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The Out-of-Hand Omnipresent Ome

In 1909, the Danish biologist Wilhelm Johannsen coined the terms gene, to describe the unit of heredity, and genotype as the entire genetic profile of an organism. Seven years later, the term biome appeared, used to describe an ecological community of organisms and environments. As technology progressed, it became possible to do high-throughput molecular biology, and we began exploring the genomes of various microbes. This essentially entailed sequencing and annotating the entire genetic com

By | June 16, 2003

In 1909, the Danish biologist Wilhelm Johannsen coined the terms gene, to describe the unit of heredity, and genotype as the entire genetic profile of an organism. Seven years later, the term biome appeared, used to describe an ecological community of organisms and environments.

As technology progressed, it became possible to do high-throughput molecular biology, and we began exploring the genomes of various microbes. This essentially entailed sequencing and annotating the entire genetic compositions of our favorite model systems and comparing them to one another. Naturally, this method of global study and comparison was called genomics, and a trend was born. Since then, the suffix ome has come to mean any collection or aggregation of similar biological entities.

It's also getting annoyingly ubiquitous. One can almost envision a room full of scientists, chanting the word om like centuries of mystics before them.

I remember when I first heard the term proteome. A seminar speaker, in referring to the nearly completed Human Genome Project, stated that the next frontier would be the study and characterization of the proteome and that this discipline would allow a clearer understanding of life. The term struck me as a bit pompous, but I conceded that no other succinct term existed for the study of the entire protein composition of a given system.

Months later, at another seminar, microarray analyses were presented, and the mRNA content of cells grown under differing conditions were referred to as the transcriptomes. The word sounded awkward to me; certainly, I thought, we can do better than this. Not long after, I was talking to a colleague who was working on RNAs transcribed from nonprotein coding genes; his field was, of course, the RNAome. I politely informed him that a term for this, the transcriptome, already existed but he had his rebuttal ready. Apparently, his understanding was that the transcriptome referred only to protein-coding RNAs, while the RNAome included all cellular RNA species, making the transcriptome a mere subset of the RNAome. The ome was becoming omnipresent, and I was beginning to get angry.

High-throughput proteomic studies, most notably in yeast, allow the elucidation of protein-protein interactions on a global scale. Mind-numbingly large networks could be found on journal covers everywhere, and if you could find your favorite protein in the spider's web of data, you could presumably see every other protein with which it is associated. Its name: the interactome. "Why not?" I thought. About this time, it occurred to me that scientists were getting too cute, and unfortunately, they had done so before.

In 1975, Ed Southern developed the powerful technique for blotting gel-electrophoresed, size-fractionated DNA onto nylon membranes for subsequent probing of specific sequences. This was called Southern blotting, and rightfully so. When similar techniques were developed for blotting and probing RNA and proteins, we did not stray from compass directions, and so were born northerns and westerns, respectively. I also have seen published data from northwesterns and southwesterns. I fear that somewhere out there, a graduate student is burning the midnight oil, feverishly trying to develop the eastern blot-- carbohydrates, perhaps, or lipids?

We've created our own lexicon before. In 1665, Robert Hooke deemed the individual hollow subunits of cork to be called cells, solely because they reminded him of the rooms in which monks lived. Frankly, who cared what he called them? Any word would have sufficed.

In the past it was necessary to invent such terms; an entirely novel structure or phenomenon warranted an entirely novel name. However, we currently have a full and rich biological vocabulary, containing words for most any process, pathway, or structure we need described. These terms can even be combined to describe new discoveries or technologies, such as ribozymes (enzymatic ribonucleic acids) and hybridomas (antibody-producing clonal tumor cells). But the precedent has been set and the freedom to create biological terms out of thin air will continue to be abused. In light of past history, the omes shouldn't have surprised me, but I still contend that it was a new low.

My anti-omic movement is common knowledge in my department, and it was with much glee that a colleague of mine showed me an article title featuring the term behaviorome.1 My shoulders slumped in defeat, and I concluded that this dread suffix would survive, ad infinitum. I was almost instantly vindicated when, in the same issue, a report appeared that contained a word both difficult to look at and pronounce: metabolomics.2

I humbly ask that we make an effort to avoid the further perversion of the ome. My fear is that in the not-so-distant future, an overzealous linguist will embark on a study of the biological vernacular--and how else to name such a field but the omeome. What will we do then?

Thomas Mennella is a doctoral student in the Department of Biological Sciences, University at Albany, State University of New York.

References
1. D. Macer, "The behaviorome mental map project," The Scientist, 17[8]:18, April 21, 2003.

2. A. Adams, "Metabolomics: Small-molecule 'omics, The Scientist, 17[8]:38-40, April 21, 2003.

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