This is a short commentary on -omes, in the spirit of reminding.
-omes are the collections of all things in a class associated with an instance of another class. For example, all the genes in a single organism is the ‘genome.’ Because of a variety of complexities in the definition of a gene since 1920, ‘genome’ is tricky, but because it is one of the earliest ‘-omes’ the example is important.
Metabolomes are of all metabolites in an organism. Transcriptomes are all the transcripts. Microbiomes are all the microbes associated with an organism or location (at a specific time). A subset, viromes, are all the viruses.
Meta-omes are the collections of those things in a particular population of the second class. Metagenomes are all the genes in a population of organisms. Metamicrobiomes could be the set of microbes across a population of hosts or locations.
Badomics is making up -omes that are nonsense or pointless (http://www.gigasciencejournal.com/content/1/1/6). The usual motivation is that -ome and -omics sound cool and there is some authority by association. One could imagine that the toiletome is all the toilets in a building and a metatoiletome would be all the toilets in a development, town, or other community. However, this seems like a pretty silly nomenclature (for plenty of silliness, http://www.ark-genomics.org/badomics-generator). Atmospheromics would be even sillier, because for any planet there is at most one atmosphere. A mathematician can logically state that both the empty set and the set containing one element exist – ah, mathematicians (http://www.mathmos.net/misc/jokes.html) – but that doesn’t make the word useful. It would be even worse to use the word atmospherome to refer to the set of all flying animals on a planet.
The ome that has me presently outraged is the ‘vaginome’ (http://motherboard.vice.com/read/enter-the-vaginome). I cannot denigrate this terminology sufficiently without being indecorous. There is no sensible vaginome. Some humans have one vagina, many have none, and the cases of more than one are at best very few. To refer to the bacterial or microbial community of the vagina as the vaginome is at best a basic misunderstanding of scientific terminology. If it were possible to retract a word from journalism, that would be the appropriate action at this time.
6 thoughts on “Bad-omics”
I enjoyed reading your article, but one statement struck me as being slightly inaccurate:
“Some humans have one vagina, many have none”. Last time I checked, the distribution was roughly 50/50. Although when one would look at the ratios of speakers at many conferences, you might have a point.
When I write about badomics words, which used to be often (see http://phylogenomics.blogspot.com/p/my-writings-on-badomics-words.html), I ask a series of questions to try to determine if something is a bad term or not. And one of the key questions is whether or not people using the term seem to think that it is a serious term or if they seem to think it is just a fun or casual term for conversations sake. The more serious they are about terms the more scrutiny that is required. If they want others to use such a term in discussions of the topic, then that is the most serious I suppose. Generally I give the award to scientists and to other academics who seem to take the terms really seriously. And generally I lay off if something was done totally tongue in cheek.
In this case here, I just don’t think Motherboard or AV Flox really was thinking that this is a serious, scholarly term that other people should necessarily use. No they donot seem to be using it completely tongue in cheek but nor does it seem to be an attempt to force its usage on others. So I guess I am not upset about this usage here. It seems harmless and actually a little bit fun.
How do you feel about “Kittenome”? Kinda cute or just plain badomics? I am starting up a Kitty Microbiome Project (partly for outreach and education) and wonder how people will feel if we use a fair amount of satire in our crowdfunding efforts.
Kittenome is fine too. Especially if we make it clear that it is not meant to be a serious term …
Seems like Jonathan and I are not yet in accord, so I’m posting a reply.
I feel the ‘kittenome’ isn’t cute enough to warrant its use to refer to the microbiome of kittens. It is probably cute enough to refer to the population of cats in a household or neighborhood, though; and that usage helps people understand what -omes are more broadly.
The Kitty Microbiome Project is already very cute and there are many opportunities for humor.
I think you won’t find any lack of funding, either, in part because of the public health implications of the kitty microbiome.
Greg Caporaso put together a fantastic plot of the growth of -ome terms overtime. Seemed relevant to link here.