BOGHOG:the linked papers come close but still do not support the contention that the study of moonlighting proteins is relevant to protein engineering"
 * That is why I deleted the protein engineering section in the first place. You should be defending the section you created. Sw mmr1928   talk  01:03, 6 May 2011 (UTC)


 * While the "Engineering proteins" section was deleted in this edit, in the same edit the contents of this short section was moved to the lead. I recreated the section heading as a place holder in response to 's excellent peer review comments and in particular "Nothing important should be in the lead only - since it is a summary, it should all be repeated in the body of the article itself". Hence if we cannot expand on how moonlighting relates to protein engineering and support this material with a reliable source, both the sentence in the lead and the corresponding section in the article that mention protein engineering should be deleted. Boghog (talk) 07:15, 6 May 2011 (UTC)
 * Just to weigh in, I am largely in agreement with here, but you don't really need my agreement, Boghog is an extremely experienced Wikipedian and knowledgeable scientist, taking his advice will definitely help improve the article. I had a quick scan over some of the papers you linked, the ones I looked at seemed like good reviews of protein engineering but I couldn't find the word moonlight*, are moonlighting proteins referenced in the papers by a different name?  Jebus989 ✰ 08:03, 6 May 2011 (UTC)
 * I say we delete the protein engineering mention. Quick question:  How can I find the article mentioned in this page? "a paper published in the September issue of the journal Microbiology."  I am trying with no luck to search on biomed website.

I know that this is from September 2008, but could you please direct me to this article?


 * Try PubMed. Entering  "Nagaraja V [au] Moonlighting glutamate racemase" as a search term quickly lead me to this:.

I never considered a biased researcher. Do you think the researchers you call biased are knowingly promoting their subject? Should there be an organization to prevent this? Sw mmr1928  talk  12:05, 6 May 2011 (UTC)


 * There is nothing wrong with what Sriram wrote, except that it perhaps suffered from a little hyperbole. Scientists are human and as humans they have biases like everyone else. You seem to have a fundamental misunderstanding both about how science and Wikipedia operate. What may be appropriate for a scientific journal may not be appropriate for Wikipedia and vice versa.  Please keep in mind that the intended audience for a scientific journal are scientists and Wikipedia is the general public.  These two audiences are very different. Scientists are by nature skeptical and when they read statements like "x is essential for the study of y" they wink and often interpret this to mean "I have to convince the funding agencies that this is essential research that must be funded; please renew my research grant!" ;-)  Perhaps I am being overly cynical, but this is often how the game is played. Wikipedia on the other hand tries to present facts in an objective and neutral way, in part, because many who read these articles may not be experts in the field and could easily be mislead.  Hence exaggerations, even if they are minor, have no place in Wikipedia, unless they include an in-line attribution to an authoritative source. Boghog (talk) 19:51, 6 May 2011 (UTC)


 * OK, I just noticed that your instructor appears to be Sriram. I was confused at first since the two papers that you cited by Sriram listed UCLA as the affiliation, but I now see he has moved to the University of Maryland. Please note that citing your instructor represents a potential conflict of interest since you have a direct relationship with him. On the  other hand, only two out of the dozen or so papers that you cite are coauthored by Sriram, so I do not think this represents a serious conflict.  Nevertheless our disagreements above illustrate one of the potential pitfalls of being too close to the topic that you are writing about.  My apologizes if I have offended either of you in anyway, but my intentions were merely to make sure that this article maintains a neutral and objective tone.  Boghog (talk) 00:38, 7 May 2011 (UTC)