Wikipedia:Reference desk/Archives/Science/2016 December 9

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December 9

How many levels of carbons are there in isoleucine?

I watched this video where the woman explains (16:20) that the Leucine has carbon alpha, beta, gamma and delta 1(D1) & delta 2 (D2). She jumped on the description of the levels of carbons of ISOleucine. Can I say that it has 4 levels of carbons in the following order: carbon alpha, beta, carbon gamma 1 (G1), carbon gamma 2 (G2) and carbon delta? (we never count the carbons of basic amino acid structure i.e carboxylic group, we start to count carbons from the alpha carbons) 93.126.88.30 (talk) 04:06, 9 December 2016 (UTC)

Sure, that's a reasonable description of isoleucine following the pattern of the given leucene example. DMacks (talk) 06:01, 9 December 2016 (UTC)

Yes. I should say though that it is rare for people to keep track of gamma and delta carbons in this way: instead, the main chain is simply numbered per IUPAC and side chains are described simply as methyl groups. On the other hand, I should mention that an alpha carbon is not limited to amino acids or the context of biochemistry, as it is of very great importance to organic chemistry. For example, acetone is (very) mildly acidic because the alpha carbons (on either end) can potentially release a proton and become double bonded to the central carbon leaving a negative charge on the oxygen (an enolate), and this conjugate base is then a potent nucleophile and could serve as a donor in an aldol condensation or many other reactions.

I should add that her approach on the delta carbons seems old-fashioned, as does the old usage of the term "imino acid" I noticed while flipping forward at 13:24 - see [1] where I was given a correction on that point. But I haven't watched any substantial portion overall. Wnt (talk) 13:54, 9 December 2016 (UTC)

Indeed, I have to agree with Wnt's assessment here on the use of Greek letters as a means of identifying carbons. In actual practice, it is rare to use any convention beyond its usefulness. Yes, one COULD assign Greek letters to every carbon in a molecule, but I have rarely (if every) encountered anyone using a letter passed beta, never mind delta. There just isn't any useful reason to do so. If you need to indicate carbons at other places in the chain, there's a perfectly useful system (the IUPAC systematic name) to do so. You'll notice that the Wikipedia article is titled alpha and beta carbon; it's just weird among chemists to get much beyond that. --Jayron32 15:29, 9 December 2016 (UTC)

Thank you all, I learnt from you a lot of information - you are really amazing with your knowledge and also patient to explain to dummies like me. Thank you again! 93.126.88.30 (talk) 16:59, 9 December 2016 (UTC)

@Jayron32, BTW you wrote that if I need to indicate carbons at other places in the chain, there's a perfectly useful system. It's very interesting for me to what is this way. I entered the link that you put and I didn't found myself there because it's a huge page. May you focus me please? 93.126.88.30 (talk) 16:59, 9 December 2016 (UTC)

Sure. The IUPAC rules work thusly 1) Identify the longest chain of carbons, use the alkane of that length as the base chain. 2) Number that chain from one end, such that the substituent groups (i.e. branches and heteroatoms not on the main chain) have the lowest possible numbers 3) Number and name the substituents as prefixes and suffixes on the base alkane. Under IUPAC rules, leucine is "2-Amino-4-methylpentanoic acid" The longest chain is five carbons. That's pentane Since the carboxylic acid is there (pentanoic acid), that's on the end, so that is carbon "1" in our chain. Numbering the other 5 going out from there there's an NH3 group on carbon 2 and a CH3 group on carbon 4. Most of the biological amino acids are "2-amino carboxylic acids" under IUPAC rules; alanine is 2-Aminopropanoic acid (a three carbon chain is propane), cysteine is like 2-amino-3-mercaptopropanoic acid, etc. --Jayron32 20:59, 9 December 2016 (UTC)

Our main article on this naming process is IUPAC nomenclature of organic chemistry. It walks through the process Jayron32 notes, of finding the parent (longest chain), identifying the various substituents and other functional groups, and then stringing the words together to describe which groups are where on the parent. DMacks (talk) 21:04, 9 December 2016 (UTC)

FYI, I already linked that. He read it and got lost in the TLDR nature of the article. That's why I simplified it. --Jayron32 21:12, 9 December 2016 (UTC)

Also, I should note, that the connection between IUPAC and the alpha/beta system is not consistent. For the alpha/beta system, the carbon that is part of the carboxyl group is not considered part of the carbon chain, so one calls the next carbon over the alpha. For IUPAC, that means that in amino acids, alpha is always carbon 2. However, in something like an alcohol (like say 1-Pentanol) the alpha carbon is the one attached to the hydroxy group, so in that case alpha = 1. Thus, if you did a lithium aluminum hydride reduction of your leucine and turned the carboxyl group into a hydroxy group, like this, you'd go from "alpha-amino-carboxylic acid" to a "beta-amino-alcohol". That sounds like the amino moved. But with the IUPAC system, you'd go from a "2-amino-carboxylic acid" to a "2-amino-alcohol". Much simpler and more consistent. --Jayron32 21:12, 9 December 2016 (UTC)

To paraphrase my engineering friends, "the great thing about systematic methods is that there are so many systems to choose from". DMacks (talk) 21:19, 9 December 2016 (UTC)

Thank you. btw, regarding to methionine according to the method of this woman, can we say that the carbon of methyl group which is attached to the sulfur- is delta carbon or it's correct to say that since it's attached to the sulfur then the counting of the carbons is stopped? 93.126.88.30 (talk) 01:11, 10 December 2016 (UTC)

The later letters in the alphabet do linger on in some old names, most famously, "gamma-hydroxybutyrate" (GHB, an undesirable variant of alcohol that had a brief fad popularity as a party drug and subsequently was vilified and highly prohibited as a so-called rape drug) Wnt (talk) 17:02, 9 December 2016 (UTC)

up through gamma/delta or so, maybe one or two more, are still commonly used in some areas for lactones (to describe the ringsize or reaction that forms it, not to name the whole molecule). And gamma is also used when discussing deprotonation of enones and related structures (for example doi:10.1002/ejoc.200500145). DMacks (talk) 20:28, 9 December 2016 (UTC)

Yeah, there's a few. But not many. They're the exception rather than the rule. --Jayron32 20:59, 9 December 2016 (UTC)

I found this usage of alpha, beta, gamma and delta carbons - on University of Arizona site. They use it exactly for isoleucine.93.126.88.30 (talk) 03:01, 10 December 2016 (UTC)

Yes, though I suspect there may not have been enough thinking involved, since they label the sulfur atom in methionine as δ (what?!?) so that the last carbon can be labelled as ε. The labelling for molecules with too many functional groups gets confusing and I do not think this or any system involving Greek letters will be universally understood for such a molecule! Double sharp (talk) 03:11, 10 December 2016 (UTC)

Yes, but at least for me it helps to remember the amino acids. I can assume that in general chemistry it's impossible and not practical, but as I said for some purposes they are convenient for use. Regarding to the using the epsilon for the methyl's carbon which is attached to the sulfur, it's nice observation and I'm also wondering about it. If you read aforementioned, then you can see that I asked if according to the method of this woman, we can say that the carbon of methyl group which is attached to the sulfur- is delta carbon or it's correct to say that since it's attached to the sulfur then the counting of the carbons is stopped. So far I don't really know what is acceptable in such case. 93.126.88.30 (talk) 03:47, 10 December 2016 (UTC)

I don't know either, because outside lactonisation (in which γ and δ are very common, and I've seen ε and ζ less frequently) and a few other cases (usually not going past γ) the Greek letters simply aren't used. I'd call that carbon "the one in the -SCH₃ group", because I wouldn't know what to call it in the Greek-letter system (and I suspect most people wouldn't know either). Double sharp (talk) 07:56, 10 December 2016 (UTC)

I found an interesting thing. The way of University of Arizona using the epsilon is also mentioned on this article "Several simple 3D experiments are used to provide J correlations between methionine C epsilon methyl carbons and either the C gamma H2 protons or C beta and C gamma.". Then I can assume that this way is not considered as a mistake but a another way to describe it. I'm just wondering why the use "carbons" (in plural) while referring to C epsilon methyl. 93.126.88.30 (talk) 20:19, 10 December 2016 (UTC)

That article talks about not just analyzing methionine itself, but also in the context of the protein calmodulin. The subject is different conformations of methionine, so having a single molecule that contains several of them held in different specific conformations is a nicer model than a less-constrained case. So I read the plural "methionines" as approximately "the methionine residues in calmodulin". DMacks (talk) 20:50, 10 December 2016 (UTC)

Then basically you say that we can not prove from this article that the methyl's carbon of standard methionine is epsilon. Isn't it?93.126.88.30 (talk) 00:09, 11 December 2016 (UTC)

Predicting solar eclipses

When was the first solar eclipse predicted reliably? Google found me some potential answers, e.g. [2] and Eclipse of Thales. But now I'm left wondering: when was it first possible to predict the specific minutes of the eclipse, whether minutes of totality or minutes of partiality, for a specific location? Who first achieved this, and where in the world? Nyttend (talk) 05:43, 9 December 2016 (UTC)

Solar eclipse of May 3, 1715. Count Iblis (talk) 06:08, 9 December 2016 (UTC)

See also here. Count Iblis (talk) 06:13, 9 December 2016 (UTC)

(ec)Our article mentions Edmund Halley, but his fairly accurate prediction was apparenty preceded by that of William Whiston. According to this Guardian article:

Flamsteed's lunar tables were later used by William Whiston and, corrected with Newtonian theory, used to produce another predictive eclipse map, also published by Senex in March 1715. Whiston’s text was more technical than Halley’s and his map less immediately appealing to “The Inquisitive” he called on to help observe, but he seems to have got there first (and twice).

Halley's first map (Low-res)

Whiston's map (3mb)

Halley's second map, corrected and with prediction for the next eclipse (6mb)

How accurate Flamsteed's tables, Whiston's map or Halley's second map were, I do not know.

ps. Actually, looking at Whiston's map, he says So that the Middle of the General Eclipse in common or apparent Time will be 50' 56″ after nine in the Morning, differing from Dr Halley's Computation near 9 min. So maybe the Grauniad is wrong and Halley did get there first?

pps. Have updated our article on the Solar eclipse of May 3, 1715 to mention Whiston.

ppps. A better source for the Halley/Whiston predictions here

pppps. As to the first good prediction of length of totality, that may be for the next eclipse in May 22, 1724. Halley notes in his map: The Curious are desired to Observe it, and especially the duration of the Total Darkness, with all the care they can; for therby the Situation and dimensions of the Shadow will be nicely determin'd; and by means thereof, we may be enabled to Predict the like Appearances for the future, to a greater degree of certainty than can be pretended to at present, for want of such Observations. --Hillbillyholiday ^talk 07:27, 9 December 2016 (UTC)

After further research I found that Philippe de La Hire invented an eclipse calculator in 1704, with which (according to this less-than convincing site) he may have predicted the May 1706 eclipse to within 1' 30″. I can't find any other source that confirms this, but it seems that reasonably accurate predictions were possible by then. Apparently Jean Le Fèvre was better than La Hire at predicting eclipses (link), but I can't find any solid proof of this either. Also here is a pdf with predictive maps by Symon van de Moolen (1705) and Andreas van Luchtenburg (1706). The first known predictive eclipse map is Erhard Weigel's 1654 map, which was 100km off (Celestial Shadows: Eclipses, Transits, and Occultations a good overview of the subject). Perhaps an article on Eclipse prediction is in order using some material already here?

The historical improvements in measuring lunar longitude relate to the potential accuracy of predictions: In 1474 Regiomontanus was 1.3° off, twice as good as Ptolemy, but by c.1630 Horrocks had reached 12', a 6.5x improvement on Regiomontanus. By 1702 Newton got to within 7', by 1753 Mayer had 1.5', and by 1787 Mason had 6″, a 15x improvement on Mayer giving an error in the shadow-path axis of roughly 5km on the ground. --Hillbillyholiday ^talk 12:13, 9 December 2016 (UTC)

• While it couldn't generally do accurate-to-the-minute calculations (except in rare cases where it got lucky), you may be interested in this detailed analysis of the eclipse-predicting capabilities of the Antikythera mechanism. Smurrayinchester 10:18, 9 December 2016 (UTC)

It would appear that solar eclipse prediction is not yet entirely exact, at least in terms of time of day predictions for 2500 years ago - ancient documents indicated times that are off from about 7 hours from what was expected based on tidal slowing of the Earth's rotation, due presumably to changes since the end of the last major glaciation... just saw this news story [3] citing [4] Wnt (talk) 20:24, 9 December 2016 (UTC)

Erm, sorry, I mean from what is expected; I meant that the current predictions of past eclipses turn out to be wrong by seven hours as indicated by checking ancient documents. Wnt (talk) 21:03, 9 December 2016 (UTC)

You can also consider the most dominant perturbations of the lunar orbit due to Jupiter which would have been impossible to take into account without using classical mechanics developed by Newton (the influence of the Sun is much larger but this was effectively taken into account by empirical formulas). Jupiter causes a perturbation of the position of Moon during one orbit of the order of 1 km. This means that the shadow of the Moon on the Earth will shift by a distance of the order of a kilometer due to Jupiter. Count Iblis (talk) 20:39, 9 December 2016 (UTC)

Long term predictions of of the movements of ANY bodies in the solar system are impossible. It is an n-body problem, and for the number of moving parts in the solar system, it can't be done. After several thousands of years, you're going to become progressively further and further afield of your predictions even if you could take into account all of the various effects. --Jayron32 20:47, 9 December 2016 (UTC)

See our article Delta T#Earth's rate of rotation for more information. Software is available which enables "the direct computation of high precision ephemerides over a time span of several millennia".[5]. 81.129.14.217 (talk) 22:49, 10 December 2016 (UTC)

What do speculation of raw materials?

do not feed. --Jayron32 14:36, 9 December 2016 (UTC)
The following discussion has been closed. Please do not modify it.
What do speculation of raw materials, in particular what do speculation of remains natural reserves of natural raw materials, such as natural gas, oil and others?--91.76.180.75 (talk) 13:37, 9 December 2016 (UTC) Please try to clarify the question. I am nor sure of the exact nature of your inquiry. Bus stop (talk) 13:44, 9 December 2016 (UTC) Denies speculation of raw materials, in particular denies speculation of remains natural reserves of natural raw materials the benefits all other participants of the economy?--91.76.180.75 (talk) 13:55, 9 December 2016 (UTC) Are you asking what the consequences are of the large-scale ownership of naturally occurring raw materials by the wealthier members of society? If that is the question, I think the answers are multitudinous, with the possibility of both positive and negative consequences. Please tell me if I am understanding the question as you intend it. Bus stop (talk) 14:05, 9 December 2016 (UTC) Denies speculation of raw materials, in particular denies speculation of remains natural reserves of natural raw materials the benefits me personally and all of us?--91.76.180.75 (talk) 14:16, 9 December 2016 (UTC) I am not sure what "denies speculation" means. What type of speculation are you referring to? Commodities are traded in the commodity markets. It is true that someone could "deny" participation in the commodity market while secretly holding positions in commodities. But I am not sure what particular situation we are discussing. Can you perhaps provide a link to a news story if this is covered elsewhere? Bus stop (talk) 14:30, 9 December 2016 (UTC) Please note: This is a person who has been doing this sort of thing (asking questions in garbled English) for years. We've come to a decision as a community that it is not productive to entertain questions from this one person anymore. Closing. --Jayron32 14:36, 9 December 2016 (UTC)

What was Brenda wearing?

People ask medical questions here, and these can be answered under limited circumstances. My goal is to improve the inadequate article Hospital gown, though I haven't had a lot of luck. This would represent a case where someone is wearing something different from a hospital gown (maybe) which, given a proper source, would be useful information to add to the article. There are situations where a hospital gown would be necessary, and others where it wouldn't or one would wear something different. I feel this idea is something useful for the article. In the case of Brenda, a character on Beverly Hills, 90210 (played by Shannen Doherty who had breast cancer for real years later) there was a breast cancer scare which required a biopsy. I did some research on what someone would wear for a biopsy, and while every source indicated one would wear a hospital gown (though they didn't necessarily say how the breast is uncovered for the biopsy), Brenda was covered by a sheet and we could see her head and shoulders, but nothing covering her shoulders, as if she was in bed with a guy.— Vchimpanzee • talk • contributions • 17:39, 9 December 2016 (UTC)

Even if you found out what someone normally would wear for a biopsy, adding such info to the article would be "original research". Also, how does having bare shoulders in a hospital bed equate to having a bed-partner? ←Baseball Bugs ^{What's up, Doc?} carrots→ 17:45, 9 December 2016 (UTC)

It doesn't. I was just making the point that it happened all the time on that show. I was trying to find actual sources that would improve the article. I thought maybe someone could point me in the right direction because I'm not having much luck.— Vchimpanzee • talk • contributions • 17:55, 9 December 2016 (UTC)

You would need to find a source that explains why she was depicted bare-shouldered instead of wearing a hospital gown. That could be a challenge. ←Baseball Bugs ^{What's up, Doc?} carrots→ 17:59, 9 December 2016 (UTC)

I guess what I'm looking for is a source that explains why the show would have depicted her not wearing a gown, based on the reality of what might actually be done. I was hoping to find someone who might speculate rather than give a specific answer, but would know of a source which might lead to the information I need for the article. — Vchimpanzee • talk • contributions • 18:25, 9 December 2016 (UTC)

A nursing textbook might work for improving the Wikipedia article. I had been looking at online journals and not finding much. I go to several libraries at colleges that have nursing programs.— Vchimpanzee • talk • contributions • 18:56, 9 December 2016 (UTC)

Again, trying to add something about what you think she "should have been" wearing amounts to original research and probably won't be allowed. And keep in mind that the show is fictional, so there's no reason to expect it to conform to some sort of real-world routine. ←Baseball Bugs ^{What's up, Doc?} carrots→ 19:43, 9 December 2016 (UTC)

I can't really picture complaining about any inaccuracy that left more of her exposed to the viewer, and it is definitely not important enough to mention in an article about hospital gowns in general. You're pushing relevance just to include it in an article about that episode of the TV series, if we have one (and I wouldn't be surprised...) Wnt (talk) 20:27, 9 December 2016 (UTC)

I think everyone is interpreting my question backwards. This isn't about Brenda, but whether it represents reality, and only reality would be relevant to the article. I'll follow up if I get answers, but I think everyone is too focused on Wikipedia here. If I got the answer about Brenda, I might be able to use that to find the relevant information for Wikipedia later.— Vchimpanzee • talk • contributions • 20:33, 9 December 2016 (UTC)

I'm still failing to see how knowing what specific garment ANYONE would wear for a biopsy (even if we COULD find a reliable source) is something that belongs in an encyclopedia article. Just because it's true, and EVEN if it is verifiable, doesn't mean we should write it. What are you trying to do with this information (if we can find it for you). --Jayron32 20:44, 9 December 2016 (UTC)

I'm not sure at this point. It sounds like my theory on how to improve the article is not being accepted.— Vchimpanzee • talk • contributions • 20:53, 9 December 2016 (UTC)

I'm sure that a misplaced sense of modesty does kill a few cancer patients each year, so if we could provide some reassurance that a breast biopsy does not mean having fifty medical students standing around taking selfies and Vine videos with your bare bosoms there is a small but non-zero chance it could save a life. So I won't say useless, exactly. But without a source beyond a TV episode, obviously we're not getting there. Wnt (talk) 21:00, 9 December 2016 (UTC)

See, it's not the TV episode that's the source. I was hoping to find a web site or possibly someone who knew something here, which would lead to a real source and something concrete for the article. I think Wnt is getting there.— Vchimpanzee • talk • contributions • 21:02, 9 December 2016 (UTC)

I think people are being too hard on this question. If there are indeed different types of hospital gowns worn for specific procedures, that would definitely be relevant to the Wikipedia article on the subject. Someguy1221 (talk) 21:47, 9 December 2016 (UTC)

That's what I'm thinking too. I was looking for a good source for that. I'm going back to the biopsy information when I get time. Some of that might be a better fit on a breast cancer article, but I'm not confident enough to attempt medical edits.

As for my comment about Brenda being in bed with guys, I have a theory she was dressed like that for the same reason they put pretty girls in bed with guys.

There was another show-- a family show where this would definitely not be the objective, where an older but still attractive woman was about to have breast cancer surgery, and she was shown with bare shoulders as well. I'm curious about the decision to do that as well. I'm just thinking it represents reality.— Vchimpanzee • talk • contributions • 20:55, 12 December 2016 (UTC)

So after all that, is your question essentially, "Is there a standard style of gown that women getting a breast biopsy wear? And if so, does it leave their shoulder(s) bare?" If so, a Google image search quickly indicates that there are multiple ways of performing the procedure (probably dependent on where the lump is located), including different positions and differing amounts of clothing. Matt Deres (talk) 17:27, 13 December 2016 (UTC)