text:
Wikiversity:Nominations for checkuser/SB Johnny

Note: Checkuser access was given to User:SB_Johnny and User:JWSchmidt on September 11 2007. You can request checkuser actions at Requests for CheckUser.

I nominate SB Johnny for CheckUser at Wikiversity. SB_Johnny is a major participant at Wikiversity (see Bloom Clock), has been a custodian since August 2006 and is an experienced CheckUser at Wikibooks. Many of our persistent vandals are blocked at our Wikimedia Foundation sister projects before they attack Wikiversity. It will be useful to have SB_Johnny as a CheckUser at Wikiversity who is aware of what is happening at other projects (SB_Johnny is also an administrator at Wikimedia Commons). --JWSchmidt 15:08, 21 August 2007 (UTC)

Accept/decline the nomination
Nominated CheckUser candidate: please indicate if you accept the nomination. Note the requirements at CheckUser policy.
 * I Accept, gladly. My hands have been feeling a bit tied lately (see my answer to question #1, below). --SB_Johnny | PA! 15:46, 21 August 2007 (UTC)

Questions for the candidate

 * 1) Wikiversity got through its first year with only minor vandalism. Why is this a good time to start having CheckUsers for Wikiversity? --JWSchmidt 15:08, 21 August 2007 (UTC)

The reason we need local checkusers is that Wikiversity has grown big enough now to attract the attention of some of the more harmful troublemakers. Two of these problem users have appeared on Wikiversity within the past month or so after having been blocked from other Wikimedia projects after CU results were acquired there. CU is really just a defensive tool, since it identifies vandals and others who make multiple accounts for ill intent, though it also can have the effect of protecting good-faith editors, since it can be used in place of autoblocks (which can easily misfire if a bad vandal was using an AOL IP, for example).

In theory, we have always been able to request checks from the stewards on meta, however when I recently made such a request, it took 11 days before the request was finally fulfilled (User:Whiteknight can confirm this... that log will not be visible to non-checkusers).

I've had CU access on en.Wikibooks since January, and while I rarely have need to use it (another of our CUs there is a multi-project vandal fighter), it's been quite useful on those rare occaisions that I've needed it. Vandalism has seriously gone down on Wikibooks in particular since User:Herbythyme started using it there for vandal tracking, and we can hopefully reduce it here as well (which may be even more important here since some of our learning materials are aimed at very young people).--SB_Johnny | PA! 15:46, 21 August 2007 (UTC)

 * I can confirm Johnny's statement about the CU: The check request was made on meta on 17 July and was actually performed by Drini on 28 July. --Whiteknight 15:55, 21 August 2007 (UTC)

 * SB, would compliance with this be an issue for you? --HappyCamper 15:55, 22 August 2007 (UTC)

 * No problem at all. I'm already in compliance as a Checkuser on Wikibooks, actually :). --SB_Johnny | PA! 16:03, 22 August 2007 (UTC)

 * How would you differentiate between disruptive and non-disruptive sock puppets and how would you deal with each? --Remi 18:34, 27 August 2007 (UTC)
 * Well, a non-disruptive sockpuppet would probably never come to my attention while wearing my checkuser hat. It's not a tool you use pre-emptively, but rather only useful when you see (or at least strongly suspect) that a someone is using multiple accounts in bad faith, and want to have a bit more evidence for that before you make accusations.
 * I personally have 2 sockpuppet accounts on Wikiversity: User:SBJ and User:SB_Johnny-LM. They're useful for certain purposes (primarily for logging bloom clock entries from 3 distinct regions), but they're certainly not deceptive in any way. And someone might want to use a public account for logging on the bloom clock while using a more anonymous account when working on a project about domestic abuse.
 * This is all more or less off the track though: the vast majority of CU checks are made on serial troublemakers who simply use another account after their primary is blocked. With CU you can "nip it in the bud" by blocking the source IP, or in some cases avoid collateral blocks to good contributors who are unfortunate enough to share a troublemaker's IP (autoblock is the B-29 to CU's smart cruise missile). --SB_Johnny | PA! 18:52, 27 August 2007 (UTC)

 * Why should only two users be given this privilege, as opposed to giving it to everyone ? (One argument might be that stalkers could use it to track down their prey, but blocking the stalker's IP might be a better way to deal with this.) StuRat 17:05, 31 August 2007 (UTC)
 * JWSchmidt gave the technical answer to this (which is quite correct), but there's more to it than that. Privacy is a funny thing, and here's 3 examples:
 * User:Whiteknight is a good example of someone who doesn't mind using and publishing his real name (User:Andrew_Whitworth).
 * I myself am for most purposes an "anonymous editor", in that I do not widely publish my real name. The Wikimedia Foundation does know who I am (in fact they have my name, address, telephone number, and a photo of me), and while I'm perfectly comfortable with that, I'm not as confortable as Whiteknight is.
 * User:Darklama is on the other extreme... he's an excellent contributor and I consider him a friend, but I don't even know his name.
 * So I guess the answer is this: if we only wanted to allow people to contribute if they weren't interested in anonymity, there'd be no reason not to give everyone checkuser. People like me might stick around, but probably not. People like darklama would be outta here like a bat out of hell. So the best compromise is to give the tools to people who are known to and trusted by the community, and who can be relied upon to use the tools only when they need them, rather than "out of curiosity". Whether or not you think privacy is a valid concern for people to entertain, people really are concerned about it, and should feel confident that Checkusers are few in number, conservative in their use of the tools, and accountable to the Foundation for their actions (which they are, and which is why the Foundation knows exactly who I am and how to find me as a Checkuser on Wikibooks). --SB_Johnny | talk 21:09, 31 August 2007 (UTC)

 * But we're only talking about being able to find editors' IP addresses and other screen names, not names, ages, phone numbers, and home addresses. Unless they've put that info out there and associated it with their IP, that info should still be private. StuRat 15:55, 1 September 2007 (UTC)

 * Well, it can trace things down to a LAN (an office, for example), and has some features built in that can get you pretty close. It could also be used to expose a perfectly legitimate alternate account (say, for example, someone was contributing to a research project about domestic abuse or recovery from rape, and didn't want to use their "public face account"). I'll agree with you to the extent that I personally could care less if someone knows my IP, but I've also had requests on a couple of occaisions from people who asked me to delete a revision of a Wikibooks page because they managed to lose their login while editing and wanted their IP hidden. Whether or not it's really anything to worry about, some people really do worry about it, so we need to respect that. --SB_Johnny | talk 00:10, 2 September 2007 (UTC)

 * I have one caveat: is there a mechanism for appeals? Just in case someone's IP has also been abused? Shir-El too 19:48, 2 September 2007 (UTC)

Community discussion

 * 1) Support. Just vaguely noting that there has been a substantial decline in vandalism for July and August 2007. However I agree that we need a CU and that SB Johnny should have CU status. McCormack 15:54, 21 August 2007 (UTC)
 * Further noting that Wikimedia Foundation rules require that any project must have either zero or two CU's, not one. As Whiteknight is a CU on other projects and active at WV, what are the chances that he will also be nominated and accept the nomination? McCormack 16:01, 21 August 2007 (UTC)
 * The chances are zero. I'm primarily a wikibookian, even if some of my work does spill over to this project as well. I would not accept any nomination here, either custodian or CU, because I wouldnt be able to devote a fair amount of my time to helping this project the way a good candidate should. --Whiteknight 16:52, 21 August 2007 (UTC)
 * Two or more, actually (there are currently 4 on Wikibooks, and many more than that number on Wikipedia). Whiteknight would of course bring more experience to the job, but I can assure you from experience that experience isn't really necessary. Also, Whiteknight isn't even a Custodian here, and you really can't make effective use of checkuser tools without sysop tools. --SB_Johnny | PA! 16:53, 21 August 2007 (UTC)
 * 1) support. I nominated SB_Johnny and I support his candidacy for the reasons given in my nomination statement, above. --JWSchmidt 15:57, 21 August 2007 (UTC)
 * 2) support. Enthusiastic support. On WB Johnny has demonstrated himself to being a hard worker and a responsible user. He is both a bcrat and a CU on wikibooks, two jobs which he performs responsibly. He will make a great asset to this community with the CU tools. --Whiteknight 16:52, 21 August 2007 (UTC)
 * 3) Support I know Johnny from off-Wikiversity and trust him implicity.  He would be a good and experienced choice for the CheckUser tools here.  Cbrown1023    talk   01:06, 22 August 2007 (UTC)
 * 4) Support he is deeply involved with wikiversity, and is familiar with the tool.Hillgentleman|Talk 06:53, 22 August 2007 (UTC)
 * 5) Support I also agree that we need some CU(s) here@WikiVersity and that SB Johnny should have CheckUser status. --Chief Mike 09:11, 22 August 2007 (UTC)
 * 6) Support Lost time by stopping vandalism is time for fun  of the vandels. --User:Sundance_Raphael 15:17, 22 August 2007 (UTC)
 * 7) Support - I'm confident you have the experience and knowledge required for access to the tool. --Michael Billington (talk • contribs) 23:05, 22 August 2007 (UTC)
 * 8) Support I heard good things from John about you. So, I hope you fight vandalism also great. You have my vote. Erkan Yilmaz ( evaluate me!,  discussion ) 19:47, 23 August 2007 (UTC)
 * 9) Support He sucked me into Wikiversity from Wikibooks where he is very trusted. --Jomegat 02:04, 24 August 2007 (UTC)
 * 10) Support As someone who nominated Johnny for his first CUs rights I would do nothing less.  A little impulsive at times however I would trust him with these rights without any concern.  He (& I) know at lot more about them than we did.  I think it is important that some of the smaller wikis obtain these rights.  Steward support/interest can be very patchy and as vandals are dealt with better on wikis with CUs they will move to less well "defended" ones.  The community need have no concerns and would be advised to support this. --Herby talk thyme 07:34, 25 August 2007 (UTC)
 * 11) Support No reason to oppose, and I appreciate Johnny's reliability and maturity in such matters. The Wikiversity community clearly accepts his nomination as well. --Draicone (talk) 12:34, 26 August 2007 (UTC)
 * 12) Support Nothing to say that hasn't already been said. --Luai lashire 15:29, 26 August 2007 (UTC)
 * 13) Support I trust SB Johnny, and he has plenty of experience in this area.. Cormaggio talk 17:56, 27 August 2007 (UTC)
 * 14) Support Trust. yes. CQ 19:00, 27 August 2007 (UTC)
 * 15) Support I have very few edits here... but I have worked with SB_Johnny on other wikis, as well as on checkuser matters, (I hold checkuser on Commons, Meta and en:wp) and like the approach used. When counting supports you may or may not want to discount mine, but I strongly support the notion that Wikiversity needs to have two checkusers, and support this user for the job, and would advocate regulars give him the support needed. ++Lar: t/c 21:32, 27 August 2007 (UTC)
 * 16) Support I support having tried and true custodians having check user rights. --Remi 11:16, 28 August 2007 (UTC)
 * 17) I fully support and trust SB_Johnny with checkuser tools, and I'm sure he'll do a great job. guillom 13:19, 29 August 2007 (UTC)
 * 18) Support  But then I support giving everyone this tool, as it seems to have the power to do more good than harm, if given to everyone, despite wiki privacy policies which appear to make it impossible to give everyone equal rights.  Perhaps these policies need to be changed. StuRat 15:52, 1 September 2007 (UTC)
 * 19) Support, already has it on wikibooks, might make muliproject check user requests easier.--Rayc 02:18, 2 September 2007 (UTC)
 * 20) Support He has the trust and respect of all the voices heard so far, and one piece of visual obscenity dumped on the Brouse page is more than enough to justify CU's. Shir-El too 19:41, 2 September 2007 (UTC)
 * I'm not sure what you'd be "appealing"... you mean blocks made using evidence gained from CU? Assuming I understand the question, I can only say that CU doesn't have anything to do with blocking, it's just a tool used to figure out whether or not an IP should be blocked. In that sense CU can not only help find and block IPs that are the source of trouble, but also make sure that we don't inadvertently block an IP which is being used by constructive contributors to our project. Without CU, our only way of blocking an IP used by a registered (but malicious) user is to use autoblock, which is more or less shooting in the dark and hoping not to hit the neigbor instead of the thief. --SB_Johnny | talk 22:39, 2 September 2007 (UTC)
 * By appealing I meant as in 'court of appeals': just in case an IP was abused by someone other than the legitimate 'owner', is there a way for that 'owner' to contact whoever blocked the IP and request a re-evaluation? I'm new to the Wiki world and ignorant of IP technology, so excuse if I'm talking through my hat. On the other hand the possibility of someone being 'frozen out' without recourse is disturbing; something of the kind happened in France many years ago, with tragic results. Thank you, Shir-El too 13:26, 6 September 2007 (UTC)
 * Ah, I think I see where you're going. If someone wants to discuss a problematic block, they just add unblock to their talk page (they receive instructions on how to do this when they try to edit and find themselves blocked). It's just as easy to unblock as it is to block, and there are some safegaurds built into the checkuser tool that let us know a bit more than just the IP used by the accounts. On wikibooks I've generally given the benefit of the doubt the first time, but not the second time (i.e., if I unblock the IP and it's used again for bad behavior, I block it again, and don't pay attention to unblock requests from that IP for a while). --SB_Johnny | talk 12:13, 9 September 2007 (UTC)
 * Thank you: this answers my concern. Good Luck in your new post. Shir-El too 22:47, 9 September 2007 (UTC)
 * 1) Support No reason to oppose. I'm new here - but I see a volunteer offering to help spend time to fight vandalism, who has gained support of other volunteers.  It looks like every vote counts so here's my thumbs-up. Ikluft 10:04, 3 September 2007 (UTC)
 * 2) Support. -- Dionysios  (talk), Date: 2007-09-03 (September 3, 2007) Time:  1141 UTC
 * 3) Support -- Banerjee 21:09, 6 September 2007 (UTC)
 * 4) Support — Tutchek 12:44, 9 September 2007 (UTC)
 * 5) Support SB_Johnny's experience on English Wikibooks demonstrates his ability to be trusted with the tools. --dark[[Image:Yin yang.svg|12px]]lama 19:16, 9 September 2007 (UTC)

 As this is Wikiversity's first official discussion of acquiring local checkusers, please remember that we need two users with the tools (Wikimedia policy dictates that projects are not permitted to have only one checkuser). If it is later decided that we need more checkusers, they can be approved individually.


text:
Wikiversity:Nominations for checkuser/JWSchmidt

Note: Checkuser access was given to User:SB_Johnny and User:JWSchmidt on September 11 2007. You can request checkuser actions at Requests for CheckUser.

I nominate JWSchmidt for Checkuser as well. He is one of our most active contributors and custodians, and is here almost every day for long periods of time when he can be available for situations where use of the tool becomes necessary. Unlike me, he is also an administrator on en.Wikipedia, and so will be able to search for deleted edits attributed to any given IP (this is something I generally do on both Commons and Wikiversity after getting a positive CU result on wikibooks, since it can help establish editing patterns). Finally, JWSchmidt is among those Wikimedians who are somewhat wary of the Checkuser tool, and would be very conservative in its use here (as should all Checkusers be conservative).

Just a note that JWSchmidt and others had earlier voiced a preference that our checkusers be experienced checkusers from other projects. I'd like to point out that this really isn't necessary: the tool is rather simple to use. For me, technical experience is not the issue (I learned how to use it within an hour or so), trust is by far the most important thing, activity second, technical ability a distant third. JWSchmidt is absolutely and completely trustworthy. --SB_Johnny | PA! 16:45, 21 August 2007 (UTC)

Accept/decline the nomination
Nominated CheckUser candidate: please indicate if you accept the nomination. Note the requirements at CheckUser policy.

I accept the nomination. Most of what I have to say about CheckUser is in my discussion comments at Wikiversity talk:CheckUser policy. Short summary: I'm skeptical about the way the CheckUser system is handled by the Wikimedia Foundation. The CheckUser system has been abused in the past and it will continue to be abused until some changes are made. Because of the existing opportunities for abuse of the CheckUser system I'm reluctant to become associated with the existing CheckUser system, but I have not been able to effectively work towards improvements of the system from the outside. Maybe if the Wikiversity community approves my candidacy then I will be able to work from inside the CheckUser system to make some changes. My basic idea for changes to the CheckUser system is that after CheckUser data are collected and used it would be beneficial to make a public record of what data were collected and how the data were used. The changes I'm talking about do not involve any violation of the privacy policy and they would not interfer with with protection of the wiki projects from vandals. Its simply a matter of openness in order to protect the CheckUser system from abuse. --JWSchmidt 17:06, 21 August 2007 (UTC)

Questions for the candidate

 * JWS, would compliance with this be an issue for you? --HappyCamper 15:54, 22 August 2007 (UTC)

 * I think that Foundation Resolution is the minimal path that the Wikimedia Foundation could take towards protecting itself from liability resulting from possible leaks of private information by wiki volunteers. My only doubts about that resolution are if it goes far enough in protecting the Foundation, but I'm sure they had it carefully reviewed by lawyers. The Foundation Office in Florida has my real world name and contact information on file. I have been in the "over 18" category for a couple of decades. As this community discussion goes along, if it looks like I will be given CheckUser status, I will have to send documentation of my age to the Foundation Office. I have no problem with that. --JWSchmidt 16:59, 22 August 2007 (UTC)
 * I sent the required information to the Florida Office about a week ago (smail mail), so it should now be in their hands. --JWSchmidt 01:40, 10 September 2007 (UTC)
 * How would you differentiate between disruptive and non-disruptive sock puppets and how would you deal with each? --Remi 18:34, 27 August 2007 (UTC)
 * A page move vandal might create several accounts and wait three days in order to have the ability to move pages. If Wikiversity started having page move vandalism by several user accounts, CheckUser data might reveal that multiple vandal accounts had been created from a single IP address. It might be wise to block additional "sleeper accounts" that had been created by such an IP even before they are actually used by a page move vandal. Another form of possible abuse is from creating multiple accounts and using them to unfairly influence community discussions. I am aware of cases of this kind of abuse that have been discovered at Wikipedia. Someday this might become a problem at Wikiversity. Abuse of multiple accounts can result in a block of the accounts at Wikipedia. Someday, Wikiversity will probably have a similar policy. Many wiki editors have multiple accounts and they never cause a problem or mis-use their multiple accounts. In my experience, most of these multiple accounts are used for purposes such as to prevent the use of names that might be confused with the user name of an existing project participant or to perform test editing without the special user rights of your primary account. In my view, there is no need to "deal with" such accounts that are not used for vandalism or vote stacking. --JWSchmidt 19:31, 27 August 2007 (UTC)

 * Why should only two users be given this privilege, as opposed to giving it to everyone ? (One argument might be that stalkers could use it to track down their prey, but blocking the stalker's IP might be a better way to deal with this.) StuRat 17:02, 31 August 2007 (UTC)

 * The Wikimedia Foundation's privacy policy suggests that if you want to edit and protect your privacy (not reveal your real world location/identity) then you should log in and use a pseudonym as your wiki username. However, even if you try to keep your IP address hidden while editing, "your IP address will be stored on the wiki servers and can be seen by Wikimedia's server administrators and by users who have been granted CheckUser access. Your IP address, and its connection to any usernames that share it may be released under certain circumstances". Those "certain circumstances" are listed in the privacy policy, but someone with CheckUser access could violate the policy, so only a small group of trusted members of the Wikimedia volunteer community are given CheckUser access. --JWSchmidt 20:29, 31 August 2007 (UTC)

 * I see why people don't want their names, ages, phone numbers, and street addresses known (I'm one of them), but I don't see how you get from their IP address to that. AFAIK, the most you can get from that is an approximate location (city, maybe) and ISP, unless the user posted the info they want to keep secret under that IP elsewhere. StuRat 23:51, 31 August 2007 (UTC)
 * According to this Wikipedia article there are some places where IP addresses are legally defined as private information. Since Wikimedia servers are used all over the world, there might be valid legal reasons for the Wikimedia Foundation keeping IP addresses of registered/logged-in users private. As for how an IP address could be used to identify the real world location/identity of an editor, a common approach seems to involve using the IP address as one datum along with other clues learned from someone's internet usage habits. --JWSchmidt 00:53, 1 September 2007 (UTC)

Community discussion
--Chief Mike 09:21, 22 August 2007 (UTC)
 * 1) Neutral. JWS was originally the person who expressed his own doubts to me about this, as he was against too great a centralisation of power in any one person (am I correct, JWS?). I agree with the point he then made to me. If any one person incorporates WV-leadership, it is JWS - and that's the problem - we need checks and balances, and CU is definitely one of these check-and-balance powers. However I can also rule myself firmly out of candidacy, so I can offer no solution to the problem of needing a 2nd CU. McCormack 17:05, 21 August 2007 (UTC)
 * Interesting point, but CU really doesn't have anything to do with "power"... it's just a detective tool. I'm quite certain that the only other Wikibookian CU that would accept CU tools here is User:Herbythyme, but he's not very active here (he does have a rather long resumé though... CU on wb and commons, very active admin on meta, etc.). Besides, and balancing needed here is already present in me... John and I are friends, but it's probably no secret that we are polar opposites when it comes to certain topics. --SB_Johnny | PA! 17:16, 21 August 2007 (UTC)
 * "against centralisation of power" <-- I think it is a source of unease for some wiki participants when they see what looks like a small "inside group" in control of maintenance at a wiki project. These kinds of concerns about appearances were a driving force behind trying to make Wikiversity custodianship "no big deal". If we can get more wiki editors involved in helping with wiki maintenance then there is less of an appearance of a small group of insiders in control of everything. In addition to what I said above (in my nomination acceptance) about not being totally happy with the CheckUser system itself, I also have the problem that I am not a diligent vandal fighter. I serve as an administrator and I devote time to helping protect Wikiversity from vandalism because I feel I should pitch in and help with such tasks. I'm much more interested in editing than vandal fighting and I have to admit that my heart is not really in vandal fighting. I'd be happy to see someone else such as McCormack or Herbythyme accept a nomination for CheckUser so that I would not have to. However, I'm willing to do the best I can if the community gives me the nod. --JWSchmidt 17:24, 21 August 2007 (UTC)
 * Quote: CU really doesn't have anything to do with "power"... it's just a detective tool. Think about what you just said! CU is a form of intelligence about users. Task: create a sentence relating the words "information", "power", "intelligence". Applied to vandals, it's just common police work. Applied to vote-rigging (as it should also be), it's an important political power. McCormack 06:24, 2 September 2007 (UTC)
 * 1) Support. For what little my vote is worth here, I know I'm not the consummate wikiversity participant. On WB when I requested CU tools, it wasnt because I wanted them for myself, it was because I wanted the other nominee to have them (a vandal-fighting user who absolutely deserved them). I felt I was one of the only other users who could amass 25 votes in a reasonable amount of time. Wikiversity is a relatively small project, and getting the 25 votes is going to be supremely difficult and time-consuming. Once you get CUs, everybody will see the benefit of them, new candidates will arise and will have the benefit of being mentored by the previous generations of them. I think JWS is an excellent candidate because (a) he is popular enough to get the necessary votes, (b) he doesnt want the "power" and is therefore deserving of it,  and (c) he is an excellent wikimedian who should not only be trusted, but set up as an example for what new users can aspire to become. --Whiteknight 01:59, 22 August 2007 (UTC)
 * 2) Support. I think JWS is an excellent candidate for CU status, as he is one of the most active admins and anti-vandal fighters. I think he'll do good work with this powerful tool, remaining his always respectful self. Historybuff 06:04, 22 August 2007 (UTC)
 * 3) Support he is deeply involved with wikiversity, and is keenly aware of the effects of the tool. And it is far more urgent than the bureaucratship.  Hillgentleman|Talk 06:55, 22 August 2007 (UTC)
 * 4) Support I also agree that we need some CU(s) here@WikiVersity and that JWSchmidt should have CheckUser status.
 * 1) Support Lost time by stopping vandalism is time for fun  of the vandels. --User:Sundance_Raphael 15:17, 22 August 2007 (UTC)
 * 2) Support Fight vandalism and thank you for the nice IRC chat. Erkan Yilmaz ( evaluate me!,  discussion ) 19:43, 23 August 2007 (UTC)
 * 3) Support --Herby talk thyme 07:35, 25 August 2007 (UTC)
 * 4) Support The best CU we could ever have on wikiversity. (Snowball clause, anyone?) --Draicone (talk) 12:46, 26 August 2007 (UTC)
 * 5) Support (as nominator... forgot to vote!) --SB_Johnny | PA! 13:03, 26 August 2007 (UTC)
 * 6) Support He gets my vote.  --Luai lashire 15:34, 26 August 2007 (UTC)
 * 7) Support While I'm as yet undecided about his proposals to modify CU policy, I still trust JWSchmidt's use of this tool. Cormaggio talk 17:59, 27 August 2007 (UTC)
 * 8) Support I trust JWS, too and support the addition of the CheckUser functionality. The proposals to modify CU policy, are a separate discussion? Link please? CQ 19:05, 27 August 2007 (UTC)
 * See my comments at Wikiversity talk:CheckUser policy. --JWSchmidt 01:49, 10 September 2007 (UTC)
 * 1) I have very few edits here so you may want to discount my support but I do think JWS makes a good candidate... that JWS has doubts and concerns ought to make one sleep a lot better at night, CUs ought to be careful and thoughtful, not trigger happy... and that SB_Johnny is his nominator ought to seal the deal. Wikiversity needs two good CU candidates and JWS seems an ideal candidate to me. I hope others will choose to support his candidacy. ++Lar: t/c 21:35, 27 August 2007 (UTC)
 * 2) Support I support having tried and true custodians having check user rights. --Remi 11:16, 28 August 2007 (UTC)
 * 3) I fully support John helping Wikiversity using checkuser tools. guillom 13:20, 29 August 2007 (UTC)
 * 4) Support  But then I support giving everyone this tool, as it seems to have the power to do more good than harm, if given to everyone, despite wiki privacy policies which appear to make it impossible to give everyone equal rights.  Perhaps these policies need to be changed. StuRat 15:48, 1 September 2007 (UTC)
 * 5) Support, need more than one in case of inactivity.--Rayc 02:20, 2 September 2007 (UTC)
 * 6) Support For all of the above. StuRat: if everyone had this tool, you'd have no privacy. Worse, you'd be snowed-under thousands of "spam". Shir-El too 20:12, 2 September 2007 (UTC)
 * 7) Support No reason to oppose. As I said above with the support for SB Johnny, I see a volunteer offering to help spend time to fight vandalism, who has gained support of other volunteers. I'm particularly encouraged to see someone who intends to use authority and privilege with restraint.  Ikluft 10:13, 3 September 2007 (UTC)
 * 8) Support. -- Dionysios  (talk), Date: 2007-09-03 (September 3, 2007) Time:  1141 UTC
 * 9) Support --- Banerjee 21:08, 6 September 2007 (UTC)
 * 10) Support — I have no doubts that JWS is able to take on this job. --Michael Billington (talk • contribs) 07:20, 9 September 2007 (UTC)
 * 11) Support — Tutchek 12:35, 9 September 2007 (UTC)
 * 12) Support --mikeu 18:47, 9 September 2007 (UTC)
 * 13) Support If SB_Johnny trusts JWSchmidt enough to nominate him for the tools then thats enough for me. Additionally JWSchmidt shows reluctance to want to use the tools which is a good sign. --dark[[Image:Yin yang.svg|12px]]lama 19:20, 9 September 2007 (UTC)

 As this is Wikiversity's first official discussion of acquiring local checkusers, please remember that we need two users with the tools (Wikimedia policy dictates that projects are not permitted to have only one checkuser). If it is later decided that we need more checkusers, they can be approved individually.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


title: File:DatabasesizeJune2007.png


text:
Photography/Digital Workflow

"Digital Workflow" is the process by which photographs are taken, downloaded, identified (see also DAM), edited, delivered, printed, backed up and stored. This can consist of any number of software programs such as the computer operating systems connectivity functions, the software shipped with the camera from the manufacture such as Canon's "Digital Photo Professional" to "Digital Darkrooms" like "Aperture" (Apple), Photoshop (Adobe), GIMP (open source) or "Lightroom" (Adobe). There are many other less common programs that perform both general photo editing and very specific editing tasks such as sharpening, adding filters, or enlargement. Digital workflows allow photographers to shoot in RAW,and process their pictures exactly as needed.

title: Photography/Digital Workflow


text:
Photography/Digital Asset Management (DAM)

DAM is an acronym for "Digital Asset Management" which is a generic term for the process of collecting "Digital Assets" or photographs, identifying them with pertinent information called "Metadata" such as keywords, location, subject, project and the like, and storing them in a manner that permits for quick and effective retrieval. One can also assign a rating to the photographs so that the best ones can be easily identified. Different developers have created database type programs to perform most of these functions.

To companies that sell products, digital assets are typically linked to a specific product and/or part number identifying the product. In addition, digital assets are not limited to photography but can include any type of digital asset that is related to a product and provides information to the buyer that assists them in making a purchase. Other types of digital assets might include PDF files, schematic drawings showing dimensions of the product, illustrations, CAD drawings and many other types of files to support the product.


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Digital Darkroom

A "Digital Darkroom" is a computer workspace where photographs are edited for publication. Different programmes are used for this, one of the most popular being Photoshop. However, many freeware alternatives are to be found across the internet.

Free and open-source software

 * Darktable
 * digiKam
 * GNU Image Manipulation Program
 * Hugin
 * RawTherapee

title: Digital Darkroom


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Geographic Information System/Metadata

General Information
Metadata is information that describes data in ArcGIS. You can find appropriate items with a search and evaluate which of the items in your search results is the correct one to use.

In an item's metadata you can record whatever information is important for the reader to know about that item. This might include information about how accurate and recent the item is, restrictions associated with using and sharing the item.

Improper evaluation of metadata can lead to inaccurate representation of the data you are using for the project at hand, which can in turn lead to the discredit of your work.

Acquiring Metadata
Since metadata comes along with most of the GIS data you acquire from anywhere, acquiring it is not very difficult. Usually when you are searching for GIS data or shape files, the metadata that corresponds to it is in the same folder/ page. Any website or database that your are looking in will probably have a guided way for you to acquire the necessary metadata. This is probably the least difficult aspect related to metadata.

Viewing Metadata
It is important to know where to find and view the metadata that you're working with, because each source you use may organize it differently withing the data set. Most GIS data sets or items will have metadata, including tools, toolboxes, folders, geodatabases, text files, and file types. After it's created, metadata is copied, moved, and deleted along with the data item when it is worked with in ArcGIS. Metadata for GIS resources is useful if it's done correctly. It can help you intuitively organize your resources and assess the cost to maintain them, improve communication and share your items, and find resources that are available and choose which one you need to use.

When working with ArcGIS, you can view an item's metadata in the Description tab, within the item you want to examine. You will see an HTML page that you can interact with as you would any other page in a web browser.

After viewing an item's metadata, you can start editing it if you have permission to do so, using the edit button withing the description tab.

Any success with GIS analysis depends on your ability to analyze metadata, therefore you must know how to view it.

Publishing Metadata
An items metadata can be published to websites, databases, organizations, etc. If you can't find metadata withing the item description in ArcGIS Desktop while working on a project, some common options for publishing metadata where you may find what you're looking for include: ArcGIS Online, Data.gov, geoportals, an ArcIMS metadata service, etc. In order to publish it to any of these places, the metadata needs to be properly inspected and examined to make sure it is accurate and that it correctly identifies the item it is supposed to.

title: Geographic Information System/Metadata


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User:Juandev/Spanish I

Okay, here are some data to Spanish I, which is in fact Spanish: An Introduction.

Previos knoweledge

 * Typing - Elementary Typing (10 % ready)
 * Wikimedia -
 * Wikiversity - Introduction to Wikiversity (100%), Introduction (100%)

title: User:Juandev/Spanish I


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User:Lisafults

Lisa Fults       Statement: Learning lifes lessons, feeling lifes joy, experiencing lifes pain. This an exciting portal to information, which will give of all unequaled power

title: User:Lisafults


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User talk:Danwallace

Hello Danwallace, and welcome to Wikiversity! If you need help, feel free to visit my talk page, or contact us and ask questions. When leaving comments for others to read, remember to sign and date; it helps everyone keep track of who is writing messages. The signature icon in the edit window makes it simple. To help you get started:
 * Take a guided tour and learn how to edit;
 * Explore our learning projects;
 * Browse our portals, schools, and research pages; and
 * Read and help develop our community policies.

Also, don't forget to experiment with the links to your left. Be bold, and see you around Wikiversity! --McCormack 19:30, 21 August 2007 (UTC)

Metadata
Metadata could apply to things other than photography - could you suggest a better title for the page? Thanks! McCormack 19:32, 21 August 2007 (UTC)

title: User talk:Danwallace


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Template:Mechanics of materials/Intro

Though Mechanics of Materials includes the deformation and motion of all materials, this topic is usually interpreted to mean introductory solid mechanics. All material behavior can be included in this subdivision with appropriate links to special material behavior.

title: Template:Mechanics of materials/Intro


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Portal:Mechanics of materials/Subjects

 * Strength of materials
 * Elasticity
 * Plasticity

title: Portal:Mechanics of materials/Subjects


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Template:Mechanics of materials/Featured learning resource

Strength of materials


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Portal:Mechanics of materials/Quotes

"In almost all cases occurring in practice, the strains are small" - Landau and Lipschitz, Theory of Elasticity.

Professor in a Strength of Material class to a student : OK, Now that you are standing, tell me which members of your body are in tension and which members are in compression ? Student: I dont know about compression prof, but surely my brain is experiencing extreme tension.

title: Portal:Mechanics of materials/Quotes


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Portal:Mechanics of materials/Division news

 * July 21, 2007 - Subdivision founded!


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Portal:Mechanics of materials/Participants

The histories of Wikiversity pages indicate who the active participants are. If you are an active participant in this subdivision, you can list your name here (this can help small subdivisions grow and the participants communicate better; for large subdivisions a list of active participants is not needed).
 * Capoeirista.muralha


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Portal:Mechanics of materials/Learning projects

Strength of materials $$\bullet$$ Introduction to Elasticity $$\bullet$$ Micromechanics of composites $$\bullet$$


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Portal:Mechanics of materials/Discussion forum

 * Please help create content for a course on Advanced Strength of Materials. -- Banerjee 19:54, 21 August 2007 (UTC)


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Portal:Mechanics of materials/WikiProjects

Strength of materials


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Template:Mechanics of materials/Research projects

 * Please add any research ideas that you have on mechanics of materials here.


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Portal:Mechanics of materials/Things you can do

 * Add content for Strength of materials
 * Create content for a course on Advanced Strength of Materials.


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Template:Mechanics of materials/Mechanics of materials External links

iMechanica:The web of mechanics and mechanicians


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Strength of materials

Welcome to this learning project about !

Learning Project Summary

 * Project code:
 * Suggested Prerequisites:
 * Statics
 * Introduction to dynamics
 * Time investment: 6 months
 * Portal:Engineering and Technology
 * School:Engineering
 * Department:Mechanical Engineering
 * Stream:Solid Mechanics
 * Level: Second year undergraduate

Content summary
This learning project is an introduction to the study of strength of materials. It discusses the simple and easy to use method for determining the stresses and strains in materials and how materials fail.

Goals
This learning project aims to teach the student how to calculate stresses and strains that materials undergo when loaded. After taking this course, a student should be able to understand the different types of stresses including normal, torsion, bending and shearing. They should also be able to solve for deflections in elastic materials, and understand how a materials yields and eventually fails under load.

Lessons

 * Lesson 1: Stresses and strains
 * Lesson 2: Elastic properties and plane stress
 * Lesson 3: Stress transformations and Mohr's circle
 * Lesson 3a: Introduction to Axial Loading
 * Lesson 4: Structures with Axial Loading
 * Lesson 5: Introduction to Torsion
 * Lesson 6: Torsion in Structures
 * Lesson 7: Shear Forces and Bending Moments
 * Lesson 8: Introduction to Stresses in Beams
 * Lesson 9: Stresses in Beams
 * Lesson 10: Analysis of Stress and Strain
 * Lesson 11: Applications of Plane Stress
 * Lesson 12: Introduction to Beam Deflection
 * Lesson 13: Beam Deflection
 * Lesson 14: Statically Indeterminate Beams
 * Lesson 15: Introduction to Beam Deflection
 * Lesson 16: Columns
 * Appendix A: Centroids and Moments of Inertia

Assignments

 * Assignment 1: ...

Tests and Quizzes

 * Quiz 1
 * Quiz 2
 * Test 1
 * etc.

Active participants
Active participants in this Learning Group
 * Capoeirista.muralha

{| width="100%" style="background:#FFFCCF; border:1px solid #DAA520"

Learning materials
Learning materials and learning projects are located in the main Wikiversity namespace. Simply make a link to the name of the lesson (lessons are independent pages in the main namespace) and start writing!

You should also read about the Wikiversity:Learning model. Lessons should center on leagrning activities for Wikiversity participants. Learning materials and learning projects can be used by multiple projects - and you are encouraged to cooperate with other departments that use the same learning resource.

 * }

title: Strength of materials


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Wikiversity:Candidates for Custodianship/Darklama

While nominating (rather than requesting) has not been our tradition on Wikiversity, I would like to nominate and mentor Darklama to be a custodian for us. Darklama is a trusted administrator on en.Wikibooks, and is by far more technically sophisticated when it comes to javascript and css than any of our active custodians. We really should have one "hacker-admin" readily available for us to solve tehnical issues: sebmol helped us with this in our early days, but he's not as active as he used to be, and over the past several months the only way we've been able to get help on technical issues is by one of the other Custodians getting in touch with darklama on irc and begging for pointers.

Darklama has made it clear to me that he will not be active as a Custodian outside of helping us with technical issues, but we really just need help on the tech side, and I couldn't imagine a more trustworthy person, or one with such enthusiasm for helping solve difficult problems.--SB_Johnny | PA! 20:03, 21 August 2007 (UTC)

 * I accept this nomination on the terms mentioned by SB_Johnny, to help on the tech side of things as best I can and have SB_Johnny as my "mentor". --dark[[Image:Yin yang.svg|12px]]lama 20:09, 21 August 2007 (UTC)

Questions and discussion

 * I think it makes sense for Darklama to be a Wikiversity custodian. Darklama has long been helpful in dealing with technical software issues at Wikiversity, often by way of IRC discussions. Custodianship should be "no big deal", but having Darklama in position to edit pages in the mediawiki namespace would be a "big deal".....a real asset for Wikiversity. Even though you are easy to reach by way of IRC, I think it is a good idea for all custodians to activate the email contact setting in the Wikiversity user preferences. --JWSchmidt 20:10, 21 August 2007 (UTC)

User:Darklama is now a probationary custodian. sebmol ? 13:29, 23 August 2007 (UTC)


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Strength of materials/Lesson 1

Lesson 1: Stress and strain
In this lesson we will review the concepts of stress and strain and suggest some improvements over the definitions from elementary strength of materials.

Stress
In elementary strength of materials we define the stress ($$\sigma$$) as

\sigma = \cfrac{P}{A} $$ where $$P$$ is the resisting force and $$A$$ is the area on which it acts. From Newtons third Law, it is easy to see that resisting force is same as that of the force applied. If the resisting force is not same as that of the force applied then we are supposed to take the resisting force value. For ex. Water is almost incompressible. So resisting force it offers is Zero (as it moves sideways or in some other possible direction). Then the Stress acting is Zero as the resisting force is Zero..What are the assumptions that we make when we use this definition? Some of the assumptions made are:

 * 1) The body is homogeneous, i.e., it is made of the same material in all its parts.
 * 2) The body is isotropic, i.e., the properties of the material do not depend on direction.
 * 3) The cross section $$A$$ is constant.
 * 4) The body is straight.
 * 5) The load is applied axially along the center line of the body, etc.

In essence, we assume that the body is a one-dimensional rod. Even in that situation we are implicitly saying that the stress is just an  average over the whole body.

A better way to think about stress is as a  point quantity. If we can do that then we can deal with bodies that have different stresses at different points - which is what one sees in real life. So how do we go about defining such a point stress?

What we do is to imagine a tiny block of material inside the body and then define the stresses in that tiny block. Such a block is more commonly known as an  infinitesimal element of the body.

In an infinitesimal element of a body, we can assume that the stresses are constant (because they don't change much over the length of the element). We can also resolve any applied force into components that act normal and tangential to the faces of the element. And we can choose the element to be such that the cross section is constant. So we can meet all the requirements of the elementary strength of materials definition of stress while making it applicable for each point in a body.

The updated definition of stress is

\sigma = \lim_{A \rightarrow 0} \cfrac{P}{A} $$ We have just chosen the area on which the force acts to be so small that we can think of the stress as acting at a point.

Types of Stresses
Since there can be both normal and tangential components of force acting on the infinitesimal element, we can have  normal stresses and  shear stresses acting on the element. Suppose that we call the normal component $$N$$ and the shear component $$S$$. Then the normal stress is defined as

\sigma = \lim_{A \rightarrow 0} \cfrac{N}{A} $$ and the shear stress ($$\tau $$) is defined as

\tau = \lim_{A \rightarrow 0} \cfrac{S}{A} $$

What are the units of stress? Since the units of force may be "lbf" or "N" and the units of area may be "in$$^2$$" or "m$$^2$$", the units of stress may be

\cfrac{\text{lbf}}{\text{in}^2} \equiv \text{psi} \qquad \text{or} \qquad \cfrac{\text{N}}{\text{m}^2} \equiv \text{Pa} ~. $$

Now let us consider a rod under uniaxial tension. The question is, is there a shear stress in the bar?

In fact, there is always a orientation inside the bar along which there is a shear stress though it may not look like it. You can see that this is indeed the case by taking a section along the bar that is inclined at an angle less that 90$$^o$$ to the axis. In that case, the applied force $$P$$ can be resolved into components $$N$$ and $$S$$ normal and tangential to the section. Clearly, that indicates that there has to be a shear stress in the bar. If you do an experiment in the lab and pull on a bar until it breaks, you will often see that the fracture surface is inclined to the direction of application of force. This indicates that there is a shear stress in the bar.

This suggests an important point.  You have to know the orientation of the infinitesimal element to find the critical stress in a body.

Stress components at a point
Since an infinitesimal element has six faces, we can resolve the applied force into components in each of the faces. By convention, we resolve the applied force into components along the directions of the coordinate axis. Since there are three axes in three dimensions there will be three such force components on each face giving a total of 18 forces on the element.

For equilibrium of forces we need forces acting in opposite directions to be equal. That reduces the number of unique force components to 9 with three normal force components and six shear force components. Also, from the balance of moments, we can show that the shear force components acting on planes perpendicular to the coordinate axes must be of equal magnitude. There are three such planes and hence the number of unique shear force components reduces to three.

You can get a feel for the situation by looking at the adjacent figure. There are three normal stresses corresponding to the three normal forces. These are labeled $$\sigma_x$$, $$\sigma_y$$, and $$\sigma_z$$ where the subscript indicates the plane on which the normal force acts.

The three shear stresses are $$\tau_{xy}$$, $$\tau_{yz}$$, and $$\tau_{zx}$$ where the first subscript indicates the plane on which the shear forces acts and the second indicates the direction of the force.

From moment equilibrium, we have

\tau_{xy} = \tau_{yx} ~; \tau_{yz} = \tau_{zy} ~; \tau_{zx} = \tau_{xz} $$

The three things to note at this point are:

 * 1) Stress is a point quantity and varies from point to point.
 * 2) The stress depends on the orientation.
 * 3) The stress has six components.

Strain
In elementary strength of materials, the strain is defined as the change in length over the original length.

\varepsilon = \cfrac{\Delta l}{l_0} = \cfrac{l_f - l_0}{l_0} $$ Just as we did for the stress, we can define the strain as a point quantity by choosing a small element and allowing the initial length of that element to go to zero. Thus our new definition of strain is

\varepsilon = \lim_{l_0 \rightarrow 0} \cfrac{\Delta l}{l_0} $$

Types of Strain
To retain the parallelism with stresses we have to define normal strains and shear strains.

The normal strains indicate how much line segments in the infinitesimal element in the $$x$$, $$y$$, $$z$$ directions change. These strains are labeled $$\varepsilon_x$$, $$\varepsilon_y$$, and $$\varepsilon_z$$.

The shear strains indicate the change in angle of a right angle initially in the $$x-y$$, $$y-z$$, and $$z-x$$ planes. These angles are measured in radians and the strains are labelled $$\gamma_{xy}$$, $$\gamma_{yz}$$ and $$\gamma_{zx}$$. The adjacent figure shows how shear strain is measured in the $$x-y$$ plane. In this case

\gamma_{xy} = \cfrac{\pi}{2} - \theta_f $$

The units of strain are dimensionless. However, people often write strain in terms of $$in/in$$ or $$mm/mm$$. Since strains are small for most engineering applications (between 1 and 2 percent), people often use microstrains so that they don't have to deal with tiny numbers.

It is a bit confusing that the normal strains deal with changes in length while the shear strains deal with changes in angle. In fact, all strains deal with changes in length. However, for the very small strains that we find in engineering, the change in length due to shear and the change in angle are approximately the same. For a more accurate descriptions of strains you can look at the courses on Introduction to Elasticity or Continuum mechanics.

title: Strength of materials/Lesson 1


text: File:InfElement.png

title: File:InfElement.png


text: File:ShearBar.png

title: File:ShearBar.png


text: File:ElementStress.png

title: File:ElementStress.png


text: File:ShearStrain.png

title: File:ShearStrain.png


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Category:Strength of materials

This category is meant for content dealing with strength of materials.

title: Category:Strength of materials


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Micromechanics of composites/Average stress power in a RVE with finite strain

Average stress power in a RVE
Recall the equation for the balance of energy (with respect to the reference configuration)

\rho_0~\dot{e} = \boldsymbol{P}^T:\dot{\boldsymbol{F}} - \boldsymbol{\nabla}_0 \bullet \mathbf{q} + \rho_0~s ~. $$ The quantity $$\boldsymbol{P}^T:\dot{\boldsymbol{F}}$$ is the stress power.

The average stress power is defined as

{ \langle \boldsymbol{P}^T:\dot{\boldsymbol{F}} \rangle := \cfrac{1}{V_0}\int_{\partial{\Omega}_0}\boldsymbol{P}^T:\dot{\boldsymbol{F}}~\text{dV} ~. } $$ Here $$\boldsymbol{P}^T$$ is an arbitrary self-equilibrating nominal stress field that satisfies the balance of momentum (without any body forces or inertial forces) and $$\dot{\boldsymbol{F}}$$ is the time rate of change of $$\boldsymbol{F}$$. The reference configuration can be arbitrary. Also, the nominal stress and the rate $$\dot{\boldsymbol{F}}$$ need not be related.

Note that in that case

{ \text{tr}(\langle \boldsymbol{P}^T:\dot{\boldsymbol{F}} \rangle) = \cfrac{1}{V_0}\int_{\partial{\Omega}_0}\text{tr}(\boldsymbol{P}\cdot\dot{\boldsymbol{F}})~\text{dV} = \cfrac{1}{V_0}\int_{\partial{\Omega}_0}\text{tr}(\dot{\boldsymbol{F}}\cdot\boldsymbol{P})~\text{dV} = \text{tr}(\langle \dot{\boldsymbol{F}}\cdot\boldsymbol{P} \rangle) ~. } $$

We can express the stress power in terms of boundary tractions and boundary velocities using the relation (see Appendix)

\int_{\partial{\Omega}} \mathbf{v}\otimes(\boldsymbol{S}^T\cdot\mathbf{n})~\text{dA} = \int_{\Omega} [\boldsymbol{\nabla} \mathbf{v}\cdot\boldsymbol{S} + \mathbf{v}\otimes(\boldsymbol{\nabla} \bullet \boldsymbol{S}^T)]~\text{dV} ~. $$ In this case, we have $$\partial{\Omega} \rightarrow \partial{\Omega}_0$$, $$\Omega \rightarrow \Omega_0$$, $$\boldsymbol{\nabla} \rightarrow \boldsymbol{\nabla}_0$$, $$\mathbf{v} \rightarrow \dot{\mathbf{x}}$$, $$\boldsymbol{S} \rightarrow \boldsymbol{P}$$, and $$\mathbf{n} \rightarrow \mathbf{N}$$. Then

\int_{\partial{\Omega}} \dot{\mathbf{x}}\otimes(\boldsymbol{P}^T\cdot\mathbf{N})~\text{dA} = \int_{\Omega} [\boldsymbol{\nabla}_0~ \dot{\mathbf{x}}\cdot\boldsymbol{P} + \dot{\mathbf{x}}\otimes(\boldsymbol{\nabla}_0 \bullet \boldsymbol{P}^T)]~\text{dV} ~. $$ Using the balance of linear momentum (in the absence of body and inertial forces), we get

\int_{\partial{\Omega}} \dot{\mathbf{x}}\otimes(\boldsymbol{P}^T\cdot\mathbf{N})~\text{dA} = \int_{\Omega} \boldsymbol{\nabla}_0~ \dot{\mathbf{x}}\cdot\boldsymbol{P}~\text{dV} ~. $$ Recalling that

\dot{\boldsymbol{F}} = \frac{\partial }{\partial t}\left(\frac{\partial \mathbf{x}}{\partial \mathbf{X}}\right) = \frac{\partial }{\partial \mathbf{X}}\left(\frac{\partial \mathbf{x}}{\partial t}\right) = \boldsymbol{\nabla}_0~ \dot{\mathbf{x}} $$ we then have

\int_{\Omega} \dot{\boldsymbol{F}}\cdot\boldsymbol{P}~\text{dV} = \int_{\partial{\Omega}} \dot{\mathbf{x}}\otimes(\boldsymbol{P}^T\cdot\mathbf{N})~\text{dA} ~. $$ If $$\bar{\mathbf{T}}$$ is a self equilibrating traction applied on the boundary that leads to the stress field $$\boldsymbol{P}$$, i.e., $$\bar{\mathbf{T}} = \boldsymbol{P}^T\cdot\mathbf{N}$$, then we have

{ \int_{\Omega} \dot{\boldsymbol{F}}\cdot\boldsymbol{P}~\text{dV} = \int_{\partial{\Omega}} \dot{\mathbf{x}}\otimes\bar{\mathbf{T}}~\text{dA} ~. } $$ Note that the fields $$\dot{\boldsymbol{F}}$$ and $$\boldsymbol{P}$$ need not be related and hence the velocities $$\dot{\mathbf{x}}$$ and the tractions $$\bar{\mathbf{T}}$$ are not related.

If the boundary velocity field $$\dot{\mathbf{x}}$$ leads to the rate $$\dot{\boldsymbol{F}}$$, using the identity (see Appendix)

\langle \dot{\boldsymbol{F}}\cdot\boldsymbol{P} \rangle - \langle \dot{\boldsymbol{F}}\rangle\cdot\langle \boldsymbol{P} \rangle = \langle (\dot{\boldsymbol{F}} - \langle \dot{\boldsymbol{F}}\rangle)\cdot(\boldsymbol{P} - \langle \boldsymbol{P} \rangle) \rangle $$ we can show that (see Appendix)

\begin{align} \langle \dot{\boldsymbol{F}}\cdot\boldsymbol{P} \rangle - \langle \dot{\boldsymbol{F}}\rangle\cdot\langle \boldsymbol{P} \rangle & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} [\dot{\mathbf{x}} - \langle \dot{\boldsymbol{F}}\rangle\cdot\mathbf{X}]\otimes \left\{ [\boldsymbol{P} - \langle \boldsymbol{P} \rangle]^T\cdot\mathbf{N} \right\}~\text{dA} \\ & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} [\dot{\mathbf{x}} - \langle \dot{\boldsymbol{F}}\rangle\cdot\mathbf{X}]\otimes (\boldsymbol{P}^T\cdot\mathbf{N})~\text{dA} \\ & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} \dot{\mathbf{x}}\otimes \left\{ [\boldsymbol{P} - \langle \boldsymbol{P} \rangle]^T\cdot\mathbf{N}\right\}~\text{dA} ~. \end{align} $$

Remark
Using similar arguments, if we assume that $$\boldsymbol{F}$$ is a deformation that is compatible with an applied boundary displacement $$\mathbf{u} = \mathbf{x} - \mathbf{X}$$,we can show that

\begin{align} \langle \boldsymbol{F}\cdot\boldsymbol{P} \rangle - \langle \boldsymbol{F}\rangle\cdot\langle \boldsymbol{P} \rangle & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} [\mathbf{x} - \langle \boldsymbol{F}\rangle\cdot\mathbf{X}]\otimes \left\{ [\boldsymbol{P} - \langle \boldsymbol{P} \rangle]^T\cdot\mathbf{N} \right\}~\text{dA} \\ & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} [\mathbf{x} - \langle \boldsymbol{F}\rangle\cdot\mathbf{X}]\otimes (\boldsymbol{P}^T\cdot\mathbf{N})~\text{dA} \\ & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} \mathbf{x}\otimes \left\{ [\boldsymbol{P} - \langle \boldsymbol{P} \rangle]^T\cdot\mathbf{N}\right\}~\text{dA} ~. \end{align} $$

We can arrive at $$\langle \dot{\boldsymbol{F}}\cdot\boldsymbol{P} \rangle = \langle \dot{\boldsymbol{F}}\rangle\cdot\langle \boldsymbol{P} \rangle$$ or $$\langle \boldsymbol{F}\cdot\boldsymbol{P} \rangle = \langle \boldsymbol{F}\rangle\cdot\langle \boldsymbol{P} \rangle$$ if either of the following conditions is satisfied at the boundary:

 * 1) $$\dot{\mathbf{x}} = \langle \dot{\boldsymbol{F}}\rangle\cdot\mathbf{X} $$ or $$\mathbf{x} = \langle \boldsymbol{F}\rangle\cdot\mathbf{X}$$.
 * 2) $$\boldsymbol{P}\cdot\mathbf{N} = \langle \boldsymbol{P} \rangle^T\cdot\mathbf{N}$$.

Linear boundary velocities/displacements
If a linear velocity field is prescribed on the boundary $$\partial{\Omega}_0$$, we can express this field as

\dot{\mathbf{x}}(\mathbf{X},t) = \dot{\boldsymbol{G}}(t)\cdot\mathbf{X} \qquad\qquad \forall \mathbf{X} \in \partial{\Omega}_0~. $$ Now,

\begin{align} \langle \dot{\boldsymbol{F}}\rangle & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} \dot{\mathbf{x}}\otimes\mathbf{N}~\text{dA} \\ & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} (\dot{\boldsymbol{G}}\cdot\mathbf{X})\otimes\mathbf{N}~\text{dA} \\ & = \dot{\boldsymbol{G}}\cdot\left(\cfrac{1}{V_0}\int_{\partial{\Omega}_0} \mathbf{X}\otimes\mathbf{N}~\text{dA}\right)~. \end{align} $$ Recall that

\int_{\Omega_0} \boldsymbol{\nabla}_0~ \mathbf{X}~\text{dV} = \int_{\partial{\Omega}_0}\mathbf{X}\otimes\mathbf{N}~\text{dA}~. $$ Therefore,

\begin{align} \langle \dot{\boldsymbol{F}}\rangle & = \dot{\boldsymbol{G}}\cdot\left(\cfrac{1}{V_0}\int_{\Omega_0} \boldsymbol{\nabla}_0~ \mathbf{X}~\text{dA}\right) \\ & = \dot{\boldsymbol{G}}\cdot\left(\cfrac{1}{V_0}\int_{\Omega_0} \boldsymbol{\mathit{1}}~\text{dA}\right) = \dot{\boldsymbol{G}} ~. \end{align} $$ Hence,

\langle \dot{\boldsymbol{F}}\rangle = \dot{\boldsymbol{G}} \qquad\implies\qquad \dot{\mathbf{x}} - \langle \dot{\boldsymbol{F}}\rangle\cdot\mathbf{X} = \mathbf{0} ~. $$ Then,

\begin{align} \langle \dot{\boldsymbol{F}}\cdot\boldsymbol{P} \rangle - \langle \dot{\boldsymbol{F}}\rangle\cdot\langle \boldsymbol{P} \rangle & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} [\dot{\mathbf{x}} - \langle \dot{\boldsymbol{F}}\rangle\cdot\mathbf{X}]\otimes (\boldsymbol{P}^T\cdot\mathbf{N})~\text{dA} \\ & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} [\dot{\mathbf{x}} - \dot{\boldsymbol{G}}\cdot\mathbf{X}]\otimes (\boldsymbol{P}^T\cdot\mathbf{N})~\text{dA}= \mathbf{0} \end{align} $$ Hence,

{ \langle \dot{\boldsymbol{F}}\cdot\boldsymbol{P} \rangle = \langle \dot{\boldsymbol{F}}\rangle\cdot\langle \boldsymbol{P} \rangle ~. } $$ Similarly, if a linear displacement field is prescribed on the boundary such that

\mathbf{u}(\mathbf{X},t) = \boldsymbol{G}(t)\cdot\mathbf{X} - \mathbf{X} \qquad\implies\qquad \mathbf{x}(\mathbf{X}) = \boldsymbol{G}(t)\cdot\mathbf{X} \qquad\qquad \forall \mathbf{X} \in \partial{\Omega}_0 $$ we can show that

\langle \boldsymbol{F}\rangle = \boldsymbol{G} \qquad\implies\qquad \mathbf{x} - \langle \boldsymbol{F}\rangle\cdot\mathbf{X} = \mathbf{0} ~. $$ This leads to the equality

{ \langle \boldsymbol{F}\cdot\boldsymbol{P} \rangle = \langle \boldsymbol{F}\rangle\cdot\langle \boldsymbol{P} \rangle ~. } $$ Recall that, the average Kirchhoff stress is given by $$ \langle \overline{\boldsymbol{\tau}} \rangle = \langle \boldsymbol{F}\rangle\cdot\langle \boldsymbol{P} \rangle $$. Therefore, if a uniform boundary displacement is prescribed, we have

\langle \overline{\boldsymbol{\tau}} \rangle = \langle \boldsymbol{F}\rangle\cdot\langle \boldsymbol{P} \rangle = \langle \boldsymbol{F}\cdot\boldsymbol{P} \rangle = \langle \boldsymbol{\tau} \rangle $$ or,

{ \langle \overline{\boldsymbol{\tau}} \rangle = \langle \boldsymbol{\tau} \rangle ~. } $$

Uniform boundary tractions
A uniform boundary traction field in the reference configuration can be represented as

\bar{\mathbf{T}}(\mathbf{X},t) = \boldsymbol{G}^T(t)\cdot\mathbf{N}(\mathbf{X}) \qquad\forall~\mathbf{X}\in\partial{\Omega}_0 ~. $$ Now,

\begin{align} \langle \boldsymbol{P} \rangle & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} \mathbf{X}\otimes\bar{\mathbf{T}}~\text{dA} \\ & = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} \mathbf{X}\otimes(\boldsymbol{G}^T\cdot\mathbf{N}~\text{dA} \\ & = \left(\cfrac{1}{V_0}\int_{\partial{\Omega}_0} \mathbf{X}\otimes\mathbf{N}~\text{dA}\right) \cdot\boldsymbol{G} \\ & = \boldsymbol{\mathit{1}}\cdot\boldsymbol{G} = \boldsymbol{G} ~. \end{align} $$ Since the surface tractions are related to the nominal stress by $$\bar{\mathbf{T}}(\mathbf{X},t) = \boldsymbol{P}^T(\mathbf{X},t)\cdot\mathbf{N}(\mathbf{X})$$, we must have

\langle \boldsymbol{P} \rangle = \boldsymbol{P} ~. $$ Therefore,

\langle \dot{\boldsymbol{F}}\cdot\boldsymbol{P} \rangle - \langle \dot{\boldsymbol{F}}\rangle\cdot\langle \boldsymbol{P} \rangle = \cfrac{1}{V_0}\int_{\partial{\Omega}_0} \dot{\mathbf{x}}\otimes \left\{ [\boldsymbol{P} - \langle \boldsymbol{P} \rangle]^T\cdot\mathbf{N}\right\}~\text{dA}= \mathbf{0} $$ or,

{ \langle \dot{\boldsymbol{F}}\cdot\boldsymbol{P} \rangle = \langle \dot{\boldsymbol{F}}\rangle\cdot\langle \boldsymbol{P} \rangle ~. } $$ Similarly,

{ \langle \boldsymbol{F}\cdot\boldsymbol{P} \rangle = \langle \boldsymbol{F}\rangle\cdot\langle \boldsymbol{P} \rangle ~. } $$ Hence, using the same argument as for the previous case, we have

{ \langle \overline{\boldsymbol{\tau}} \rangle = \langle \boldsymbol{\tau} \rangle ~. } $$


text:
Micromechanics of composites/Proof 1

Tensor-vector identity - 1

[(\mathbf{v}\bullet\mathbf{a})(\boldsymbol{S}\bullet\mathbf{b})]\cdot\mathbf{n} = \mathbf{a}\cdot[\{\mathbf{v}\otimes(\boldsymbol{S}^T\bullet\mathbf{n})\}\cdot\mathbf{b}] ~. $$

Proof:

Using the identity $$ \mathbf{a}\cdot(\boldsymbol{A}^T\cdot\mathbf{b}) = \mathbf{b}\cdot(\boldsymbol{A}\cdot\mathbf{a})$$ we have

\mathbf{n}\cdot[(\mathbf{v}\bullet\mathbf{a})(\boldsymbol{S}\bullet\mathbf{b})] = \mathbf{b}\cdot[(\mathbf{v}\cdot\mathbf{a})(\boldsymbol{S}^T\cdot\mathbf{n})] ~. $$ Also, using the definition $$ (\mathbf{u}\otimes\mathbf{v})\cdot\mathbf{a} = (\mathbf{a}\cdot\mathbf{v})\mathbf{u} $$ we have

(\mathbf{v}\cdot\mathbf{a})(\boldsymbol{S}^T\cdot\mathbf{n}) = [(\boldsymbol{S}^T\cdot\mathbf{n})\otimes\mathbf{v}]\cdot\mathbf{a}~. $$ Therefore,

\mathbf{n}\cdot[(\mathbf{v}\bullet\mathbf{a})(\boldsymbol{S}\bullet\mathbf{b})] = \mathbf{b}\cdot[\{(\boldsymbol{S}^T\cdot\mathbf{n})\otimes\mathbf{v}\}\cdot\mathbf{a}]~. $$ Using the identity $$ \mathbf{a}\cdot(\boldsymbol{A}^T\cdot\mathbf{b}) = \mathbf{b}\cdot(\boldsymbol{A}\cdot\mathbf{a})$$ we have

\mathbf{b}\cdot[\{(\boldsymbol{S}^T\cdot\mathbf{n})\otimes\mathbf{v}\}\cdot\mathbf{a}] = \mathbf{a}\cdot[\{(\boldsymbol{S}^T\cdot\mathbf{n})\otimes\mathbf{v}\}^T\cdot\mathbf{b}]~. $$ Finally, using the relation $$(\mathbf{u}\otimes\mathbf{v})^T = \mathbf{v}\otimes\mathbf{u}$$, we get

\mathbf{a}\cdot[\{(\boldsymbol{S}^T\cdot\mathbf{n})\otimes\mathbf{v}\}^T\cdot\mathbf{b}] = \mathbf{a}\cdot[\{\mathbf{v}\otimes(\boldsymbol{S}^T\cdot\mathbf{n})\}\cdot\mathbf{b}]~. $$ Hence,

{ [(\mathbf{v}\bullet\mathbf{a})(\boldsymbol{S}\bullet\mathbf{b})]\cdot\mathbf{n} = \mathbf{a}\cdot[\{\mathbf{v}\otimes(\boldsymbol{S}^T\bullet\mathbf{n})\}\cdot\mathbf{b}]} \qquad \qquad \qquad \square $$

title: Micromechanics of composites/Proof 1


text:
Micromechanics of composites/Proof 2

Tensor-vector identity 2
Let $$\mathbf{v}$$ be a vector field and let $$\boldsymbol{S}$$ be a second-order tensor field. Let $$\mathbf{a}$$ and $$\mathbf{b}$$ be two arbitrary vectors. Show that

\boldsymbol{\nabla} \bullet [(\mathbf{v}\cdot\mathbf{a})(\boldsymbol{S}\cdot\mathbf{b})] = \mathbf{a}\cdot[\{\boldsymbol{\nabla} \mathbf{v}\cdot\boldsymbol{S} + \mathbf{v}\otimes(\boldsymbol{\nabla} \bullet \boldsymbol{S}^T)\}\cdot\mathbf{b}] ~. $$

Proof:

Using the identity $$\boldsymbol{\nabla} \bullet (\varphi~\mathbf{u}) = \mathbf{u}\cdot\boldsymbol{\nabla} \varphi + \varphi~\boldsymbol{\nabla} \bullet \mathbf{u}$$ we have

\boldsymbol{\nabla} \bullet [(\mathbf{v}\cdot\mathbf{a})(\boldsymbol{S}\cdot\mathbf{b})] = (\boldsymbol{S}\cdot\mathbf{b})\cdot\boldsymbol{\nabla} (\mathbf{v}\cdot\mathbf{a}) + (\mathbf{v}\cdot\mathbf{a})~\boldsymbol{\nabla} \bullet (\boldsymbol{S}\cdot\mathbf{b}) ~. $$ From the identity $$\boldsymbol{\nabla} (\mathbf{u}\cdot\mathbf{v}) = \boldsymbol{\nabla}\mathbf{u}^T\cdot\boldsymbol{\nabla} \mathbf{v} + \boldsymbol{\nabla} \mathbf{v}^T\cdot\mathbf{u}$$, we have $$\boldsymbol{\nabla} (\mathbf{v}\cdot\mathbf{a}) = \boldsymbol{\nabla} \mathbf{v}^T\cdot\mathbf{a} + \boldsymbol{\nabla} \mathbf{a}^T\cdot\mathbf{v}$$.

Since $$\mathbf{a}$$ is constant, $$\boldsymbol{\nabla} \mathbf{a} = 0$$, and we have

(\boldsymbol{S}\cdot\mathbf{b})\cdot\boldsymbol{\nabla} (\mathbf{v}\cdot\mathbf{a})= (\boldsymbol{S}\cdot\mathbf{b})\cdot(\boldsymbol{\nabla} \mathbf{v}^T\cdot\mathbf{a})~. $$ From the relation $$ \mathbf{a}\cdot(\boldsymbol{A}^T\cdot\mathbf{b}) = \mathbf{b}\cdot(\boldsymbol{A}\cdot\mathbf{a})$$ we have

(\boldsymbol{S}\cdot\mathbf{b})\cdot(\boldsymbol{\nabla} \mathbf{v}^T\cdot\mathbf{a}) = \mathbf{a}\cdot[\boldsymbol{\nabla} \mathbf{v}\cdot(\boldsymbol{S}\cdot\mathbf{b})] ~. $$ Using the relation $$\boldsymbol{A}\cdot(\boldsymbol{B}\cdot\mathbf{b}) = (\boldsymbol{A}\cdot\boldsymbol{B})\cdot\mathbf{b}$$, we get

\boldsymbol{\nabla} \mathbf{v}\cdot(\boldsymbol{S}\cdot\mathbf{b}) = (\boldsymbol{\nabla} \mathbf{v}\cdot\boldsymbol{S})\cdot\mathbf{b} ~. $$ Therefore, the final form of the first term is

(\boldsymbol{S}\cdot\mathbf{b})\cdot\boldsymbol{\nabla} (\mathbf{v}\cdot\mathbf{a})= \mathbf{a}\cdot[(\boldsymbol{\nabla} \mathbf{v}\cdot\boldsymbol{S})\cdot\mathbf{b}] ~. $$ For the second term, from the identity $$\boldsymbol{\nabla} \bullet (\boldsymbol{S}^T\cdot\mathbf{v}) = \boldsymbol{S}:\boldsymbol{\nabla} \mathbf{v} + \mathbf{v}\cdot(\boldsymbol{\nabla} \bullet \boldsymbol{S})$$ we get, $$\boldsymbol{\nabla} \bullet (\boldsymbol{S}\cdot\mathbf{b}) = \boldsymbol{S}^T:\boldsymbol{\nabla} \mathbf{b} + \mathbf{b}\cdot(\boldsymbol{\nabla} \bullet \boldsymbol{S}^T)$$.

Since $$\mathbf{b}$$ is constant, $$\boldsymbol{\nabla} \mathbf{b} = 0$$, and we have

(\mathbf{v}\cdot\mathbf{a})~\boldsymbol{\nabla} \bullet (\boldsymbol{S}\cdot\mathbf{b}) = (\mathbf{v}\cdot\mathbf{a})~[\mathbf{b}\cdot(\boldsymbol{\nabla} \bullet \boldsymbol{S}^T)] = \mathbf{a}\cdot[\{\mathbf{b}\cdot(\boldsymbol{\nabla} \bullet \boldsymbol{S}^T)\}~\mathbf{v}] ~. $$ From the definition $$ (\mathbf{u}\otimes\mathbf{v})\cdot\mathbf{a} = (\mathbf{a}\cdot\mathbf{v})\mathbf{u} $$, we get

[\mathbf{b}\cdot(\boldsymbol{\nabla} \bullet \boldsymbol{S}^T)]~\mathbf{v} = [\mathbf{v}\otimes(\boldsymbol{\nabla} \bullet \boldsymbol{S}^T)]\cdot\mathbf{b} ~. $$ Therefore, the final form of the second term is

(\mathbf{v}\cdot\mathbf{a})~\boldsymbol{\nabla} \bullet (\boldsymbol{S}\cdot\mathbf{b}) = \mathbf{a}\cdot[\mathbf{v}\otimes(\boldsymbol{\nabla} \bullet \boldsymbol{S}^T)]\cdot\mathbf{b} ~. $$ Adding the two terms, we get

\boldsymbol{\nabla} \bullet [(\mathbf{v}\cdot\mathbf{a})(\boldsymbol{S}\cdot\mathbf{b})] = \mathbf{a}\cdot[(\boldsymbol{\nabla} \mathbf{v}\cdot\boldsymbol{S})\cdot\mathbf{b}] + \mathbf{a}\cdot[\mathbf{v}\otimes(\boldsymbol{\nabla} \bullet \boldsymbol{S}^T)]\cdot\mathbf{b} ~. $$ Therefore,

{ \boldsymbol{\nabla} \bullet [(\mathbf{v}\cdot\mathbf{a})(\boldsymbol{S}\cdot\mathbf{b})] = \mathbf{a}\cdot[\{\boldsymbol{\nabla} \mathbf{v}\cdot\boldsymbol{S} + \mathbf{v}\otimes(\boldsymbol{\nabla} \bullet \boldsymbol{S}^T)\}\cdot\mathbf{b}] } \qquad\qquad\qquad\square $$

title: Micromechanics of composites/Proof 2


text:
Draft:Original research/Amino acids

An amphoteric organic acid containing the amino group is an amino acid.

Amino acids make up proteins.

Amino acids and proteins are the building blocks of life.

Amino acid, any of a group of organic molecules that consist of a basic amino group (―), an acidic carboxyl group (―COOH), and an organic R group (or side chain) that is unique to each amino acid. The term amino acid is short for α-amino [alpha-amino] carboxylic acid. Each molecule contains a central carbon (C) atom, called the α-carbon, to which both an amino and a carboxyl group are attached. The remaining two bonds of the α-carbon atom are generally satisfied by a hydrogen (H) atom and the R group. When proteins are digested or broken down, amino acids are left. The human body uses amino acids to make proteins to help the body:

Proteins are of primary importance to the continuing functioning of life on Earth. Proteins catalyze the vast majority of chemical reactions that occur in the cell. They provide many of the structural elements of a cell, and they help to bind cells together into tissues. Some proteins act as contractile elements to make movement possible. Others are responsible for the transport of vital materials from the outside of the cell (“extracellular”) to its inside (“intracellular”). Proteins, in the form of antibodies, protect animals from disease and, in the form of interferon, mount an intracellular attack against viruses that have eluded destruction by the antibodies and other immune system defenses. Many hormones are proteins. Last but certainly not least, proteins control the activity of genes (“gene expression”).

This plethora of vital tasks is reflected in the incredible spectrum of known proteins that vary markedly in their overall size, shape, and charge. By the end of the 19th century, scientists appreciated that, although there exist many different kinds of proteins in nature, all proteins upon their hydrolysis yield a class of simpler compounds, the building blocks of proteins, called amino acids. The simplest amino acid is called glycine, named for its sweet taste (glyco, “sugar”). It was one of the first amino acids to be identified, having been isolated from the protein gelatin in 1820. In the mid-1950s scientists involved in elucidating the relationship between proteins and genes agreed that 20 amino acids (called standard or common amino acids) were to be considered the essential building blocks of all proteins. The last of these to be discovered, threonine, had been identified in 1935.

Amino acids are classified into three groups:

(i) Essential amino acids, (ii) Nonessential amino acids, and (iii) Conditional amino acids

Essential amino acids cannot be made by the body. As a result, they must come from food. The 9 essential amino acids are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

Nonessential means that our bodies produce an amino acid, even if we do not get it from the food we eat. Nonessential amino acids include: alanine, asparagine, aspartic acid, and glutamic acid.

Conditional amino acids are usually not essential, except in times of illness and stress. Conditional amino acids include: arginine, cysteine, glutamine, tyrosine, glycine, ornithine, proline, and serine. You do not need to eat essential and nonessential amino acids at every meal, but getting a balance of them over the whole day is important. A diet based on a single plant item will not be adequate, but we no longer worry about pairing proteins (such as beans with rice) at a single meal. Instead we look at the adequacy of the diet overall throughout the day.

Standard Amino Acids: One of the most useful manners by which to classify the standard (or common) amino acids is based on the polarity (that is, the distribution of electric charge) of the R group (e.g., side chain).

Group I: Nonpolar amino acids, Group I amino acids are glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, and tryptophan. The R groups of these amino acids have either aliphatic or aromatic groups. This makes them hydrophobic (“water fearing”). In aqueous solutions, globular proteins will fold into a three-dimensional shape to bury these hydrophobic side chains in the protein interior. The chemical structures of Group I amino acids are:

Group I amino acids: biochemistry, chemical compound

Isoleucine is an isomer of leucine, and it contains two chiral carbon atoms. Proline is unique among the standard amino acids in that it does not have both free α-amino and free α-carboxyl groups. Instead, its side chain forms a cyclic structure as the nitrogen atom of proline is linked to two carbon atoms. (Strictly speaking, this means that proline is not an amino acid but rather an α-imino acid.) Phenylalanine, as the name implies, consists of a phenyl group attached to alanine. Methionine is one of the two amino acids that possess a sulfur atom. Methionine plays a central role in protein biosynthesis (translation) as it is almost always the initiating amino acid. Methionine also provides methyl groups for metabolism. Tryptophan contains an indole ring attached to the alanyl side chain.

Group II: Polar, uncharged amino acids Group II amino acids are serine, cysteine, threonine, tyrosine, asparagine, and glutamine. The side chains in this group possess a spectrum of functional groups. However, most have at least one atom (nitrogen, oxygen, or sulfur) with electron pairs available for hydrogen bonding to water and other molecules. The chemical structures of Group II amino acids are:

Group II amino acids: biochemistry, chemical compound

Two amino acids, serine and threonine, contain aliphatic hydroxyl groups (that is, an oxygen atom bonded to a hydrogen atom, represented as ―OH). Tyrosine possesses a hydroxyl group in the aromatic ring, making it a phenol derivative. The hydroxyl groups in these three amino acids are subject to an important type of posttranslational modification: phosphorylation (see below Nonstandard amino acids). Like methionine, cysteine contains a sulfur atom. Unlike methionine’s sulfur atom, however, cysteine’s sulfur is very chemically reactive (see below Cysteine oxidation). Asparagine, first isolated from asparagus, and glutamine both contain amide R groups. The carbonyl group can function as a hydrogen bond acceptor, and the amino group can function as a hydrogen bond donor.

Group III: Acidic amino acids The two amino acids in this group are aspartic acid and glutamic acid. Each has a carboxylic acid on its side chain that gives it acidic (proton-donating) properties. In an aqueous solution at physiological pH, all three functional groups on these amino acids will ionize, thus giving an overall charge of −1. In the ionic forms, the amino acids are called aspartate and glutamate. The chemical structures of Group III amino acids are

Group III amino acids: biochemistry, chemical compound

The side chains of aspartate and glutamate can form ionic bonds (“salt bridges”), and they can also function as hydrogen bond acceptors. Many proteins that bind metal ions (“metalloproteins”) for structural or functional purposes possess metal-binding sites containing aspartate or glutamate side chains or both. Free glutamate and glutamine play a central role in amino acid metabolism. Glutamate is the most abundant excitatory neurotransmitter in the central nervous system.

Group IV: Basic amino acids The three amino acids in this group are arginine, histidine, and lysine. Each side chain is basic (i.e., can accept a proton). Lysine and arginine both exist with an overall charge of +1 at physiological pH. The guanidino group in arginine’s side chain is the most basic of all R groups (a fact reflected in its pKa value of 12.5). As mentioned above for aspartate and glutamate, the side chains of arginine and lysine also form ionic bonds. The chemical structures of Group IV amino acids are

Group IV amino acids: biochemistry, chemical compound

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The imidazole side chain of histidine allows it to function in both acid and base catalysis near physiological pH values. None of the other standard amino acids possesses this important chemical property. Therefore, histidine is an amino acid that most often makes up the active sites of protein enzymes.

The majority of amino acids in Groups II, III, and IV are hydrophilic (“water loving”). As a result, they are often found clustered on the surface of globular proteins in aqueous solutions.

Amino Acid Reactions: Amino acids via their various chemical functionalities (carboxyls, amino, and R groups) can undergo numerous chemical reactions. However, two reactions (peptide bond and cysteine oxidation) are of particular importance because of their effect on protein structure.

Peptide bond: Amino acids can be linked by a condensation reaction in which an ―OH is lost from the carboxyl group of one amino acid along with a hydrogen from the amino group of a second, forming a molecule of water and leaving the two amino acids linked via an amide—called, in this case, a peptide bond. At the turn of the 20th century, German chemist Emil Fischer first proposed this linking together of amino acids. Note that when individual amino acids are combined to form proteins, their carboxyl and amino groups are no longer able to act as acids or bases, since they have reacted to form the peptide bond. Therefore, the acid-base properties of proteins are dependent upon the overall ionization characteristics of the individual R groups of the component amino acids.

Amino acids joined by a series of peptide bonds are said to constitute a peptide. After they are incorporated into a peptide, the individual amino acids are referred to as amino acid residues. Small polymers of amino acids (fewer than 50) are called oligopeptides, while larger ones (more than 50) are referred to as polypeptides. Hence, a protein molecule is a polypeptide chain composed of many amino acid residues, with each residue joined to the next by a peptide bond. The lengths for different proteins range from a few dozen to thousands of amino acids, and each protein contains different relative proportions of the 20 standard amino acids.

Condensation reaction in which three molecules of the amino acid glycine produce a tripeptide chain, with the elimination of two molecules of water. Condensation reaction in which three molecules of the amino acid glycine produce a tripeptide chain, with the elimination of two molecules of water. Encyclopædia Britannica, Inc.

Cysteine oxidation: The thiol (sulfur-containing) group of cysteine is highly reactive. The most common reaction of this group is a reversible oxidation that forms a disulfide. Oxidation of two molecules of cysteine forms cystine, a molecule that contains a disulfide bond. When two cysteine residues in a protein form such a bond, it is referred to as a disulfide bridge. Disulfide bridges are a common mechanism used in nature to stabilize many proteins. Such disulfide bridges are often found among extracellular proteins that are secreted from cells. In eukaryotic organisms, formation of disulfide bridges occurs within the organelle called the endoplasmic reticulum.

Biochemistry
Def. a compound that releases at least one hydrogen ion (H+), or donates a proton, accepts an electron in reactions, when dissolved in water is called an acid.

Def. capable of reacting chemically either as an acid or a base is called amphoteric.

Organic chemistry
Def. any of various compounds derived from ammonia (NH3) by replacement of hydrogen (H) by one or more univalent hydrocarbon radicals is called an amine.

Def. a compound derived from ammonia by replacement of a hydrogen by a metal, containing the anion NH2- is called an amide.

Def. containing the group NH2 or a substituted group NHR or NR2 united to a radical group (R) other than an acid radical is called amino.

Most organic acids (carboxylic or fatty acids) contain the carboxyl group (-COOH).

Theoretical amino acids
Def. a simple organic compound containing both a carboxyl (-COOH) and an amino (-NH2) group is called an amino acid.

Chemistry
One way amino acids are classified is dextro (D) versus levo (L). This refers to the arrangement of certain radicals relative to the COOH portion.

Dextro has NH2 or the charged NH3+ on the right or on the bottom when the double bonded oxygen is on top.

Compounds
Def. 2-aminopropanoic acid with the chemical formula: CH3 CH(NH2)COOH is called alanine.

Def. 3-aminopropanoic acid, (NH2)CH2 CH2 COOH, is called β-alanine.

Def. 2-aminobutanedioic acid, COOHCH2 CH(NH2)COOH, or symmetrically HOOCCH(NH2)CH2COOH, is called aspartic acid.

Def. 2-aminopentanedioic acid, HOOC(CH2)2 (NH2)COOH, is called glutamic acid.

Def. 2,6-Diaminohexanoic acid, CH2OH CH (NH2)COOH, is called lysine.

Def. 2-amino-3-hydroxypropanic acid, HO2CCH(NH2)CH2OH, is called serine.

Lysine anabolisms
Lysine (Lys or K), is an α-amino acid that contains an α-amino group (−NH3+ protonated under physiologicl conditions), an α-carboxylic acid group (which is in the deprotonated −COO− form under biological conditions), and a side chain lysyl ((CH2)4NH2), classifying it as a charged (at physiological pH), aliphatic amino acid.

Lysine is an essential amino acid, with an element formula of C6H14N2O2.

In plants and most bacteria, lysine is synthesized from aspartic acid (aspartate):

Lysine is a base. The ε-amino group often participates in hydrogen bonding and as a general base in catalysis. The ε-ammonium group (NH3+) is attached to the fourth carbon from the α-carbon, which is attached to the carboxyl (C=OOH) group.

Enzymes involved in this biosynthesis include:

 * 1) Aspartokinase
 * 2) Aspartate-semialdehyde dehydrogenase
 * 3) 4-hydroxy-tetrahydrodipicolinate synthase
 * 4) dihydrodipicolinate reductase or 4-hydroxy-tetrahydrodipicolinate reductase
 * 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
 * 1) Succinyldiaminopimelate transaminase
 * 2) Succinyl-diaminopimelate desuccinylase
 * 3) Diaminopimelate epimerase
 * 4) Diaminopimelate decarboxylase

 * L-aspartate is first converted to L-aspartyl-4-phosphate by aspartokinase (or aspartate kinase). Adenosine triphosphate (ATP) is needed as an energy source for this step.
 * β-Aspartate semialdehyde dehydrogenase converts this into β-aspartyl-4-semialdehyde (or β-aspartate-4-semialdehyde). Energy from Nicotinamide adenine dinucleotide phosphate (NADPH) is used in this conversion.
 * 4-hydroxy-tetrahydrodipicolinate synthase adds a pyruvate group to the β-aspartyl-4-semialdehyde, and a water molecule is removed. This causes cyclization and gives rise to (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate.
 * This product is reduced to 2,3,4,5-tetrahydrodipicolinate (or Δ1-piperidine-2,6-dicarboxylate, in the figure: (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate) by dihydrodipicolinate reductase or 4-hydroxy-tetrahydrodipicolinate reductase. This reaction consumes an NADPH molecule and releases a second water molecule.
 * Tetrahydrodipicolinate N-acetyltransferase opens this ring and gives rise to N-succinyl-L-2-amino-6-oxoheptanedionate (or N-acyl-2-amino-6-oxopimelate). Two water molecules and one acyl-CoA (succinyl-CoA) enzyme are used in this reaction.
 * N-succinyl-L-2-amino-6-oxoheptanedionate is converted into N-succinyl-LL-2,6-diaminoheptanedionate (N-acyl-2,6-diaminopimelate). This reaction is catalyzed by the enzyme succinyl diaminopimelate aminotransferase. A glutamic acid molecule is used in this reaction and an oxoacid is produced as a byproduct.
 * N-succinyl-LL-2,6-diaminoheptanedionate (N-acyl-2,6-diaminopimelate) is converted into LL-2,6-diaminoheptanedionate (L,L-2,6-diaminopimelate) by succinyl diaminopimelate desuccinylase (acyldiaminopimelate deacylase). A water molecule is consumed in this reaction and a succinate is produced as a by-product.
 * LL-2,6-diaminoheptanedionate is converted by diaminopimelate epimerase into meso-2,6-diamino-heptanedionate (meso-2,6-diaminopimelate).
 * Finally, meso-2,6-diamino-heptanedionate is converted into L-lysine by diaminopimelate decarboxylase.

In fungi, euglenoids and some prokaryotes lysine is synthesized via the alpha-aminoadipate pathway.

Homocitrate is initially synthesised from acetyl-CoA and 2-oxoglutarate by homocitrate synthase. This is then converted to homoaconitate by homoaconitate hydratase (homoaconitase) and then to homoisocitrate by homoisocitrate dehydrogenase. A nitrogen atom is added from glutamate by aminoadipate aminotransferase to form the alpha-aminoadipic acid (α-aminoadipate) from which this pathway gets its name. This is then reduced by L-aminoadipate-semialdehyde dehydrogenase (aminoadipate reductase) via an acyl-enzyme intermediate to a semialdehyde. Reaction with glutamate by one class of saccharopine dehydrogenase yields saccharopine which is then cleaved by a second saccharopine dehydrogenase to yield lysine and oxoglutarate.

Metallosphaera cuprina
"The genome of the metal sulfide-oxidizing, thermoacidophilic strain Metallosphaera cuprina Ar-4 has been completely sequenced and annotated."

Lysine biosynthesis enzymes are

 * 1) Aspartokinase Gene ID: 10492721.
 * 2) Aspartate-semialdehyde dehydrogenase Gene ID: 10492720.
 * 3) 4-hydroxy-tetrahydrodipicolinate synthase Gene ID: 10492422.
 * 4) dihydrodipicolinate reductase or 4-hydroxy-tetrahydrodipicolinate reductase [EC 1.17.1.8]
 * 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [EC:2.3.1.117]
 * 1) Succinyldiaminopimelate transaminase [EC:2.6.1.11 2.6.1.17]
 * 2) Succinyl-diaminopimelate desuccinylase [EC:3.5.1.18]
 * 3) Diaminopimelate epimerase [EC:5.1.1.7]
 * 4) Diaminopimelate decarboxylase [EC:4.1.1.20]

Metallosphaera cuprina gene to enzyme match-up
E.C. numbers can be searched using KEGG Enzyme.

 * 1) Gene ID: 10492201 is MCUP_RS00020 nicotinamide-nucleotide adenylyltransferase Mcup_0004 [EC:2.7.7.1].
 * 2) Gene ID: 10492208 is MCUP_RS00055 threonine ammonia-lyase Mcup_0011 [EC:4.3.1.17 4.3.1.19].
 * 3) Gene ID: 10492218 is MCUP_RS00115 diaminohydroxyphosphoribosylaminopyrimidine reductase Mcup_0021 [EC:3.5.4.26 1.1.1.193].
 * 4) Gene ID: 10492243 is MCUP_RS00245 riboflavin synthase Mcup_0046 [EC:2.5.1.9].
 * 5) Gene ID: 10492277 is MCUP_RS00425 aldo/keto reductase Mcup_0081.
 * 6) Gene ID: 10492364 is MCUP_RS00875 alcohol dehydrogenase Mcup_0169 (NADP+) [EC:1.1.1.2].
 * 7) Gene ID: 10492386 is MCUP_RS00980 hypothetical protein Mcup_0191.
 * 8) Gene ID: 10492404 is MCUP_RS01065 CoA-disulfide reductase Mcup_0209 [EC:1.8.1.14].
 * 9) Gene ID: 10492412 is MCUP_RS01105 3-oxoacyl-ACP reductase Mcup_0217 [EC:1.1.1.100].
 * 10) Gene ID: 10492422 is MCUP_RS01150 dihydrodipicolinate synthase family protein or 4-hydroxy-tetrahydrodipicolinate synthase Mcup_0227 [EC:4.3.3.7].
 * 11) Gene ID: 10492489 is MCUP_RS01510 lysine biosynthesis enzyme LysX Mcup_0295 [EC:6.3.2.43].
 * 12) Gene ID: 10492516 is MCUP_RS01655 2-polyprenylphenol hydroxylase Mcup_0322.
 * 13) Gene ID: 10492603 is aroE shikimate dehydrogenase Mcup_0409 [EC:4.2.1.10 1.1.1.25].
 * 14) Gene ID: 10492647 is MCUP_RS02325 3-oxoacyl-ACP reductase Mcup_0453 [EC:1.1.1.100].
 * 15) Gene ID: 10492660 is MCUP_RS02390 3-oxoacyl-ACP reductase Mcup_0467 [EC:1.1.1.100].
 * 16) Gene ID: 10492705 is MCUP_RS02610 ribonucleoside-diphosphate reductase [EC:1.17.4.1], adenosylcobalamin-dependent [EC:1.17.4.1] Mcup_0512.
 * 17) Gene ID: 10492720 is MCUP_RS02695 aspartate-semialdehyde dehydrogenase Mcup_0527 [EC:1.2.1.11]; PRK08664 Location:1 → 348: PRK08664; aspartate-semialdehyde dehydrogenase; Reviewed.
 * 18) Gene ID: 10492721 is MCUP_RS02700 aspartate kinase Mcup_0528 [EC:2.7.2.4]; COG0527 Location:1 → 438: LysC; Aspartokinase [Amino acid transport and metabolism].
 * 19) Gene ID: 10492728 is MCUP_RS02735 acylphosphatase Mcup_0535 [EC:3.6.1.7].
 * 20) Gene ID: 10492734 is MCUP_RS02765 anthranilate synthase component I Mcup_0541 [EC:4.1.3.27].
 * 21) Gene ID: 10492739 is MCUP_RS02790 dehydrogenase Mcup_0546.
 * 22) Gene ID: 10492755 is MCUP_RS02865 S26 family signal peptidase Mcup_0562 [EC:3.4.21.89].
 * 23) Gene ID: 10492771 is MCUP_RS02970 hydroxymethylglutaryl-CoA reductase (NADPH) Mcup_0580 [EC:1.1.1.34].
 * 24) Gene ID: 10492799 is MCUP_RS03115 hypothetical protein Mcup_0608.
 * 25) Gene ID: 10492806 is MCUP_RS03150 thiol reductase thioredoxin Mcup_0615 [EC:1.8.1.8].
 * 26) Gene ID: 10492838 is MCUP_RS03335 threonine--tRNA ligase Mcup_0647 [EC:6.1.1.3].
 * 27) Gene ID: 10492872 is MCUP_RS03505 DsrE family protein Mcup_0681.
 * 28) Gene ID: 10492875 is MCUP_RS03520 heterodisulfide reductase Mcup_0684 [EC:1.8.98.1].
 * 29) Gene ID: 10492876 is MCUP_RS03525 heterodisulfide reductase subunit B Mcup_0685 [EC:1.8.98.1].
 * 30) Gene ID: 10492879 is MCUP_RS03540 heterodisulfide reductase subunit C Mcup_0688 [EC:1.8.98.1].
 * 31) Gene ID: 10492880 is MCUP_RS03545 disulfide reductase Mcup_0689.
 * 32) Gene ID: 10492918 is MCUP_RS03695 oxidoreductase Mcup_0727.
 * 33) Gene ID: 10493002 is MCUP_RS04100 succinate-semialdehyde dehydrogenase Mcup_0811 [EC:1.2.1.16 1.2.1.79 1.2.1.20].
 * 34) Gene ID: 10493114 is MCUP_RS04635 NAD(P)-dependent oxidoreductase Mcup_0923 [EC:1.1.1.30].
 * 35) Gene ID: 10493216 is MCUP_RS05050 FAD-dependent oxidoreductase Mcup_1025 [EC:1.8.5.4].
 * 36) Gene ID: 10493261 is MCUP_RS05240 pyridine nucleotide-disulfide oxidoreductase Mcup_1070 [EC:1.2.1.43].
 * 37) Gene ID: 10493372 is MCUP_RS05540 beta-ketoacyl-ACP reductase Mcup_1181 [EC:1.1.1.62 1.1.1.239].
 * 38) Gene ID: 10493374 is MCUP_RS05550 rubredoxin Mcup_1183 [EC:1.18.1.1].
 * 39) Gene ID: 10493379 is MCUP_RS05575 flavin reductase Mcup_1188 [EC:1.5.1.36].
 * 40) Gene ID: 10493392 is MCUP_RS05635 pyrroline-5-carboxylate reductase Mcup_1201 [EC:1.5.1.2].
 * 41) Gene ID: 10493407 is MCUP_RS05700 alcohol dehydrogenase Mcup_1216 (NADP+) [EC:1.1.1.2].
 * 42) Gene ID: 10493417 is MCUP_RS05750 thiol reductase thioredoxin Mcup_1226 [EC:1.11.1.15].
 * 43) Gene ID: 10493454 is fabG 3-ketoacyl-ACP reductase Mcup_1263 [EC:1.1.1.100].
 * 44) Gene ID: 10493470 is MCUP_RS06010 vitamin K epoxide reductase Mcup_1279 [EC:1.17.4.4].
 * 45) Gene ID: 10493478 is MCUP_RS06050 nitrite reductase Mcup_1288 [EC:1.7.1.15].
 * 46) Gene ID: 10493482 is MCUP_RS06070 component of anaerobic dehydrogenase Mcup_1292.
 * 47) Gene ID: 10493515 is MCUP_RS06215 mercury(II) reductase Mcup_1326 [EC:1.16.1.1].
 * 48) Gene ID: 10493544 is MCUP_RS06335 ferredoxin--NADP(+) reductase Mcup_1355 [EC:1.18.1.2].
 * 49) Gene ID: 10493553 is MCUP_RS06375 dTDP-4-dehydrorhamnose reductase Mcup_1364 [EC:1.1.1.133].
 * 50) Gene ID: 10493582 is MCUP_RS06525 disulfide reductase Mcup_1393 [EC:1.8.4.-].
 * 51) Gene ID: 10493583 is MCUP_RS06530 succinate dehydrogenase Mcup_1394 [EC:1.8.99.2].
 * 52) Gene ID: 10493584 is MCUP_RS06535 succinate dehydrogenase flavoprotein subunit Mcup_1395 [EC:1.3.5.1 1.3.5.4].
 * 53) Gene ID: 10493616 is MCUP_RS06695 aspartate-semialdehyde dehydrogenase Mcup_1427 [EC:1.2.1.75] malonyl-CoA reductase (malonate semialdehyde-forming) 1.2.1.76 succinate-semialdehyde dehydrogenase (acylating); PRK08664 Location:2 → 354: PRK08664; aspartate-semialdehyde dehydrogenase; Reviewed.
 * 54) Gene ID: 10493619 is MCUP_RS06710 peptide-methionine (S)-S-oxide reductase Mcup_1430 [EC:1.8.4.11].
 * 55) Gene ID: 10493642 is MCUP_RS06820 DNA-binding protein Mcup_1453.
 * 56) Gene ID: 10493691 is MCUP_RS07050 alcohol dehydrogenase Mcup_1502 (NADP+) [EC:1.1.1.2].
 * 57) Gene ID: 10493694 is MCUP_RS07065 DNA polymerase IV Mcup_1505 [EC:2.7.7.7].
 * 58) Gene ID: 10493700 is MCUP_RS07095 thioredoxin-disulfide reductase Mcup_1511 [EC:1.8.1.9].
 * 59) Gene ID: 10493802 is MCUP_RS07585 FAD-dependent oxidoreductase Mcup_1613 [EC:1.8.5.4].
 * 60) Gene ID: 10493824 is MCUP_RS07690 aldo/keto reductase Mcup_1635.
 * 61) Gene ID: 10493838 is MCUP_RS07760 alcohol dehydrogenase (NADP+) Mcup_1649 [EC:1.1.1.2].
 * 62) Gene ID: 10493847 is MCUP_RS07805 flavoprotein Mcup_1658 [EC:1.5.5.1].
 * 63) Gene ID: 10493859 is MCUP_RS07865 NADH oxidase Mcup_1670 [EC:1.6.3.3].
 * 64) Gene ID: 10493870 is MCUP_RS07920 alcohol dehydrogenase Mcup_1681 (NADP+) [EC:1.1.1.2].
 * 65) Gene ID: 10493881 is MCUP_RS07975 enoyl-CoA hydratase Mcup_1692 [EC:5.3.3.18].
 * 66) Gene ID: 10493903 is MCUP_RS08085 oxidoreductase Mcup_1714 [EC:1.3.1.34].
 * 67) Gene ID: 10493920 is MCUP_RS08170 hypothetical protein Mcup_1731.
 * 68) Gene ID: 10493946 is MCUP_RS08300 2-ketoisovalerate ferredoxin oxidoreductase Mcup_1758 [EC:1.2.7.1].
 * 69) Gene ID: 10493950 is MCUP_RS08320 4Fe-4S ferredoxin Mcup_1762 [EC:1.8.7.1].
 * 70) Gene ID: 10494003 is MCUP_RS08555 D-glycerate dehydrogenase Mcup_1815.
 * 71) Gene ID: 10494014 is MCUP_RS08605 nucleotide pyrophosphohydrolase Mcup_1826 [EC:3.6.1.11 3.6.1.40].
 * 72) Gene ID: 10494032 is pyrG CTP synthetase Mcup_1844 [EC:6.3.4.2].
 * 73) Gene ID: 10494046 is MCUP_RS08765 glutamyl-tRNA reductase Mcup_1858 [EC:1.2.1.70].
 * 74) Gene ID: 10494054 is MCUP_RS08800 peptidyl-tRNA hydrolase Mcup_1866 [EC:3.1.1.29].
 * 75) Gene ID: 10494093 is MCUP_RS09005 lysine biosynthesis enzyme LysX Mcup_1905 [EC:6.3.2.43].
 * 76) Gene ID: 10494094 is MCUP_RS09010 sulfonate ABC transporter Mcup_1906 [EC:3.6.3.-].
 * 77) Gene ID: 10494097 is MCUP_RS09025 N-acetyl-gamma-glutamyl-phosphate reductase Mcup_1909 [EC:1.2.1.38].
 * 78) Gene ID: 10494159 is MCUP_RS09350 hypothetical protein Mcup_1971.
 * 79) Gene ID: 32167125 is MCUP_RS09805 DNA-directed RNA polymerase subunit P Mcup_0095 [EC:2.7.7.6].
 * 80) Gene ID: 32167145 is MCUP_RS09905 YHS domain-containing protein Mcup_1601.
 * 81) Gene ID: 32167149 is MCUP_RS09925 30S ribosomal protein S14 Mcup_1953.
 * 82) Gene ID: 32167150 is MCUP_RS09930 50S ribosomal protein L37e Mcup_1997.

Hypotheses

 * 1) Genes are used to produce amino acids.
 * 2) Archaea have a different pathway to produce lysine than bacteria, fungi, or plants.

title: Draft:Original research/Amino acids