October 27, 2004

-ome is where the art is

I've spent the past three days at the SOFG-2004 conference, among folks who are wrestling not only with the genome, but also with the proteome, the transcriptome, the reactome, and the metabolome (or is it the metabonome?). X-ome in this sense means something like "the overall ensemble of Xs". Though it's not quite that simple, since the reactome is "a knowledgebase of biological processes", i.e. reactions. So perhaps X-ome, in the modern sense, is "a systematic digital compendium of things denoted by some word derived from the stem X".

As usual, there's a bit of historical dirt in the morphological mix. For instance, I've been confused about the distinction between metabonomics and metabolomics, which seem to be used interchangeably to refer the ensemble of information about metabolites and their interconnections. Google tells me that

These very similar terms have arisen at about the same time in different area of bioscience research, mainly animal biochemistry and microbial/plant biochemistry respectively. Although both involve the multiparametric measurement of metabolites they are not philosophically identical as metabonomics deals with integrated, multicellular, biological systems including communicating extracellular environments and metabolomics deals with simple cell systems and, at least in terms of published data, mainly intracellular metabolite concentrations.

And to get the form metabonome, I think we have to postulate a mis-parsing of genome as ge+nome and metabolism as metabo+lism, so as to give us metabo+nome: an -omic eggcorn or folk etymology. This is the only use of an invented affix -nome that I've seen so far.

From an on-line -omes and omics glossary, I've learned that other recent coinages include behaviourome, cellome, clinome, complexome, cryptome, crystallome, ctyome, degradome, enzymome,epigenome, epitome, expressome, fluxome, foldome, functome, glycome, immunome, ionome, interactome, kinome, ligandome, localizome, metallome, methylome, morphome, nucleome, ORFeome, parasitome, peptidome, phenome, phostatome, physiome, regulome, saccharome, secretome, signalome, systeome, toponome, toxicome, translatome, transportome, vaccinome, and variome.

Not all the derivations are obvious: thus good old epitome gets overloaded because epitomics is defined as "a new field of science that studies all epitopes of the proteome in an organism. ... An epitope is a functional recognition site that binds by a specific monoclonal antibody." And my current favorite X-ome is a sort of pun:

At present, a large proportion of genes can only be described as members of the unknome -- those with currently no functional information!  [Dov Greenbaum "Interrelating Different Types of  Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001]

Terminological oddities aside, the intrepid -omicists deserve admiration. Like the intellectual adventurers of the enlightenment, they foresee that an encyclopedic compendium of the facts of nature will reveal hidden truths. They go boldly botanizing in the nucleus and the cytoplasm and even the far reaches of the extracellular matrix, like Humboldt on Tenerife or Darwin in the Galapagos. Darwin suggested the source of their zeal when he wrote in his autobiography that "no pursuit at Cambridge was followed with nearly so much eagerness or gave me so much pleasure as collecting beetles".

According to the American Heritage Dictionary, the -ome suffix comes from Greek via New Latin -ōma, -ōmat-. The original Greek meaning of the -ome morpheme foreshadows the notion of a large ensemble of items: e.g. phyllon "leaf", phyllôma "foliage". But according to the OED, -ome spent some time in less relevant corners of biology, as an

anglicized form of -OMA (partly through influence of G. -om, F. -ome), occurring chiefly in Bot. in terms such as CAULOME, HADROME, PHYLLOME, RHIZOME, and usu. signifying a structure or group of cells forming a normal part of the anatomy, in contrast with the abnormality implied by -oma (cf. MYCETOME, an organ in insects, MYCETOMA, a fungal skin disease). It also occurs in a few obs. forms of words now written -oma, e.g. FIBROME, TUBERCULOME.

The oldest -ome word I could find is rhizome "A prostrate or subterranean root-like stem emitting roots and usually producing leaves at its apex; a rootstock." with citations from 1845, though phyllome follows not too much later:

1858 MAYNE Expos. Lex., Phylloma. Herschel terms thus..the whole of the germs destined to produce the leaves which come from the bud..when it is developed: a phyllome.

By the early 20th century, we have biome in the sense of "biotic community":

1916 F. E. CLEMENTS Plant Succession 319 Human evidence of past climates and biotic communities, or biomes, must come to be of very great value.

The first use of genome in the sense of "the sum-total of the genes in ... a set [of chromosomes]" was in 1930, where it was used to refer to one of the (haploid) sets of chromosomes in a diploid organism:

1930 Cytologia I. 14 Chromosomes from different sets (or genoms) of Triticum vulgare show affinity toward each other.

This meaning was still standard in the 1960s:

1965 A. M. SRB et al. Gen. Genetics (ed. 2) vii. 190 Among organisms with chromosomes, each species has a characteristic set of genes, or genome. In diploids a genome is found in each normal gamete. It consists of a full set of the different kinds of chromosomes.

The -omic flowering is very recent, and almost entirely limited to the life sciences. Thus the compilation of data that forms the subject matter of economics is by no means the econome, nor is the ensemble of taxonomies the taxonome. And no one has yet suggested to my eight-year-old son that his compendium of information on his favorite games could be called the Pokémome.


Posted by Mark Liberman at October 27, 2004 01:06 AM