Welcome Sophophora melanogaster
April 10, 2010 3:47 PM Subscribe
You may not recognize the difference between Sophophora melanogaster and the common fruit fly. That's because there isn't. The International Commission on Zoological Nomenclature is proposing a name change from Drosophila melanogaster on scientific grounds, but it's ruffling the antennae of some scientists.
I'm not sure how the biologists do it, but at my company, such renaming proposals must be accompanied with patches to update all existing occurrences in the code base.
posted by ryanrs at 4:27 PM on April 10, 2010 [3 favorites]
posted by ryanrs at 4:27 PM on April 10, 2010 [3 favorites]
It would be a big mess. The spider I'm currently working on has had at least 16 names, and tracking it down through the ages has been a headache. I still don't know what to call it.
posted by dhruva at 4:49 PM on April 10, 2010
posted by dhruva at 4:49 PM on April 10, 2010
My husband says, "Great, now I have to change all my labs."
posted by theredpen at 5:05 PM on April 10, 2010
posted by theredpen at 5:05 PM on April 10, 2010
This is why you don't use business keys. "But but but, family names Social Security Numbers county names genus names never change!"
Yes, yes, they do. Synthetic keys don't change, because they have no meaning, they're designed to have no meaning, the meaninglessness is the feature. They're unique, and meaningless.
This is why you should use synthetic keys, because without changing the key, we can change the key's referent in one place. (And this is why you should never expose synthetic keys, because exposed they acquire meaning and so become compromised.)
posted by orthogonality at 5:08 PM on April 10, 2010 [3 favorites]
Yes, yes, they do. Synthetic keys don't change, because they have no meaning, they're designed to have no meaning, the meaninglessness is the feature. They're unique, and meaningless.
This is why you should use synthetic keys, because without changing the key, we can change the key's referent in one place. (And this is why you should never expose synthetic keys, because exposed they acquire meaning and so become compromised.)
posted by orthogonality at 5:08 PM on April 10, 2010 [3 favorites]
That's nice for databases, #21280, but not so good for human communication.
posted by ryanrs at 5:13 PM on April 10, 2010 [2 favorites]
posted by ryanrs at 5:13 PM on April 10, 2010 [2 favorites]
#21820, you mean. Ah, human communication! Gotta love it.
posted by thejoshu at 5:14 PM on April 10, 2010 [2 favorites]
posted by thejoshu at 5:14 PM on April 10, 2010 [2 favorites]
What's the difference? Those numbers are supposed to be meaningless.
posted by ryanrs at 5:17 PM on April 10, 2010 [1 favorite]
posted by ryanrs at 5:17 PM on April 10, 2010 [1 favorite]
Mine is named Alonzo and he likes bananas soaked in Johnnie Walker Red.
posted by longsleeves at 5:19 PM on April 10, 2010 [2 favorites]
posted by longsleeves at 5:19 PM on April 10, 2010 [2 favorites]
Can't read the article. Too many buzz words.
posted by Splunge at 5:24 PM on April 10, 2010 [2 favorites]
posted by Splunge at 5:24 PM on April 10, 2010 [2 favorites]
Drosophila melanogaster is number 7227 actually....
I don't think this is a good idea. My understanding is the type specimen for Drosophila is D. funebris and the splitters at the ICZN decided that they can't break convention to change it to D. melanogaster even though it is much more widely used. It makes sense to change a paraphyletic genus to two monophyletic ones, but they should take into account convention as well as tradition when giving out new names.
If something in taxonomy needs sorting out, it is the anamorph/teleomorph split in fungi. This leads to fungi which have a sexual form having a different genus/species name from their asexual relatives for pretty much no good reason.
posted by scodger at 5:27 PM on April 10, 2010
I don't think this is a good idea. My understanding is the type specimen for Drosophila is D. funebris and the splitters at the ICZN decided that they can't break convention to change it to D. melanogaster even though it is much more widely used. It makes sense to change a paraphyletic genus to two monophyletic ones, but they should take into account convention as well as tradition when giving out new names.
If something in taxonomy needs sorting out, it is the anamorph/teleomorph split in fungi. This leads to fungi which have a sexual form having a different genus/species name from their asexual relatives for pretty much no good reason.
posted by scodger at 5:27 PM on April 10, 2010
clumpers v. splitters! It's not just for birds!
posted by localroger at 5:29 PM on April 10, 2010
posted by localroger at 5:29 PM on April 10, 2010
This is pretty stupid. Why not just call it Why not just call it Drosophila Melanogaster* with a little note that says it's actually in the Sophophora group?
I mean, being able to look up information on something seems much more important then knowing the exact classification by looking at the name, particularly something that's been studied so much.
posted by delmoi at 5:35 PM on April 10, 2010
I mean, being able to look up information on something seems much more important then knowing the exact classification by looking at the name, particularly something that's been studied so much.
posted by delmoi at 5:35 PM on April 10, 2010
Everyone says "Druhsofula" to refer to these flies. It's one of the most commonly used organisms in the world & the backbone of genetics and microbiology.
Grrrr. Changing its name is a SPECTACULARLY STUPID IDEA.
Stupid bureaucrats sucking the joy out of nomenclature. They're everywhere.
It's as if IUPAC (Chemical Naming Convention body) insisted that everyone say "dihyrdogen monoxide" when referring to water.
posted by lalochezia at 5:49 PM on April 10, 2010
Grrrr. Changing its name is a SPECTACULARLY STUPID IDEA.
Stupid bureaucrats sucking the joy out of nomenclature. They're everywhere.
It's as if IUPAC (Chemical Naming Convention body) insisted that everyone say "dihyrdogen monoxide" when referring to water.
posted by lalochezia at 5:49 PM on April 10, 2010
I'm not sure how the biologists do it, but at my company, such renaming proposals must be accompanied with patches to update all existing occurrences in the code base.
That looks to be precisely the problem - going through and changing the name in every database, etc. it appears in would be next to impossible.
posted by DecemberBoy at 5:53 PM on April 10, 2010
That looks to be precisely the problem - going through and changing the name in every database, etc. it appears in would be next to impossible.
posted by DecemberBoy at 5:53 PM on April 10, 2010
Why not just call it Drosophila Melanogaster* with a little note that says it's actually in the Sophophora group?
I'm assuming that's what the proposal to protect the name was, which failed, but they don't explain exactly how that would work. I'm assuming something like you propose.
posted by DecemberBoy at 5:56 PM on April 10, 2010
I'm assuming that's what the proposal to protect the name was, which failed, but they don't explain exactly how that would work. I'm assuming something like you propose.
posted by DecemberBoy at 5:56 PM on April 10, 2010
Oh god, I just read the full text [pdf] of the ICZN judgment. I was hoping for the last sentence to be "Yng, who voted AGAINST, said he did it for shits and giggles because it had been a bitch of a week."
The second comment of the Nature piece has it just right,by the way.
posted by cromagnon at 6:17 PM on April 10, 2010
The second comment of the Nature piece has it just right,by the way.
posted by cromagnon at 6:17 PM on April 10, 2010
Here's a bit of heresy... dogs have been bred to the point where there is speciation. St. Bernards are no longer the same species as Double-nosed Andean Tigerhounds. If an Abyssinian Wolf is a distinct species from Canis Lupus... and most (not all, but most) zoologists specializing in the field agree that it is, then a Great Dane is not the same species as a Beagle. The fact that humans had a hand in the speciation is irrelevant... Natural Selection is not always natural in a world where hominids (and others! Hello, ants!) have been running selective breeding experiments running hundreds of thousands of years, and it's high time biology recognized this.
posted by Slap*Happy at 6:28 PM on April 10, 2010
posted by Slap*Happy at 6:28 PM on April 10, 2010
Grrrr. Changing its name is a SPECTACULARLY STUPID IDEA.
Not really: I understand that the change is necessary to ensure the nomenclature is consistent with the actual evolutionary relationships occurring amongst the taxa formerly known as Drosophila. This sort of thing occurs ALL THE TIME in taxonomy, for example, the recent renaming of the African acacia. The idea is to ensure that the taxonomy of the group reflects its evolutionary history.
I'm sure many of us will feel a bit sad that Drosophila melanogasta is to be renamed. However, I assure you that which we call a Drosophila by any other name will smell as much like growth medium as it ever did before.
posted by Alice Russel-Wallace at 6:32 PM on April 10, 2010 [1 favorite]
Not really: I understand that the change is necessary to ensure the nomenclature is consistent with the actual evolutionary relationships occurring amongst the taxa formerly known as Drosophila. This sort of thing occurs ALL THE TIME in taxonomy, for example, the recent renaming of the African acacia. The idea is to ensure that the taxonomy of the group reflects its evolutionary history.
I'm sure many of us will feel a bit sad that Drosophila melanogasta is to be renamed. However, I assure you that which we call a Drosophila by any other name will smell as much like growth medium as it ever did before.
posted by Alice Russel-Wallace at 6:32 PM on April 10, 2010 [1 favorite]
Interesting that this drops right during the big fly meeting, when most of the world's Drosophilists are in talks all day and otherwise occupied.
The proscriptivist in me is currently fighting it out with the would be Sophophorist. While re-grouping may be more precise and correct (we'll see if that bears out in further analysis), it would, I'm sure be a nightmare for information retrivial and cohesion. Why not leave drosophila alone and rename the other subgenera?
My guess is that it will be entirely ignored by anyone who actually works with Drosophilids and left to the hardcore phylogenetic wankers.
posted by Cold Lurkey at 7:00 PM on April 10, 2010
The proscriptivist in me is currently fighting it out with the would be Sophophorist. While re-grouping may be more precise and correct (we'll see if that bears out in further analysis), it would, I'm sure be a nightmare for information retrivial and cohesion. Why not leave drosophila alone and rename the other subgenera?
My guess is that it will be entirely ignored by anyone who actually works with Drosophilids and left to the hardcore phylogenetic wankers.
posted by Cold Lurkey at 7:00 PM on April 10, 2010
Interesting, thanks for posting.
The posts regarding the topic on the website for International Commission on Zoological Nomenclature (the ruling party) are a good read:
Drosophila Fallén, 1823 (Insecta, Diptera): proposed conservation of usage:
The purpose of this application, under Article 70.2 of the Code, is to conserve the current usage of the widely used name Drosophila Fallén, 1823 (a genus of flies widely used in biological research, particularly in genetics and developmental biology) by the designation of Drosophila melanogaster Meigen, 1830 as the type species of Drosophila. Detailed phylogenetic studies show that the genus Drosophila as currently defined is paraphyletic. Splitting the genus requires that the subgenus Sophophora Sturtevant, 1939 must be ranked as a separate genus. The type species of Sophophora is by original designation Drosophila melanogaster Meigen, 1830. Ranking Sophophora as a genus and changing the name of Drosophila melanogaster to Sophophora melanogaster would result in major nomenclatural instability due to the breadth and vast number of publications, using this combination. In addition, many refer to ‘Drosophila’ when ‘Drosophila melanogaster’ is actually meant; the two names are used interchangeably. It is therefore proposed that Drosophila melanogaster Meigen, 1830 is designated as the type species of Drosophila.
Comments on the proposed conservation of the usage of the generic name of Drosophila Fallén:
03/2008: It seems likely that were the Commission not to vote in support of the conservation of Drosophila, such action would lead not only to unprecedented nomenclatural instability, but also to a widespread lack of confidence in both the actions and the purpose of the Commission itself.
06/2008 (in response): In my opinion their arguments are oversimplified or not justified. The species of Drosophila (s.s.) have also played a major role in science and the classification is not as messy as it is suggested.
The author then goes on to make a pretty good case, including this comment about the common usage:
Thus it is clear that, for geneticists, the name ‘Drosophila’ does not mean specifically D. melanogaster but the family DROSOPHILIDAE (and so includes D. melanogaster). Fly geneticists used to refer to the model species as ‘melanogaster’ instead of ‘Drosophila’ because the research community is aware that many species are used as study material. Research is also carried out on albomicans, ananassae, immigrans, indianus, kikkawai, mojavensis, virilis and, whichever genus individual species belong to, all are considered to be ‘Drosophila’. This usage suggests that, even under the name of Sophophora melanogaster, the species will still be considered as a ‘Drosophila’ and the term can be used in the titles and keywords of future publications. We should also note Bulletin of Zoological Nomenclature 65(2) June 2008 137 that ‘drosophila’ (without initial upper case and not italicized) would be more appropriate.
After reading through them, I personally think that the Commission made the right decision.
posted by kisch mokusch at 7:42 PM on April 10, 2010
The posts regarding the topic on the website for International Commission on Zoological Nomenclature (the ruling party) are a good read:
Drosophila Fallén, 1823 (Insecta, Diptera): proposed conservation of usage:
The purpose of this application, under Article 70.2 of the Code, is to conserve the current usage of the widely used name Drosophila Fallén, 1823 (a genus of flies widely used in biological research, particularly in genetics and developmental biology) by the designation of Drosophila melanogaster Meigen, 1830 as the type species of Drosophila. Detailed phylogenetic studies show that the genus Drosophila as currently defined is paraphyletic. Splitting the genus requires that the subgenus Sophophora Sturtevant, 1939 must be ranked as a separate genus. The type species of Sophophora is by original designation Drosophila melanogaster Meigen, 1830. Ranking Sophophora as a genus and changing the name of Drosophila melanogaster to Sophophora melanogaster would result in major nomenclatural instability due to the breadth and vast number of publications, using this combination. In addition, many refer to ‘Drosophila’ when ‘Drosophila melanogaster’ is actually meant; the two names are used interchangeably. It is therefore proposed that Drosophila melanogaster Meigen, 1830 is designated as the type species of Drosophila.
Comments on the proposed conservation of the usage of the generic name of Drosophila Fallén:
03/2008: It seems likely that were the Commission not to vote in support of the conservation of Drosophila, such action would lead not only to unprecedented nomenclatural instability, but also to a widespread lack of confidence in both the actions and the purpose of the Commission itself.
06/2008 (in response): In my opinion their arguments are oversimplified or not justified. The species of Drosophila (s.s.) have also played a major role in science and the classification is not as messy as it is suggested.
The author then goes on to make a pretty good case, including this comment about the common usage:
Thus it is clear that, for geneticists, the name ‘Drosophila’ does not mean specifically D. melanogaster but the family DROSOPHILIDAE (and so includes D. melanogaster). Fly geneticists used to refer to the model species as ‘melanogaster’ instead of ‘Drosophila’ because the research community is aware that many species are used as study material. Research is also carried out on albomicans, ananassae, immigrans, indianus, kikkawai, mojavensis, virilis and, whichever genus individual species belong to, all are considered to be ‘Drosophila’. This usage suggests that, even under the name of Sophophora melanogaster, the species will still be considered as a ‘Drosophila’ and the term can be used in the titles and keywords of future publications. We should also note Bulletin of Zoological Nomenclature 65(2) June 2008 137 that ‘drosophila’ (without initial upper case and not italicized) would be more appropriate.
After reading through them, I personally think that the Commission made the right decision.
posted by kisch mokusch at 7:42 PM on April 10, 2010
Minelli, voting AGAINST, noted that ‘Drosophila melanogaster’ was likely to be perceived by most people, including some biologists who did not care for taxonomy, as ‘the’ name of the species, without distinctly perceiving, or caring to distinguish, whether this meant the scientific, or the vernacular name.So basically this whole thing is a whiny feud between taxonomists and research biologists, the former being spergy Wikipedia nerds who want science to adhere to some rules written up by old dead white dudes 200 years ago, and the latter who just want to do their science without this renaming bullshit. Except the taxonomists run the naming guild, so, neener neener.
posted by shii at 7:57 PM on April 10, 2010 [1 favorite]
They change plant names all the time. Two that come to mind: The Queen Palm and Indian Hawthorn, which went from Raphiolepis to Rhapiolepis, but is now Rhaphiolepis.
This stuff will drive you nuts at first, but after a while you just don't give a damn anymore. Plus, you know who the old hands are when they refer to Cocus plumosa in their plant lists.
Of course it's all based on morphology anyway and not actual genetics...so you get things like the "botanical wonder"...a plant that is a cross between different Genuses (Genera?)...
posted by Xoebe at 9:06 PM on April 10, 2010
This stuff will drive you nuts at first, but after a while you just don't give a damn anymore. Plus, you know who the old hands are when they refer to Cocus plumosa in their plant lists.
Of course it's all based on morphology anyway and not actual genetics...so you get things like the "botanical wonder"...a plant that is a cross between different Genuses (Genera?)...
posted by Xoebe at 9:06 PM on April 10, 2010
This is nothing; I heard the scientists demoted an actual planet a few years back.
posted by TedW at 9:21 PM on April 10, 2010 [2 favorites]
posted by TedW at 9:21 PM on April 10, 2010 [2 favorites]
I've been working on an update of an encyclopaedia of forage plants that was written in the 70s. 25% of the taxons cited 40 years ago have been modified since. Some taxons have been merged, others have been split, others have been moved to another genus etc.
The irony is that vernacular names end up being more useful for searching information than taxonomic names in some cases, particularly when changes affect major species.
posted by elgilito at 1:25 AM on April 11, 2010
The irony is that vernacular names end up being more useful for searching information than taxonomic names in some cases, particularly when changes affect major species.
posted by elgilito at 1:25 AM on April 11, 2010
Drosophila melanogaster is number 7227
Actually, she's number 97209.
posted by Obscure Reference at 5:12 AM on April 11, 2010
Actually, she's number 97209.
posted by Obscure Reference at 5:12 AM on April 11, 2010
Oh, people, people. Will no one have pity on the taxonomists? I helped change the names of some of the most common fungal pathogens, and it's not something you do on a whim. As Scodger pointed out, fungal taxonomy is in flux. Back in the day, taxonomists assumed that morphological similarity mirrored phylogeny, and that's largely true, especially if you're a large animal taxonomist. Fungal scientists looked at fungi with similar conidiophores and said "these organisms must be similar; let's put them in the same genus". However, when you work with microscopic organisms, there aren't a lot of parts, and those parts are influenced by micro-physical constraints that aren't intuitive to large animals. We don't worry a lot about the surface tension of water or the dynamics of air flow around a blade of grass, but those are things that influence the height of a conidiophore or the shape of a spine in a tiny organism. Now that mycologists can compare the genetic material of the organisms they've lumped together on the basis of morphology, they've discovered a few discrepencies. If you are a practical person, you can say that morphology is a valid way to group things, but if you want names to mirror phylogeny, then you have to change them as more information becomes available, and if it's inconvenient, so be it.
In the case of the organisms I study, we used to group them by the kind of spines present on the sexual stage. Taxonomists tend to feel that things like spines exist ENTIRELY for the benefit of taxonomists. However, it turns out that fungi do not worry about taxonomists. It turns out that their sexual stage has spines when the organims grow on a woody host, and doesn't have spines when they grow on a herbaceous host. That's because the spines help anchor the sexual stage to the host's bark over the winter so the sexual spores can pop out in the spring and land on the newly emerging leaves. However, in a host with no bark, there's no point in having spines, and spines are "expensive", so the organism has lost its spines every time a mutation allows it to jump to a herbaceous host.
So I am a hated person for changing the names, but I contend that the story is now much more interesting, and I am unrepentant. Anyway, I *have* been punished. I am now sent every paper about the taxonomy of this organism as a peer reviewer because everyone knows I'm the only person who understands the names.
posted by acrasis at 6:33 AM on April 11, 2010 [1 favorite]
In the case of the organisms I study, we used to group them by the kind of spines present on the sexual stage. Taxonomists tend to feel that things like spines exist ENTIRELY for the benefit of taxonomists. However, it turns out that fungi do not worry about taxonomists. It turns out that their sexual stage has spines when the organims grow on a woody host, and doesn't have spines when they grow on a herbaceous host. That's because the spines help anchor the sexual stage to the host's bark over the winter so the sexual spores can pop out in the spring and land on the newly emerging leaves. However, in a host with no bark, there's no point in having spines, and spines are "expensive", so the organism has lost its spines every time a mutation allows it to jump to a herbaceous host.
So I am a hated person for changing the names, but I contend that the story is now much more interesting, and I am unrepentant. Anyway, I *have* been punished. I am now sent every paper about the taxonomy of this organism as a peer reviewer because everyone knows I'm the only person who understands the names.
posted by acrasis at 6:33 AM on April 11, 2010 [1 favorite]
This is shameful. Bzzzz.
posted by DMelanogaster at 8:43 AM on April 11, 2010
posted by DMelanogaster at 8:43 AM on April 11, 2010
on the one hand, i thought the uproar over the pluto thing was silly; on the other, Drosophila melanogaster is the only name i remember of all those we had to memorize in that goddamn biology class.
posted by fallacy of the beard at 9:56 AM on April 11, 2010
posted by fallacy of the beard at 9:56 AM on April 11, 2010
The taxa formerly known as Drosophila
If I had a say, that there would have my vote. Other than that, I don't care what they're called - I just wish they'd get the hell out of m kitchen!
posted by empatterson at 1:11 PM on April 11, 2010
If I had a say, that there would have my vote. Other than that, I don't care what they're called - I just wish they'd get the hell out of m kitchen!
posted by empatterson at 1:11 PM on April 11, 2010
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