Nomenclature overhaul in the life sciences

Factual Questions
1

A thread in IMHO about tips to remember anatomical labels has me wondering, why isn’t there a project to overhaul medical and biological nomenclature?

I remember from my biology classes till grade 12 and from my neuroscience readings later, that the nomenclature does have some logic to it, but the roots and modifiers seem to be Latin and Greek derived.

Since English seems to be pretty much the lingua franca of science research and education, why doesn’t the medical community devise a system (a bit similar to what IUPAC did to Chemistry) to create labels that have common layman English vocabulary as the root words and the modifiers also derivatives of English adjectives. Furthermore, make nomenclature systematic, in the sense that from the breakdown of a term, a person well-versed in the principles behind the system, can locate the element of interest. Wouldn’t it be more intuitive for most students? Is there any such effort underway?

2

IUPAC nomenclature isn’t derived from English – most of it is Latin or Greek with a lot of neologisms. (It’s not IUPAC, but aldehyde comes from alcohol dehydrogenatum.) But the roots aren’t hard to learn. The advantage of IUPAC nomenclature is that it makes sense, not that the names are derived from everyday English words, which would be of no benefit to non-English-speaking chemists.

Reforming anatomical nomenclature would have to be similar. Hundreds of years of depending on (mostly) Latin has left English rather weak for describing anatomy in detail. If we just translated the Latin terms, you’d get silly names like ‘trapeze-muscle’, ‘widest back-muscle’, ‘strainer-bone’ – things like that. So I really don’t think using an English system of anatomy would be helpful, even for native English speakers. Like IUPAC nomenclature, it has to be something that makes sense. But that’s hard to do for the thousands of named body parts that don’t have a systematic relationship between them, like chemicals (or organisms) do.

There is something of a movement in anatomy to rid the nomenclature of eponyms, such as otopharyngeal tube instead of Eustachian tube. You can find a detailed list of the replacements for eponymous terms here.

Personally, I hope the trend against eponyms continues (as much as I’d like to have a name reaction). Chemistry has a highly logical, systematic method of naming molecules, but not of naming reactions. It’s possible to generate names that tell you each tiny detail about a molecule’s structure, but nearly every reaction in organic chemistry is named after a person. To make it even worse, a lot of people have more than one reaction named after them – and a lot of organic chemists have been named Fischer or Hof(f)man(n).

There seems to be no movement to change this. There’s really no reason why reactions have to be named after people, except that chemists love to safeguard their science against enthusiastic undergraduates, and the eponyms make organic chemistry into something to be memorized rather than understood.

Genes are the only thing in science I think desperately needs systematic nomenclature more than organic reactions. Genes can be named anything from p45378 to Rel to sonic hedgehog. (I made up two of those.) Most proteins have a name that makes sense – alcohol dehydrogenase dehydrogenates alcohols. But genes are still named the same way the alchemists used to name chemicals. Corrosive sublimate of mercury, and things like that.

3

I should have been more clear. What I meant by a bit similar to IUPAC was that it made naming compounds systematic., and not the language of roots.

Couldn’t there be a system based on spatial location and/or structure like limb-upper-middle joint. Of course, my example is unwieldy and absurd,but hopefully you get the picture. Using a top-down hierarchy or something similar.

4

Hate to break it to you, but the only one of those that isn’t real is p45378. Rel is part of the NF-[symbol]k[/symbol]B family and sonic hedgehog is involved in signaling.

I’d agree that the system of naming genes needs to be overhauled, but then we’d lose all those funky Drosophila gene names, like cactus and 18wheeler, and that would make learning genetics much more boring. :slight_smile:

5

What bugs me is in biochemistry, there is a strong insistance in using out-dated nomenclature to describe molecular structure. As someone who is more interested in organic chemistry, this is rediculously frustrating to me. The example from just the other day - the conversion of D-methylmalonylCoA to L-methylmalonylCoA. I am fine with using common names (who wants to learn the IUPAC name for the CoA part??) but D and L mean absolutely NOTHING structurally. They rotate plane polarized light RIGHT (D) or LEFT (L), but this doesn’t actually tell me what the stereocentre of interest is. Is it really that difficult to use the R/S (+/-) system? Sure, it’s an extra character, but at least then I could draw the molecule correctlly!

Same goes for amino acids and sugars. In 4 years of studying biochemistry, I don’t think I’ve ever actually seen a drawing of the amino acids that included the stereocentre configurating for the backbone part. It’s as if biochemists are totally happy to just gloss over these details, when, really, they are quite important since only one of each configuration is only ever used!! Do you not think this could help in terms of enzymology and active site structure and determination? Your body thinks it’s important - why don’t you?

6

Hate to break it to you, but there is (usually) very strict nomenclature rules for gene names. The problem is that it is fixed by model organism. Since genes are conserved by evolution, the same gene names get imported across models, and the nomenclature gets muddled. But if you have a reasonable grasp of how things are named in the major model organisms, things make sense.

In Drosophila, genes are named after their mutant phenotypes. white mutants have white eyes, even though the White protein transports red pigment into the eyes (it makes the eyes red). This is backwards at first, but makes some genetic sense once you get used to it. Gene names are italicized, their protein products are capitalized and non-italicized. Alleles are designated by superscript, usually a number but can be anything. If the first mutant was recessive, then the gene has a lower case name (like white); if dominant it is capitalized (like Drop which has a drop-shaped eye). Gene names imported (like Cdk7, gene name imported from yeast) are also capitalized, or sometimes started with a lower case “d” for Drosophila (like dParkin from humans). These are all of the rules. With yeast, genes have a three letter designant and then a number – CDC2 or CDK7. In humans, the gene can be called anything, but it is always formalized in upper case letters (and numbers) like PRKN. Mouse works similarly but the gene names are usually not all in caps. In nematodes, there are only a few classes of mutants, and the gene is categorized in one of these and then given a number (let-1, unc-18, egl-4), plus a very long formalized allele designation depending on the lab which discovered it.

Let’s take hedgehog for an example. Nusslein-Volhard discovered it and hundreds of other genes in a large screen. They were screening embryo morphology. Some are named in a straightforward manner – bicoid has two tails, corkscrew, hunchback. Being German and hungry, many of them are named after German foods – gurken, kugulei, gooseberry. hedgehog embryos apparently are spiky. Perhaps they have duplicated denticle belts or something.

There are many copies of the hedgehog gene in humans – evolution has duplicated its important role. These were named in tribute to the Drosophila protein – Indian hedgehog (IHH), Desert hedgehog (DHH), and of course Sonic Hedgehog (SHH). This is sometimes the case, sometimes it isn’t. It depends on which was discovered first, how often it was published and many other factors. So Drosophila rolled is also called ERK or MAPKK. But *Drosophila EGFR{/i] is just EGFR or EGFR(number) based on which human/mouse copy.

7

Ms Macphisto: It was more like ‘made up without bothering to check’. I’m not surprised that Rel is a real gene, being a three-letter name. But “part of the NF-kB family” (how did you make a kappa?) illustrates my point. If I say that a molecule is an alkylpyridine or a benzylcyclohexyloxetane, someone who knows something about chemical nomenclature can understand those names without having heard of the particular family of molecules I’m discussing. You can’t know what NF-kB is without having heard of it in detail. Really, this is just a property of genes – genomics, like anatomy, deals with things that are difficult to name systematically. Chemistry deals with things that are inherently possible to break down into fragments and name.

mnemosyne: I’d be happy if nomenclature was the only outdated part of biochemistry. They also love to draw molecules with 90° bond angles and like to write carbons and hydrogens explicitly. To make it even worse, the system of drawing mechanisms is different in biochemistry than in organic chemistry – they like to draw arrows from atoms rather than bonds. Having to learn two ways of drawing arrows is very annoying. I lost large numbers of marks for drawing arrows in biochemical mechanisms as if they were organic reactions.

Trivial names (like CoA) are acceptable and often necessary for anything biological. I agree that the D,L system should no longer be used, but in a lot of cases it’s only practical to give a +,- designator for a large molecule. For some biomolecules, using R,S would mean having to assign 20 or 30 stereocenters. That might not even be of much use if the numbering of the molecule wasn’t clear. So it’s probably better to use a relative stereochemical label and remember the absolute stereochemistry of the stereocenter of interest separately.

Technically, those amino acid structures you saw did include stereochemical information. They’re Fischer projections of the D[sub]S[/sub],L[sub]S[/sub] type, showing the molecule’s stereochemistry relative to glycine. (Rather than glyceraldehyde, the usual basis for Fischer projections.) Now, as you probably know, Fischer projections are evil and confusing – two adjacent stereocenters which have the same orientation on paper in a Fischer projection actually have the opposite orientation in a molecule. (I believe that anyone who draws a Fischer projection in the twenty-first century should be stripped of their degrees.)

In some of my courses, amino acids were drawn in the biochemical manner, with 90° bond angles, explicit C and H – Fischer projections, basically. In others, they were drawn properly – zigzag structures with dashed and wedged bonds to indicated 3D orientation. The difference is one of biochemistry versus biological chemistry.

This reminds me of one time I was asked to give the IUPAC name for alanine. I know “(2S)-2-aminopropanoic acid” was the correct answer, and I gave it. But “(2S)-alanine” is also correct, because ‘alanine’ is a reserved name according to the IUPAC Blue Book (1993).

8

Thankfully, I haven’t had problems regarding how to draw reaction arrows, other than having to think more in biochem classes about what they mean when they draw things a certain way! If a prof ever took marks off because I did bond arrows, I’d argue it, all the way up to the Dean if I had to (who is NOT a biochemist!).

I never thought about the Fischer projections…I HATE Fischer projections! I like dashes and wedges. I know the complication of using the R/S system for larger molecules, but often we are only considering one stereocentre (like which type of amino acid is used in making proteins) and so I’d like to see it shown in a way that matters!

I’m a biochemist by degree, but it is not what I will make a living at, so I guess I shouldn’t be too bothered. I do really hate the D and L, though! And explicit hydrogens. Though I know from a class Im currently in that if you just draw the zigzags, there are actually people who don’t know what that means, even in 4th year courses (in which it should be common background knowledge).

And don’t get me started on the electricity convention of the direction of current flow. I don’t understand why people insist to sticking to a WRONG convention!

9

Roches - first the easy part. I got the [symbol]k[/symbol] by doing {symbol}k{/symbol} (with square instead of curly brackets of course).

As for NF-[symbol]k[/symbol]B, the full name is nuclear factor kappa B, which does make more sense since it’s a transcription factor and the protein was likely first identified in a nuclear extract, though please don’t quote me on that. Actually, that’s probably about as logical as naming of genes and proteins is going to get, until you get people like me throwing around the abbreviations without thinking about it, which really does happen far too frequently and I suspect is a large part of the problem.

Come to think of it, that’s another problem in biology - people have built abbreviations based on other abbreviations, to the point that it looks ridiculous if you have to write the full name out. One example: there’s TNF (tumor necrosis factor) that interacts with TNFR (tumor necrosis factor receptor). All fine so far. But then the signals from TNFR are transmitted by TRAF (tumor necrosis factor receptor associated factor). Now that makes sense, but it just doesn’t sound right.

10

Because it isn’t wrong? There are a lot of arbitrary conventions in physics, and in each case, you just have to choose one and stick to it consistently. Setting cat fur to negative and glass rod to positive is one of those arbitrary conventions, and it’s just as logical and sensible as the other way around.

And Latin does have an advantage over English in scientific names, in that it’s not commonly used. If there’s a species named “Rana verda” (I don’t know if there actually is; I just made that one up), then a zoologist is going to know what I mean when I ask for a specimen of one. But if we used English names for a species, and I asked for a Green frog, then it’d be unclear whether I wanted that particular species, or just any old Kermit.

11

Because it isn’t wrong? There are a lot of arbitrary conventions in physics, and in each case, you just have to choose one and stick to it consistently. Setting cat fur to negative and glass rod to positive is one of those arbitrary conventions, and it’s just as logical and sensible as the other way around.

And Latin does have an advantage over English in scientific names, in that it’s not commonly used. If there’s a species named “Rana verda” (I don’t know if there actually is; I just made that one up), then a zoologist is going to know what I mean when I ask for a specimen of one. But if we used English names for a species, and I asked for a Green frog, then it’d be unclear whether I wanted that particular species, or just any old Kermit.

12

I never said that plain English words had to be used. I said, use English for roots and modifiers, since most (and would-be) scientists know English. In this case, the terminology could be Frogus Greenus Scotlandus, you get the picture.

13

Basing a convention of the flow of positive charges when we know its actually negative charges that flow is sort of silly. Sure the initial designation of “this is positive, this is negative” was arbitrary, but since the particles HAVE been defined that way, would it not be better to do so in all cases, rather than have an exception “just because that’s how it was first done”?

It’s just annoying, that’s all. I like it when things are standardized, and that’s one thing that isn’t, and it bugs me.

14

Except ALL scientists ( biologists, anyway ) already know the Latin and Latinized-Greek system, including the non-English speaking ones ( of which there are still a good number, I’m sure ). There is just no utility to switching from established convention, which aside from tradition, would completely confuse anyone trained in your new Anglicized system who had to then paw through decades of work written using the old way.

The only people who would derive any significant benefit from your changes would be English-speaking lay people, who have no real reason to care.

If it ain’t broke, don’t fix it ( or alternatively if it takes a lot more effort to “fix” something than benefit that would be derived from “fixing” it ).

  • Tamerlane
15

That said, there are a few traditions that I believe could do with some updating. I’ve never been a fan of the Botanical Code’s insistence on the formal description of new species of plant ( and by extension, fungi ) be written up in Latin, something the Zoological Code has dumped. That does seems a bit archaic and unnecessary to me.

  • Tamerlane
16

The same argument that’s used to stifle change in many fields. Coz that’s the way it has been. The people who would have a problem with it are already-trained scientists and medical students within the next 15-20 years who might have to learn both systems (but the Anglicized one should be easy to learn). Once the transition period is effectively over, the new easier system will shift the focus of budding high school biology students from memorization to concepts. I can firsthand verify the reason that a lot of my smart fellow students, didn’t consider a biology career as seriously as computers or physics, was because most of the effort in biology class was devoted to remembering what were the goddamed names. And that made biology very boring.

Any major change entails a mixed-use transition period. But if the benefits of the new system are worthy enough, the focus should be on smoothening the transition, not eliminating the change.

17

That’s not the argument. The argument is that there is no great advantage to switching to your system.

Evolutionary biologists ( if not med students ), paleontologists and the like will always have to deal with the old system, because it is a historical science where old data is always relevant, if not vital.

Nonsense. The amount of change in memorization would be trivial. It truly isn’t that difficult to remember Latin names once you get used to it and there isn’t much less memorization involved in switching it to English.

Didn’t bore me :). If that is the only reason they were dissuaded from pursueing biology then I would venture to say it wasn’t the right career path for them in the first place.

I’m afraid I just don’t see many benefits.

  • Tamerlane
18

Vaguely remembered nitpick: it’s not always negatively charged electrons that carry current. For instance, electrolytes. And I seem to recall something about holes in electron shells in semiconductors. I wish the arrow did go the other way, but its overstating to say that its completely wrong: it is a convention, and while it might be nicer the other way, its not just tidier, its not inherently wrong.

19

By this logic, there can never be a new system, coz if a new system is implemented, it will be tedious to translate older documents. Not a compelling argument. With the information management technologies in place and being developed, it won’t be a stretch to scan old documents and over the period of a decade, table a old-new dictionary. It’ll require a technical effort, but it can be done.

Sez you. When I was referencing Squire’s Fundamental Neuroscience, at first, some of the terms were esoteric. Once, I knew the Latin meanings, it became quite easier to remember. Now imagine, instead of learning 101 terms and their latin meanings, I could just look at a term and from it’s construction, figure out the element. I will across a significant lesser number of terms of totally unknown roots. Seems to be a good leap.

You are suggesting that nomenclature is a minor stumbling block in high school biology. Hardly. You might understand the concepts, but the nomenclature could prevent you from remembering what exactly they apply to. And not crossing up the processes among different classes of organisms.

20

It’s not an exception. Under the present convention, if you have positive charges moving in the positive direction, you have a positive current, and if you have negative charges moving in the postive direction, you have a negative current. I = lambda*v. Of course, one can argue that the more mobile atomic particles should be called “positive”, but then again, one can also argue that the more massive atomic particles should be called “positive”. So we stick with the convention that we have.

How did we get onto this tangent again?