From alphomics to omomics

From the New York Times:

‘Ome,’ the Sound of the Scientific Universe

By James Gorman

The age of “omes” is here. It began with the genome, continued with the proteome, branched out with the memome and reached full flowering with the notion of the omome.

This probably sounds like raw material for nonsense poetry, but it’s a real biological and linguistic trend that makes sense, once you get the idea of just what an “ome” is.

The genome is the place to start. It is the totality of all the genes, whether in an organism or in something else, like a tumor. The human genome, mapped out about a decade ago, includes all the genes that make a human being.

Creating a map of the whole genome was a monumental achievement, and during work on that project and after its completion, the omification of science took off. Joshua Lederberg, a geneticist and Nobel laureate who died in 2008, and Alexa T. McCray, now an associate professor at Harvard Medical School, saw it coming, and talked about the origin of the suffix “ome” in a 2001 essay, “ ’Ome Sweet ’Omics — A Genealogical Treasury of Words,” in The Scientist.

The word “genome” was first used in 1920, by Hans Winkler, a German scientist, to mean all the material on the chromosomes in a sperm or egg, but did not become really popular until the end of the last century, when genome mapping began. Various experts had differing ideas on where the suffix came from, but it seems to be one that was made up. In any case, it clearly meant the totality of something. Dr. Lederberg, who coined a few scientific terms himself, contributed “microbiome” — all the microbes that live in and on humans — to the growing trend.

An epidemic of neologia ensued. Thus were born the proteome and the secretome and the glycome, and numerous other omes that are pretty much impossible to keep track of. Interactome. Regulome. Connectome. Epigenome. The list goes on. In fact, it goes on for about 18 pages if you go to the Omics.org site and print out its list of omes and omics.

The list could be said to be the omome, the ome of all the omes, a word which, in a moment of indulgent fantasy, I thought perhaps I had invented. Apparently not. “Omome,” or “omeome,” is on the Omics.org list, although the Web site given as a source led nowhere. Another possible inventor is Martin Krzywinski, a scientist at the Genome Sciences Center in Vancouver, British Columbia. He has created some extraordinary visual representations of genomes, and also invents new words. Among the coinings he offers on his site are “omome,” “omeomics,” “omicsophy,” which I don’t think will ever take off, and, just Thursday, “metaomomics,” which I don’t even want to think about.

I loved the idea of the omome, but I thought it needed a reality check. I called Mark Gerstein at Yale. His lab is deeply involved in bioinformatics, the use of computing to make sense of the vast amounts of information produced in pursuit of the various omes. Dr. Gerstein also has an interest in the way scientific terminology develops.

The omome, he said, was a fun idea, but he doubted anyone was making a living in omomics. Despite the humor in speculative omification, he said, the proliferation of real omic disciplines marked the spread of a “very important scientific idea.” He said, “All the omes derive to some extent from the genome,” and key to all of them is that an ome represents “the entirety of the thing being studied.”

The mapping of genomes, he said, inspired scientists to use the same approach in studying proteins, metabolites and their biochemical connections, to name a few. And as they pursued this “omic idea,” the focus of biological research shifted in the direction of studying complete systems and networks, rather than individual parts, discrete genes or proteins.

His comments reminded me of a recent conversation I had when I was reporting on the evolution of polar bears. One scientist wanted to make it clear to me that she was studying genomics, whereas another researcher was studying only genes. Only genes, I thought? What a difference an ome can make.