Sciencemadness Discussion Board - The Social Norm of Capitalization

The Social Norm of Capitalization

watson.fawkes - 5-12-2010 at 13:50

I suggest two social norms for capitalization. A social norm means that members may urge compliance independently, with requiring an official policy.

All chemical compounds should use proper element capitalization. I know what "naoh" probably refers to, and it's likely not a misspelling of the guy with an ark. Nevertheless, it's still harder to read. My attitude, rarely expressed directly to members who do this, is "If you can't be bothered to hit the shift key, I can't be bothered to care about your question."
All abbreviations should be spelled out in full at least once before they are used, especially in subject lines that open new threads and appear on summary pages and in HTML titles. I suggest the spell-first, abbreviation-in-parentheses-following (SP-AiPF) convention for clarity. SP-AiPF is pretty widespread already. My attitude, similarly mostly silent, is "If you can't be bothered to explain yourself, I can't be bothered to care."

To my mind, these are some of the least burdensome consequences of a general care in writing for many other people to read. There's already a social norm here that members should at least some research before asking a question. How much less work is it to take an extra moment to ask a question legibly?

aonomus - 5-12-2010 at 14:07

I commend you for the fact you still have hope for people to use proper spelling and capitalization. I don't have that hope.

Plus, the people most likely to offend are also the least likely to read this sub-forum.

I'd say make it mandatory for major infractions (ie: entire posts with no capitalization, punctuation, and butchered spelling get warnings) and ignore the occasional slip ups (IUPAC naming pedantics and SP-AIPF). Promote the fact that people should Google something before asking it in a 1 sentence post.

Nicodem - 5-12-2010 at 14:32

Good to see I'm not the only one who gets pissed by the continuous abuse of element's symbols, for they are symbols and not letters. Thus, without proper capitalization they mean shit. I wanted to complain myself already several times, but did not because I don’t think the people who are too lazy to use the shift key will ever bother reading it, or changing for better. It still hurts to read crap like “h2so4” or “naoh” all the time, but my attitude is to ignore such posts where the poster shows obvious signs of illiteracy. That’s more or less the response I give when they are lazy or kewlish or otherwise annoying. Except when I’m in the mood though, when I might waste some time preaching even though knowing it is a complete waste of time (but at least it gives me the illusion of having fulfilled the moderator’s duty).

I don’t see an easy and efficient way to avoid post like that by any change in moderating policy. I have been trying for years to enforce even the most basic scientific method, the use of references, yet I feel I had close to no effect. This experience led me to believe it is not possible to change lazy people by any simple approach, especially if you have to deal with hordes of lazy people.

watson.fawkes - 5-12-2010 at 14:41

Quote: Originally posted by Nicodem

I have been trying for years to enforce even the most basic scientific method, the use of references, yet I feel I had close to no effect.

I believe you've had a significant effect, actually, not by changing the lazy people but by chasing them away. If you can't change lazy people (not in any great quantity, at least), the second best you can do is keep them from polluting your own social environment. It doesn't benefit the lazy, but it does benefit the non-lazy. It's not as good an outcome, but it's better and it's realistic. So therefore, thank you.

watson.fawkes - 5-12-2010 at 14:46

Quote: Originally posted by aonomus

Plus, the people most likely to offend are also the least likely to read this sub-forum.

Yet we may lead them here. Part of my thinking is that links to this thread might be posted in response to particularly egregious or flagrant examples, if not in the hope changing the perpetrator, at least in strengthening the expectations of good behavior.

aonomus - 5-12-2010 at 15:38

Considering that most of the illiterates' eyes glaze over when being preached to (lest they become defensive), essentially they think 'tl;dr'.

Perhaps a screenshot of a horrible forum post vs a good forum post with some infographics and flashy crap is exactly what the kewls need to 'change'. That, or the Clockwork Orange treatment with a crash course on the English language.

Govern with an iron fist = kewls leave and don't come back. Forum stagnates, fewer people join the hobby
Lack of control = smart people leave and go to another forum with less crap
Moderate control with the entire forum population self policing new posters and 'encouraging' proper posting etiquette = ?

movin up

cyanureeves - 5-12-2010 at 18:06

sounds good. this will force me to learn.but hope yall dont give up just yet cause theres a bunch of good stuff ill miss out from other people who are very apt in chemistry but not grammar or english.tolerance is rewarding too,its inviting.inviting who huh?i use naoh alot its shorter than sodium hydroxeyesofacrosseyedtoad.i googled a symbol i saw here yesterday that looked mean as hell and it was just ethanol.NaOH. i like it! the universal language of love almost.

bfesser - 5-12-2010 at 18:45

Watson.Fawkes:

Hear hear!

gnitseretni - 5-12-2010 at 19:57

People should use proper grammar, PERIOD!

Posts like the one below are a real eyesore!

Quote: Originally posted by cyanureeves

sounds good. this will force me to learn.but hope yall dont give up just yet cause theres a bunch of good stuff ill miss out from other people who are very apt in chemistry but not grammar or english.tolerance is rewarding too,its inviting.inviting who huh?i use naoh alot its shorter than sodium hydroxeyesofacrosseyedtoad.i googled a symbol i saw here yesterday that looked mean as hell and it was just ethanol.NaOH. i like it! the universal language of love almost.

bquirky - 5-12-2010 at 21:51

What a charmed life you all must lead if Grammer on the internet is your biggest problem

hissingnoise - 6-12-2010 at 02:52

Indeed! While I find poorly written posts irritating to read I often choose irritation.
Carelessly written posts by English speakers make me wonder if their carelessness persists when they handle reactive substances.
Allowances should, of course, be made when the poster doesn't have English as a first language . . .
I don't, however, find it a major problem!

Ephoton - 6-12-2010 at 02:58

well I read this thread.

still I read as much as I can when I have the time.

grammer is one of my problems but I can see your point.

still I use element symbols properly.

maby im better at coded language than written.

does that make me unworthy of such a place as this.

I hope not I like quite a lot of you and kind of hoped that some of you

felt the same

Arthur Dent - 6-12-2010 at 05:23

I've been accused of being a grammar nazi on occasions, and English isn't even my native language! I do a lot of translation work and live in a bilingual city (Montreal)...

I wholeheartedly agree with watson.fawkes that the language, grammar (sic) and syntax on some posts makes them hard to decipher sometimes, and I am much less likely to grant any form of credibility to the poster if the post looks like something texted on an iPhone by a 13 yr. old teen girl. I mean, if one sucks at English and it's their native tongue, I bet that their knowledge of chemistry wouldn't be any better...

There are posts written by people whose native tongue is not English and they often make a brave effort to make it legible but some of them make me smile because when you read them aloud, they sound like a Yakov Smirnoff monologue! LOL (pretty much dated myself there...)

Watson.fawkes has a good point that people on this forum should indeed use the "long" name of a reagent at least once, especially when it comes to organic chemistry. When I look up a chemical I am unfamiliar with, it's easier if I have a proper reference to it than some cryptic abbreviation that looks like a cat dragged its paws on a keyboard!

I usually allow quite a bit of latitude in the grammar used in posts, but when a post looks almost intentionally written by a demented monkey, or is obviously written by a dumb little "kewl" with a post count of one, who just discovered the reaction between baking soda and vinegar in mommy's cupboard, I tend to skip this post or the whole thread because I feel it's a waste of my time and of all of the other "real" members of this forum.

" i wnt mak GP wat i do?? plzzz!!1!! "

I am glad to participate or help inexperienced members in their quest to synthetize a reagent or build a piece of equipment, but when the grammar of the post is horrendous, I don't feel I want to make the effort to help if that person can't at least make the effort to use the Caps key once in a while on their keyboard... and the "texting" abbreviations just make my friggin' skin crawl!

As I said, this may be because of my background as translator/copy-proofing work in French and in English, but I consider proper grammar as important as the usage of the words "please" and "thank you". My grammar isn't perfect and I'll do the occasional blurb, but I do make an effort to use Shakespeare and Molière's language the way it's supposed to.

Robert

[Edited on 6-12-2010 by Arthur Dent] (typos, LOL)

[Edited on 6-12-2010 by Arthur Dent]

[Edited on 6-12-2010 by Arthur Dent]

Ephoton - 6-12-2010 at 05:32

maske ?

Je ne comprends pas

ya gotta love this place.

[Edited on 6-12-2010 by Ephoton]

Arthur Dent - 6-12-2010 at 05:34

Yeah, you got me there...

I meant make... LOL

hissingnoise - 6-12-2010 at 05:49

Quote: Originally posted by Arthur Dent

... and the "texting" abbreviations just make my friggin' skin crawl!

o i h8 dat 2

madscientist - 6-12-2010 at 05:49

Biggest problem to me is a lack of paragraph breaks. Huge blocks of sloppily written text can be difficult to read.

Poor grammar, overuse of cryptic lingo etc. can be a little annoying but it doesn't bother me that much.

We still like you Ephoton!

vulture - 6-12-2010 at 08:46

Ditto.

Science stands or falls with proper communication. I often find it sad that native English speakers show great disrespect for their own language, yet those are also the people who will shout "habla ingles" at foreigners...

Ephoton - 6-12-2010 at 08:50

At least you guys push me to better my self rather than screaming for
recipes

I like that.

bbartlog - 6-12-2010 at 10:59

Agree with the use of proper capitalization. And reasonable grammar, and so on. Further, even if people get offended, I think it makes sense to tell them: there's an implicit quid pro quo, where the amount of effort people spend trying to answer your questions is going to be strongly correlated with the amount of effort you put into your posts. Not only that, but some people really do lack awareness of how they come across and would benefit from being reminded that their sloppiness makes them look stupider than they really are.

Quote:

I have been trying for years to enforce even the most basic scientific method, the use of references, yet I feel I had close to no effect.

There may not be improvement, but sometimes the best that can be done is to prevent the slide into complete degeneracy.

madscientist - 6-12-2010 at 11:13

So long as the content is good, it's still a positive contribution.

I do encourage adhering to standards that make posts readable - no huge blocks of text, proper capitalization, no use of undefined acronyms (outside of ones standardized in the literature: DMSO, LAH, etc.), reasonably decent spelling. We do have a spell checker that highlights misspelled words as a post is written.

I'm not going to crack the whip though unless someone is truly teetering on unreadability, writing as if they have been ripping bong hits of phosphine.

Magpie - 6-12-2010 at 11:22

When you pose a question or ask for help on this forum I would think that you are after the highest quality response that you can get. So why would you present that request in poor grammer or cell phone jive? This will just get you junk answers from people that talk like you. If that's good enough you should just go to the junk forums to start.

Quote: Originally posted by bbartlog

Not only that, but some people really do lack awareness of how they come across and would benefit from being reminded that their sloppiness makes them look stupider than they really are.

I get this same feeling when I see someone wearing a baseball cap backwards. It immediately knocks their IQ down by 20 points.

Quote:

I have been trying for years to enforce even the most basic scientific method, the use of references, yet I feel I had close to no effect.

Nicodem, I believe this is having a positive effect - keep at it, please.

Ozone - 6-12-2010 at 13:43

Coincidentally, this arrived in my email today. I decided that it was relevant to this conversation...and amusing.

"Grammar:

Those of us who fall into the world of hi-tech should take note of the importance of correct grammar.

I have noticed that many who text messages & email, have forgotten the "art" of capitalization.

Capitalization is the difference between helping your Uncle Jack off a horse and helping your uncle jack off a horse."

Cheers,

O3

hissingnoise - 7-12-2010 at 04:24

Quote: Originally posted by madscientist

We do have a spell checker that highlights misspelled words as a post is written.

Yeah, the one that tells me I'm misspelling certain words when I know I'm using the correct spelling.

turd - 7-12-2010 at 15:49

Quote: Originally posted by madscientist

We do have a spell checker that highlights misspelled words as a post is written.

Which is completely useless since my computer's language is not set to English.

I think we should all make an effort to write clearly but let's not overdo it and turn this message board into yet another bleak peer reviewed journal. The most effective way of sucking joy out of science.

aonomus - 7-12-2010 at 16:34

To me, the point of the arguement for better posting standards is twofold.

1. Have readers exert less effort while reading posts and attempting to aid people
2. Have posters exert more effort so that they are more likely to get answers to their questions

For the most part, I like to see people actually exert effort. In many cases I won't even bother replying whether or not I know the answer because I feel I shouldn't bother exerting effort for someone else who demonstrably failed to do so. Non-English speakers aside, people who come from English speaking countries are the main issue at hand.

gsd - 8-12-2010 at 08:05

Quote: Originally posted by Magpie

I get this same feeling when I see someone wearing a baseball cap backwards. It immediately knocks their IQ down by 20 points.

Well Magpie how many IQ points your will knock-out for this fellow?

gsd

Magpie - 8-12-2010 at 13:51

That guy would get a loud pro-longed belly laugh from me. That's a classic.

Ephoton - 8-12-2010 at 21:49

at least his neck is not sun burnt ;P

unionised - 9-12-2010 at 12:42

I presume this
"All abbreviations should be spelled out in full at least once before they are used, especially in subject lines that open new threads and appear on summary pages and in HTML titles."
was included in the first post for the benefit of those who enjoy irony.

HTML (hyper text markup language)

arsphenamine - 10-12-2010 at 12:58

Quote: Originally posted by unionised

I presume this
"All abbreviations should be spelled out in full at least once before they are used, especially in subject lines that open new threads and appear on summary pages and in HTML titles."
was included in the first post for the benefit of those who enjoy irony.

HTML (hyper text markup language)

Agreed.

HTML is an FLA (as distinct from the ubiquitous TLA, although 'FLA' is a TLA, but I digress).

The original point, though, was that it would help if folks were less prolix
using DMG instead of dimethylglyme (or glyoxime) prior to explication.
HTML is a well-recognized four letter acronym (FLA) while DMG is not.

I can somewhat forgive DNPH since dinitrophenylhydrazine approaches
the territory where the Principle Of Maximum Laziness holds sway.

One unmentioned point is that few here seem to use chemistry drawing
tools. Often, a simple picture can take the place of verbiage.

[Edited on 10-12-2010 by arsphenamine]

hissingnoise - 10-12-2010 at 13:07

Hmmm, you haven't changed a bit since I saw you last . . .

arsphenamine - 10-12-2010 at 14:28

Quote: Originally posted by hissingnoise

Hmmm, you haven't changed a bit since I saw you last . . .

*blush!*

You think so?

Check out the model shots under my stage name, salvarsan.

madscientist - 10-12-2010 at 14:52

It would indeed be nice to see more use of quality drawings.

http://www.symyx.com/downloads/downloadable/

You have to register, but it's worth it - their product "Symyx Draw" (based on ISIS Draw) is free and of high quality. It's much easier than trying to scratch out crappy drawings in MS Paint, or posting huge IUPAC names for others to decipher.

Freeware chemical drawing programs

arsphenamine - 10-12-2010 at 15:54

ACD/labs ChemSketch
http://www.acdlabs.com/resources/freeware/chemsketch/

ChemAxon MarvinSketch
http://www.chemaxon.com/download/marvin/

Both of them require registration. If you can prove university affiliation,
you can get academic license discounts on their commercial products.

ChemSketch's authors have a close affiliation with IUPAC so their built-in
structure-to-name applet is the industrial standard.

I favor MarvinSketch for its cleaner user interface and ability
to export/import in many different formats, and for the ease with which you
can express reaction roadmaps. It can generate names from structures
as well, but gets confused when you draw chemically valid but non-
existent compounds. Theoretical chemists, take note.

It's easy to cruft up a structure and name it in formal IUPAC

({3-[2-(dimethylamino)ethyl]-1H-indol-4-yl}oxy)phosphonic acid

or, if you need to do online searches, as a SMILES string:

CN(C)CCc1c[nH]c2cccc(OP(O)(O)=O)c12

or traditionally as psilocybin.

Nicodem - 11-12-2010 at 13:09

Quote: Originally posted by unionised

In my field of organic chemistry we do use lots of abbreviations and acronyms and I agree that this can be a source of confusion. However, some abbreviations became so natural that those who use them either believe that everybody even closely affiliated to chemistry knows what they mean or that they can have no other meaning to other people. For example, most if not all, would know that "Me" stands for methyl, but when it comes to "Ar" or "Ac" (which to organic chemists means just aryl and acetyl), you will hardly find an organic chemist which consciously realizes these are also symbols for elements. Yet, an inorganic chemist will first think of these being element symbols rather than a shorthand for a structural moiety.
Some acronyms are so generic that it is hard to believe that there is any chemist who does not know its meaning. Thus most chemists use acronyms for solvents and this become so natural that you will see the naming of THF, DMF, DMSO, etc. in some articles without them ever being spelled out with the full name.

Anyway, here is list of acronyms and abbreviations for organic chemistry: http://www.chem.wisc.edu/areas/reich/handouts/acronyms.pdf
And here you can search for acronyms and abbreviations in general: http://www.acronymfinder.com/

watson.fawkes - 11-12-2010 at 18:43

Quote: Originally posted by Nicodem

Anyway, here is list of acronyms and abbreviations for organic chemistry: http://www.chem.wisc.edu/areas/reich/handouts/acronyms.pdf
And here you can search for acronyms and abbreviations in general: http://www.acronymfinder.com/

I think we might to transcribe our own list of well-known abbreviations, particularly because we get so many beginners on the board. At the very least, it would be a designated place to point people to, and some might even find it themselves.

arsphenamine - 12-12-2010 at 07:53

Quote: Originally posted by watson.fawkes

Quote: Originally posted by Nicodem

+1

For this level of intellectual inbreeding, a scorecard is essential and
a sense of humor helps.

Programmers have 0xDEADBEEF and OrgSyn chemists have DEADCAT.

You have to respect a field that creates such world class
mnemonics/acronyms as TOSMIC and LICKOR.

The latter is notable since "Lithium-potassium alkoxide reagents"
has no 'C' anywhere.

Reminds me of AlNiCo III, which contains copper instead of cobalt,
but nobody wanted to call it AlNiCu.

Also, Tf derives from "triflate," itself derived from "Trifluoro sulfonate" --
a lexical second derivative with regard to etymology.

turd - 12-12-2010 at 09:38

Quote: Originally posted by arsphenamine

({3-[2-(dimethylamino)ethyl]-1H-indol-4-yl}oxy)phosphonic acid

What a terrible, unwieldy way of naming the phosphoric acid ester of 4-hydroxy-N,N-dimethyltrypramine.

Apart from historic interest and a few journals demanding it, has the formal IUPAC nomenclature any relevance to the modern chemist? I see the point of a 1:1 molecule to name relation in times before the dawn of electronic databases. But nowadays, do they still annoy students with this? Seems like a waste of time. And it's probably not even useful as an internal representation in electronic databases.

Quote:

For example, most if not all, would know that "Me" stands for methyl, but when it comes to "Ar" or "Ac" (which to organic chemists means just aryl and acetyl), you will hardly find an organic chemist which consciously realizes these are also symbols for elements. Yet, an inorganic chemist will first think of these being element symbols rather than a shorthand for a structural moiety.

Sadly, most inorganic and especially analytic chemists I know seem to believe that Ac stands for acetate(sic!), as in NaAc for sodium acetate. The mind boggles when the same people label their acetic acid bottles with "AcOH" instead of "AcH".

Quote:

Reminds me of AlNiCo III, which contains copper instead of cobalt,
but nobody wanted to call it AlNiCu.

Hear, hear. Are you into quasi-crystals or "simply" magnetism?
Edit: Should have googled before - AlNiCo is an iron alloy and has nothing to do with quasi-crystals.

[Edited on 12-12-2010 by turd]

arsphenamine - 12-12-2010 at 13:48

Quote:

({3-[2-(dimethylamino)ethyl]-1H-indol-4-yl}oxy)phosphonic acid

What a terrible, unwieldy way of naming the phosphoric acid ester of 4-hydroxy-N,N-dimethyltrypramine.

Apart from historic interest and a few journals demanding it, has the formal IUPAC nomenclature any relevance to the modern chemist?

I have felt that pain, often in the gluteous maximus.

[mode="wizard"]
If you know its true name, you can conjure with it.
[/mode]

Chemical modeling and searching need unambiguous names if you want to share your knowledge quickly.

From IUPAC, we get 1,4,7,10,13,16-hexaoxa cyclooctadecane when we knew all along it was 18-crown-6.

In school, they told us that its oxygens like to fit around a K+ ion.
With a quick Avogadro draft or SMILES cut-and-paste, you can
run a few 1000's of force field iterations and watch it happen.

Two honking huge organizations like unambiguous naming for compound
searches in their PubChem and ChemSpider online databases. The IUPAC
naming, godawful as it is, is still more readable than the SMILES, SMART,
and InChI specifier grammars.

These specifiers allow you to construct a model on which you can perform all manner of calculations since the software is getting cheap enough for the hobbyist. For example, it is possible to get useful estimates of 3D visualization, pKa, NMR spectra, conformational analysis in different solvents, electron field topologies, vibrational energies/modes/frequencies ... and that's just the free stuff.

If BigPharma bankrolls you, drug simulation and pharmacokinetics simulation are just two that come to mind.

The good news is that you don't have to know it all.
You can sharpen your existing knowledge with some very good
freeware such as Avogadro and GAMESS.

Quote:

Reminds me of AlNiCo III, which contains copper instead of cobalt,
but nobody wanted to call it AlNiCu.

Hear, hear. Are you into quasi-crystals or "simply" magnetism?
Edit: Should have googled before - AlNiCo is an iron alloy and has nothing to do with quasi-crystals.

Last I heard, but not read, Alnico is a mix of two co-aligned metallic crystals, one with low field-high coercivity, and one with high field-low coercivity. I'd love to know more but more urgent things await.

[Edited on 12-12-2010 by arsphenamine]

turd - 13-12-2010 at 12:29

Quote: Originally posted by arsphenamine

Wow, that's stone-age.

In Beilstein/Gmelin/Crossfire and CA/SciFinder you typically use a structure drawing applet which is much more flexible. You can do things like putting an arbitrary alkyl-chain at this and that position. With IUPAC nomenclature this is impossible, since an alkyl-chain may completely change the canonical name of the molecule.

Quote:

Magnetic structure and symmetry is very interesting. Unfortunately you need good neutron diffraction data, which means either huge crystals or powder data, which limits you to simple structures. And of course few amateurs have access to a neutron source.

arsphenamine - 13-12-2010 at 14:04

Quote: Originally posted by turd

Wow, that's stone-age.

If you haven't been to the IUPAC site, hold your criticism.

To be fair, they let you upload your model file in one of the common formats.
And, to be pragmatic, you can cut and paste a SMILES string very conveniently if the molecule isn't too large.

And, though it rankles to admit it, organic chemistry is itself "stone-age."

For proof, you need look no farther than the merging of chemistry and
biochemistry departments at many universities. It is much the same with
electrical engineering and computer science.

If you wanted to put a thumbnail image of a compound on this forum, what
would you use?

turd - 13-12-2010 at 15:38

I'm not criticizing, I'm wondering. To give an example: I want to search all reactions of the form

O2N-CH=CH-R --> H2N-CH2-CH2-R

where R is an arbitrary organic rest. Canonical IUPAC names do not seem very helpful for this search, whereas it is trivially performed with the structure plugin of Scifinder.

watson.fawkes - 13-12-2010 at 16:28

Quote: Originally posted by turd

Canonical IUPAC names do not seem very helpful for this search, whereas it is trivially performed with the structure plugin of Scifinder.

You've inadvertently hit the nail on the head, IUPAC names are created for the express purpose of being canonical names, that is, to provide common and unambiguous names of reference for communication between two chemists, and in particular, between a chemist author and reader. For this purpose, you're going to get one kind of naming structure. Such a naming structure should not be expected to be universal across all purposes. Different representations, different purposes. The subgraph-matching problem you pose needs a different representation than an IUPAC name, sure, but this doesn't diminish in any way the value of such names as reference names.

On the other hand, your purpose has "R" notation in it, and it might behoove IUPAC to make canonical names for "compounds with unknowns", by analogy a kind of algebraic expression for chemistry.

arsphenamine - 13-12-2010 at 18:23

Quote: Originally posted by turd

I'm not criticizing, I'm wondering. To give an example: I want to search all reactions of the form

O2N-CH=CH-R --> H2N-CH2-CH2-R

where R is an arbitrary organic rest. Canonical IUPAC names do not seem very helpful for this search, whereas it is trivially performed with the structure plugin of Scifinder.

Well...um...yeah.

An arbitrary analog is not an unambiguously specified == unique compound.
A custom tailor job doesn't belong in the one-size-fits-all bin.

The SMILES method is worth a little examination,
particularly since many chemical sketch/draw/ model applications let you
paste in a SMILES string.

Searching for analogs requires, to my limited knowledge, either a SMART
string (a regular expression language) or Markush Structure queries.
There are undoubtedly many more query schemes.

Have a look at PubChem to see if any of their options are familiar or
conventient to your work. http://pubchem.ncbi.nlm.nih.gov/

turd - 14-12-2010 at 01:04

Quote: Originally posted by watson.fawkes

Yes, but exactly in this context I don't understand the usefulness of a canonical naming. On the contrary, I think it hurts. Of course naming has to be unambiguous (i.e. the relationship connecting names and compounds should be a function). Of course the nomenclature should be able to name any thinkable compound (i.e. the function should be surjective). But IUPAC also specifies rules to make the function injective and therefore bijective. Two reasons I don't think this is useful in the context of author-reader:

With a non-canonical naming, we can emphasize certain aspects of our compound. E.g. we can emphasize the amine (2-hydroxyethylamine) or the alcohol (2-aminoethanol).
A canonical naming will invariably in some cases become very unwieldy. Take for example the naming arsphenamine has given for psylocybin. If I had to read something like this in a paper, the first thought that would cross my mind is "asshole". Publications should be clear and easy to read and never cryptic. Never should I have to sit half an hour to work out what molecule the author is talking about.

So the only reason for a canonical naming I can come up with is for indexing in reference works (and of course a raison d'être for committees). But with Scifinder et. al., this seems to be of less and less relevance to the modern chemist. That was my point - nothing more, nothing less.

PS: Actually, I think for brievety it's also useful soften the function part. Chloroethanol could designate Cl-CH2-CH2-OH or CH3-CHClOH, but as chemists, we know which one the author is talking about.

watson.fawkes - 14-12-2010 at 08:20

Quote: Originally posted by turd

But IUPAC also specifies rules to make the function injective and therefore bijective. [...]

With a non-canonical naming, we can emphasize certain aspects of our compound. [...]
A canonical naming will invariably in some cases become very unwieldy. [...]

So the only reason for a canonical naming I can come up with is for indexing in reference works (and of course a raison d'être for committees).

I agree that the properties of canonical names aren't good for either of the cases you list. The social norm to use canonical names, therefore, should not be to use them exclusively. The relationship between a colloquial name and a canonical name is very much like that between a name and its abbreviation or acronym. When you a colloquial name for the first time, you should identify it with a canonical name. Thereafter, use of the canonical name in the context of that particular writing is unambiguous. For academic writing, this could be done once in the abstract (if needed) or body, since a "paper" represents a clear boundary for creating a disambiguation context.

The purpose of this practice aligns with the self-interest of an author to draw attention to their work, because doing an exhaustive search for a compound will always find its canonical name but be less successful in finding synonyms. It's for exactly this reason that IUPAC bijective naming is the right thing, because it supports this important purpose. It's not the only purpose, though, and canonical naming is not a universal solution. Tracking synonyms is certainly useful, necessary even for historical work, but is practically incapable of yielding 100% reliability as canonical names are.

Nicodem - 14-12-2010 at 08:26

Quote: Originally posted by turd

I'm not criticizing, I'm wondering. To give an example: I want to search all reactions of the form

O2N-CH=CH-R --> H2N-CH2-CH2-R

where R is an arbitrary organic rest. Canonical IUPAC names do not seem very helpful for this search, whereas it is trivially performed with the structure plugin of Scifinder.

Actually there exists a nomenclature equivalent of Markush structures. In the above case it would be "transforming beta-substituted nitroethenes to beta-substituted ethylamines". You can narrow it further to beta-alkyl, beta-aryl, beta-heteroatom substituted, beta-dialkylamino, beta-alkoxy, etc... This is a valid way to describe general transformations in the literature, however you will only find pertaining references if the authors ever wrote these in the text. Similarly, you will ever find references using structure search if the reactions were properly abstracted, which is not always the case (just compare reaction search hits between SciFinder and Beilstein, and you will see what I mean). As annoying as the formalism of IUPAC nomenclature is, it is still the best there is, and to those who don't have proper access to CA and Beilstein, it also represents an efficient way to find references by using publisher's ever more efficient keyword based search engines by searching for a specific compound using proper IUPAC nomenclature.

Ephoton - 18-12-2010 at 00:20

I do love diagrams will do thanx arsphenamine.

Nicodem you are always miles beyond me

I can only wish to rise to such hights alas I am going to be a thorn in

vultures foot for ever.

sigh to be disabled

[Edited on 18-12-2010 by Ephoton]

madscientist - 20-12-2010 at 14:20

Something I forgot to mention - use the tags (minus the spaces). They make posts a lot more pleasant to read.

Ph2C=CHCH2CH(CO2CH3)2

vs

Ph2C=CHCH2CH(CO2CH3

2

It's not necessary, but it certainly is nice.

[Edited on 20-12-2010 by madscientist]

Nicodem - 28-12-2010 at 03:15

Regarding the proper use of chemical symbols, there is an interesting recent thread titled "H202?" in the Energetic materials section that seems exemplary to the objections raised in this thread. The 1-post member obviously made no typo exchanging "O" for "0", but apparently honestly believes that hydrogen peroxide is represented by "H-twohundredtwo" as he repeats that in the post. All this would be nothing but funny if it wasn't a question on "simply looking to synth some HMTD". As if this would not be sad enough, he then goes on with this selfhumiliation by declaring: "i understand the risks involved ( i have looked at previous topics on peroxide compounds)".

This is a nice example on how lack of proper spelling, no capitalization and misuse of symbols can lead to dangerous situations, eventually death. When ignorance and hazarding with life is combined, such things are not funny any more.

Nicodem - 12-3-2011 at 01:56

There is something in regard to this thread's topic that I have been wandering for years, but never dared asking.

Are there actually people who believe the symbol for chlorine is "CL"?

At first I be believed all those annoying "HCL", "CuCL2", etc., are only typos and didn't pay much attention to it, but then due to the shear amount of this same presumed typos, I started to have doubts about it. You can see this all over the internet, on all forums, and I would like to ask those that do this errors to honestly answer if these are typos or misconceptions.

hissingnoise - 12-3-2011 at 05:51

Quote: Originally posted by Nicodem

. . . I would like to ask those that do this errors to honestly answer if these are typos or misconceptions.

Everyone makes mistakes (and typos), Nicodem!
If you reread your own post you'll find a few . . .

Nicodem - 12-3-2011 at 06:24

Yes, I'm aware that everyone, me included, makes lots of mistakes. But that was not the question. What keeps me puzzled about the "CL" thing is that it keeps on appearing all the time. You don't see symbols of other elements being misrepresented the same way and so commonly. So, for the other elements, I'm quite sure it is just a typo when they are mistakenly written.
I mean, can it really be just a typo, if it is mistakenly written so many times in the same post or even in the same sentence? Is that statistically reasonable? And if it is a typo, then how come it is so widespread? Does it have something to do with the position of the letters C and L on the standard keyboard coupled with some widespread stereotyped lack of typing coordination in humans? Does this typo evolved because people just like to repeat other's mistakes? Am I the only one who finds this unusual? Is it nothing special and I'm just being paranoid? Ah, never mind this last question, I already know the answer. But seriously, I do want to know more about this phenomenon.

hissingnoise - 12-3-2011 at 07:42

All mistakes and typos have some irritant value; the ones that piss me off most though, are the ones I make myself . . .

Magpie - 12-3-2011 at 13:02

For CL I think this is due to the rhythm of typing as for HCL and CH3CL. For the use of the personal pronoun i this seems to be laziness + irritant value.

Chordate - 12-3-2011 at 23:51

I offer an alternate theory: Cl is probably one of if not the most common two letter element symbol used on these boards. This gives it ample opportunities for error, and and if it bothers you, you will notice the mistakes far more than the correct uses.

Finnnicus - 18-6-2013 at 23:28

Ooh, old(ish) thread.
How does everyone feel about subscripting chemical formulas?

Subscript & Superscript

bfesser - 1-7-2013 at 06:38

I feel that there's now no excuse not to use subscript and superscript in posting. Some time ago, I coded up some buttons that you will see on the "Post Reply" page under the "Text Color:" dropdown (xy and xy

, and <a href="viewthread.php?tid=18651#pid242812">Polverone was gracious enough to fix my errors and implement them</a>. For those who can type BBCode tags, you can use [sub][/sub] and [sup][/sup]. Or for HTML junkies like myself, use and .

<a href="viewthread.php?tid=15528#pid201809">Subscript</a> thread

[Edited on 7/6/13 by bfesser]